gromacs →
2019.4-1 →
armhf → 2019-12-15 00:14:39
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| gromacs 2019.4-1 (armhf) Sat, 14 Dec 2019 23:23:11 +0000 |
+==============================================================================+
Package: gromacs
Version: 2019.4-1
Source Version: 2019.4-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-021685d2-dbf0-4489-9357-88445a942b9a' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.3 MB in 9s (2599 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 33.5 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2019.4-1 (dsc) [2578 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2019.4-1 (tar) [33.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2019.4-1 (diff) [36.1 kB]
Fetched 33.5 MB in 6s (5633 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-HUVhuv/gromacs-2019.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-HUVhuv' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-hV2JYf/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-hV2JYf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hV2JYf/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9211 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 19 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13002 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-hV2JYf/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Sources [572 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ Packages [655 B]
Fetched 2560 B in 0s (11.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath cmake
cmake-data cpp-9 debhelper dh-autoreconf dh-strip-nondeterminism dwz file
g++-9 gcc-9 gcc-9-base gettext gettext-base gfortran gfortran-9 groff-base
hwloc-nox ibverbs-providers intltool-debian libarchive-zip-perl libarchive13
libasan5 libatomic1 libblas-dev libblas3 libboost-dev libboost1.67-dev
libbrotli1 libbsd0 libcc1-0 libcroco3 libcurl3-gnutls libdebhelper-perl
libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev
libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7
libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-single3
libfile-stripnondeterminism-perl libgcc-9-dev libgcc1 libgfortran-9-dev
libgfortran5 libglib2.0-0 libgomp1 libgssapi-krb5-2 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu63 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpich-dev libmpich12
libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200
libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1
libpmix2 libprocps7 libpsl5 libpthread-stubs0-dev librhash0 librtmp1
libsigsegv2 libssh2-1 libssl1.1 libstdc++-9-dev libstdc++6
libsub-override-perl libtinfo5 libtool libubsan1 libuchardet0 libuv1
libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev
libxdmcp-dev libxdmcp6 libxml2 m4 man-db mpich ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client po-debconf procps sensible-utils
x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build gcc-9-locales dh-make gcc-9-doc gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-9-doc libcoarrays-dev
groff lrzip liblapack-doc libboost-doc libboost1.67-doc
libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev
libboost-context1.67-dev libboost-coroutine1.67-dev
libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libfftw3-doc krb5-doc krb5-user libtool-doc openmpi-doc pciutils
libstdc++-9-doc gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less
www-browser mpich-doc opencl-icd keychain libpam-ssh monkeysphere
ssh-askpass libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev
publicsuffix xauth libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base gfortran gfortran-9 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.67-dev libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3
libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-9-dev
libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins
libhwloc15 libibverbs-dev libibverbs1 libicu63 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libltdl-dev
libltdl7 libmagic-mgc libmagic1 libmpich-dev libmpich12 libncurses6
libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev
libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps7
libpsl5 libpthread-stubs0-dev librhash0 librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libuv1
libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev
libxdmcp-dev libxdmcp6 libxml2 m4 man-db mpich ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client po-debconf procps
sbuild-build-depends-gromacs-dummy sensible-utils x11proto-core-dev
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libatomic1 libcc1-0 libgcc-9-dev
libgcc1 libgomp1 libstdc++-9-dev libstdc++6 libubsan1
13 upgraded, 119 newly installed, 0 to remove and 6 not upgraded.
Need to get 89.4 MB of archives.
After this operation, 330 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hV2JYf/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [948 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 9.2.1-21+rpi1 [38.0 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.2.1-21+rpi1 [195 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libgcc1 armhf 1:9.2.1-21+rpi1 [37.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 9.2.1-21+rpi1 [73.8 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 9.2.1-21+rpi1 [8160 B]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.2.1-21+rpi1 [348 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 9.2.1-21+rpi1 [112 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf g++-9 armhf 9.2.1-21+rpi1 [8207 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-9-dev armhf 9.2.1-21+rpi1 [1707 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libgcc-9-dev armhf 9.2.1-21+rpi1 [640 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gcc-9 armhf 9.2.1-21+rpi1 [7715 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf cpp-9 armhf 9.2.1-21+rpi1 [7458 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 9.2.1-21+rpi1 [414 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191025-1 [79.3 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.1p1-1 [713 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.15.4-1+rpi1 [1580 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.0-1+b1 [292 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-5 [257 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.8-1 [132 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.33.1-2 [112 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.15.4-1+rpi1 [2540 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-4 [140 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.3-2 [1137 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-21+rpi1 [231 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.2.1-21+rpi1 [279 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.2.1-21+rpi1 [8099 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-11 [387 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.1.0+dfsg-2+rpi1 [112 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 2.1.0+dfsg-2+rpi1 [145 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 26.0-2 [47.1 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 26.0-2 [23.8 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-1 [113 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b8 [4464 B]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.11-stable-1 [165 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.11-stable-1 [124 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.11-stable-1 [98.7 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.11-stable-1 [54.7 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.11-stable-1 [59.7 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.11-stable-1 [279 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-11 [159 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.1.0+dfsg-2+rpi1 [172 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.7 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.1.0+dfsg-2+rpi1 [17.0 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 26.0-2 [165 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-1 [2981 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.3-3 [1028 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.3-3 [332 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.3-3 [1198 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.4-1+b1 [370 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.2-4+rpi1+b1 [1680 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.2-4+rpi1 [168 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.2-4+rpi1+b1 [183 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.2-4+rpi1+b1 [906 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.8-1 [691 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2018.4-4 [251 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2018.4-4 [3128 B]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.13.1-2 [169 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.8-1 [760 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libstdc++6:armhf (9.2.1-21+rpi1) ...
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Setting up libexpat1:armhf (2.2.9-1) ...
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Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
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Setting up libglib2.0-0:armhf (2.62.3-2) ...
No schema files found: doing nothing.
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Setting up libdebhelper-perl (12.7.1) ...
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Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.37-6) ...
Setting up libgomp1:armhf (9.2.1-21+rpi1) ...
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Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up libasan5:armhf (9.2.1-21+rpi1) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.33.1-2) ...
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libevent-core-2.1-7:armhf (2.1.11-stable-1) ...
Setting up libatomic1:armhf (9.2.1-21+rpi1) ...
Setting up libevent-2.1-7:armhf (2.1.11-stable-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libltdl7:armhf (2.4.6-11) ...
Setting up libfftw3-double3:armhf (3.3.8-2) ...
Setting up libgfortran5:armhf (9.2.1-21+rpi1) ...
Setting up libubsan1:armhf (9.2.1-21+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libmpich12:armhf (3.3-3) ...
Setting up sensible-utils (0.0.12+nmu1) ...
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update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
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Setting up cpp-9 (9.2.1-21+rpi1) ...
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Setting up libelf1:armhf (0.176-1.1) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libjsoncpp1:armhf (1.7.4-3) ...
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Setting up x11proto-dev (2018.4-4) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
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Setting up liblapack3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
Setting up libxau-dev:armhf (1:1.0.8-1+b2) ...
Setting up libtool (2.4.6-11) ...
Setting up libarchive13:armhf (3.4.0-1+b1) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up libedit2:armhf (3.1-20191025-1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.11-stable-1) ...
Setting up m4 (1.4.18-4) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libgcc-9-dev:armhf (9.2.1-21+rpi1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up x11proto-core-dev (2018.4-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libevent-dev (2.1.11-stable-1) ...
Setting up liblapack-dev:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libhwloc15:armhf (2.1.0+dfsg-2+rpi1) ...
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-4) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gcc-9 (9.2.1-21+rpi1) ...
Setting up libibverbs1:armhf (26.0-2) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libxcb1-dev:armhf (1.13.1-2) ...
Setting up libstdc++-9-dev:armhf (9.2.1-21+rpi1) ...
Setting up ibverbs-providers:armhf (26.0-2) ...
Setting up openssh-client (1:8.1p1-1) ...
Setting up hwloc-nox (2.1.0+dfsg-2+rpi1) ...
Setting up libx11-dev:armhf (2:1.6.8-1) ...
Setting up libgfortran-9-dev:armhf (9.2.1-21+rpi1) ...
Setting up libcurl3-gnutls:armhf (7.67.0-2) ...
Setting up libhwloc-plugins:armhf (2.1.0+dfsg-2+rpi1) ...
Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-11) ...
Setting up g++-9 (9.2.1-21+rpi1) ...
Setting up cmake (3.15.4-1+rpi1) ...
Setting up libhwloc-dev:armhf (2.1.0+dfsg-2+rpi1) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up gfortran-9 (9.2.1-21+rpi1) ...
Setting up libpmix2:armhf (3.1.4-1+b1) ...
Setting up mpich (3.3-3) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up po-debconf (1.0.21) ...
Setting up libopenmpi3:armhf (4.0.2-4+rpi1+b1) ...
Setting up libibverbs-dev:armhf (26.0-2) ...
Setting up gfortran (4:9.2.1-3.1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libmpich-dev:armhf (3.3-3) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up libboost-dev:armhf (1.67.0.2+b8) ...
Setting up openmpi-bin (4.0.2-4+rpi1+b1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.0.2-4+rpi1+b1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.1) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-21+rpi1 gcc-9_9.2.1-21+rpi1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-21+rpi1 libstdc++6_9.2.1-21+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 chrpath_0.16-2 cmake_3.15.4-1+rpi1 cmake-data_3.15.4-1+rpi1 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-21+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-4 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-21+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-21+rpi1 gcc-9-base_9.2.1-21+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.2.1-21+rpi1 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.23 hwloc-nox_2.1.0+dfsg-2+rpi1 ibverbs-providers_26.0-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libarchive13_3.4.0-1+b1 libasan5_9.2.1-21+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-21+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-5+rpi1 libblas-dev_3.9.0-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b8 libboost1.67-dev_1.67.0-13 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-21+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdpkg-perl_1.19.7 libedit2_3.1-20191025-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.11-stable-1 libevent-core-2.1-7_2.1.11-stable-1 libevent-dev_2.1.11-stable-1 libevent-extra-2.1-7_2.1.11-stable-1 libevent-openssl-2.1-7_2.1.11-stable-1 libevent-pthreads-2.1-7_2.1.11-stable-1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-21+rpi1 libgcc1_1:9.2.1-21+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-21+rpi1 libgfortran5_9.2.1-21+rpi1 libglib2.0-0_2.62.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-21+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_2.1.0+dfsg-2+rpi1 libhwloc-plugins_2.1.0+dfsg-2+rpi1 libhwloc15_2.1.0+dfsg-2+rpi1 libibverbs-dev_26.0-2 libibverbs1_26.0-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.9.0-1 liblapack3_3.9.0-1 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 libltdl-dev_2.4.6-11 libltdl7_2.4.6-11 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpich-dev_3.3-3 libmpich12_3.3-3 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libopenmpi-dev_4.0.2-4+rpi1+b1 libopenmpi3_4.0.2-4+rpi1+b1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-3 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpmix2_3.1.4-1+b1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpthread-stubs0-dev_0.4-1 libreadline7_7.0-5 libreadline8_8.0-3 librhash0_1.3.8-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 librust-bitflags-dev_1.2.1-1 librust-cloudabi+default-dev_0.0.3-1 librust-cloudabi-dev_0.0.3-1 librust-fuchsia-zircon-dev_0.3.3-2 librust-fuchsia-zircon-sys-dev_0.3.3-2 librust-libc-dev_0.2.62-1 librust-phf-codegen-dev_0.7.23-1 librust-phf-generator-dev_0.7.23-1 librust-phf-shared-dev_0.7.23-2+b1 librust-rand-0.5+alloc-dev_0.5.5-2+rpi1 librust-rand-0.5+std-dev_0.5.5-2+rpi1 librust-rand-0.5-dev_0.5.5-2+rpi1 librust-rand-core-0.2+alloc-dev_0.2.2-1 librust-rand-core-0.2+std-dev_0.2.2-1 librust-rand-core-0.2-dev_0.2.2-1 librust-rand-core-dev_0.3.0-1 librust-siphasher-dev_0.2.3-1 librust-winapi-dev_0.3.6-1 librust-winapi-i686-pc-windows-gnu-dev_0.4.0-1 librust-winapi-x86-64-pc-windows-gnu-dev_0.4.0-1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.9-3 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-21+rpi1 libstdc++6_9.2.1-21+rpi1 libsub-override-perl_0.09-2 libsystemd0_243-8+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-21+rpi1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.33.1-2 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libx11-dev_2:1.6.8-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-2 libxcb1-dev_1.13.1-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mount_2.34-0.1 mpich_3.3-3 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_4.0.2-4+rpi1+b1 openmpi-common_4.0.2-4+rpi1 openssh-client_1:8.1p1-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 3 01:14:58 2019 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2019.4-1.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2019.4.orig.tar.gz
dpkg-source: info: unpacking gromacs_2019.4-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying doxygen.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-021685d2-dbf0-4489-9357-88445a942b9a
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2019.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON)
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- hwloc version: 2.1.0
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.1.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Can not build documentation with Python 3
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:229 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- hwloc version: 2.1.0
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.1.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Can not build documentation with Python 3
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 2.1.0
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.1.0", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:229 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 2.1.0
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.1.0", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 2.1.0
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.1.0", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 9.2.1
-- The CXX compiler identification is GNU 9.2.1
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:229 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 2.1.0
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.1.0", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
15188 | "%4d-%02d-%02d %02d:%02d:%02d",
| ^~~~
In file included from /usr/include/stdio.h:867,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 9%] Built target mdrun_test_objlib
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
397 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
212 | findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
290 | findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
361 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
309 | vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/__/external/vmd_molfile/vmddlopen.c.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2255 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
378 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
399 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
163 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
173 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
293 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
423 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
443 | void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
463 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
474 | double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
483 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
487 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
131 | CoordState::sampleUmbrellaGridpoint(const Grid &grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1231 | void BiasState::sampleProbabilityWeights(const Grid &grid,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | void BiasState::sampleCoordAndPmf(const Grid &grid,
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1074 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
226 | void CorrelationTensor::addData(double weight,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams ¶ms,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.4 -o ../../lib/libgromacs.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -fopenmp -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.4.0.0 ../../lib/libgromacs.so.4 ../../lib/libgromacs.so
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
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/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:371:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
371 | put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
372 | atomsArrayRef);
| ~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:371:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 5%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulationdatabase.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
15188 | "%4d-%02d-%02d %02d:%02d:%02d",
| ^~~~
In file included from /usr/include/stdio.h:867,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 7%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target mdrun_test_objlib
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3460414 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
235 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
282 | void set_ddbox(const gmx_domdec_t &dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
296 | low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | &dd.nc, box, calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | ddbox);
| ~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
308 | void set_ddbox_cr(const t_commrec &cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
317 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
318 | dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
247 | void dd_collect_vec(gmx_domdec_t *dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
310 | dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
315 | dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
320 | dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
128 | ddSendrecv(const gmx_domdec_t *dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3015 | set_ddbox(*dd, false, state.box, true, state.x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2137 | static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2358 | set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2383 | set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::LocalAtomSetManager*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2953 | gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2979 | set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2980 | mtop, ir,
| ~~~~~~~~~
2981 | box, xGlobal,
| ~~~~~~~~~~~~~
2982 | &ddbox);
| ~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
598 | ddSendrecv(dd, d, dddirBackward,
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
599 | sendBuffer, receiveBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
664 | ddSendrecv(dd, d, dddirForward,
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
665 | sendBuffer, receiveBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | void dd_move_x(gmx_domdec_t *dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
386 | ddSendrecv(dd, d, dddirBackward,
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
387 | sendBuffer, receiveBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
408 | void dd_move_f(gmx_domdec_t *dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
472 | ddSendrecv(dd, d, dddirForward,
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
473 | sendBuffer, receiveBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
259 | ddSendrecv(dd, d, dddirBackward,
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
260 | gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
261 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2236 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
2237 | work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
207 | rvec *makeRvecArray(gmx::ArrayRef<const gmx::RVec> v,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3244 | set_ddbox(*dd, true,
| ~~~~~~~~~^~~~~~~~~~~
3245 | DDMASTER(dd) ? state_global->box : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3246 | true, xGlobal,
| ~~~~~~~~~~~~~~
3247 | &ddbox);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3297 | set_ddbox(*dd, bMasterState, state_local->box,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3298 | true, state_local->x, &ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3316 | set_ddbox(*dd, bMasterState, state_local->box,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3317 | bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3336 | comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3337 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3364 | comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3365 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3419 | nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3420 | 0,
| ~~
3421 | comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
3422 | comm->zones.size[0].bb_x1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
3423 | comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3424 | 0, dd->ncg_home,
| ~~~~~~~~~~~~~~~~
3425 | comm->zones.dens_zone0,
| ~~~~~~~~~~~~~~~~~~~~~~~
3426 | fr->cginfo,
| ~~~~~~~~~~~
3427 | state_local->x,
| ~~~~~~~~~~~~~~~
3428 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3429 | fr->nbv->grp[eintLocal].kernel_type,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3430 | fr->nbv->nbat);
| ~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1413 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1473 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1531 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
212 | findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
397 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
290 | findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
309 | vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
361 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/__/external/vmd_molfile/vmddlopen.c.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:51:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<edpar> {anonymous}::read_edi_file(const char*, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:959:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
959 | bool pullCheckPbcWithinGroup(const pull_t &pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:959:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2255 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
378 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
399 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
163 | tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
173 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
293 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
423 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
443 | void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
463 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
464 | forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
474 | double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
483 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
487 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1231 | void BiasState::sampleProbabilityWeights(const Grid &grid,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | void BiasState::sampleCoordAndPmf(const Grid &grid,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
131 | CoordState::sampleUmbrellaGridpoint(const Grid &grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1074 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
226 | void CorrelationTensor::addData(double weight,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
78 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
210 | double HistogramSize::newHistogramSize(const BiasParams ¶ms,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_anadock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anadock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyndom.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyndom.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tune_pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:1702:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1702 | put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
1703 | positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:1702:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:373:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
373 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:373:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:316:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
316 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:316:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:67:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
67 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:99:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
99 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:174:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
174 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:206:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
206 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp-impl.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp-impl.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void enter_function(t_params*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void enter_function(t_params*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert-molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert-molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, gmx_atomprop_t, real, real)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert-molecules.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert-molecules.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:537:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
537 | pullCheckPbcWithinGroup(*pull_work,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
538 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
539 | mtop->natoms),
| ~~~~~~~~~~~~~~
540 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:564:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
564 | pullCheckPbcWithinGroup(*pull_work,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
565 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(x),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
566 | mtop->natoms),
| ~~~~~~~~~~~~~~
567 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:610:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
610 | AnalysisDataStorageFrameData::addPointSet(int dataSetIndex, int firstColumn,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:750:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
750 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
751 | makeConstArrayRef(values_).
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
752 | subArray(begin, end-begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:750:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/report-methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report-methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/chargegroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation-utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
109 | BoxDeformation::apply(ArrayRef<RVec> x,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start, int homenr, gmx::ArrayRef<gmx::RVec> x, const real q[], const real qB[],
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka *at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
848 | t_blocka make_at2con(const gmx_moltype_t &moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
698 | void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda *fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const gmx_bool*, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
781 | void andersen_tcoupl(const t_inputrec *ir, int64_t step,
| ^~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdsetup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
247 | void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
269 | dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
274 | dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
280 | dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1416 | void nbnxn_put_on_grid(nbnxn_search_t nbs,
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1520 | void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1536 | nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
1537 | zone, c0, c1,
| ~~~~~~~~~~~~~
1538 | nullptr,
| ~~~~~~~~
1539 | zones->cg_range[zone],
| ~~~~~~~~~~~~~~~~~~~~~~
1540 | zones->cg_range[zone+1],
| ~~~~~~~~~~~~~~~~~~~~~~~~
1541 | -1,
| ~~~
1542 | atinfo,
| ~~~~~~~
1543 | x,
| ~~
1544 | 0, nullptr,
| ~~~~~~~~~~~
1545 | nb_kernel_type,
| ~~~~~~~~~~~~~~~
1546 | nbat);
| ~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ns.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin *b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin *b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1144 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1145 | mdstep, nrnb, wcycle, top, groups,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1146 | state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1147 | forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1148 | state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~
1149 | fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1150 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1151 | ddOpenBalanceRegion, ddCloseBalanceRegion);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1254 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1255 | 1, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~
1256 | top, groups, state->box, posWithPadding[Try], &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1257 | forceWithPadding[Try], force_vir,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1258 | md, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1259 | fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1260 | shellfc_flags,
| ~~~~~~~~~~~~~~
1261 | ddOpenBalanceRegion, ddCloseBalanceRegion);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
796 | computeSpecialForces(FILE *fplog,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2722:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2722 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2120:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2120 | void do_force(FILE *fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1175 | nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1176 | 0, vzero, box_diag,
| ~~~~~~~~~~~~~~~~~~~
1177 | nullptr, 0, mdatoms->homenr, -1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1178 | fr->cginfo, x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1179 | 0, nullptr,
| ~~~~~~~~~~~
1180 | nbv->grp[eintLocal].kernel_type,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1181 | nbv->nbat);
| ~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1187 | nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1188 | fr->cginfo, x.unpaddedArrayRef(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | nbv->grp[eintNonlocal].kernel_type,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | nbv->nbat);
| ~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1575 | computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1576 | step, t, wcycle,
| ~~~~~~~~~~~~~~~~
1577 | fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1578 | flags, &forceWithVirial, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1579 | ed, bNS);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1627:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1627 | dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2048:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2048 | computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2049 | step, t, wcycle,
| ~~~~~~~~~~~~~~~~
2050 | fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2051 | flags, &forceWithVirial, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2052 | ed, bNS);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2059:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2059 | dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2070:26: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2070 | dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1575 | computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1576 | step, t, wcycle,
| ~~~~~~~~~~~~~~~~
1577 | fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1578 | flags, &forceWithVirial, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1579 | ed, bNS);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2875:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2875 | extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0)
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2973:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2973 | initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2973:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2979 | initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3047:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
3047 | initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3047:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3053:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
3053 | initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3053:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
57 | do_md_trajectory_writing(FILE *fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
164 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
165 | step, t, state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1781 | upd->deform->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_update_t*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1920 | extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1944 | andersen_tcoupl(ir, step, cr, md, v, rate,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1945 | upd->sd->randomize_group, upd->sd->boltzfac);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
85 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wnblist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/disre.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
758 | void constructVsitesGlobal(const gmx_mtop_t &mtop,
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/gpubonded-impl.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-forces.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/manage-threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/position-restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate-spline-moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald-utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long-range-correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-load-balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-pp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-solve.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spline-work.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spread.cpp
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program-impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/integrator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
551 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | top_global, step, static_cast<double>(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | &state->s, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->f);
| ~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
564 | dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
869 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
870 | count, nrnb, wcycle, top, &top_global->groups,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
871 | ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
872 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
873 | ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
874 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
875 | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
876 | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~
877 | DOMAINDECOMP(cr) ?
| ~~~~~~~~~~~~~~~~~~
878 | DdOpenBalanceRegionBeforeForceComputation::yes :
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
879 | DdOpenBalanceRegionBeforeForceComputation::no,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
880 | DOMAINDECOMP(cr) ?
| ~~~~~~~~~~~~~~~~~~
881 | DdCloseBalanceRegionAfterForceComputation::yes :
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
882 | DdCloseBalanceRegionAfterForceComputation::no);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
936 | sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:880:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
880 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
881 | step, nrnb, wcycle, top, groups,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
882 | state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
883 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
884 | state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~
885 | fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
886 | (bNS ? GMX_FORCE_NS : 0) | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
887 | ddOpenBalanceRegion, ddCloseBalanceRegion);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1031:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1031 | sum_dhdl(enerd, state->lambda, ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1056:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1056 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1057 | ir, state, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1058 | top_global, fr,
| ~~~~~~~~~~~~~~~
1059 | outf, mdebin, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~
1060 | checkpointHandler->isCheckpointingStep(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1061 | bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~
1062 | mdrunOptions.writeConfout,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
1063 | bSumEkinhOld);
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1094:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1094 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1304:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1304 | sum_dhdl(enerd, state->lambda, ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
377 | initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
582 | do_force(fplog, cr, ms, ir, awh, enforcedRotation,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | step, nrnb, wcycle, top, groups,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
585 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~
587 | fr, ppForceWorkload, vsite, mu_tot, t, ed,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
588 | GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
589 | ddOpenBalanceRegion, ddCloseBalanceRegion);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
599 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
600 | ir, state, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
601 | top_global, fr,
| ~~~~~~~~~~~~~~~
602 | outf, mdebin, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~
603 | isCheckpointingStep, doRerun, isLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
604 | mdrunOptions.writeConfout,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
605 | bSumEkinhOld);
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
663 | sum_dhdl(enerd, state->lambda, ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1932 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1933 | top_global, step, static_cast<real>(step), &ems.s, state_global, observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
551 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | top_global, step, static_cast<double>(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | &state->s, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->f);
| ~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
551 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | top_global, step, static_cast<double>(step),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | &state->s, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->f);
| ~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
465 | do_force(fplog, cr, ms, ir, awh, enforcedRotation,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
466 | step, nrnb, wcycle, top, groups,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
467 | state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
468 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
469 | state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~
470 | fr, ppForceWorkload, vsite, mu_tot, t, ed,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
471 | GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
472 | ddOpenBalanceRegion, ddCloseBalanceRegion);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
482 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
483 | ir, state, state_global, observablesHistory,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
484 | top_global, fr,
| ~~~~~~~~~~~~~~~
485 | outf, mdebin, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~
486 | isCheckpointingStep, doRerun, isLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
487 | mdrunOptions.writeConfout,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
488 | bSumEkinhOld);
| ~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
544 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
554 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
569 | sum_dhdl(enerd, state->lambda, ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/mdmodules.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
647 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
648 | step, nrnb, wcycle, top, &top_global->groups,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
649 | state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
650 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
651 | state_global->lambda,
| ~~~~~~~~~~~~~~~~~~~~~
652 | nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
654 | (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) |
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
655 | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
656 | DdOpenBalanceRegionBeforeForceComputation::no,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
657 | DdCloseBalanceRegionAfterForceComputation::no);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:922:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
922 | cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | &mtop, inputrec,
| ~~~~~~~~~~~~~~~~
924 | box, positionsFromStatePointer(globalState.get()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
925 | &atomSets);
| ~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1278:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1278 | constructVsitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
260 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs_d.so.4 -o ../../lib/libgromacs_d.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -fopenmp -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.4.0.0 ../../lib/libgromacs_d.so.4 ../../lib/libgromacs_d.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/share/template /<<PKGBUILDDIR>>/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
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[ 2%] Built target tng_io_obj
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'.
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Scanning dependencies of target gmock
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[ 2%] Built target lmfit_objlib
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
[ 3%] Built target mdrun_test_objlib
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'.
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make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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[ 6%] Built target libgromacs_external
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
[ 6%] Built target mdrun_objlib
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'.
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Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
[ 19%] Built target libgromacs_generated
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 19%] Built target onlinehelp-test-shared
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 20%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target libgromacs
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o
/usr/bin/ranlib ../../../lib/libgmock.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target applied-forces-test
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target listed-forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target mdlib-test
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target domdec-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target commandline-test
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target hardware-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
70 | void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
| ^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
97 | void compareViews(ArrayRef<T> input,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
109 | void compareViews(ArrayRef < BasicVector < T>> input,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
119 | }};
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
131 | }};
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
142 | }};
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
517 | TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
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/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
517 | TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
461 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
461 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
467 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
467 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
489 | EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
489 | EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
494 | EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
494 | EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
461 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
461 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
467 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
467 | EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
489 | EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
489 | EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
494 | EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
176 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
494 | EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-mpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
Scanning dependencies of target utility-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target pull-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target fileio-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target options-test
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_trjconv.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target awh-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target pdb2gmx-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
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/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target selection-test
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report-methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target energyanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color=
[ 96%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
Scanning dependencies of target legacy-mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target legacy-mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target trajectoryanalysis-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target mdrun-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (16 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariants
1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (25 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (1 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (1 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (1 ms)
1: [----------] 4 tests from XvgTests (5 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (47 ms total)
1: [ PASSED ] 59 tests.
1/40 Test #1: TestUtilsUnitTests ............... Passed 0.07 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (1 ms total)
2: [ PASSED ] 1 test.
2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.02 sec
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3: [==========] Running 50 tests from 8 test cases.
3: [----------] Global test environment set-up.
3: [----------] 1 test from VerletBufferConstraintTest
3: [ RUN ] VerletBufferConstraintTest.EqualMasses
3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
3: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
3:
3: [----------] 3 tests from PrintEbin
3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (1 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (0 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (1 ms)
3: [----------] 3 tests from PrintEbin (2 ms total)
3:
3: [----------] 4 tests from ShakeTest
3: [ RUN ] ShakeTest.ConstrainsOneBond
3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
3: [----------] 4 tests from ShakeTest (0 ms total)
3:
3: [----------] 1 test from NullSignalTest
3: [ RUN ] NullSignalTest.NullSignallerWorks
3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
3: [----------] 1 test from NullSignalTest (0 ms total)
3:
3: [----------] 7 tests from SignalTest
3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
3: [----------] 7 tests from SignalTest (1 ms total)
3:
3: [----------] 9 tests from UpdateGroups
3: [ RUN ] UpdateGroups.ethaneUA
3: [ OK ] UpdateGroups.ethaneUA (0 ms)
3: [ RUN ] UpdateGroups.methane
3: [ OK ] UpdateGroups.methane (0 ms)
3: [ RUN ] UpdateGroups.ethane
3: [ OK ] UpdateGroups.ethane (0 ms)
3: [ RUN ] UpdateGroups.butaneUA
3: [ OK ] UpdateGroups.butaneUA (0 ms)
3: [ RUN ] UpdateGroups.waterThreeSite
3: [ OK ] UpdateGroups.waterThreeSite (0 ms)
3: [ RUN ] UpdateGroups.waterFourSite
3: [ OK ] UpdateGroups.waterFourSite (0 ms)
3: [ RUN ] UpdateGroups.fourAtomsWithSettle
3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
3: [ RUN ] UpdateGroups.waterFlexAngle
3: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
3: [ RUN ] UpdateGroups.twoMoltypes
3: [ OK ] UpdateGroups.twoMoltypes (0 ms)
3: [----------] 9 tests from UpdateGroups (0 ms total)
3:
3: [----------] 1 test from UpdateGroupsCog
3: [ RUN ] UpdateGroupsCog.ComputesCogs
3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms)
3: [----------] 1 test from UpdateGroupsCog (2 ms total)
3:
3: [----------] 24 tests from WithParameters/SettleTest
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms)
3: [----------] 24 tests from WithParameters/SettleTest (2 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 50 tests from 8 test cases ran. (7 ms total)
3: [ PASSED ] 50 tests.
3/40 Test #3: MdlibUnitTest .................... Passed 0.03 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4: [==========] Running 3 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 3 tests from ElectricFieldTest
4: [ RUN ] ElectricFieldTest.Static
4: [ OK ] ElectricFieldTest.Static (0 ms)
4: [ RUN ] ElectricFieldTest.Oscillating
4: [ OK ] ElectricFieldTest.Oscillating (0 ms)
4: [ RUN ] ElectricFieldTest.Pulsed
4: [ OK ] ElectricFieldTest.Pulsed (0 ms)
4: [----------] 3 tests from ElectricFieldTest (0 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 3 tests from 1 test case ran. (1 ms total)
4: [ PASSED ] 3 tests.
4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.02 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 15 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 15 tests from BondedTest
5: [ RUN ] BondedTest.BondAnglePbcNone
5: [ OK ] BondedTest.BondAnglePbcNone (0 ms)
5: [ RUN ] BondedTest.BondAnglePbcXy
5: [ OK ] BondedTest.BondAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.BondAnglePbcXyz
5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcNone
5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXy
5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXyz
5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcNo
5: [ OK ] BondedTest.IfuncBondsPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXy
5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXyz
5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcNo
5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXy
5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ
5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo
5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms)
5: [----------] 15 tests from BondedTest (3 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 15 tests from 1 test case ran. (3 ms total)
5: [ PASSED ] 15 tests.
5/40 Test #5: ListedForcesTest ................. Passed 0.02 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6: [==========] Running 55 tests from 6 test cases.
6: [----------] Global test environment set-up.
6: [----------] 3 tests from CommandLineHelpModuleTest
6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms)
6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
6: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total)
6:
6: [----------] 6 tests from CommandLineHelpWriterTest
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
6: [----------] 6 tests from CommandLineHelpWriterTest (3 ms total)
6:
6: [----------] 6 tests from CommandLineModuleManagerTest
6: [ RUN ] CommandLineModuleManagerTest.RunsModule
6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
6: [----------] 6 tests from CommandLineModuleManagerTest (4 ms total)
6:
6: [----------] 13 tests from CommandLineParserTest
6: [ RUN ] CommandLineParserTest.HandlesSingleValues
6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesString
6: [ OK ] CommandLineParserTest.HandlesString (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (1 ms)
6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
6: [----------] 13 tests from CommandLineParserTest (2 ms total)
6:
6: [----------] 6 tests from CommandLineProgramContextTest
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
6:
6: [----------] 21 tests from ParseCommonArgsTest
6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (1 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (2 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
6: [----------] 21 tests from ParseCommonArgsTest (8 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 55 tests from 6 test cases ran. (23 ms total)
6: [ PASSED ] 55 tests.
6/40 Test #6: CommandLineUnitTests ............. Passed 0.04 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 9 tests from 2 test cases.
7: [----------] Global test environment set-up.
7: [----------] 7 tests from HashedMap
7: [ RUN ] HashedMap.InsertsFinds
7: [ OK ] HashedMap.InsertsFinds (0 ms)
7: [ RUN ] HashedMap.NegativeKeysWork
7: [ OK ] HashedMap.NegativeKeysWork (0 ms)
7: [ RUN ] HashedMap.InsertsErases
7: [ OK ] HashedMap.InsertsErases (0 ms)
7: [ RUN ] HashedMap.InsertsOrAssigns
7: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
7: [ RUN ] HashedMap.Clears
7: [ OK ] HashedMap.Clears (0 ms)
7: [ RUN ] HashedMap.LinkedEntries
7: [ OK ] HashedMap.LinkedEntries (0 ms)
7: [ RUN ] HashedMap.ResizesTable
7: [ OK ] HashedMap.ResizesTable (0 ms)
7: [----------] 7 tests from HashedMap (0 ms total)
7:
7: [----------] 2 tests from LocalAtomSetManager
7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
7: [----------] 2 tests from LocalAtomSetManager (0 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 9 tests from 2 test cases ran. (0 ms total)
7: [ PASSED ] 9 tests.
7/40 Test #7: DomDecTests ...................... Passed 0.02 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 257 tests from 10 test cases.
8: [----------] Global test environment set-up.
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (6 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total)
8:
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (3 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (3 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (3 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (3 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (3 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (5 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (5 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (5 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (4 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (5 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (5 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (4 ms)
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (120 ms total)
8:
8: [----------] 144 tests from SaneInput/PmeGatherTest
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms)
8: [----------] 144 tests from SaneInput/PmeGatherTest (154 ms total)
8:
8: [----------] 16 tests from SaneInput/PmeSolveTest
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (4 ms)
8: [----------] 16 tests from SaneInput/PmeSolveTest (51 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (17 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (30 ms total)
8:
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (47 ms total)
8:
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms)
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (57 ms total)
8:
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (73 ms total)
8:
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (10 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (14 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (16 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (21 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (24 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (10 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (13 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (16 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (19 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (23 ms)
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (226 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 257 tests from 10 test cases ran. (802 ms total)
8: [ PASSED ] 257 tests.
8/40 Test #8: EwaldUnitTests ................... Passed 0.89 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 14 tests from 4 test cases.
9: [----------] Global test environment set-up.
9: [----------] 2 tests from ManyFFTTest
9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (8 ms)
9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (14 ms)
9: [----------] 2 tests from ManyFFTTest (23 ms total)
9:
9: [----------] 1 test from FFTTest
9: [ RUN ] FFTTest.Real2DLength18_15Test
9: [ OK ] FFTTest.Real2DLength18_15Test (5 ms)
9: [----------] 1 test from FFTTest (6 ms total)
9:
9: [----------] 1 test from FFFTest3D
9: [ RUN ] FFFTest3D.Real5_6_9
9: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
9: [----------] 1 test from FFFTest3D (3 ms total)
9:
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (4 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (9 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (12 ms)
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (34 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 14 tests from 4 test cases ran. (67 ms total)
9: [ PASSED ] 14 tests.
9/40 Test #9: FFTUnitTests ..................... Passed 0.09 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 60 tests from 19 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Swap
10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Comparison
10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Swap
10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Comparison
10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Swap
10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Comparison
10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Swap
10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Comparison
10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
10:
10: [----------] 1 test from HostAllocatorUntypedTest
10: [ RUN ] HostAllocatorUntypedTest.Comparison
10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from HostAllocatorUntypedTest (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/2 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 60 tests from 19 test cases ran. (14 ms total)
10: [ PASSED ] 60 tests.
10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.04 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 4 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 4 tests from HardwareTopologyTest
11: [ RUN ] HardwareTopologyTest.Execute
11: [ OK ] HardwareTopologyTest.Execute (12 ms)
11: [ RUN ] HardwareTopologyTest.HwlocExecute
11: [ OK ] HardwareTopologyTest.HwlocExecute (11 ms)
11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (12 ms)
11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
11: /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp:205: Failure
11: Expected: (c.size) > (0), actual: 0 vs 0
11: /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp:205: Failure
11: Expected: (c.size) > (0), actual: 0 vs 0
11: [ FAILED ] HardwareTopologyTest.NumaCacheSelfconsistency (11 ms)
11: [----------] 4 tests from HardwareTopologyTest (47 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 4 tests from 1 test case ran. (48 ms total)
11: [ PASSED ] 3 tests.
11: [ FAILED ] 1 test, listed below:
11: [ FAILED ] HardwareTopologyTest.NumaCacheSelfconsistency
11:
11: 1 FAILED TEST
11/40 Test #11: HardwareUnitTests ................***Failed 0.06 sec
[==========] Running 4 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 4 tests from HardwareTopologyTest
[ RUN ] HardwareTopologyTest.Execute
[ OK ] HardwareTopologyTest.Execute (12 ms)
[ RUN ] HardwareTopologyTest.HwlocExecute
[ OK ] HardwareTopologyTest.HwlocExecute (11 ms)
[ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
[ OK ] HardwareTopologyTest.ProcessorSelfconsistency (12 ms)
[ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
/<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp:205: Failure
Expected: (c.size) > (0), actual: 0 vs 0
/<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp:205: Failure
Expected: (c.size) > (0), actual: 0 vs 0
[ FAILED ] HardwareTopologyTest.NumaCacheSelfconsistency (11 ms)
[----------] 4 tests from HardwareTopologyTest (47 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 1 test case ran. (48 ms total)
[ PASSED ] 3 tests.
[ FAILED ] 1 test, listed below:
[ FAILED ] HardwareTopologyTest.NumaCacheSelfconsistency
1 FAILED TEST
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 112 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from EmptyArrayRefWithPaddingTest
12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
12:
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (1 ms total)
12:
12: [----------] 6 tests from StructureSimilarityTest
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
12: [----------] 6 tests from StructureSimilarityTest (0 ms total)
12:
12: [----------] 21 tests from FunctionTest
12: [ RUN ] FunctionTest.StaticLog2
12: [ OK ] FunctionTest.StaticLog2 (0 ms)
12: [ RUN ] FunctionTest.Log2I32Bit
12: [ OK ] FunctionTest.Log2I32Bit (1 ms)
12: [ RUN ] FunctionTest.Log2I64Bit
12: [ OK ] FunctionTest.Log2I64Bit (0 ms)
12: [ RUN ] FunctionTest.GreatestCommonDivisor
12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
12: [ RUN ] FunctionTest.InvsqrtFloat
12: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
12: [ RUN ] FunctionTest.InvsqrtDouble
12: [ OK ] FunctionTest.InvsqrtDouble (1 ms)
12: [ RUN ] FunctionTest.InvsqrtInteger
12: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
12: [ RUN ] FunctionTest.InvcbrtFloat
12: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
12: [ RUN ] FunctionTest.InvcbrtDouble
12: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
12: [ RUN ] FunctionTest.InvcbrtInteger
12: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
12: [ RUN ] FunctionTest.SixthrootFloat
12: [ OK ] FunctionTest.SixthrootFloat (0 ms)
12: [ RUN ] FunctionTest.SixthrootDouble
12: [ OK ] FunctionTest.SixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.SixthrootInteger
12: [ OK ] FunctionTest.SixthrootInteger (1 ms)
12: [ RUN ] FunctionTest.InvsixthrootFloat
12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootDouble
12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootInteger
12: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
12: [ RUN ] FunctionTest.Powers
12: [ OK ] FunctionTest.Powers (0 ms)
12: [ RUN ] FunctionTest.ErfInvFloat
12: [ OK ] FunctionTest.ErfInvFloat (0 ms)
12: [ RUN ] FunctionTest.ErfInvDouble
12: [ OK ] FunctionTest.ErfInvDouble (0 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms)
12: [----------] 21 tests from FunctionTest (6 ms total)
12:
12: [----------] 2 tests from InvertMatrixTest
12: [ RUN ] InvertMatrixTest.IdentityIsImpotent
12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertMatrixTest.ComputesInverse
12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
12: [----------] 2 tests from InvertMatrixTest (0 ms total)
12:
12: [----------] 2 tests from InvertBoxMatrixTest
12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanCopyAssign
12: [ OK ] PaddedVectorTest/0.CanCopyAssign (1 ms)
12: [ RUN ] PaddedVectorTest/0.CanMoveAssign
12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanSwap
12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanCopyAssign
12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanMoveAssign
12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanSwap
12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanCopyAssign
12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanMoveAssign
12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanSwap
12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanCopyAssign
12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanMoveAssign
12: [ OK ] PaddedVectorTest/3.CanMoveAssign (1 ms)
12: [ RUN ] PaddedVectorTest/3.CanSwap
12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/3 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanCopyAssign
12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanMoveAssign
12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanSwap
12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanCopyAssign
12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanMoveAssign
12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanSwap
12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanCopyAssign
12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanMoveAssign
12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanSwap
12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/6 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanCopyAssign
12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanMoveAssign
12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanSwap
12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanCopyAssign
12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanMoveAssign
12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanSwap
12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanCopyAssign
12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanMoveAssign
12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanSwap
12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total)
12:
12: [----------] 33 tests from RVecTest
12: [ RUN ] RVecTest.CanBeStoredInVector
12: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAsMutable_rvec
12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Array
12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
12: [ RUN ] RVecTest.CanAddRVecToRvec
12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanAddAssignRVecToRvec
12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractRVecFromRvec
12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanDotProductRVecByRvec
12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanCrossProductRVecByRvec
12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVecInplace
12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
12: [ RUN ] RVecTest.CanScaleRVec
12: [ OK ] RVecTest.CanScaleRVec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVec
12: [ OK ] RVecTest.CanDivideRVec (0 ms)
12: [ RUN ] RVecTest.CanDoUnitvFromRVec
12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanSqLengthOfRVec
12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanLengthOfRVec
12: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToRVec
12: [ OK ] RVecTest.CanCastToRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToDVec
12: [ OK ] RVecTest.CanCastToDVec (0 ms)
12: [ RUN ] RVecTest.CanLeftScalarMultiply
12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanRightScalarMultiply
12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanGetUnitvFromRVec
12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanGetSqLengthOfRVec
12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanGetLengthOfRVec
12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoCrossProductOfRVec
12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoDotProductOfRVec
12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
12: [ RUN ] RVecTest.WorksAs_dvec_Reference
12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_ivec_Reference
12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Reference
12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
12: [ RUN ] RVecTest.CopyConstructorWorks
12: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
12: [ RUN ] RVecTest.CopyAssignmentWorks
12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
12: [ RUN ] RVecTest.MoveConstructorWorks
12: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
12: [ RUN ] RVecTest.MoveAssignmentWorks
12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
12: [----------] 33 tests from RVecTest (1 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 112 tests from 20 test cases ran. (12 ms total)
12: [ PASSED ] 112 tests.
12/40 Test #12: MathUnitTests .................... Passed 0.04 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 17 tests from ThreadAffinityTest
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
13: NOTE: Affinity setting failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
13: NOTE: Affinity setting for 1/2 threads failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms)
13: [----------] 17 tests from ThreadAffinityTest (15 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 1 test case ran. (16 ms total)
13: [ PASSED ] 17 tests.
13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.03 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 13 tests from 2 test cases.
14: [----------] Global test environment set-up.
14: [----------] 6 tests from ThreadAffinityMultiRankTest
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (8 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (12 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (16 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (13 ms)
14: [----------] 6 tests from ThreadAffinityMultiRankTest (60 ms total)
14:
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (18 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (11 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (17 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (54 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (8 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (9 ms)
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (122 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 13 tests from 2 test cases ran. (182 ms total)
14: [ PASSED ] 13 tests.
14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.20 sec
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 22 tests from 4 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from TextTableFormatterTest
15: [ RUN ] TextTableFormatterTest.HandlesBasicCase
15: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesIndentation
15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
15: [----------] 6 tests from TextTableFormatterTest (3 ms total)
15:
15: [----------] 3 tests from HelpManagerTest
15: [ RUN ] HelpManagerTest.HandlesRootTopic
15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
15: [ RUN ] HelpManagerTest.HandlesSubTopics
15: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
15: [ RUN ] HelpManagerTest.HandlesInvalidTopics
15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
15: [----------] 3 tests from HelpManagerTest (1 ms total)
15:
15: [----------] 2 tests from HelpTopicFormattingTest
15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms)
15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
15:
15: [----------] 11 tests from HelpWriterContextTest
15: [ RUN ] HelpWriterContextTest.FormatsParagraphs
15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralText
15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsBulletList
15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsGridTable
15: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsTitles
15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
15: [----------] 11 tests from HelpWriterContextTest (4 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 22 tests from 4 test cases ran. (10 ms total)
15: [ PASSED ] 22 tests.
15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.03 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 110 tests from 18 test cases.
16: [----------] Global test environment set-up.
16: [----------] 5 tests from AbstractOptionStorageTest
16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
16: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
16:
16: [----------] 8 tests from FileNameOptionTest
16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (1 ms)
16: [----------] 8 tests from FileNameOptionTest (1 ms total)
16:
16: [----------] 15 tests from FileNameOptionManagerTest
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total)
16:
16: [----------] 1 test from OptionsTest
16: [ RUN ] OptionsTest.FailsOnNonsafeStorage
16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
16: [----------] 1 test from OptionsTest (0 ms total)
16:
16: [----------] 9 tests from OptionsAssignerTest
16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (1 ms)
16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMissingValue
16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesExtraValue
16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesGroups
16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesSections
16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
16: [----------] 9 tests from OptionsAssignerTest (1 ms total)
16:
16: [----------] 4 tests from OptionsAssignerBooleanTest
16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
16: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
16:
16: [----------] 13 tests from OptionsAssignerIntegerTest
16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
16: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
16:
16: [----------] 5 tests from OptionsAssignerDoubleTest
16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
16:
16: [----------] 9 tests from OptionsAssignerStringTest
16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (1 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
16:
16: [----------] 6 tests from OptionsAssignerEnumTest
16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
16:
16: [----------] 8 tests from RepeatingOptionSectionTest
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total)
16:
16: [----------] 1 test from TimeUnitManagerTest
16: [ RUN ] TimeUnitManagerTest.BasicOperations
16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
16: [----------] 1 test from TimeUnitManagerTest (0 ms total)
16:
16: [----------] 4 tests from TimeUnitBehaviorTest
16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (1 ms)
16: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
16:
16: [----------] 2 tests from TreeValueSupportAssignTest
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
16:
16: [----------] 1 test from TreeValueSupportAssignErrorTest
16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
16:
16: [----------] 5 tests from TreeValueSupportCheckTest
16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
16: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
16:
16: [----------] 6 tests from TreeValueSupportAdjustTest
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total)
16:
16: [----------] 8 tests from TreeValueSupportTest
16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsInt64Option
16: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsStringOption
16: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsFloatOption
16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumOption
16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
16: [----------] 8 tests from TreeValueSupportTest (3 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 110 tests from 18 test cases ran. (16 ms total)
16: [ PASSED ] 110 tests.
16/40 Test #16: OptionsUnitTests ................. Passed 0.04 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 44 tests from 10 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from ExponentialDistributionTest
17: [ RUN ] ExponentialDistributionTest.Output
17: [ OK ] ExponentialDistributionTest.Output (0 ms)
17: [ RUN ] ExponentialDistributionTest.Logical
17: [ OK ] ExponentialDistributionTest.Logical (0 ms)
17: [ RUN ] ExponentialDistributionTest.Reset
17: [ OK ] ExponentialDistributionTest.Reset (0 ms)
17: [ RUN ] ExponentialDistributionTest.AltParam
17: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
17:
17: [----------] 4 tests from GammaDistributionTest
17: [ RUN ] GammaDistributionTest.Output
17: [ OK ] GammaDistributionTest.Output (0 ms)
17: [ RUN ] GammaDistributionTest.Logical
17: [ OK ] GammaDistributionTest.Logical (0 ms)
17: [ RUN ] GammaDistributionTest.Reset
17: [ OK ] GammaDistributionTest.Reset (0 ms)
17: [ RUN ] GammaDistributionTest.AltParam
17: [ OK ] GammaDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from GammaDistributionTest (1 ms total)
17:
17: [----------] 4 tests from NormalDistributionTest
17: [ RUN ] NormalDistributionTest.Output
17: [ OK ] NormalDistributionTest.Output (0 ms)
17: [ RUN ] NormalDistributionTest.Logical
17: [ OK ] NormalDistributionTest.Logical (0 ms)
17: [ RUN ] NormalDistributionTest.Reset
17: [ OK ] NormalDistributionTest.Reset (0 ms)
17: [ RUN ] NormalDistributionTest.AltParam
17: [ OK ] NormalDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from NormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from SeedTest
17: [ RUN ] SeedTest.makeRandomSeed
17: [ OK ] SeedTest.makeRandomSeed (0 ms)
17: [----------] 1 test from SeedTest (0 ms total)
17:
17: [----------] 6 tests from TabulatedNormalDistributionTest
17: [ RUN ] TabulatedNormalDistributionTest.Output14
17: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Output16
17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Logical
17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Reset
17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.AltParam
17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
17: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
17:
17: [----------] 1 test from TabulatedNormalDistributionTableTest
17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
17: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
17:
17: [----------] 6 tests from ThreeFry2x64Test
17: [ RUN ] ThreeFry2x64Test.Logical
17: [ OK ] ThreeFry2x64Test.Logical (0 ms)
17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
17: [ RUN ] ThreeFry2x64Test.Reseed
17: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
17: [ RUN ] ThreeFry2x64Test.Discard
17: [ OK ] ThreeFry2x64Test.Discard (0 ms)
17: [ RUN ] ThreeFry2x64Test.InvalidCounter
17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
17: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
17:
17: [----------] 4 tests from UniformIntDistributionTest
17: [ RUN ] UniformIntDistributionTest.Output
17: [ OK ] UniformIntDistributionTest.Output (1 ms)
17: [ RUN ] UniformIntDistributionTest.Logical
17: [ OK ] UniformIntDistributionTest.Logical (0 ms)
17: [ RUN ] UniformIntDistributionTest.Reset
17: [ OK ] UniformIntDistributionTest.Reset (0 ms)
17: [ RUN ] UniformIntDistributionTest.AltParam
17: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
17:
17: [----------] 5 tests from UniformRealDistributionTest
17: [ RUN ] UniformRealDistributionTest.GenerateCanonical
17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Output
17: [ OK ] UniformRealDistributionTest.Output (0 ms)
17: [ RUN ] UniformRealDistributionTest.Logical
17: [ OK ] UniformRealDistributionTest.Logical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Reset
17: [ OK ] UniformRealDistributionTest.Reset (0 ms)
17: [ RUN ] UniformRealDistributionTest.AltParam
17: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
17: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
17:
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 44 tests from 10 test cases ran. (15 ms total)
17: [ PASSED ] 44 tests.
17/40 Test #17: RandomUnitTests .................. Passed 0.05 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 1 test from 1 test case.
18: [----------] Global test environment set-up.
18: [----------] 1 test from RestraintManager
18: [ RUN ] RestraintManager.restraintList
18: [ OK ] RestraintManager.restraintList (0 ms)
18: [----------] 1 test from RestraintManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 1 test from 1 test case ran. (0 ms total)
18: [ PASSED ] 1 test.
18/40 Test #18: RestraintTests ................... Passed 0.02 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 16 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms)
19: [ RUN ] SplineTableTest/0.Sinc
19: [ OK ] SplineTableTest/0.Sinc (2 ms)
19: [ RUN ] SplineTableTest/0.LJ12
19: [ OK ] SplineTableTest/0.LJ12 (27 ms)
19: [ RUN ] SplineTableTest/0.PmeCorrection
19: [ OK ] SplineTableTest/0.PmeCorrection (3 ms)
19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
19: [ RUN ] SplineTableTest/0.TwoFunctions
19: [ OK ] SplineTableTest/0.TwoFunctions (54 ms)
19: [ RUN ] SplineTableTest/0.ThreeFunctions
19: [ OK ] SplineTableTest/0.ThreeFunctions (61 ms)
19: [----------] 8 tests from SplineTableTest/0 (153 ms total)
19:
19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (3 ms)
19: [ RUN ] SplineTableTest/1.Sinc
19: [ OK ] SplineTableTest/1.Sinc (1 ms)
19: [ RUN ] SplineTableTest/1.LJ12
19: [ OK ] SplineTableTest/1.LJ12 (5 ms)
19: [ RUN ] SplineTableTest/1.PmeCorrection
19: [ OK ] SplineTableTest/1.PmeCorrection (2 ms)
19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
19: [ RUN ] SplineTableTest/1.TwoFunctions
19: [ OK ] SplineTableTest/1.TwoFunctions (8 ms)
19: [ RUN ] SplineTableTest/1.ThreeFunctions
19: [ OK ] SplineTableTest/1.ThreeFunctions (10 ms)
19: [----------] 8 tests from SplineTableTest/1 (32 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 16 tests from 2 test cases ran. (185 ms total)
19: [ PASSED ] 16 tests.
19/40 Test #19: TableUnitTests ................... Passed 0.20 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 1 test case.
20: [----------] Global test environment set-up.
20: [----------] 3 tests from GpuIdStringHandlingTest
20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork
20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (1 ms)
20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid
20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow
20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms)
20: [----------] 3 tests from GpuIdStringHandlingTest (2 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 1 test case ran. (2 ms total)
20: [ PASSED ] 3 tests.
20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.02 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 325 tests from 52 test cases.
21: [----------] Global test environment set-up.
21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.Move
21: [ OK ] AllocatorTest/0.Move (0 ms)
21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/0 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.Move
21: [ OK ] AllocatorTest/1.Move (0 ms)
21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/1 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.Move
21: [ OK ] AllocatorTest/2.Move (0 ms)
21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/2 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.Move
21: [ OK ] AllocatorTest/3.Move (0 ms)
21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/3 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.Move
21: [ OK ] AllocatorTest/4.Move (0 ms)
21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/4 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/5.Move
21: [ OK ] AllocatorTest/5.Move (0 ms)
21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/5 (1 ms total)
21:
21: [----------] 1 test from AllocatorUntypedTest
21: [ RUN ] AllocatorUntypedTest.Comparison
21: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
21: [----------] 1 test from AllocatorUntypedTest (0 ms total)
21:
21: [----------] 1 test from EmptyArrayRefTest
21: [ RUN ] EmptyArrayRefTest.IsEmpty
21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyArrayRefTest (0 ms total)
21:
21: [----------] 1 test from EmptyConstArrayRefTest
21: [ RUN ] EmptyConstArrayRefTest.IsEmpty
21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (1 ms)
21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (1 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
21:
21: [----------] 4 tests from KeyValueTreeSerializerTest
21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
21: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total)
21:
21: [----------] 6 tests from TreeValueTransformTest
21: [ RUN ] TreeValueTransformTest.SimpleTransforms
21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromString
21: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
21: [ RUN ] TreeValueTransformTest.ScopedTransformRules
21: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
21: [----------] 6 tests from TreeValueTransformTest (2 ms total)
21:
21: [----------] 1 test from TreeValueTransformErrorTest
21: [ RUN ] TreeValueTransformErrorTest.ConversionError
21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
21:
21: [----------] 2 tests from RegexBasicTest
21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported
21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms)
21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported
21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms)
21: [----------] 2 tests from RegexBasicTest (2 ms total)
21:
21: [----------] 5 tests from LoggerTest
21: [ RUN ] LoggerTest.EmptyLoggerWorks
21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
21: [ RUN ] LoggerTest.LogsToStream
21: [ OK ] LoggerTest.LogsToStream (0 ms)
21: [ RUN ] LoggerTest.LogsToFile
21: [ OK ] LoggerTest.LogsToFile (1 ms)
21: [ RUN ] LoggerTest.LevelFilteringWorks
21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
21: [ RUN ] LoggerTest.LogsToMultipleStreams
21: [ OK ] LoggerTest.LogsToMultipleStreams (1 ms)
21: [----------] 5 tests from LoggerTest (2 ms total)
21:
21: [----------] 4 tests from MutexBasicTest
21: [ RUN ] MutexBasicTest.CanBeMade
21: [ OK ] MutexBasicTest.CanBeMade (0 ms)
21: [ RUN ] MutexBasicTest.CanBeLocked
21: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeTryLocked
21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
21: [----------] 4 tests from MutexBasicTest (0 ms total)
21:
21: [----------] 3 tests from MutexTaskTest
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
21: [----------] 3 tests from MutexTaskTest (0 ms total)
21:
21: [----------] 4 tests from PathTest
21: [ RUN ] PathTest.StripSourcePrefixWorks
21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks
21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathWorks
21: [ OK ] PathTest.GetParentPathWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathAndBasenameWorks
21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms)
21: [----------] 4 tests from PathTest (0 ms total)
21:
21: [----------] 2 tests from PhysicalNodeCommunicatorTest
21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
21:
21: [----------] 7 tests from StringUtilityTest
21: [ RUN ] StringUtilityTest.StartsWith
21: [ OK ] StringUtilityTest.StartsWith (0 ms)
21: [ RUN ] StringUtilityTest.EndsWith
21: [ OK ] StringUtilityTest.EndsWith (0 ms)
21: [ RUN ] StringUtilityTest.StripSuffixIfPresent
21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
21: [ RUN ] StringUtilityTest.StripString
21: [ OK ] StringUtilityTest.StripString (0 ms)
21: [ RUN ] StringUtilityTest.SplitString
21: [ OK ] StringUtilityTest.SplitString (1 ms)
21: [ RUN ] StringUtilityTest.SplitDelimitedString
21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
21: [----------] 7 tests from StringUtilityTest (2 ms total)
21:
21: [----------] 2 tests from FormatStringTest
21: [ RUN ] FormatStringTest.HandlesBasicFormatting
21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
21: [ RUN ] FormatStringTest.HandlesLongStrings
21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
21: [----------] 2 tests from FormatStringTest (0 ms total)
21:
21: [----------] 1 test from StringFormatterTest
21: [ RUN ] StringFormatterTest.HandlesBasicFormatting
21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
21: [----------] 1 test from StringFormatterTest (0 ms total)
21:
21: [----------] 1 test from formatAndJoinTest
21: [ RUN ] formatAndJoinTest.Works
21: [ OK ] formatAndJoinTest.Works (0 ms)
21: [----------] 1 test from formatAndJoinTest (0 ms total)
21:
21: [----------] 1 test from JoinStringsTest
21: [ RUN ] JoinStringsTest.Works
21: [ OK ] JoinStringsTest.Works (0 ms)
21: [----------] 1 test from JoinStringsTest (0 ms total)
21:
21: [----------] 6 tests from ReplaceAllTest
21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesNoMatches
21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
21: [----------] 6 tests from ReplaceAllTest (0 ms total)
21:
21: [----------] 10 tests from TextLineWrapperTest
21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectly
21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndent
21: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms)
21: [----------] 10 tests from TextLineWrapperTest (3 ms total)
21:
21: [----------] 6 tests from TextWriterTest
21: [ RUN ] TextWriterTest.WritesLines
21: [ OK ] TextWriterTest.WritesLines (0 ms)
21: [ RUN ] TextWriterTest.WritesLinesInParts
21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
21: [ RUN ] TextWriterTest.WritesWrappedLines
21: [ OK ] TextWriterTest.WritesWrappedLines (1 ms)
21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
21: [ RUN ] TextWriterTest.TracksNewlines
21: [ OK ] TextWriterTest.TracksNewlines (0 ms)
21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
21: [----------] 6 tests from TextWriterTest (1 ms total)
21:
21: [----------] 1 test from TypeTraitsTest
21: [ RUN ] TypeTraitsTest.IsIntegralConstant
21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
21: [----------] 1 test from TypeTraitsTest (0 ms total)
21:
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
21:
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
21:
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (1 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
21:
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
21:
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 325 tests from 52 test cases ran. (35 ms total)
21: [ PASSED ] 325 tests.
21/40 Test #21: UtilityUnitTests ................. Passed 0.09 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 2 tests from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from PhysicalNodeCommunicatorTest
22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
22: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 2 tests from 1 test case ran. (3 ms total)
22: [ PASSED ] 2 tests.
22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.02 sec
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 17 tests from 4 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from FileMD5Test
23: [ RUN ] FileMD5Test.CanComputeMD5
23: [ OK ] FileMD5Test.CanComputeMD5 (2 ms)
23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms)
23: [----------] 2 tests from FileMD5Test (2 ms total)
23:
23: [----------] 9 tests from ReadTest
23: [ RUN ] ReadTest.get_eint_ReadsInteger
23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_eint64_ReadsInteger
23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsInteger
23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsFloat
23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
23: [ RUN ] ReadTest.get_ereal_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not a
23: real value
23:
23:
23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
23: [----------] 9 tests from ReadTest (1 ms total)
23:
23: [----------] 2 tests from TngTest
23: [ RUN ] TngTest.CanOpenTngFile
23: [ OK ] TngTest.CanOpenTngFile (0 ms)
23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
23: [----------] 2 tests from TngTest (0 ms total)
23:
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (2 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (5 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (11 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 17 tests from 4 test cases ran. (14 ms total)
23: [ PASSED ] 17 tests.
23/40 Test #23: FileIOTests ...................... Passed 0.03 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 5 tests from 1 test case.
24: [----------] Global test environment set-up.
24: [----------] 5 tests from PullTest
24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
24: [----------] 5 tests from PullTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 5 tests from 1 test case ran. (1 ms total)
24: [ PASSED ] 5 tests.
24/40 Test #24: PullTest ......................... Passed 0.02 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 12 tests from 4 test cases.
25: [----------] Global test environment set-up.
25: [----------] 1 test from BiasTest
25: [ RUN ] BiasTest.DetectsCovering
25: [ OK ] BiasTest.DetectsCovering (1 ms)
25: [----------] 1 test from BiasTest (1 ms total)
25:
25: [----------] 1 test from gridTest
25: [ RUN ] gridTest.neighborhood
25: [ OK ] gridTest.neighborhood (3 ms)
25: [----------] 1 test from gridTest (3 ms total)
25:
25: [----------] 8 tests from WithParameters/BiasTest
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms)
25: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
25:
25: [----------] 2 tests from WithParameters/BiasStateTest
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
25: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 12 tests from 4 test cases ran. (12 ms total)
25: [ PASSED ] 12 tests.
25/40 Test #25: AwhTest .......................... Passed 0.03 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 86 tests from 3 test cases.
26: [----------] Global test environment set-up.
26: [----------] 41 tests from SimdScalarTest
26: [ RUN ] SimdScalarTest.load
26: [ OK ] SimdScalarTest.load (0 ms)
26: [ RUN ] SimdScalarTest.loadU
26: [ OK ] SimdScalarTest.loadU (0 ms)
26: [ RUN ] SimdScalarTest.store
26: [ OK ] SimdScalarTest.store (0 ms)
26: [ RUN ] SimdScalarTest.storeU
26: [ OK ] SimdScalarTest.storeU (0 ms)
26: [ RUN ] SimdScalarTest.setZero
26: [ OK ] SimdScalarTest.setZero (0 ms)
26: [ RUN ] SimdScalarTest.andNot
26: [ OK ] SimdScalarTest.andNot (0 ms)
26: [ RUN ] SimdScalarTest.fma
26: [ OK ] SimdScalarTest.fma (0 ms)
26: [ RUN ] SimdScalarTest.fms
26: [ OK ] SimdScalarTest.fms (0 ms)
26: [ RUN ] SimdScalarTest.fnma
26: [ OK ] SimdScalarTest.fnma (0 ms)
26: [ RUN ] SimdScalarTest.fnms
26: [ OK ] SimdScalarTest.fnms (0 ms)
26: [ RUN ] SimdScalarTest.maskAdd
26: [ OK ] SimdScalarTest.maskAdd (0 ms)
26: [ RUN ] SimdScalarTest.maskzMul
26: [ OK ] SimdScalarTest.maskzMul (0 ms)
26: [ RUN ] SimdScalarTest.maskzFma
26: [ OK ] SimdScalarTest.maskzFma (0 ms)
26: [ RUN ] SimdScalarTest.abs
26: [ OK ] SimdScalarTest.abs (0 ms)
26: [ RUN ] SimdScalarTest.max
26: [ OK ] SimdScalarTest.max (0 ms)
26: [ RUN ] SimdScalarTest.min
26: [ OK ] SimdScalarTest.min (0 ms)
26: [ RUN ] SimdScalarTest.round
26: [ OK ] SimdScalarTest.round (0 ms)
26: [ RUN ] SimdScalarTest.trunc
26: [ OK ] SimdScalarTest.trunc (0 ms)
26: [ RUN ] SimdScalarTest.reduce
26: [ OK ] SimdScalarTest.reduce (0 ms)
26: [ RUN ] SimdScalarTest.testBits
26: [ OK ] SimdScalarTest.testBits (0 ms)
26: [ RUN ] SimdScalarTest.anyTrue
26: [ OK ] SimdScalarTest.anyTrue (0 ms)
26: [ RUN ] SimdScalarTest.selectByMask
26: [ OK ] SimdScalarTest.selectByMask (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMask
26: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
26: [ RUN ] SimdScalarTest.blend
26: [ OK ] SimdScalarTest.blend (0 ms)
26: [ RUN ] SimdScalarTest.cvtR2I
26: [ OK ] SimdScalarTest.cvtR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvttR2I
26: [ OK ] SimdScalarTest.cvttR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvtI2R
26: [ OK ] SimdScalarTest.cvtI2R (0 ms)
26: [ RUN ] SimdScalarTest.cvtF2D
26: [ OK ] SimdScalarTest.cvtF2D (0 ms)
26: [ RUN ] SimdScalarTest.cvtD2D
26: [ OK ] SimdScalarTest.cvtD2D (0 ms)
26: [ RUN ] SimdScalarTest.loadI
26: [ OK ] SimdScalarTest.loadI (0 ms)
26: [ RUN ] SimdScalarTest.loadUI
26: [ OK ] SimdScalarTest.loadUI (0 ms)
26: [ RUN ] SimdScalarTest.storeI
26: [ OK ] SimdScalarTest.storeI (0 ms)
26: [ RUN ] SimdScalarTest.storeUI
26: [ OK ] SimdScalarTest.storeUI (0 ms)
26: [ RUN ] SimdScalarTest.andNotI
26: [ OK ] SimdScalarTest.andNotI (0 ms)
26: [ RUN ] SimdScalarTest.testBitsI
26: [ OK ] SimdScalarTest.testBitsI (0 ms)
26: [ RUN ] SimdScalarTest.selectByMaskI
26: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMaskI
26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
26: [ RUN ] SimdScalarTest.blendI
26: [ OK ] SimdScalarTest.blendI (0 ms)
26: [ RUN ] SimdScalarTest.cvtB2IB
26: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
26: [ RUN ] SimdScalarTest.cvtIB2B
26: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
26: [ RUN ] SimdScalarTest.expandScalarsToTriplets
26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
26: [----------] 41 tests from SimdScalarTest (1 ms total)
26:
26: [----------] 8 tests from SimdScalarUtilTest
26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
26: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
26:
26: [----------] 37 tests from SimdScalarMathTest
26: [ RUN ] SimdScalarMathTest.copysign
26: [ OK ] SimdScalarMathTest.copysign (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPair
26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
26: [ RUN ] SimdScalarMathTest.inv
26: [ OK ] SimdScalarMathTest.inv (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrt
26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
26: [ RUN ] SimdScalarMathTest.log
26: [ OK ] SimdScalarMathTest.log (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2
26: [ OK ] SimdScalarMathTest.exp2 (0 ms)
26: [ RUN ] SimdScalarMathTest.exp
26: [ OK ] SimdScalarMathTest.exp (0 ms)
26: [ RUN ] SimdScalarMathTest.erf
26: [ OK ] SimdScalarMathTest.erf (0 ms)
26: [ RUN ] SimdScalarMathTest.erfc
26: [ OK ] SimdScalarMathTest.erfc (0 ms)
26: [ RUN ] SimdScalarMathTest.sincos
26: [ OK ] SimdScalarMathTest.sincos (0 ms)
26: [ RUN ] SimdScalarMathTest.sin
26: [ OK ] SimdScalarMathTest.sin (0 ms)
26: [ RUN ] SimdScalarMathTest.cos
26: [ OK ] SimdScalarMathTest.cos (0 ms)
26: [ RUN ] SimdScalarMathTest.tan
26: [ OK ] SimdScalarMathTest.tan (0 ms)
26: [ RUN ] SimdScalarMathTest.asin
26: [ OK ] SimdScalarMathTest.asin (0 ms)
26: [ RUN ] SimdScalarMathTest.acos
26: [ OK ] SimdScalarMathTest.acos (0 ms)
26: [ RUN ] SimdScalarMathTest.atan
26: [ OK ] SimdScalarMathTest.atan (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2
26: [ OK ] SimdScalarMathTest.atan2 (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrection
26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.invSingleAccuracy
26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.logSingleAccuracy
26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.expSingleAccuracy
26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
26: [----------] 37 tests from SimdScalarMathTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 86 tests from 3 test cases ran. (4 ms total)
26: [ PASSED ] 86 tests.
26/40 Test #26: SimdUnitTests .................... Passed 0.03 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 6 tests from 6 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from CompatibilityHelper
27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles
27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms)
27: [----------] 1 test from CompatibilityHelper (0 ms total)
27:
27: [----------] 1 test from NotNullConstruction
27: [ RUN ] NotNullConstruction.Works
27: [ OK ] NotNullConstruction.Works (0 ms)
27: [----------] 1 test from NotNullConstruction (0 ms total)
27:
27: [----------] 1 test from NotNullCasting
27: [ RUN ] NotNullCasting.Works
27: [ OK ] NotNullCasting.Works (0 ms)
27: [----------] 1 test from NotNullCasting (0 ms total)
27:
27: [----------] 1 test from NotNullAssignment
27: [ RUN ] NotNullAssignment.Works
27: [ OK ] NotNullAssignment.Works (0 ms)
27: [----------] 1 test from NotNullAssignment (0 ms total)
27:
27: [----------] 1 test from MakeNotNull
27: [ RUN ] MakeNotNull.Works
27: [ OK ] MakeNotNull.Works (0 ms)
27: [----------] 1 test from MakeNotNull (0 ms total)
27:
27: [----------] 1 test from NotNull
27: [ RUN ] NotNull.WorksInContainers
27: [ OK ] NotNull.WorksInContainers (0 ms)
27: [----------] 1 test from NotNull (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 6 tests from 6 test cases ran. (1 ms total)
27: [ PASSED ] 6 tests.
27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.02 sec
test 28
Start 28: GmxAnaTest
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
28: Test timeout computed to be: 600
28: [==========] Running 26 tests from 5 test cases.
28: [----------] Global test environment set-up.
28: [----------] 5 tests from Entropy
28: [ RUN ] Entropy.Schlitter_300_NoLinear
28: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
28: [ RUN ] Entropy.Schlitter_300_Linear
28: [ OK ] Entropy.Schlitter_300_Linear (1 ms)
28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_200_Linear
28: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
28: [----------] 5 tests from Entropy (1 ms total)
28:
28: [----------] 3 tests from MsdTest
28: [ RUN ] MsdTest.threeDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.threeDimensionalDiffusion (4 ms)
28: [ RUN ] MsdTest.twoDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
28: [ RUN ] MsdTest.oneDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.oneDimensionalDiffusion (3 ms)
28: [----------] 3 tests from MsdTest (10 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: trr version: GMX_trn_file (single precision)
28:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (6 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (4 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (4 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (29 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (8 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (7 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (7 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm)
28: -> frame 0 time 0.000
't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (6 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (7 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (44 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (3 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (4 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm)
28: -> frame 0 time 0.000
't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (3 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (16 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 26 tests from 5 test cases ran. (100 ms total)
28: [ PASSED ] 26 tests.
28/40 Test #28: GmxAnaTest ....................... Passed 0.12 sec
test 29
Start 29: GmxPreprocessTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 26 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 4 tests from GenconfTest
29: [ RUN ] GenconfTest.nbox_Works
29: [ OK ] GenconfTest.nbox_Works (2 ms)
29: [ RUN ] GenconfTest.nbox_norenumber_Works
29: [ OK ] GenconfTest.nbox_norenumber_Works (2 ms)
29: [ RUN ] GenconfTest.nbox_dist_Works
29: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
29: [ RUN ] GenconfTest.nbox_rot_Works
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: [ OK ] GenconfTest.nbox_rot_Works (2 ms)
29: [----------] 4 tests from GenconfTest (8 ms total)
29:
29: [----------] 5 tests from InsertMoleculesTest
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 8 atoms)!
29:
29: Added 1 molecules (out of 1 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
29:
29: Output configuration contains 8 atoms in 4 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (5 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 2 atoms)!
29:
Try 2 success (now 4 atoms)!
29:
Try 3 success (now 6 atoms)!
29:
Try 4 success (now 8 atoms)!
29:
Try 5 success (now 10 atoms)!
29:
29: Added 5 molecules (out of 5 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
29:
29: Output configuration contains 10 atoms in 10 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 8 atoms)!
29:
Try 2 success (now 10 atoms)!
29:
29: Added 2 molecules (out of 2 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
29:
29: Output configuration contains 10 atoms in 4 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (5 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 650 atoms)!
29:
Try 2 success (now 652 atoms)!
29:
Try 3 success (now 654 atoms)!
29:
Try 4 success (now 656 atoms)!
29:
29: Added 4 molecules (out of 4 requested)
29: Replaced 8 residues (24 atoms)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
29:
29: Output configuration contains 632 atoms in 212 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (20 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
29:
29:
Try 1 success (now 2 atoms)!
29:
Try 2 success (now 4 atoms)!
29:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
29:
Try 13 success (now 6 atoms)!
29:
29: Added 3 molecules (out of 4 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
29:
29: Output configuration contains 6 atoms in 3 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (5 ms)
29: [----------] 5 tests from InsertMoleculesTest (39 ms total)
29:
29: [----------] 12 tests from GetIrTest
29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: Ignoring obsolete mdp entry 'title'
29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (7 ms)
29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme
29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (7 ms)
29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (6 ms)
29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (7 ms)
29: [ RUN ] GetIrTest.EmptyInputWorks
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.EmptyInputWorks (6 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricField
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricField (7 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (7 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (6 ms)
29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys
29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (3 ms)
29: [ RUN ] GetIrTest.ImplicitSolventNoWorks
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ImplicitSolventNoWorks (7 ms)
29: [ RUN ] GetIrTest.ImplicitSolventYesWorks
29: [ OK ] GetIrTest.ImplicitSolventYesWorks (7 ms)
29: [ RUN ] GetIrTest.HandlesMimic
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.HandlesMimic (7 ms)
29: [----------] 12 tests from GetIrTest (77 ms total)
29:
29: [----------] 5 tests from SolvateTest
29: [ RUN ] SolvateTest.cs_box_Works
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 1x1x1 boxes
29: Solvent box contains 270 atoms in 90 residues
29: Removed 129 solvent atoms due to solvent-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 47 residues
29: Generated solvent containing 141 atoms in 47 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
29:
29: Output configuration contains 141 atoms in 47 residues
29: Volume : 1.331 (nm^3)
29: Density : 1056.36 (g/l)
29: Number of solvent molecules: 47
29:
29: [ OK ] SolvateTest.cs_box_Works (19 ms)
29: [ RUN ] SolvateTest.cs_cp_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 886 residues
29: Generated solvent containing 2658 atoms in 886 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
29:
29: Output configuration contains 2664 atoms in 888 residues
29: Volume : 27.2709 (nm^3)
29: Density : 974.777 (g/l)
29: Number of solvent molecules: 886
29:
29: [ OK ] SolvateTest.cs_cp_Works (71 ms)
29: [ RUN ] SolvateTest.cs_cp_p_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 886 residues
29: Generated solvent containing 2658 atoms in 886 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
29:
29: Output configuration contains 2664 atoms in 888 residues
29: Volume : 27.2709 (nm^3)
29: Density : 974.777 (g/l)
29: Number of solvent molecules: 886
29:
29: Processing topology
29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top)
29: [ OK ] SolvateTest.cs_cp_p_Works (72 ms)
29: [ RUN ] SolvateTest.shell_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 1902 solvent atoms more than 1.000000 nm from solute.
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 252 residues
29: Generated solvent containing 756 atoms in 252 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
29:
29: Output configuration contains 762 atoms in 254 residues
29: Volume : 27.2709 (nm^3)
29: Density : 279.3 (g/l)
29: Number of solvent molecules: 252
29:
29: [ OK ] SolvateTest.shell_Works (40 ms)
29: [ RUN ] SolvateTest.update_Topology_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 3x3x3 boxes
29: Solvent box contains 14952 atoms in 4984 residues
29: Removed 2787 solvent atoms due to solvent-solvent overlap
29: Removed 30 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 2 different molecule types:
29: HOH ( 3 atoms): 1876 residues
29: SOL ( 3 atoms): 2169 residues
29: Generated solvent containing 0 atoms in 0 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
29:
29: Output configuration contains 12141 atoms in 4047 residues
29: Volume : 125 (nm^3)
29: Density : 968.963 (g/l)
29: Number of solvent molecules: 4045
29:
29: Processing topology
29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
29: [ OK ] SolvateTest.update_Topology_Works (267 ms)
29: [----------] 5 tests from SolvateTest (469 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 26 tests from 4 test cases ran. (593 ms total)
29: [ PASSED ] 26 tests.
29/40 Test #29: GmxPreprocessTests ............... Passed 0.61 sec
test 30
Start 30: Pdb2gmxTest
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmxTest.xml"
30: Test timeout computed to be: 480
30: [==========] Running 80 tests from 6 test cases.
30: [----------] Global test environment set-up.
30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
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Atomtype 6
Atomtype 7
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Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (1072 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
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Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
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Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
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Atomtype 116
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Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
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Atomtype 132
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Atomtype 136
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Atomtype 141
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Atomtype 176
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Atomtype 180
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Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
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Atomtype 215
Atomtype 216
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Atomtype 218
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Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
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Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
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Atomtype 464
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Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
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Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
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Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
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Atomtype 660
Atomtype 661
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Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
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Atomtype 679
Atomtype 680
Atomtype 681
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Atomtype 687
Atomtype 688
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Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
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Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
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Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (1227 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (1114 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
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Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
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Atomtype 764
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Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
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Atomtype 806
Atomtype 807
Atomtype 808
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Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (999 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
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Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
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Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
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Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
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Atomtype 164
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Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
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Atomtype 171
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Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
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Atomtype 185
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Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
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Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
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Atomtype 205
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Atomtype 211
Atomtype 212
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Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
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Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
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Atomtype 264
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Atomtype 272
Atomtype 273
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Atomtype 276
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Atomtype 278
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Atomtype 282
Atomtype 283
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Atomtype 291
Atomtype 292
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Atomtype 297
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Atomtype 301
Atomtype 302
Atomtype 303
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Atomtype 305
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Atomtype 307
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Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
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Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
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Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
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Atomtype 342
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Atomtype 344
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Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
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Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
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Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
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Atomtype 385
Atomtype 386
Atomtype 387
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Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
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Atomtype 403
Atomtype 404
Atomtype 405
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Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
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Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
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Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
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Atomtype 445
Atomtype 446
Atomtype 447
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Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (1170 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
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Atomtype 159
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Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
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Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
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Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
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Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
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Atomtype 251
Atomtype 252
Atomtype 253
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Atomtype 255
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Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
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Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
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Atomtype 280
Atomtype 281
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Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
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Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
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Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
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Atomtype 356
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Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
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Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
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Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
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Atomtype 444
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Atomtype 446
Atomtype 447
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Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
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Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
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Atomtype 464
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Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
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Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
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Atomtype 511
Atomtype 512
Atomtype 513
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Atomtype 516
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Atomtype 519
Atomtype 520
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Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
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Atomtype 607
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Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
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Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (1320 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (1209 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (1082 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (1080 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (1226 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
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Atomtype 230
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Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
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Atomtype 241
Atomtype 242
Atomtype 243
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Atomtype 250
Atomtype 251
Atomtype 252
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Atomtype 255
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Atomtype 264
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Atomtype 297
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Atomtype 300
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Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
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Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
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Atomtype 323
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Atomtype 325
Atomtype 326
Atomtype 327
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Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
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Atomtype 341
Atomtype 342
Atomtype 343
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Atomtype 352
Atomtype 353
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Atomtype 355
Atomtype 356
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Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
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Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
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Atomtype 396
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Atomtype 401
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Atomtype 403
Atomtype 404
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Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
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Atomtype 416
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Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
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Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
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Atomtype 459
Atomtype 460
Atomtype 461
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Atomtype 496
Atomtype 497
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Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
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Atomtype 516
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Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
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Atomtype 529
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Atomtype 532
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Atomtype 538
Atomtype 539
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Atomtype 542
Atomtype 543
Atomtype 544
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Atomtype 549
Atomtype 550
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Atomtype 553
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Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
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Atomtype 603
Atomtype 604
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Atomtype 610
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Atomtype 619
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Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
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Atomtype 645
Atomtype 646
Atomtype 647
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Atomtype 650
Atomtype 651
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Atomtype 701
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Atomtype 703
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Atomtype 711
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Atomtype 713
Atomtype 714
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Atomtype 728
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Atomtype 737
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Atomtype 745
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Atomtype 750
Atomtype 751
Atomtype 752
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Atomtype 754
Atomtype 755
Atomtype 756
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Atomtype 759
Atomtype 760
Atomtype 761
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Atomtype 763
Atomtype 764
Atomtype 765
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Atomtype 767
Atomtype 768
Atomtype 769
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Atomtype 771
Atomtype 772
Atomtype 773
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Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
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Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (1112 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
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Atomtype 71
Atomtype 72
Atomtype 73
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Atomtype 75
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Atomtype 77
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Atomtype 79
Atomtype 80
Atomtype 81
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Atomtype 83
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Atomtype 86
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Atomtype 91
Atomtype 92
Atomtype 93
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Atomtype 97
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Atomtype 99
Atomtype 100
Atomtype 101
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Atomtype 103
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Atomtype 106
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Atomtype 111
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Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
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Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (989 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
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Atomtype 86
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Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (1151 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (1328 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (1239 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (1109 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (1110 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (1247 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (1145 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
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Atomtype 236
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Atomtype 314
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Atomtype 366
Atomtype 367
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Atomtype 426
Atomtype 427
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Atomtype 440
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Atomtype 450
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Atomtype 454
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Atomtype 503
Atomtype 504
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Atomtype 564
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Atomtype 567
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Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
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Atomtype 590
Atomtype 591
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Atomtype 640
Atomtype 641
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Atomtype 751
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Atomtype 781
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Atomtype 790
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Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
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Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
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Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (1027 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
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Atomtype 51
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Atomtype 131
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Atomtype 135
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Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
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Atomtype 154
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Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
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Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
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Atomtype 171
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Atomtype 173
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Atomtype 176
Atomtype 177
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Atomtype 181
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Atomtype 186
Atomtype 187
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Atomtype 189
Atomtype 190
Atomtype 191
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Atomtype 193
Atomtype 194
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Atomtype 196
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Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
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Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
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Atomtype 264
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Atomtype 277
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Atomtype 280
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Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
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Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (1201 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (1348 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (1160 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
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Atomtype 182
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Atomtype 187
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Atomtype 192
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Atomtype 194
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Atomtype 196
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Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
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Atomtype 309
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Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
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Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
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Atomtype 360
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Atomtype 362
Atomtype 363
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Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
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Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
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Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
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Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
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Atomtype 460
Atomtype 461
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Atomtype 471
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Atomtype 480
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Atomtype 484
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Atomtype 487
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Atomtype 500
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Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
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Atomtype 512
Atomtype 513
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Atomtype 515
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Atomtype 544
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Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (1088 ms)
30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (27757 ms total)
30:
30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (581 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (680 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (589 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (538 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Marked 37 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 37 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (610 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Marked 53 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 51 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (738 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Marked 36 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 36 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (623 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Marked 33 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 31 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (569 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (544 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (684 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (590 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (541 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Marked 37 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 37 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (613 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Marked 53 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 51 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (683 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Marked 36 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 36 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (625 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Marked 33 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 31 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (573 ms)
30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (9786 ms total)
30:
30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (599 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (709 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (613 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (565 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Marked 39 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 39 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (636 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Marked 57 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 55 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (751 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Marked 38 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 38 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (647 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Marked 35 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 33 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (591 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (602 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (705 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (612 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (529 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Marked 39 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 39 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (635 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Marked 57 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 55 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (757 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Marked 38 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 38 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (645 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Marked 35 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 33 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (596 ms)
30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (10214 ms total)
30:
30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 255, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 691 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 691 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.132 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (1168 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 291, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 788 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 788 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.366 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (1318 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 262, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 727 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 727 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.124 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (1205 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 233, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 634 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 634 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.888 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (1043 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 255, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 691 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 691 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.132 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (1257 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 291, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 788 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 788 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.366 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (1399 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 262, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 727 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 727 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.124 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (1301 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 233, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 634 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 634 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.888 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (1163 ms)
30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (9855 ms total)
30:
30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 663 dihedrals, 48 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.115 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (1149 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 778 dihedrals, 49 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (1298 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 696 dihedrals, 39 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.130 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (1175 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 618 dihedrals, 38 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.885 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (1035 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 663 dihedrals, 48 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.115 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (1244 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 778 dihedrals, 49 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (1380 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 696 dihedrals, 39 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.130 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (1246 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 618 dihedrals, 38 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.885 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (1149 ms)
30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (9687 ms total)
30:
30: [----------] 8 tests from ChainSep/Pdb2gmxTest
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 258, now 258
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 651 pairs
30: Before cleaning: 661 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 10 cmap torsion pairs
30: There are 661 dihedrals, 46 impropers, 463 angles
30: 648 pairs, 258 bonds and 0 virtual sites
30: Total mass 1882.146 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on changing chain id only (ignoring TER records).
30:
30: Merged chains into joint molecule definitions at 2 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Identified residue PHE6 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Start terminus PHE-6: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 258 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (1158 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 50, now 50
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 123 pairs
30: Before cleaning: 123 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 123 dihedrals, 9 impropers, 88 angles
30: 123 pairs, 50 bonds and 0 virtual sites
30: Total mass 434.421 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 10 donors and 7 acceptors were found.
30: There are 7 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS8
30: NE223
30: MET12 SD55 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 125, now 125
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 317 pairs
30: Before cleaning: 322 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 5 cmap torsion pairs
30: There are 322 dihedrals, 19 impropers, 227 angles
30: 314 pairs, 125 bonds and 0 virtual sites
30: Total mass 846.083 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 258 atoms and 16 residues
30: Total mass in system 1882.146 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on changing chain id only (ignoring TER records).
30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 4 28
30: 2 'B' 7 58
30: 3 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (28 atoms, 4 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 51 atoms
30: Chain time...
30: Processing chain 2 'B' (58 atoms, 7 residues)
30: Identified residue PHE6 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus PHE-6: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 7 residues with 124 atoms
30: Chain time...
30: Processing chain 3 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 51 atoms 4 residues
30: Including chain 2 in system: 124 atoms 7 residues
30: Including chain 3 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (148 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 258, now 258
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 651 pairs
30: Before cleaning: 661 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 10 cmap torsion pairs
30: There are 661 dihedrals, 46 impropers, 463 angles
30: 648 pairs, 258 bonds and 0 virtual sites
30: Total mass 1882.146 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records only (ignoring chain id).
30:
30: Merged chains into joint molecule definitions at 2 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus ILE-9: COO-
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 258 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (1139 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 10 donors and 12 acceptors were found.
30: There are 13 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3
30: SG9
30: HIS8 NE251 1.055
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 115, now 115
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 288 pairs
30: Before cleaning: 293 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 6 cmap torsion pairs
30: There are 293 dihedrals, 23 impropers, 203 angles
30: 285 pairs, 115 bonds and 0 virtual sites
30: Total mass 888.952 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 60, now 60
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 152 pairs
30: Before cleaning: 152 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 1 cmap torsion pairs
30: There are 152 dihedrals, 5 impropers, 112 angles
30: 152 pairs, 60 bonds and 0 virtual sites
30: Total mass 391.552 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 258 atoms and 16 residues
30: Total mass in system 1882.146 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records only (ignoring chain id).
30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 8 61
30: 2 'B' 3 25
30: 3 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (61 atoms, 8 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus ILE-9: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 8 residues with 114 atoms
30: Chain time...
30: Processing chain 2 'B' (25 atoms, 3 residues)
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 3 residues with 61 atoms
30: Chain time...
30: Processing chain 3 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 114 atoms 8 residues
30: Including chain 2 in system: 61 atoms 3 residues
30: Including chain 3 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (147 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 260, now 260
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 650 pairs
30: Before cleaning: 660 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 8 cmap torsion pairs
30: There are 660 dihedrals, 45 impropers, 466 angles
30: 647 pairs, 260 bonds and 0 virtual sites
30: Total mass 1900.162 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30:
30: Merged chains into joint molecule definitions at 3 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Identified residue PHE6 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Start terminus PHE-6: NH3+
30: End terminus ILE-9: COO-
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 261 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (1153 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 50, now 50
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 123 pairs
30: Before cleaning: 123 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 123 dihedrals, 9 impropers, 88 angles
30: 123 pairs, 50 bonds and 0 virtual sites
30: Total mass 434.421 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 6 donors and 4 acceptors were found.
30: There are 3 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 67, now 67
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 164 pairs
30: Before cleaning: 169 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 169 dihedrals, 13 impropers, 118 angles
30: 161 pairs, 67 bonds and 0 virtual sites
30: Total mass 472.547 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 60, now 60
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 152 pairs
30: Before cleaning: 152 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 1 cmap torsion pairs
30: There are 152 dihedrals, 5 impropers, 112 angles
30: 152 pairs, 60 bonds and 0 virtual sites
30: Total mass 391.552 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 261 atoms and 16 residues
30: Total mass in system 1900.162 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
30: They will be treated as separate chains unless you reorder your file.
30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 4 28
30: 2 'B' 4 33
30: 3 'B' 3 25
30: 4 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (28 atoms, 4 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 51 atoms
30: Chain time...
30: Processing chain 2 'B' (33 atoms, 4 residues)
30: Identified residue PHE6 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Start terminus PHE-6: NH3+
30: End terminus ILE-9: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 66 atoms
30: Chain time...
30: Processing chain 3 'B' (25 atoms, 3 residues)
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 3 residues with 61 atoms
30: Chain time...
30: Processing chain 4 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 51 atoms 4 residues
30: Including chain 2 in system: 66 atoms 4 residues
30: Including chain 3 in system: 61 atoms 3 residues
30: Including chain 4 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (154 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 256, now 256
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 652 pairs
30: Before cleaning: 662 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 12 cmap torsion pairs
30: There are 662 dihedrals, 47 impropers, 460 angles
30: 649 pairs, 256 bonds and 0 virtual sites
30: Total mass 1864.131 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records and chain id changing.
30:
30: Merged chains into joint molecule definitions at 1 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (1148 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
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30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 14 donors and 15 acceptors were found.
30: There are 20 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 173, now 173
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 441 pairs
30: Before cleaning: 446 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 9 cmap torsion pairs
30: There are 446 dihedrals, 29 impropers, 312 angles
30: 438 pairs, 173 bonds and 0 virtual sites
30: Total mass 1262.488 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 255 atoms and 16 residues
30: Total mass in system 1864.131 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records and chain id changing.
30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 11 86
30: 2 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (86 atoms, 11 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 11 residues with 172 atoms
30: Chain time...
30: Processing chain 2 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 172 atoms 11 residues
30: Including chain 2 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (144 ms)
30: [----------] 8 tests from ChainSep/Pdb2gmxTest (5194 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 80 tests from 6 test cases ran. (72495 ms total)
30: [ PASSED ] 80 tests.
30/40 Test #30: Pdb2gmxTest ...................... Passed 72.53 sec
test 31
Start 31: CorrelationsTest
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 11 tests from 2 test cases.
31: [----------] Global test environment set-up.
31: [----------] 10 tests from AutocorrTest
31: [ RUN ] AutocorrTest.EacNormal
31: [ OK ] AutocorrTest.EacNormal (25 ms)
31: [ RUN ] AutocorrTest.EacNoNormalize
31: [ OK ] AutocorrTest.EacNoNormalize (20 ms)
31: [ RUN ] AutocorrTest.EacCos
31: [ OK ] AutocorrTest.EacCos (37 ms)
31: [ RUN ] AutocorrTest.EacVector
31: [ OK ] AutocorrTest.EacVector (51 ms)
31: [ RUN ] AutocorrTest.EacRcross
31: [ OK ] AutocorrTest.EacRcross (4 ms)
31: [ RUN ] AutocorrTest.EacP0
31: [ OK ] AutocorrTest.EacP0 (50 ms)
31: [ RUN ] AutocorrTest.EacP1
31: [ OK ] AutocorrTest.EacP1 (51 ms)
31: [ RUN ] AutocorrTest.EacP2
31: [ OK ] AutocorrTest.EacP2 (100 ms)
31: [ RUN ] AutocorrTest.EacP3
31: [ OK ] AutocorrTest.EacP3 (10 ms)
31: [ RUN ] AutocorrTest.EacP4
31: [ OK ] AutocorrTest.EacP4 (53 ms)
31: [----------] 10 tests from AutocorrTest (412 ms total)
31:
31: [----------] 1 test from ManyAutocorrelationTest
31: [ RUN ] ManyAutocorrelationTest.Empty
31: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
31: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 11 tests from 2 test cases ran. (419 ms total)
31: [ PASSED ] 11 tests.
31/40 Test #31: CorrelationsTest ................. Passed 0.44 sec
test 32
Start 32: AnalysisDataUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 69 tests from 14 test cases.
32: [----------] Global test environment set-up.
32: [----------] 3 tests from AnalysisDataInitializationTest
32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
32: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/0 (27 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (5 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (3 ms)
32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/1 (32 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (6 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (3 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/2 (38 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (5 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (6 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (8 ms)
32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (3 ms)
32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (3 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/3 (38 ms total)
32:
32: [----------] 4 tests from AnalysisArrayDataTest
32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (5 ms)
32: [ RUN ] AnalysisArrayDataTest.StorageWorks
32: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
32: [----------] 4 tests from AnalysisArrayDataTest (7 ms total)
32:
32: [----------] 6 tests from AverageModuleTest
32: [ RUN ] AverageModuleTest.BasicTest
32: [ OK ] AverageModuleTest.BasicTest (4 ms)
32: [ RUN ] AverageModuleTest.HandlesMultipointData
32: [ OK ] AverageModuleTest.HandlesMultipointData (5 ms)
32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (6 ms)
32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
32: [ RUN ] AverageModuleTest.CanCustomizeXAxis
32: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (5 ms)
32: [----------] 6 tests from AverageModuleTest (30 ms total)
32:
32: [----------] 2 tests from FrameAverageModuleTest
32: [ RUN ] FrameAverageModuleTest.BasicTest
32: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
32: [----------] 2 tests from FrameAverageModuleTest (10 ms total)
32:
32: [----------] 7 tests from AnalysisHistogramSettingsTest
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
32: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total)
32:
32: [----------] 2 tests from SimpleHistogramModuleTest
32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
32: [----------] 2 tests from SimpleHistogramModuleTest (13 ms total)
32:
32: [----------] 3 tests from WeightedHistogramModuleTest
32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (8 ms)
32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
32: [----------] 3 tests from WeightedHistogramModuleTest (23 ms total)
32:
32: [----------] 3 tests from BinAverageModuleTest
32: [ RUN ] BinAverageModuleTest.ComputesCorrectly
32: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (6 ms)
32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
32: [----------] 3 tests from BinAverageModuleTest (18 ms total)
32:
32: [----------] 4 tests from AbstractAverageHistogramTest
32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (12 ms)
32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (7 ms)
32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
32: [----------] 4 tests from AbstractAverageHistogramTest (34 ms total)
32:
32: [----------] 3 tests from LifetimeModuleTest
32: [ RUN ] LifetimeModuleTest.BasicTest
32: [ OK ] LifetimeModuleTest.BasicTest (5 ms)
32: [ RUN ] LifetimeModuleTest.CumulativeTest
32: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (6 ms)
32: [----------] 3 tests from LifetimeModuleTest (15 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 69 tests from 14 test cases ran. (300 ms total)
32: [ PASSED ] 69 tests.
32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.32 sec
test 33
Start 33: SelectionUnitTests
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 190 tests from 10 test cases.
33: [----------] Global test environment set-up.
33: [----------] 1 test from IndexGroupTest
33: [ RUN ] IndexGroupTest.RemovesDuplicates
33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
33: [----------] 1 test from IndexGroupTest (0 ms total)
33:
33: [----------] 15 tests from IndexBlockTest
33: [ RUN ] IndexBlockTest.CreatesUnknownBlock
33: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesAtomBlock
33: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesResidueBlock
33: [ OK ] IndexBlockTest.CreatesResidueBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock
33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion
33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (1 ms)
33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion
33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (0 ms)
33: [ RUN ] IndexBlockTest.CreatesSingleBlock
33: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (1 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
33: [----------] 15 tests from IndexBlockTest (4 ms total)
33:
33: [----------] 11 tests from IndexMapTest
33: [ RUN ] IndexMapTest.InitializesAtomBlock
33: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
33: [ RUN ] IndexMapTest.InitializesMoleculeBlock
33: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
33: [ RUN ] IndexMapTest.MapsSingleBlock
33: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
33: [ RUN ] IndexMapTest.MapsResidueBlocks
33: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
33: [ RUN ] IndexMapTest.HandlesMultipleRequests
33: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
33: [----------] 11 tests from IndexMapTest (6 ms total)
33:
33: [----------] 15 tests from NeighborhoodSearchTest
33: [ RUN ] NeighborhoodSearchTest.SimpleSearch
33: [ OK ] NeighborhoodSearchTest.SimpleSearch (35 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (34 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchBox
33: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (25 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (10 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (6 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (99 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
33: [----------] 15 tests from NeighborhoodSearchTest (230 ms total)
33:
33: [----------] 12 tests from PositionCalculationTest
33: [ RUN ] PositionCalculationTest.ComputesAtomPositions
33: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionMask
33: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms)
33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms)
33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms)
33: [----------] 12 tests from PositionCalculationTest (7 ms total)
33:
33: [----------] 30 tests from SelectionCollectionTest
33: [ RUN ] SelectionCollectionTest.HandlesNoSelections
33: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms)
33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms)
33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions
33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (0 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
33: [----------] 30 tests from SelectionCollectionTest (40 ms total)
33:
33: [----------] 14 tests from SelectionCollectionInteractiveTest
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
33: [----------] 14 tests from SelectionCollectionInteractiveTest (26 ms total)
33:
33: [----------] 66 tests from SelectionCollectionDataTest
33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResnr
33: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesChain
33: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMass
33: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesCharge
33: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBeta
33: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResname
33: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (18 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (13 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (15 ms)
33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (8 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (7 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (7 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (11 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (10 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (9 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (10 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (12 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (8 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (14 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (8 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (10 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (6 ms)
33: [----------] 66 tests from SelectionCollectionDataTest (365 ms total)
33:
33: [----------] 17 tests from SelectionOptionTest
33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms)
33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (3 ms)
33: [ RUN ] SelectionOptionTest.ChecksEmptySelections
33: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooManySelections
33: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms)
33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesAdjuster
33: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms)
33: [----------] 17 tests from SelectionOptionTest (15 ms total)
33:
33: [----------] 9 tests from SelectionFileOptionTest
33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
33: [----------] 9 tests from SelectionFileOptionTest (10 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 190 tests from 10 test cases ran. (705 ms total)
33: [ PASSED ] 190 tests.
33/40 Test #33: SelectionUnitTests ............... Passed 0.74 sec
test 34
Start 34: TrajectoryAnalysisUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 74 tests from 14 test cases.
34: [----------] Global test environment set-up.
34: [----------] 5 tests from ClustsizeTest
34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
34: There is one group in the index
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 24
34: cmid: 2, cmax: 4, max_size: 6
34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (6 ms)
34: [ RUN ] ClustsizeTest.NoMolShortCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
34: There is one group in the index
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 24
34: cmid: 1, cmax: 6, max_size: 6
34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
34: [ RUN ] ClustsizeTest.MolDefaultCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 2, cmax: 4, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms)
34: [ RUN ] ClustsizeTest.MolShortCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 1, cmax: 6, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (13 ms)
34: [ RUN ] ClustsizeTest.MolCSize
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 2, cmax: 4, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolCSize (14 ms)
34: [----------] 5 tests from ClustsizeTest (53 ms total)
34:
34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
34: Reading frames from gro file 'Test system', 8 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (9 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
34: Reading frames from gro file 'Test system', 8 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (8 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (19 ms total)
34:
34: [----------] 11 tests from AngleModuleTest
34: [ RUN ] AngleModuleTest.ComputesSimpleAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesSimpleAngles (11 ms)
34: [ RUN ] AngleModuleTest.ComputesDihedrals
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesDihedrals (11 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (14 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (13 ms)
34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (11 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (12 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
34: Reading frames from gro file 'Test system for different angles', 33 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (13 ms)
34: [ RUN ] AngleModuleTest.ComputesMultipleAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesMultipleAngles (17 ms)
34: [ RUN ] AngleModuleTest.HandlesDynamicSelections
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesDynamicSelections (12 ms)
34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (13 ms)
34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (15 ms)
34: [----------] 11 tests from AngleModuleTest (142 ms total)
34:
34: [----------] 3 tests from DistanceModuleTest
34: [ RUN ] DistanceModuleTest.ComputesDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2:
34: Number of samples: 5
34: Average distance: 1.43246 nm
34: Standard deviation: 0.96700 nm
34: [ OK ] DistanceModuleTest.ComputesDistances (15 ms)
34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2:
34: Number of samples: 5
34: Average distance: 1.43246 nm
34: Standard deviation: 0.96700 nm
34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
34: Number of samples: 4
34: Average distance: 1.81066 nm
34: Standard deviation: 0.79289 nm
34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (20 ms)
34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2 and res_cog x < 2.8:
34: Number of samples: 3
34: Average distance: 1.72076 nm
34: Standard deviation: 1.24839 nm
34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (16 ms)
34: [----------] 3 tests from DistanceModuleTest (51 ms total)
34:
34: [----------] 2 tests from FreeVolumeModuleTest
34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for 40 particles. These were set to zero.
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: cutoff = 0.18 nm
34: probe_radius = 0 nm
34: seed = 13
34: ninsert = 1000 probes per nm^3
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
34: van der Spoel and Luciano T. Costa
34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
34: -------- -------- --- Thank You --- -------- --------
34:
34: Free volume 38.02 +/- 0.00 %
34: Total volume 68.92 +/- 0.00 nm^3
34: Number of molecules 340 total mass 63491.38 Dalton
34: Average molar mass: 186.74 Dalton
34: Density rho: 1529.71 +/- 0.00 nm^3
34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
34: Fractional free volume 0.194 +/- 0.000
34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (854 ms)
34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: cutoff = 0.18 nm
34: probe_radius = 0 nm
34: seed = 17
34: ninsert = 1000 probes per nm^3
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
34: van der Spoel and Luciano T. Costa
34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
34: -------- -------- --- Thank You --- -------- --------
34:
34: Free volume 38.48 +/- 0.00 %
34: Total volume 68.92 +/- 0.00 nm^3
34: Number of molecules 340 total mass 63491.38 Dalton
34: Average molar mass: 186.74 Dalton
34: Density rho: 1529.71 +/- 0.00 nm^3
34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
34: Fractional free volume 0.200 +/- 0.000
34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (831 ms)
34: [----------] 2 tests from FreeVolumeModuleTest (1685 ms total)
34:
34: [----------] 7 tests from PairDistanceModuleTest
34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (10 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (11 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (9 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (9 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (10 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (10 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (10 ms)
34: [----------] 7 tests from PairDistanceModuleTest (70 ms total)
34:
34: [----------] 5 tests from RdfModuleTest
34: [ RUN ] RdfModuleTest.BasicTest
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.BasicTest (58 ms)
34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (45 ms)
34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (58 ms)
34: [ RUN ] RdfModuleTest.CalculatesSurf
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.CalculatesSurf (39 ms)
34: [ RUN ] RdfModuleTest.CalculatesXY
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.CalculatesXY (66 ms)
34: [----------] 5 tests from RdfModuleTest (267 ms total)
34:
34: [----------] 5 tests from SasaModuleTest
34: [ RUN ] SasaModuleTest.BasicTest
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.BasicTest (34 ms)
34: [ RUN ] SasaModuleTest.HandlesSelectedResidues
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesSelectedResidues (22 ms)
34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (18 ms)
34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (27 ms)
34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (27 ms)
34: [----------] 5 tests from SasaModuleTest (132 ms total)
34:
34: [----------] 8 tests from SelectModuleTest
34: [ RUN ] SelectModuleTest.BasicTest
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.BasicTest (20 ms)
34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (14 ms)
34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (14 ms)
34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (16 ms)
34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (15 ms)
34: [ RUN ] SelectModuleTest.NormalizesSizes
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.NormalizesSizes (12 ms)
34: [ RUN ] SelectModuleTest.WritesResidueNumbers
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
34: [ RUN ] SelectModuleTest.WritesResidueIndices
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.WritesResidueIndices (9 ms)
34: [----------] 8 tests from SelectModuleTest (110 ms total)
34:
34: [----------] 10 tests from SurfaceAreaTest
34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints12
34: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints32
34: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints42
34: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints122
34: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms)
34: [ RUN ] SurfaceAreaTest.Computes100Points
34: [ OK ] SurfaceAreaTest.Computes100Points (3 ms)
34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (11 ms)
34: [----------] 10 tests from SurfaceAreaTest (32 ms total)
34:
34: [----------] 4 tests from TopologyInformation
34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
34: [ RUN ] TopologyInformation.WorksWithGroFile
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TopologyInformation.WorksWithGroFile (7 ms)
34: [ RUN ] TopologyInformation.WorksWithPdbFile
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TopologyInformation.WorksWithPdbFile (7 ms)
34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
34:
34: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]:
34: /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
34: scheme was introduced, but the group scheme was still the default. The
34: default is now the Verlet scheme, so you will observe different behaviour.
34:
34:
34: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: For a correct single-point energy evaluation with nsteps = 0, use
34: continuation = yes to avoid constraining the input coordinates.
34:
34: Setting the LD random seed to 1185171261
34: Generated 330891 of the 330891 non-bonded parameter combinations
34: Generating 1-4 interactions: fudge = 0.5
34: Generated 330891 of the 330891 1-4 parameter combinations
34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
34:
34: NOTE 3 [file lysozyme.top, line 1465]:
34: System has non-zero total charge: 2.000000
34: Total charge should normally be an integer. See
34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
34: for discussion on how close it should be to an integer.
34:
34:
34:
34: Removing all charge groups because cutoff-scheme=Verlet
34: Number of degrees of freedom in T-Coupling group rest is 465.00
34:
34: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: NVE simulation with an initial temperature of zero: will use a Verlet
34: buffer of 10%. Check your energy drift!
34:
34:
34: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: You are using a plain Coulomb cut-off, which might produce artifacts.
34: You might want to consider using PME electrostatics.
34:
34:
34:
34: There were 5 notes
34: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.4 (single precision)
34: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.4 (single precision)
34: Analysing residue names:
34: There are: 10 Protein residues
34: Analysing Protein...
34: This run will generate roughly 0 Mb of data
34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (532 ms)
34: [----------] 4 tests from TopologyInformation (548 ms total)
34:
34: [----------] 4 tests from TrajectoryModuleTest
34: [ RUN ] TrajectoryModuleTest.BasicTest
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.BasicTest (13 ms)
34: [ RUN ] TrajectoryModuleTest.PlotsXOnly
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.PlotsXOnly (11 ms)
34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (10 ms)
34: [ RUN ] TrajectoryModuleTest.HandlesNoForces
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms)
34: [----------] 4 tests from TrajectoryModuleTest (44 ms total)
34:
34: [----------] 5 tests from UnionFinderTest
34: [ RUN ] UnionFinderTest.WorksEmpty
34: [ OK ] UnionFinderTest.WorksEmpty (1 ms)
34: [ RUN ] UnionFinderTest.BasicMerges
34: [ OK ] UnionFinderTest.BasicMerges (0 ms)
34: [ RUN ] UnionFinderTest.LargerMerges
34: [ OK ] UnionFinderTest.LargerMerges (0 ms)
34: [ RUN ] UnionFinderTest.LongRightMerge
34: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
34: [ RUN ] UnionFinderTest.LongLeftMerge
34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
34: [----------] 5 tests from UnionFinderTest (1 ms total)
34:
34: [----------] 1 test from MappedUnionFinderTest
34: [ RUN ] MappedUnionFinderTest.BasicMerges
34: [ OK ] MappedUnionFinderTest.BasicMerges (1 ms)
34: [----------] 1 test from MappedUnionFinderTest (1 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 74 tests from 14 test cases ran. (3157 ms total)
34: [ PASSED ] 74 tests.
34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 3.18 sec
test 35
Start 35: EnergyAnalysisUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 7 tests from 4 test cases.
35: [----------] Global test environment set-up.
35: [----------] 1 test from DhdlTest
35: [ RUN ] DhdlTest.ExtractDhdl
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
35: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
35: Note: file tpx version 110, software tpx version 116
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
35:
35:
35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
35: [ OK ] DhdlTest.ExtractDhdl (130 ms)
35: [----------] 1 test from DhdlTest (131 ms total)
35:
35: [----------] 1 test from OriresTest
35: [ RUN ] OriresTest.ExtractOrires
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
35: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
35: Note: file tpx version 111, software tpx version 116
35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
35: End your selection with 0
35: Selecting all 7 orientation restraints
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
35: [ OK ] OriresTest.ExtractOrires (206 ms)
35: [----------] 1 test from OriresTest (206 ms total)
35:
35: [----------] 3 tests from EnergyTest
35: [ RUN ] EnergyTest.ExtractEnergy
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
35: [ OK ] EnergyTest.ExtractEnergy (34 ms)
35: [ RUN ] EnergyTest.ExtractEnergyByNumber
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
35: Pres. DC -268.49 3 8.52175 13.2804 (bar)
35: [ OK ] EnergyTest.ExtractEnergyByNumber (34 ms)
35: [ RUN ] EnergyTest.ExtractEnergyMixed
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: [ OK ] EnergyTest.ExtractEnergyMixed (35 ms)
35: [----------] 3 tests from EnergyTest (105 ms total)
35:
35: [----------] 2 tests from ViscosityTest
35: [ RUN ] ViscosityTest.EinsteinViscosity
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Pres-XX 20.2092 65 717.193 185.978 (bar)
35: Pres-XY -47.7351 39 372.522 207.456 (bar)
35: Pres-XZ 11.477 31 379.79 6.80818 (bar)
35: Pres-YX -47.7106 39 372.525 207.5 (bar)
35: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
35: Pres-YZ -41.3534 45 401.216 114.663 (bar)
35: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
35: Pres-ZY -41.3119 45 401.196 114.743 (bar)
35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
35: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: [ OK ] ViscosityTest.EinsteinViscosity (74 ms)
35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Pres-XX 20.2092 65 717.193 185.978 (bar)
35: Pres-XY -47.7351 39 372.522 207.456 (bar)
35: Pres-XZ 11.477 31 379.79 6.80818 (bar)
35: Pres-YX -47.7106 39 372.525 207.5 (bar)
35: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
35: Pres-YZ -41.3534 45 401.216 114.663 (bar)
35: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
35: Pres-ZY -41.3119 45 401.196 114.743 (bar)
35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
35: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (62 ms)
35: [----------] 2 tests from ViscosityTest (137 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 7 tests from 4 test cases ran. (582 ms total)
35: [ PASSED ] 7 tests.
35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.60 sec
test 36
Start 36: ToolUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 4 tests from 1 test case.
36: [----------] Global test environment set-up.
36: [----------] 4 tests from ReportMethodsTest
36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
36: [ RUN ] ReportMethodsTest.WritesCorrectInformation
36:
36: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]:
36: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
36: scheme was introduced, but the group scheme was still the default. The
36: default is now the Verlet scheme, so you will observe different behaviour.
36:
36:
36: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: For a correct single-point energy evaluation with nsteps = 0, use
36: continuation = yes to avoid constraining the input coordinates.
36:
36: Setting the LD random seed to 1688161942
36: Generated 330891 of the 330891 non-bonded parameter combinations
36: Generating 1-4 interactions: fudge = 0.5
36: Generated 330891 of the 330891 1-4 parameter combinations
36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
36:
36: NOTE 3 [file lysozyme.top, line 1465]:
36: System has non-zero total charge: 2.000000
36: Total charge should normally be an integer. See
36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
36: for discussion on how close it should be to an integer.
36:
36:
36:
36: Removing all charge groups because cutoff-scheme=Verlet
36: Number of degrees of freedom in T-Coupling group rest is 465.00
36:
36: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: NVE simulation with an initial temperature of zero: will use a Verlet
36: buffer of 10%. Check your energy drift!
36:
36:
36: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: You are using a plain Coulomb cut-off, which might produce artifacts.
36: You might want to consider using PME electrostatics.
36:
36:
36:
36: There were 5 notes
36: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.4 (single precision)
36: Analysing residue names:
36: There are: 10 Protein residues
36: Analysing Protein...
36: This run will generate roughly 0 Mb of data
36: [ OK ] ReportMethodsTest.WritesCorrectInformation (499 ms)
36: [ RUN ] ReportMethodsTest.ToolEndToEndTest
36:
36: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]:
36: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
36: scheme was introduced, but the group scheme was still the default. The
36: default is now the Verlet scheme, so you will observe different behaviour.
36:
36:
36: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: For a correct single-point energy evaluation with nsteps = 0, use
36: continuation = yes to avoid constraining the input coordinates.
36:
36: Setting the LD random seed to 1062305030
36: Generated 330891 of the 330891 non-bonded parameter combinations
36: Generating 1-4 interactions: fudge = 0.5
36: Generated 330891 of the 330891 1-4 parameter combinations
36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
36:
36: NOTE 3 [file lysozyme.top, line 1465]:
36: System has non-zero total charge: 2.000000
36: Total charge should normally be an integer. See
36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
36: for discussion on how close it should be to an integer.
36:
36:
36:
36: Removing all charge groups because cutoff-scheme=Verlet
36: Number of degrees of freedom in T-Coupling group rest is 465.00
36:
36: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: NVE simulation with an initial temperature of zero: will use a Verlet
36: buffer of 10%. Check your energy drift!
36:
36:
36: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: You are using a plain Coulomb cut-off, which might produce artifacts.
36: You might want to consider using PME electrostatics.
36:
36:
36:
36: There were 5 notes
36: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.4 (single precision)
36: Analysing residue names:
36: There are: 10 Protein residues
36: Analysing Protein...
36: This run will generate roughly 0 Mb of data
36: section: Methods
36: subsection: Simulation system
36: A system of 1 molecules (156 atoms) was simulated.
36:
36: subsection: Simulation settings
36: A total of 0 ns were simulated with a time step of 1 fs.
36: Neighbor searching was performed every 10 steps.
36: The Cut-off algorithm was used for electrostatic interactions.
36: with a cut-off of 1 nm.
36: A single cut-off of 1.1 nm was used for Van der Waals interactions.
36: [ OK ] ReportMethodsTest.ToolEndToEndTest (527 ms)
36: [----------] 4 tests from ReportMethodsTest (1026 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 4 tests from 1 test case ran. (1026 ms total)
36: [ PASSED ] 4 tests.
36/40 Test #36: ToolUnitTests .................... Passed 1.05 sec
test 37
Start 37: MdrunTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
37: Test timeout computed to be: 600
37: [==========] Running 29 tests from 11 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from GromppTest
37: [ RUN ] GromppTest.EmptyMdpFileWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -342602121
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 12.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: NVE simulation: will use the initial temperature of 1046.791 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37: [ OK ] GromppTest.EmptyMdpFileWorks (74 ms)
37: [----------] 1 test from GromppTest (74 ms total)
37:
37: [----------] 1 test from ImdTest
37: [ RUN ] ImdTest.ImdCanRun
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]:
37: The Berendsen thermostat does not generate the correct kinetic energy
37: distribution. You might want to consider using the V-rescale thermostat.
37:
37: Setting the LD random seed to 1250037236
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD).
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 50, rlist from 1.121 to 1.344
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: IMD: Enabled. This simulation will accept incoming IMD connections.
37: IMD: You chose a port number < 1. Will automatically assign a free port.
37: IMD: Pulling from IMD remote is enabled (-imdpull).
37: IMD: Turning on IMD - port for incoming requests is 0.
37: IMD: Setting up incoming socket.
37: IMD: Listening for IMD connection on port 34739.
37: IMD: -imdwait not set, starting simulation.
37: starting mdrun 'spc2'
37: 2 steps, 0.0 ps.
37: turning all bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.197 0.099 199.3
37: (ns/day) (hour/ns)
37: Performance: 10.488 2.288
37: [ OK ] ImdTest.ImdCanRun (141 ms)
37: [----------] 1 test from ImdTest (141 ms total)
37:
37: [----------] 2 tests from PmeTest
37: [ RUN ] PmeTest.ReproducesEnergies
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -340687547
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
37: NVE simulation: will use the initial temperature of 1046.791 K for
37: determining the Verlet buffer size
37:
37: Estimate for the relative computational load of the PME mesh part: 1.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
37: The optimal PME mesh load for parallel simulations is below 0.5
37: and for highly parallel simulations between 0.25 and 0.33,
37: for higher performance, increase the cut-off and the PME grid spacing.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: Calculating fourier grid dimensions for X Y Z
37: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.248 0.125 199.5
37: (ns/day) (hour/ns)
37: Performance: 14.570 1.647
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.269 0.135 199.5
37: (ns/day) (hour/ns)
37: Performance: 13.450 1.784
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37:
37: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.277 0.139 199.5
37: (ns/day) (hour/ns)
37: Performance: 13.090 1.833
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10697 ms)
37: [ RUN ] PmeTest.ScalesTheBox
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -264937895
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Searching the wall atom type(s)
37: Number of degrees of freedom in T-Coupling group rest is 13.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: NVE simulation: will use the initial temperature of 966.268 K for
37: determining the Verlet buffer size
37:
37: Estimate for the relative computational load of the PME mesh part: 1.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: The optimal PME mesh load for parallel simulations is below 0.5
37: and for highly parallel simulations between 0.25 and 0.33,
37: for higher performance, increase the cut-off and the PME grid spacing.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 0 steps, 0.0 ps.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.013 0.007 186.8
37: (ns/day) (hour/ns)
37: Performance: 12.220 1.964
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: Calculating fourier grid dimensions for X Y Z
37: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
37: This run will generate roughly 0 Mb of data
37: [ OK ] PmeTest.ScalesTheBox (30807 ms)
37: [----------] 2 tests from PmeTest (41505 ms total)
37:
37: [----------] 1 test from CompelTest
37: [ RUN ] CompelTest.SwapCanRun
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
37: The Berendsen thermostat does not generate the correct kinetic energy
37: distribution. You might want to consider using the V-rescale thermostat.
37:
37: Setting the LD random seed to -657109367
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein'
37: Excluding 3 bonded neighbours molecule type 'OCT'
37: Excluding 1 bonded neighbours molecule type 'NA'
37: Excluding 1 bonded neighbours molecule type 'CL'
37: Excluding 3 bonded neighbours molecule type 'Protein'
37: Excluding 3 bonded neighbours molecule type 'OCT'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Split0 group 'Ch0' contains 83 atoms.
37: Split1 group 'Ch1' contains 83 atoms.
37: Solvent group 'SOL' contains 11931 atoms.
37: Swap group 'NA+' contains 19 atoms.
37: Swap group 'CL-' contains 19 atoms.
37: Number of degrees of freedom in T-Coupling group System is 27869.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.4 (single precision)
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: SWAP: Determining initial numbers of ions per compartment.
37: SWAP: Setting pointers for checkpoint writing
37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
37: starting mdrun 'Channel_coco in octane membrane'
37: 2 steps, 0.0 ps.
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 1 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 2.635 1.318 199.9
37: (ns/day) (hour/ns)
37: Performance: 0.983 24.407
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.4 (single precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: SWAP: Setting pointers for checkpoint writing
37: SWAP: Copying channel fluxes from checkpoint file data
37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
37: starting mdrun 'Channel_coco in octane membrane'
37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 2.399 1.200 199.9
37: (ns/day) (hour/ns)
37: Performance: 1.080 22.220
37: [ OK ] CompelTest.SwapCanRun (4320 ms)
37: [----------] 1 test from CompelTest (4320 ms total)
37:
37: [----------] 6 tests from BondedInteractionsTest
37: [ RUN ] BondedInteractionsTest.NormalBondWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -600706120
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 2 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 180.2
37: (ns/day) (hour/ns)
37: Performance: 87.724 0.274
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalBondWorks (25 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1873821629
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 2 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 180.5
37: (ns/day) (hour/ns)
37: Performance: 85.388 0.281
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (30 ms)
37: [ RUN ] BondedInteractionsTest.NormalAngleWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1814892540
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 1 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 181.0
37: (ns/day) (hour/ns)
37: Performance: 82.888 0.290
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalAngleWorks (25 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 142117326
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 1 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 180.6
37: (ns/day) (hour/ns)
37: Performance: 84.769 0.283
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (28 ms)
37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -613097871
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 181.2
37: (ns/day) (hour/ns)
37: Performance: 85.550 0.281
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (25 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 391827855
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 180.4
37: (ns/day) (hour/ns)
37: Performance: 86.427 0.278
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (31 ms)
37: [----------] 6 tests from BondedInteractionsTest (164 ms total)
37:
37: [----------] 2 tests from MdrunTerminationTest
37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -1438473825
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 1, rlist from 1.024 to 1
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 100 steps, 0.1 ps.
37:
37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.240 0.120 199.5
37: (ns/day) (hour/ns)
37: Performance: 1.435 16.724
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.4 (single precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps
37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
37:
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps).
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.178 0.089 199.3
37: (ns/day) (hour/ns)
37: Performance: 2.897 8.285
37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (246 ms)
37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1138421571
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 1, rlist from 1.024 to 1
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 100 steps, 0.1 ps.
37:
37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.183 0.092 199.3
37: (ns/day) (hour/ns)
37: Performance: 1.886 12.724
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.4 (single precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps
37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
37:
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps).
37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.177 0.089 199.7
37: (ns/day) (hour/ns)
37: Performance: 2.925 8.206
37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (216 ms)
37: [----------] 2 tests from MdrunTerminationTest (462 ms total)
37:
37: [----------] 4 tests from MimicTest
37: [ RUN ] MimicTest.OneQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1301723454
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 181.4
37: (ns/day) (hour/ns)
37: Performance: 81.619 0.294
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.OneQuantumMol (28 ms)
37: [ RUN ] MimicTest.AllQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 374981081
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 181.5
37: (ns/day) (hour/ns)
37: Performance: 78.660 0.305
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.AllQuantumMol (31 ms)
37: [ RUN ] MimicTest.TwoQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 589251710
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 181.8
37: (ns/day) (hour/ns)
37: Performance: 77.782 0.309
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.TwoQuantumMol (28 ms)
37: [ RUN ] MimicTest.BondCuts
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1815661083
37: Generated 2211 of the 2211 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 2211 of the 2211 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 66.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: NVE simulation: will use the initial temperature of 300.368 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/ala.gro'
37:
37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.003 0.002 186.2
37: (ns/day) (hour/ns)
37: Performance: 56.280 0.426
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.BondCuts (62 ms)
37: [----------] 4 tests from MimicTest (149 ms total)
37:
37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
37: Setting the LD random seed to -783689897
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.236 0.118 199.4
37: (ns/day) (hour/ns)
37: Performance: 1.462 16.421
37:
Reading frame 0 time 0.000
37: # Atoms 6
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (144 ms)
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
37: Setting the LD random seed to 1864847378
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.248 0.124 199.4
37: (ns/day) (hour/ns)
37: Performance: 1.392 17.243
37:
Reading frame 0 time 0.000
37: # Atoms 6
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (150 ms)
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
37: Setting the LD random seed to -904430880
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.215 0.108 199.4
37: (ns/day) (hour/ns)
37: Performance: 1.606 14.946
37:
Reading frame 0 time 0.000
37: # Atoms 3
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (133 ms)
37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (427 ms total)
37:
37: [----------] 3 tests from Checking/InitialConstraintsTest
37: [ RUN ] Checking/InitialConstraintsTest.Works/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -763279936
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.161 0.081 199.2
37: (ns/day) (hour/ns)
37: Performance: 2.142 11.205
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (176 ms)
37: [ RUN ] Checking/InitialConstraintsTest.Works/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 654281018
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.277 0.139 199.5
37: (ns/day) (hour/ns)
37: Performance: 1.244 19.295
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (233 ms)
37: [ RUN ] Checking/InitialConstraintsTest.Works/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: Integrator method md-vv-avek is implemented primarily for validation
37: purposes; for molecular dynamics, you should probably be using md or md-vv
37:
37: Setting the LD random seed to -1022934275
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.4 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.277 0.139 199.5
37: (ns/day) (hour/ns)
37: Performance: 1.246 19.269
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (233 ms)
37: [----------] 3 tests from Checking/InitialConstraintsTest (642 ms total)
37:
37: [----------] 3 tests from MdrunCanWrite/Trajectories
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -671155743
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.222 0.112 199.4
37: (ns/day) (hour/ns)
37: Performance: 5.423 4.426
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (209 ms)
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -433328158
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.209 0.105 199.3
37: (ns/day) (hour/ns)
37: Performance: 5.772 4.158
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (198 ms)
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 808926818
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.244 0.123 199.4
37: (ns/day) (hour/ns)
37: Performance: 4.935 4.863
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (216 ms)
37: [----------] 3 tests from MdrunCanWrite/Trajectories (625 ms total)
37:
37: [----------] 3 tests from MdrunCanWrite/NptTrajectories
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -1590847121
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.162 0.082 199.1
37: (ns/day) (hour/ns)
37: Performance: 3.179 7.550
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (175 ms)
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1262676182
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.163 0.082 199.0
37: (ns/day) (hour/ns)
37: Performance: 3.165 7.583
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (175 ms)
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -1959847802
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.4 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.229 0.115 199.3
37: (ns/day) (hour/ns)
37: Performance: 2.258 10.628
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (208 ms)
37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (558 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 29 tests from 11 test cases ran. (49068 ms total)
37: [ PASSED ] 29 tests.
37/40 Test #37: MdrunTests ....................... Passed 49.10 sec
test 38
Start 38: MdrunNonIntegratorTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
38: Test timeout computed to be: 600
38: [==========] Running 57 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -4.7990990e+01
38: Maximum force = 1.8629828e+02 on atom 13
38: Norm of force = 8.7721844e+01
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (404 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 3.02331e+02 on atom 3
38: F-Norm = 1.18024e+02
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -5.5862099e+01
38: Maximum force = 4.2728845e+02 on atom 13
38: Norm of force = 1.8453478e+02
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (462 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 22.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 3.1937714e+02
38: Maximum force = 9.9988643e+03 on atom 9
38: Norm of force = 4.6166996e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (363 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38:
38: NOTE 3 [file glycine_vacuo.top, line 12]:
38: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
38:
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 22.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 2.41575e+04 on atom 10
38: F-Norm = 1.18451e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 1.5174377e+02
38: Maximum force = 7.4208838e+03 on atom 9
38: Norm of force = 3.5693005e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (361 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 3 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -1.5698413e+02
38: Maximum force = 4.5704984e+02 on atom 17
38: Norm of force = 1.8327747e+02
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (83 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 3 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38:
38: NOTE 4 [file unknown]:
38: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 1.06801e+03 on atom 28
38: F-Norm = 4.26916e+02
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -1.6941180e+02
38: Maximum force = 2.1832491e+02 on atom 17
38: Norm of force = 7.9220732e+01
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (85 ms)
38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1759 ms total)
38:
38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents converged to Fmax < 10 in 1 steps
38: Potential Energy = -9.7425699e-01
38: Maximum force = 4.0132303e+00 on atom 1
38: Norm of force = 1.6383944e+00
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (43 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 4.01323e+00 on atom 1
38: F-Norm = 1.63839e+00
38:
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
38: Potential Energy = -9.9064207e-01
38: Maximum force = 2.5781622e+00 on atom 1
38: Norm of force = 1.0525302e+00
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (43 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38:
38: There was 1 warning
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Low-Memory BFGS Minimizer:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: Using 10 BFGS correction steps.
38:
38: F-max = 4.01323e+00 on atom 1
38: F-Norm = 1.63839e+00
38:
38:
38: writing lowest energy coordinates.
38:
38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
38: Potential Energy = -9.9064207e-01
38: Maximum force = 2.5781622e+00 on atom 1
38: Norm of force = 1.0525302e+00
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (43 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 3.1939697e+02
38: Maximum force = 9.9704248e+03 on atom 9
38: Norm of force = 4.6227540e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (364 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 2.41672e+04 on atom 10
38: F-Norm = 1.19357e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 1.5625757e+02
38: Maximum force = 7.5018242e+03 on atom 9
38: Norm of force = 3.6139019e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (361 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38:
38: There was 1 warning
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Low-Memory BFGS Minimizer:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: Using 10 BFGS correction steps.
38:
38: F-max = 2.41672e+04 on atom 10
38: F-Norm = 1.19357e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 5.6111725e+02
38: Maximum force = 1.2685491e+04 on atom 10
38: Norm of force = 6.0643622e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (362 ms)
38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1216 ms total)
38:
38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: NVE simulation: will use the initial temperature of 68.810 K for
38: determining the Verlet buffer size
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.310 0.156 199.6
38: (ns/day) (hour/ns)
38: Performance: 9.441 2.542
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr'
38:
38: trr version: GMX_trn_file (single precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 195.0
38: (ns/day) (hour/ns)
38: Performance: 292.318 0.082
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (235 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: NVE simulation: will use the initial temperature of 68.810 K for
38: determining the Verlet buffer size
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.243 0.122 199.5
38: (ns/day) (hour/ns)
38: Performance: 12.075 1.988
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 195.0
38: (ns/day) (hour/ns)
38: Performance: 294.949 0.081
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (202 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.203 0.102 199.3
38: (ns/day) (hour/ns)
38: Performance: 14.410 1.666
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.006 179.4
38: (ns/day) (hour/ns)
38: Performance: 260.468 0.092
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (185 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.213 0.107 199.4
38: (ns/day) (hour/ns)
38: Performance: 13.723 1.749
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.006 179.4
38: (ns/day) (hour/ns)
38: Performance: 259.667 0.092
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (191 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: NVE simulation: will use the initial temperature of 398.997 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.262 0.131 199.5
38: (ns/day) (hour/ns)
38: Performance: 11.193 2.144
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.005 195.1
38: (ns/day) (hour/ns)
38: Performance: 271.595 0.088
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (642 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: NVE simulation: will use the initial temperature of 398.997 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.247 0.124 199.4
38: (ns/day) (hour/ns)
38: Performance: 11.879 2.020
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.005 195.8
38: (ns/day) (hour/ns)
38: Performance: 273.270 0.088
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (634 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.273 0.137 199.5
38: (ns/day) (hour/ns)
38: Performance: 10.753 2.232
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.006 195.7
38: (ns/day) (hour/ns)
38: Performance: 260.512 0.092
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (667 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.272 0.136 199.5
38: (ns/day) (hour/ns)
38: Performance: 10.776 2.227
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.005 195.7
38: (ns/day) (hour/ns)
38: Performance: 272.798 0.088
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (666 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: NVE simulation: will use the initial temperature of 456.887 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 7 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 7 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.255 0.128 199.4
38: (ns/day) (hour/ns)
38: Performance: 11.468 2.093
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.017 0.009 197.1
38: (ns/day) (hour/ns)
38: Performance: 168.516 0.142
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (262 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: NVE simulation: will use the initial temperature of 456.887 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 7 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 7 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.231 0.116 199.3
38: (ns/day) (hour/ns)
38: Performance: 12.679 1.893
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.017 0.009 197.0
38: (ns/day) (hour/ns)
38: Performance: 167.285 0.143
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (250 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 6 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.269 0.135 199.4
38: (ns/day) (hour/ns)
38: Performance: 10.872 2.208
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.017 0.009 197.1
38: (ns/day) (hour/ns)
38: Performance: 168.437 0.142
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (315 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 6 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.221 0.111 199.3
38: (ns/day) (hour/ns)
38: Performance: 13.221 1.815
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.017 0.009 197.0
38: (ns/day) (hour/ns)
38: Performance: 167.389 0.143
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (275 ms)
38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (4524 ms total)
38:
38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.297 0.150 198.4
38: (ns/day) (hour/ns)
38: Performance: 9.810 2.446
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.023 0.012 195.6
38: (ns/day) (hour/ns)
38: Performance: 124.772 0.192
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (302 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.288 0.144 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.178 2.358
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 128.856 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (291 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.276 0.138 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.614 2.261
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.6
38: (ns/day) (hour/ns)
38: Performance: 129.383 0.185
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (283 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.276 0.138 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.609 2.262
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 128.945 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (285 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.306 0.154 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.565 2.509
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 131.283 0.183
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (301 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.254 0.128 199.2
38: (ns/day) (hour/ns)
38: Performance: 11.511 2.085
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 130.843 0.183
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (274 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.287 0.144 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.199 2.353
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 130.723 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (291 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.290 0.146 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.090 2.378
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 129.099 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (296 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.364 0.183 199.5
38: (ns/day) (hour/ns)
38: Performance: 8.047 2.983
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 129.389 0.185
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (328 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.308 0.154 199.3
38: (ns/day) (hour/ns)
38: Performance: 9.511 2.523
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 130.366 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (301 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.308 0.154 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.521 2.521
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 131.496 0.183
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (302 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.288 0.144 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.179 2.358
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 130.959 0.183
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (292 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.284 0.143 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.305 2.329
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.021 0.011 195.4
38: (ns/day) (hour/ns)
38: Performance: 138.111 0.174
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (286 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.437 0.219 199.5
38: (ns/day) (hour/ns)
38: Performance: 6.706 3.579
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 128.276 0.187
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (364 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.318 0.159 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.216 2.604
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 129.850 0.185
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (308 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.300 0.151 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.756 2.460
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 130.361 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (298 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.323 0.162 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.061 2.649
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 128.380 0.187
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (308 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.421 0.211 199.5
38: (ns/day) (hour/ns)
38: Performance: 6.958 3.449
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 128.912 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (358 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.658 0.329 199.7
38: (ns/day) (hour/ns)
38: Performance: 4.460 5.381
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 128.942 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (476 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.270 0.136 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.839 2.214
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.0
38: (ns/day) (hour/ns)
38: Performance: 130.358 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (281 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.308 0.155 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.505 2.525
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.4
38: (ns/day) (hour/ns)
38: Performance: 132.369 0.181
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (299 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.396 0.198 199.5
38: (ns/day) (hour/ns)
38: Performance: 7.409 3.240
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.4 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.6
38: (ns/day) (hour/ns)
38: Performance: 130.726 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (344 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.339 0.170 199.4
38: (ns/day) (hour/ns)
38: Performance: 8.644 2.777
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.5
38: (ns/day) (hour/ns)
38: Performance: 131.104 0.183
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (348 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.341 0.171 199.4
38: (ns/day) (hour/ns)
38: Performance: 8.586 2.795
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 129.596 0.185
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (351 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.272 0.137 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.749 2.233
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.5
38: (ns/day) (hour/ns)
38: Performance: 130.119 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (316 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.273 0.137 199.2
38: (ns/day) (hour/ns)
38: Performance: 10.708 2.241
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 194.8
38: (ns/day) (hour/ns)
38: Performance: 130.143 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (319 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.296 0.148 199.3
38: (ns/day) (hour/ns)
38: Performance: 9.897 2.425
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.1
38: (ns/day) (hour/ns)
38: Performance: 129.853 0.185
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (332 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.289 0.145 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.123 2.371
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 194.9
38: (ns/day) (hour/ns)
38: Performance: 130.402 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (327 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.351 0.176 199.4
38: (ns/day) (hour/ns)
38: Performance: 8.345 2.876
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 128.735 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (357 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.288 0.145 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.164 2.361
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 128.047 0.187
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (324 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.288 0.144 199.3
38: (ns/day) (hour/ns)
38: Performance: 10.179 2.358
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.3
38: (ns/day) (hour/ns)
38: Performance: 128.912 0.186
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (326 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.387 0.194 199.5
38: (ns/day) (hour/ns)
38: Performance: 7.565 3.173
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.1
38: (ns/day) (hour/ns)
38: Performance: 129.976 0.185
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (375 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.301 0.151 199.4
38: (ns/day) (hour/ns)
38: Performance: 9.724 2.468
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.4 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.022 0.011 195.2
38: (ns/day) (hour/ns)
38: Performance: 130.325 0.184
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (331 ms)
38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (10576 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 57 tests from 4 test cases ran. (18075 ms total)
38: [ PASSED ] 57 tests.
38/40 Test #38: MdrunNonIntegratorTests .......... Passed 18.12 sec
test 39
Start 39: LegacyGroupSchemeMdrunTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/legacy-mdrun-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml"
39: Test timeout computed to be: 600
39: [==========] Running 2 tests from 1 test case.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from Simple/TpiTest
39: [ RUN ] Simple/TpiTest.ReproducesOutput/0
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]:
39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
39: removed in a future release when all interaction forms are supported for
39: the verlet scheme. The verlet scheme already scales better, and it is
39: compatible with GPUs and other accelerators.
39:
39: Generated 331705 of the 331705 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 331705 of the 331705 1-4 parameter combinations
39: Excluding 2 bonded neighbours molecule type 'SOL'
39: Excluding 3 bonded neighbours molecule type 'methane'
39: Number of degrees of freedom in T-Coupling group System is 1308.00
39:
39: There was 1 note
39: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.4 (single precision)
39: Using 1 MPI thread
39:
39:
39: NOTE: Thread affinity was not set.
39:
39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
39: removed in a future release when 'verlet' supports all interaction forms.
39:
39: Reading frames from gro file '216 water molecules', 648 atoms.
39:
Reading frame 0 time 0.000 mu 8.698e+02 <mu> 8.698e+02
39:
Last frame 0 time 0.000
39: Analysing residue names:
39: There are: 216 Water residues
39: There are: 1 Other residues
39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm
39: Largest charge group radii for Coulomb: 0.100, 0.100 nm
39: This run will generate roughly 0 Mb of data
39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (462 ms)
39: [ RUN ] Simple/TpiTest.ReproducesOutput/1
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]:
39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
39: removed in a future release when all interaction forms are supported for
39: the verlet scheme. The verlet scheme already scales better, and it is
39: compatible with GPUs and other accelerators.
39:
39: Generated 331705 of the 331705 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 331705 of the 331705 1-4 parameter combinations
39: Excluding 2 bonded neighbours molecule type 'SOL'
39: Excluding 3 bonded neighbours molecule type 'methane'
39: Number of degrees of freedom in T-Coupling group System is 1308.00
39:
39: There was 1 note
39: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.4 (single precision)
39: Using 1 MPI thread
39:
39:
39: NOTE: Thread affinity was not set.
39:
39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
39: removed in a future release when 'verlet' supports all interaction forms.
39:
39: Reading frames from gro file '216 water molecules', 648 atoms.
39:
Reading frame 0 time 0.000 mu 9.151e+01 <mu> 9.151e+01
39:
Last frame 0 time 0.000
39: Analysing residue names:
39: There are: 216 Water residues
39: There are: 1 Other residues
39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm
39: Largest charge group radii for Coulomb: 0.100, 0.100 nm
39: This run will generate roughly 0 Mb of data
39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (515 ms)
39: [----------] 2 tests from Simple/TpiTest (978 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 2 tests from 1 test case ran. (978 ms total)
39: [ PASSED ] 2 tests.
39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 1.00 sec
test 40
Start 40: MdrunMpiTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
40: Test timeout computed to be: 600
40: [==========] Running 21 tests from 7 test cases.
40: [----------] Global test environment set-up.
40: [----------] 1 test from DomainDecompositionSpecialCasesTest
40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 955384598
40: Generated 3 of the 3 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 3 of the 3 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 9.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc2'
40: 0 steps, 0.0 ps.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.002 0.001 156.5
40: (ns/day) (hour/ns)
40: Performance: 61.589 0.390
40: This run will generate roughly 0 Mb of data
40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (42 ms)
40: [----------] 1 test from DomainDecompositionSpecialCasesTest (42 ms total)
40:
40: [----------] 4 tests from MimicTest
40: [ RUN ] MimicTest.OneQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -1155734905
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.003 0.002 160.3
40: (ns/day) (hour/ns)
40: Performance: 51.403 0.467
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.OneQuantumMol (49 ms)
40: [ RUN ] MimicTest.AllQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -409799002
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.002 0.001 181.5
40: (ns/day) (hour/ns)
40: Performance: 77.950 0.308
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.AllQuantumMol (50 ms)
40: [ RUN ] MimicTest.TwoQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -1204770717
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.003 0.002 173.5
40: (ns/day) (hour/ns)
40: Performance: 53.967 0.445
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.TwoQuantumMol (46 ms)
40: [ RUN ] MimicTest.BondCuts
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 249600165
40: Generated 2211 of the 2211 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2211 of the 2211 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 66.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: NVE simulation: will use the initial temperature of 300.368 K for
40: determining the Verlet buffer size
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/ala.gro'
40:
40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.003 0.002 186.2
40: (ns/day) (hour/ns)
40: Performance: 55.024 0.436
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.BondCuts (79 ms)
40: [----------] 4 tests from MimicTest (225 ms total)
40:
40: [----------] 1 test from MultiSimTerminationTest
40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
40: [----------] 1 test from MultiSimTerminationTest (0 ms total)
40:
40: [----------] 2 tests from PmeTest
40: [ RUN ] PmeTest.ReproducesEnergies
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40: Setting the LD random seed to 1536865878
40: Generated 279 of the 1225 non-bonded parameter combinations
40: Excluding 2 bonded neighbours molecule type 'Methanol'
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 12.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
40: NVE simulation: will use the initial temperature of 1046.791 K for
40: determining the Verlet buffer size
40:
40: Estimate for the relative computational load of the PME mesh part: 1.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
40: The optimal PME mesh load for parallel simulations is below 0.5
40: and for highly parallel simulations between 0.25 and 0.33,
40: for higher performance, increase the cut-off and the PME grid spacing.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: Calculating fourier grid dimensions for X Y Z
40: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
40: This run will generate roughly 0 Mb of data
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.246 0.124 199.5
40: (ns/day) (hour/ns)
40: Performance: 14.682 1.635
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.251 0.126 199.5
40: (ns/day) (hour/ns)
40: Performance: 14.429 1.663
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.241 0.121 199.5
40: (ns/day) (hour/ns)
40: Performance: 15.008 1.599
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10602 ms)
40: [ RUN ] PmeTest.ScalesTheBox
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 1815103676
40: Generated 279 of the 1225 non-bonded parameter combinations
40: Excluding 2 bonded neighbours molecule type 'Methanol'
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Searching the wall atom type(s)
40: Number of degrees of freedom in T-Coupling group rest is 13.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: NVE simulation: will use the initial temperature of 966.268 K for
40: determining the Verlet buffer size
40:
40: Estimate for the relative computational load of the PME mesh part: 1.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: The optimal PME mesh load for parallel simulations is below 0.5
40: and for highly parallel simulations between 0.25 and 0.33,
40: for higher performance, increase the cut-off and the PME grid spacing.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.4 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 0 steps, 0.0 ps.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.014 0.007 188.0
40: (ns/day) (hour/ns)
40: Performance: 11.846 2.026
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: Calculating fourier grid dimensions for X Y Z
40: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
40: This run will generate roughly 0 Mb of data
40: [ OK ] PmeTest.ScalesTheBox (30884 ms)
40: [----------] 2 tests from PmeTest (41487 ms total)
40:
40: [----------] 1 test from ReplicaExchangeTerminationTest
40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
40:
40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -4.7990990e+01
40: Maximum force = 1.8629828e+02 on atom 13
40: Norm of force = 8.7721844e+01
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (433 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 3.02331e+02 on atom 3
40: F-Norm = 1.18024e+02
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -5.5862099e+01
40: Maximum force = 4.2728845e+02 on atom 13
40: Norm of force = 1.8453478e+02
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (443 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 22.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 3.1937714e+02
40: Maximum force = 9.9988643e+03 on atom 9
40: Norm of force = 4.6166996e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (336 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40:
40: NOTE 3 [file glycine_vacuo.top, line 12]:
40: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
40:
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 22.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 2.41575e+04 on atom 10
40: F-Norm = 1.18451e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 1.5174377e+02
40: Maximum force = 7.4208838e+03 on atom 9
40: Norm of force = 3.5693005e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (337 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 2145 of the 2145 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2145 of the 2145 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
40:
40: NOTE 3 [file unknown]:
40: You are using constraints on all bonds, whereas the forcefield has been
40: parametrized only with constraints involving hydrogen atoms. We suggest
40: using constraints = h-bonds instead, this will also improve performance.
40:
40: Cleaning up constraints and constant bonded interactions with virtual sites
40: Removed 18 Angles with virtual sites, 21 left
40: Removed 10 Proper Dih.s with virtual sites, 44 left
40: Converted 15 Constraints with virtual sites to connections, 7 left
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 23.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -1.5698413e+02
40: Maximum force = 4.5704984e+02 on atom 17
40: Norm of force = 1.8327747e+02
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (63 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 2145 of the 2145 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2145 of the 2145 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
40:
40: NOTE 3 [file unknown]:
40: You are using constraints on all bonds, whereas the forcefield has been
40: parametrized only with constraints involving hydrogen atoms. We suggest
40: using constraints = h-bonds instead, this will also improve performance.
40:
40:
40: NOTE 4 [file unknown]:
40: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
40:
40: Cleaning up constraints and constant bonded interactions with virtual sites
40: Removed 18 Angles with virtual sites, 21 left
40: Removed 10 Proper Dih.s with virtual sites, 44 left
40: Converted 15 Constraints with virtual sites to connections, 7 left
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 23.00
40:
40: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 5 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 1.06801e+03 on atom 28
40: F-Norm = 4.26916e+02
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -1.6941180e+02
40: Maximum force = 2.1832491e+02 on atom 17
40: Norm of force = 7.9220732e+01
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (65 ms)
40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1677 ms total)
40:
40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents converged to Fmax < 10 in 1 steps
40: Potential Energy = -9.7425699e-01
40: Maximum force = 4.0132303e+00 on atom 1
40: Norm of force = 1.6383944e+00
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (25 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 4.01323e+00 on atom 1
40: F-Norm = 1.63839e+00
40:
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
40: Potential Energy = -9.9064207e-01
40: Maximum force = 2.5781622e+00 on atom 1
40: Norm of force = 1.0525302e+00
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (26 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40:
40: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40:
40: There was 1 warning
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.4 (single precision)
40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
40:
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Low-Memory BFGS Minimizer:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: Using 10 BFGS correction steps.
40:
40: F-max = 4.01323e+00 on atom 1
40: F-Norm = 1.63839e+00
40:
40:
40: writing lowest energy coordinates.
40:
40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
40: Potential Energy = -9.9064207e-01
40: Maximum force = 2.5781622e+00 on atom 1
40: Norm of force = 1.0525302e+00
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (25 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 3.1939697e+02
40: Maximum force = 9.9704248e+03 on atom 9
40: Norm of force = 4.6227540e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (344 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.4 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 2.41672e+04 on atom 10
40: F-Norm = 1.19357e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 1.5625757e+02
40: Maximum force = 7.5018242e+03 on atom 9
40: Norm of force = 3.6139019e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (337 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40:
40: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40:
40: There was 1 warning
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.4 (single precision)
40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
40:
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Low-Memory BFGS Minimizer:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: Using 10 BFGS correction steps.
40:
40: F-max = 2.41672e+04 on atom 10
40: F-Norm = 1.19357e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 5.6111725e+02
40: Maximum force = 1.2685491e+04 on atom 10
40: Norm of force = 6.0643622e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (340 ms)
40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1097 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 21 tests from 7 test cases ran. (44528 ms total)
40: [ PASSED ] 21 tests.
40:
40: YOU HAVE 4 DISABLED TESTS
40:
40/40 Test #40: MdrunMpiTests .................... Passed 44.55 sec
98% tests passed, 1 tests failed out of 40
Label Time Summary:
GTest = 194.52 sec*proc (40 tests)
IntegrationTest = 112.90 sec*proc (5 tests)
MpiTest = 0.24 sec*proc (3 tests)
SlowTest = 72.53 sec*proc (1 test)
UnitTest = 9.08 sec*proc (34 tests)
Total Test time (real) = 194.59 sec
The following tests FAILED:
11 - HardwareUnitTests (Failed)
Errors while running CTest
make: *** [debian/rules:126: build-basic] Error 1
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-12-15T00:14:30Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1804808
Build-Time: 2649
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 402
Job: gromacs_2019.4-1
Machine Architecture: armhf
Package: gromacs
Package-Time: 3079
Source-Version: 2019.4-1
Space: 1804808
Status: attempted
Version: 2019.4-1
--------------------------------------------------------------------------------
Finished at 2019-12-15T00:14:30Z
Build needed 00:51:19, 1804808k disk space