gromacs →
2016-3+b1 →
armhf → 2016-10-06 12:09:15
sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on bm-wb-04
+==============================================================================+
| gromacs 2016-3+b1 (armhf) Thu, 06 Oct 2016 11:36:47 +0000 |
+==============================================================================+
Package: gromacs
Version: 2016-3+b1
Source Version: 2016-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-b43a0684-d317-4419-8360-3abc2a9abbf5' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9327 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.3 MB]
Fetched 20.6 MB in 22s (903 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 'Svn' version control system at:
svn://anonscm.debian.org/debichem/unstable/gromacs/
Need to get 27.4 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main gromacs 2016-3 (dsc) [2574 B]
Get:2 http://172.17.0.1/private stretch-staging/main gromacs 2016-3 (tar) [27.3 MB]
Get:3 http://172.17.0.1/private stretch-staging/main gromacs 2016-3 (diff) [33.0 kB]
Fetched 27.4 MB in 2s (9734 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-DgLUw5/gromacs-2016' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-DgLUw5' 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-ASJygh/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-ASJygh/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ASJygh/gpg/trustdb.gpg: trustdb created
gpg: key 5B825F7B5086BFC4: 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 5B825F7B5086BFC4: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5B825F7B5086BFC4: 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-ASJygh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ASJygh/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ASJygh/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ASJygh/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ASJygh/apt_archive ./ Packages [433 B]
Fetched 2081 B in 0s (3553 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:
dirmngr fuse2fs gnupg-l10n libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages
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 10 not upgraded.
Need to get 762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ASJygh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 762 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14070 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: cmake, debhelper (>= 7.0.0), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libtinyxml-dev, libx11-dev, openmpi-bin, zlib1g-dev
Filtered Build-Depends: cmake, debhelper (>= 7.0.0), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libtinyxml-dev, libx11-dev, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-hUEqDy/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-gromacs-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-hUEqDy/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hUEqDy/gpg/trustdb.gpg: trustdb created
gpg: key 5B825F7B5086BFC4: 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 5B825F7B5086BFC4: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5B825F7B5086BFC4: 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-hUEqDy/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hUEqDy/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hUEqDy/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hUEqDy/apt_archive ./ Sources [427 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hUEqDy/apt_archive ./ Packages [516 B]
Fetched 2242 B in 0s (3858 B/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:
dirmngr fuse2fs gnupg-l10n libfuse2 libsasl2-modules manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base
gfortran gfortran-6 groff-base intltool-debian libarchive-zip-perl
libarchive13 libblas-common libblas-dev libblas3 libboost-dev
libboost1.61-dev libbsd0 libcroco3 libcurl3 libexpat1 libfftw3-bin
libfftw3-dev libfftw3-double3 libfftw3-single3
libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev
libibverbs1 libicu57 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libltdl-dev libltdl7 liblzo2-2
libmagic-mgc libmagic1 libmpich-dev libmpich12 libnghttp2-14 libnl-3-200
libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1
libpthread-stubs0-dev librtmp1 libsigsegv2 libssh2-1 libtinyxml-dev
libtinyxml2.6.2v5 libtool libunistring0 libx11-6 libx11-data libx11-dev
libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxml2 m4
man-db ocl-icd-libopencl1 openmpi-bin openmpi-common po-debconf
x11proto-core-dev x11proto-input-dev x11proto-kb-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation codeblocks eclipse ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-6-doc libgfortran3-dbg
libcoarrays-dev groff lrzip liblapack-doc-man liblapack-doc libboost-doc
libboost1.61-doc libboost-atomic1.61-dev libboost-chrono1.61-dev
libboost-context1.61-dev libboost-coroutine1.61-dev
libboost-date-time1.61-dev libboost-exception1.61-dev
libboost-filesystem1.61-dev libboost-graph1.61-dev
libboost-graph-parallel1.61-dev libboost-iostreams1.61-dev
libboost-locale1.61-dev libboost-log1.61-dev libboost-math1.61-dev
libboost-mpi1.61-dev libboost-mpi-python1.61-dev
libboost-program-options1.61-dev libboost-python1.61-dev
libboost-random1.61-dev libboost-regex1.61-dev
libboost-serialization1.61-dev libboost-signals1.61-dev
libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
libmpfrc++-dev libntl-dev libfftw3-doc krb5-doc krb5-user
libhwloc-contrib-plugins libtool-doc openmpi-doc pciutils libtinyxml-doc
gcj-jdk libxcb-doc less www-browser opencl-icd libmail-box-perl
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales mpich libx11-doc xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base
gfortran gfortran-6 groff-base intltool-debian libarchive-zip-perl
libarchive13 libblas-common libblas-dev libblas3 libboost-dev
libboost1.61-dev libbsd0 libcroco3 libcurl3 libexpat1 libfftw3-bin
libfftw3-dev libfftw3-double3 libfftw3-single3
libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev
libibverbs1 libicu57 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libltdl-dev libltdl7 liblzo2-2
libmagic-mgc libmagic1 libmpich-dev libmpich12 libnghttp2-14 libnl-3-200
libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0 libpipeline1
libpthread-stubs0-dev librtmp1 libsigsegv2 libssh2-1 libtinyxml-dev
libtinyxml2.6.2v5 libtool libunistring0 libx11-6 libx11-data libx11-dev
libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxml2 m4
man-db ocl-icd-libopencl1 openmpi-bin openmpi-common po-debconf
sbuild-build-depends-gromacs-dummy x11proto-core-dev x11proto-input-dev
x11proto-kb-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 95 newly installed, 0 to remove and 10 not upgraded.
Need to get 73.6 MB of archives.
After this operation, 373 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hUEqDy/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [854 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.11 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf cmake-data all 3.6.2-1 [1153 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libarchive13 armhf 3.2.1-2 [250 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.15.0-1 [72.6 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libcurl3 armhf 7.50.1-1 [251 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf cmake armhf 3.6.2-1 [2268 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libfftw3-double3 armhf 3.3.4-2+rvt+b2 [435 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libfftw3-single3 armhf 3.3.4-2+rvt+b2 [641 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-1 [2520 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10 [823 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-11+rpi1 [166 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.1.1-11+rpi1 [200 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.1.1-11+rpi1 [27.9 MB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-2.1+b1 [6843 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libfftw3-bin armhf 3.3.4-2+rvt+b2 [42.0 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libfftw3-dev armhf 3.3.4-2+rvt+b2 [1073 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libnl-3-200 armhf 3.2.27-1 [53.4 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libnl-route-3-200 armhf 3.2.27-1 [111 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libtinyxml2.6.2v5 armhf 2.6.2-3 [32.5 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libtinyxml-dev armhf 2.6.2-3 [49.1 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf x11proto-core-dev all 7.0.29-1 [728 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libxdmcp-dev armhf 1:1.1.2-1.1 [40.8 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf x11proto-input-dev all 2.3.2-1 [158 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf x11proto-kb-dev all 1.0.7-1 [233 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libxcb1-dev armhf 1.12-1 [165 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libhwloc5 armhf 1.11.4-1+rpi1 [82.8 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libhwloc-dev armhf 1.11.4-1+rpi1 [136 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf ocl-icd-libopencl1 armhf 2.2.9-2 [34.7 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libhwloc-plugins armhf 1.11.4-1+rpi1 [14.9 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libmpich12 armhf 3.2-7+rpi1 [785 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libmpich-dev armhf 3.2-7+rpi1 [1038 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libopenmpi2 armhf 2.0.1-5 [1621 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf openmpi-common all 2.0.1-5 [146 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libopenmpi-dev armhf 2.0.1-5 [997 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf openmpi-bin armhf 2.0.1-5 [195 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 73.6 MB in 7s (10.2 MB/s)
Selecting previously unselected package groff-base.
(Reading database ... 14070 files and directories currently installed.)
Preparing to unpack .../00-groff-base_1.22.3-8_armhf.deb ...
Unpacking groff-base (1.22.3-8) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../01-libbsd0_0.8.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../02-bsdmainutils_9.0.11_armhf.deb ...
Unpacking bsdmainutils (9.0.11) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../05-cmake-data_3.6.2-1_all.deb ...
Unpacking cmake-data (3.6.2-1) ...
Selecting previously unselected package liblzo2-2:armhf.
Preparing to unpack .../06-liblzo2-2_2.08-1.2_armhf.deb ...
Unpacking liblzo2-2:armhf (2.08-1.2) ...
Selecting previously unselected package libicu57:armhf.
Preparing to unpack .../07-libicu57_57.1-4_armhf.deb ...
Unpacking libicu57:armhf (57.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../08-libxml2_2.9.4+dfsg1-2_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-2) ...
Selecting previously unselected package libarchive13:armhf.
Preparing to unpack .../09-libarchive13_3.2.1-2_armhf.deb ...
Unpacking libarchive13:armhf (3.2.1-2) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../10-libkeyutils1_1.5.9-9_armhf.deb ...
Unpacking libkeyutils1:armhf (1.5.9-9) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../11-libkrb5support0_1.14.3+dfsg-2_armhf.deb ...
Unpacking libkrb5support0:armhf (1.14.3+dfsg-2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../12-libk5crypto3_1.14.3+dfsg-2_armhf.deb ...
Unpacking libk5crypto3:armhf (1.14.3+dfsg-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../13-libkrb5-3_1.14.3+dfsg-2_armhf.deb ...
Unpacking libkrb5-3:armhf (1.14.3+dfsg-2) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../14-libgssapi-krb5-2_1.14.3+dfsg-2_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../15-libnghttp2-14_1.15.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.15.0-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../16-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../17-libssh2-1_1.7.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.7.0-1) ...
Selecting previously unselected package libcurl3:armhf.
Preparing to unpack .../18-libcurl3_7.50.1-1_armhf.deb ...
Unpacking libcurl3:armhf (7.50.1-1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../19-libexpat1_2.2.0-1_armhf.deb ...
Unpacking libexpat1:armhf (2.2.0-1) ...
Selecting previously unselected package libjsoncpp1:armhf.
Preparing to unpack .../20-libjsoncpp1_1.7.4-3_armhf.deb ...
Unpacking libjsoncpp1:armhf (1.7.4-3) ...
Selecting previously unselected package cmake.
Preparing to unpack .../21-cmake_3.6.2-1_armhf.deb ...
Unpacking cmake (3.6.2-1) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../22-libfftw3-double3_3.3.4-2+rvt+b2_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.4-2+rvt+b2) ...
Selecting previously unselected package libfftw3-single3:armhf.
Preparing to unpack .../23-libfftw3-single3_3.3.4-2+rvt+b2_armhf.deb ...
Unpacking libfftw3-single3:armhf (3.3.4-2+rvt+b2) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../24-libxau6_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../25-libxdmcp6_1%3a1.1.2-1.1_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-1.1) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../26-libxcb1_1.12-1_armhf.deb ...
Unpacking libxcb1:armhf (1.12-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../27-libx11-data_2%3a1.6.3-1_all.deb ...
Unpacking libx11-data (2:1.6.3-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../28-libx11-6_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.3-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../29-libmagic-mgc_1%3a5.28-4_armhf.deb ...
Unpacking libmagic-mgc (1:5.28-4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../30-libmagic1_1%3a5.28-4_armhf.deb ...
Unpacking libmagic1:armhf (1:5.28-4) ...
Selecting previously unselected package file.
Preparing to unpack .../31-file_1%3a5.28-4_armhf.deb ...
Unpacking file (1:5.28-4) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../32-gettext-base_0.19.8.1-1_armhf.deb ...
Unpacking gettext-base (0.19.8.1-1) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../33-libsigsegv2_2.10-5_armhf.deb ...
Unpacking libsigsegv2:armhf (2.10-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../34-m4_1.4.17-5_armhf.deb ...
Unpacking m4 (1.4.17-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../35-autoconf_2.69-10_all.deb ...
Unpacking autoconf (2.69-10) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../36-autotools-dev_20160430.1_all.deb ...
Unpacking autotools-dev (20160430.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../37-automake_1%3a1.15-4_all.deb ...
Unpacking automake (1:1.15-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../38-autopoint_0.19.8.1-1_all.deb ...
Unpacking autopoint (0.19.8.1-1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../39-libtool_2.4.6-2_all.deb ...
Unpacking libtool (2.4.6-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../40-dh-autoreconf_12_all.deb ...
Unpacking dh-autoreconf (12) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../41-libarchive-zip-perl_1.59-1_all.deb ...
Unpacking libarchive-zip-perl (1.59-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../42-libfile-stripnondeterminism-perl_0.028-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.028-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../43-dh-strip-nondeterminism_0.028-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.028-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../44-libglib2.0-0_2.50.0-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.50.0-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../45-libcroco3_0.6.11-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-2) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../46-libunistring0_0.9.6+really0.9.3-0.1_armhf.deb ...
Unpacking libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../47-gettext_0.19.8.1-1_armhf.deb ...
Unpacking gettext (0.19.8.1-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../48-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../49-po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../50-debhelper_10_all.deb ...
Unpacking debhelper (10) ...
Selecting previously unselected package libgfortran3:armhf.
Preparing to unpack .../51-libgfortran3_6.1.1-11+rpi1_armhf.deb ...
Unpacking libgfortran3:armhf (6.1.1-11+rpi1) ...
Selecting previously unselected package libgfortran-6-dev:armhf.
Preparing to unpack .../52-libgfortran-6-dev_6.1.1-11+rpi1_armhf.deb ...
Unpacking libgfortran-6-dev:armhf (6.1.1-11+rpi1) ...
Selecting previously unselected package gfortran-6.
Preparing to unpack .../53-gfortran-6_6.1.1-11+rpi1_armhf.deb ...
Unpacking gfortran-6 (6.1.1-11+rpi1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../54-gfortran_4%3a6.1.1-1_armhf.deb ...
Unpacking gfortran (4:6.1.1-1) ...
Selecting previously unselected package libblas-common.
Preparing to unpack .../55-libblas-common_3.6.1-2_armhf.deb ...
Unpacking libblas-common (3.6.1-2) ...
Selecting previously unselected package libblas3.
Preparing to unpack .../56-libblas3_3.6.1-2_armhf.deb ...
Unpacking libblas3 (3.6.1-2) ...
Selecting previously unselected package libblas-dev.
Preparing to unpack .../57-libblas-dev_3.6.1-2_armhf.deb ...
Unpacking libblas-dev (3.6.1-2) ...
Selecting previously unselected package libboost1.61-dev:armhf.
Preparing to unpack .../58-libboost1.61-dev_1.61.0+dfsg-2.1+b1_armhf.deb ...
Unpacking libboost1.61-dev:armhf (1.61.0+dfsg-2.1+b1) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../59-libboost-dev_1.61.0.2_armhf.deb ...
Unpacking libboost-dev:armhf (1.61.0.2) ...
Selecting previously unselected package libfftw3-bin.
Preparing to unpack .../60-libfftw3-bin_3.3.4-2+rvt+b2_armhf.deb ...
Unpacking libfftw3-bin (3.3.4-2+rvt+b2) ...
Selecting previously unselected package libfftw3-dev:armhf.
Preparing to unpack .../61-libfftw3-dev_3.3.4-2+rvt+b2_armhf.deb ...
Unpacking libfftw3-dev:armhf (3.3.4-2+rvt+b2) ...
Selecting previously unselected package liblapack3.
Preparing to unpack .../62-liblapack3_3.6.1-2_armhf.deb ...
Unpacking liblapack3 (3.6.1-2) ...
Selecting previously unselected package liblapack-dev.
Preparing to unpack .../63-liblapack-dev_3.6.1-2_armhf.deb ...
Unpacking liblapack-dev (3.6.1-2) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../64-libltdl7_2.4.6-2_armhf.deb ...
Unpacking libltdl7:armhf (2.4.6-2) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../65-libltdl-dev_2.4.6-2_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.6-2) ...
Selecting previously unselected package libnl-3-200:armhf.
Preparing to unpack .../66-libnl-3-200_3.2.27-1_armhf.deb ...
Unpacking libnl-3-200:armhf (3.2.27-1) ...
Selecting previously unselected package libnl-route-3-200:armhf.
Preparing to unpack .../67-libnl-route-3-200_3.2.27-1_armhf.deb ...
Unpacking libnl-route-3-200:armhf (3.2.27-1) ...
Selecting previously unselected package libpciaccess0:armhf.
Preparing to unpack .../68-libpciaccess0_0.13.4-1_armhf.deb ...
Unpacking libpciaccess0:armhf (0.13.4-1) ...
Selecting previously unselected package libpthread-stubs0-dev:armhf.
Preparing to unpack .../69-libpthread-stubs0-dev_0.3-4_armhf.deb ...
Unpacking libpthread-stubs0-dev:armhf (0.3-4) ...
Selecting previously unselected package libtinyxml2.6.2v5:armhf.
Preparing to unpack .../70-libtinyxml2.6.2v5_2.6.2-3_armhf.deb ...
Unpacking libtinyxml2.6.2v5:armhf (2.6.2-3) ...
Selecting previously unselected package libtinyxml-dev:armhf.
Preparing to unpack .../71-libtinyxml-dev_2.6.2-3_armhf.deb ...
Unpacking libtinyxml-dev:armhf (2.6.2-3) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../72-xorg-sgml-doctools_1%3a1.11-1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1) ...
Selecting previously unselected package x11proto-core-dev.
Preparing to unpack .../73-x11proto-core-dev_7.0.29-1_all.deb ...
Unpacking x11proto-core-dev (7.0.29-1) ...
Selecting previously unselected package libxau-dev:armhf.
Preparing to unpack .../74-libxau-dev_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau-dev:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp-dev:armhf.
Preparing to unpack .../75-libxdmcp-dev_1%3a1.1.2-1.1_armhf.deb ...
Unpacking libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Selecting previously unselected package x11proto-input-dev.
Preparing to unpack .../76-x11proto-input-dev_2.3.2-1_all.deb ...
Unpacking x11proto-input-dev (2.3.2-1) ...
Selecting previously unselected package x11proto-kb-dev.
Preparing to unpack .../77-x11proto-kb-dev_1.0.7-1_all.deb ...
Unpacking x11proto-kb-dev (1.0.7-1) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../78-xtrans-dev_1.3.5-1_all.deb ...
Unpacking xtrans-dev (1.3.5-1) ...
Selecting previously unselected package libxcb1-dev:armhf.
Preparing to unpack .../79-libxcb1-dev_1.12-1_armhf.deb ...
Unpacking libxcb1-dev:armhf (1.12-1) ...
Selecting previously unselected package libx11-dev:armhf.
Preparing to unpack .../80-libx11-dev_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-dev:armhf (2:1.6.3-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../81-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libhwloc5:armhf.
Preparing to unpack .../82-libhwloc5_1.11.4-1+rpi1_armhf.deb ...
Unpacking libhwloc5:armhf (1.11.4-1+rpi1) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../83-libhwloc-dev_1.11.4-1+rpi1_armhf.deb ...
Unpacking libhwloc-dev:armhf (1.11.4-1+rpi1) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../84-ocl-icd-libopencl1_2.2.9-2_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.2.9-2) ...
Selecting previously unselected package libhwloc-plugins.
Preparing to unpack .../85-libhwloc-plugins_1.11.4-1+rpi1_armhf.deb ...
Unpacking libhwloc-plugins (1.11.4-1+rpi1) ...
Selecting previously unselected package libibverbs1.
Preparing to unpack .../86-libibverbs1_1.2.1-2_armhf.deb ...
Unpacking libibverbs1 (1.2.1-2) ...
Selecting previously unselected package libibverbs-dev.
Preparing to unpack .../87-libibverbs-dev_1.2.1-2_armhf.deb ...
Unpacking libibverbs-dev (1.2.1-2) ...
Selecting previously unselected package libmpich12:armhf.
Preparing to unpack .../88-libmpich12_3.2-7+rpi1_armhf.deb ...
Unpacking libmpich12:armhf (3.2-7+rpi1) ...
Selecting previously unselected package libmpich-dev.
Preparing to unpack .../89-libmpich-dev_3.2-7+rpi1_armhf.deb ...
Unpacking libmpich-dev (3.2-7+rpi1) ...
Selecting previously unselected package libopenmpi2.
Preparing to unpack .../90-libopenmpi2_2.0.1-5_armhf.deb ...
Unpacking libopenmpi2 (2.0.1-5) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../91-openmpi-common_2.0.1-5_all.deb ...
Unpacking openmpi-common (2.0.1-5) ...
Selecting previously unselected package libopenmpi-dev.
Preparing to unpack .../92-libopenmpi-dev_2.0.1-5_armhf.deb ...
Unpacking libopenmpi-dev (2.0.1-5) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../93-openmpi-bin_2.0.1-5_armhf.deb ...
Unpacking openmpi-bin (2.0.1-5) ...
Selecting previously unselected package sbuild-build-depends-gromacs-dummy.
Preparing to unpack .../94-sbuild-build-depends-gromacs-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libtinyxml2.6.2v5:armhf (2.6.2-3) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.15.0-1) ...
Setting up libtinyxml-dev:armhf (2.6.2-3) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
Setting up libblas-common (3.6.1-2) ...
Setting up libgfortran3:armhf (6.1.1-11+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.0-1) ...
No schema files found: doing nothing.
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up libgfortran-6-dev:armhf (6.1.1-11+rpi1) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up cmake-data (3.6.2-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up x11proto-kb-dev (1.0.7-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libfftw3-double3:armhf (3.3.4-2+rvt+b2) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libboost1.61-dev:armhf (1.61.0+dfsg-2.1+b1) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up libblas3 (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libssh2-1:armhf (1.7.0-1) ...
Setting up openmpi-common (2.0.1-5) ...
Processing triggers for libc-bin (2.24-3) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libltdl7:armhf (2.4.6-2) ...
Setting up libpciaccess0:armhf (0.13.4-1) ...
Setting up libfftw3-single3:armhf (3.3.4-2+rvt+b2) ...
Setting up libboost-dev:armhf (1.61.0.2) ...
Setting up libxdmcp6:armhf (1:1.1.2-1.1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.9-2) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.11) ...
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 libnl-3-200:armhf (3.2.27-1) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up liblzo2-2:armhf (2.08-1.2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libjsoncpp1:armhf (1.7.4-3) ...
Setting up gfortran-6 (6.1.1-11+rpi1) ...
Setting up libfftw3-bin (3.3.4-2+rvt+b2) ...
Setting up libmpich12:armhf (3.2-7+rpi1) ...
Setting up x11proto-core-dev (7.0.29-1) ...
Setting up libltdl-dev:armhf (2.4.6-2) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libarchive13:armhf (3.2.1-2) ...
Setting up liblapack3 (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libxau-dev:armhf (1:1.0.8-1) ...
Setting up libnl-route-3-200:armhf (3.2.27-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
Setting up libhwloc5:armhf (1.11.4-1+rpi1) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-2) ...
Setting up libhwloc-plugins (1.11.4-1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Setting up libfftw3-dev:armhf (3.3.4-2+rvt+b2) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxcb1:armhf (1.12-1) ...
Setting up x11proto-input-dev (2.3.2-1) ...
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.1.1-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libibverbs1 (1.2.1-2) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
Setting up po-debconf (1.0.19) ...
Setting up libhwloc-dev:armhf (1.11.4-1+rpi1) ...
Setting up libblas-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libmpich-dev (3.2-7+rpi1) ...
update-alternatives: using /usr/include/mpich to provide /usr/include/mpi (mpi) in auto mode
Setting up libxcb1-dev:armhf (1.12-1) ...
Setting up libopenmpi2 (2.0.1-5) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up libx11-dev:armhf (2:1.6.3-1) ...
Setting up libibverbs-dev (1.2.1-2) ...
Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libopenmpi-dev (2.0.1-5) ...
update-alternatives: renaming mpi.pc slave link from /usr/lib/arm-linux-gnueabihf/pkgconfig/mpi.pc to /usr/lib/pkgconfig/mpi.pc
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up openmpi-bin (2.0.1-5) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up libcurl3:armhf (7.50.1-1) ...
Setting up cmake (3.6.2-1) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10) ...
Setting up dh-autoreconf (12) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.24-3 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.26.1-1 bsdmainutils_9.0.11 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 cmake_3.6.2-1 cmake-data_3.6.2-1 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-3 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.1.1-11+rpi1 gnupg_2.1.15-3 gnupg-agent_2.1.15-3 gnupg-l10n_2.1.15-3 gpgv_2.1.15-3 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.3 libarchive-zip-perl_1.59-1 libarchive13_3.2.1-2 libasan1_4.9.3-14 libasan3_6.1.1-11+rpi1 libassuan0_2.4.3-1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.2-1 libboost-dev_1.61.0.2 libboost1.61-dev_1.61.0+dfsg-2.1+b1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-3 libc-dev-bin_2.24-3 libc6_2.24-3 libc6-dev_2.24-3 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.0-2 libcurl3_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.10-1 libdebconfclient0_0.217 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfftw3-bin_3.3.4-2+rvt+b2 libfftw3-dev_3.3.4-2+rvt+b2 libfftw3-double3_3.3.4-2+rvt+b2 libfftw3-single3_3.3.4-2+rvt+b2 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.1.1-11+rpi1 libgfortran3_6.1.1-11+rpi1 libglib2.0-0_2.50.0-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.4-2 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libhogweed4_3.2-1 libhwloc-dev_1.11.4-1+rpi1 libhwloc-plugins_1.11.4-1+rpi1 libhwloc5_1.11.4-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu57_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libmpich-dev_3.2-7+rpi1 libmpich12_3.2-7+rpi1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.2-1 libnghttp2-14_1.15.0-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libnpth0_1.2-3 libopenmpi-dev_2.0.1-5 libopenmpi2_2.0.1-5 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpciaccess0_0.13.4-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-2 libpthread-stubs0-dev_0.3-4 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-3+b1 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_231-4 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtinyxml-dev_2.6.2-3 libtinyxml2.6.2v5_2.6.2-3 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_231-4 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-dev_2:1.6.3-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxcb1_1.12-1 libxcb1-dev_1.12-1 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28.2-1 multiarch-support_2.24-3 nano_2.7.0-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 ocl-icd-libopencl1_2.2.9-2 openmpi-bin_2.0.1-5 openmpi-common_2.0.1-5 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-5 po-debconf_1.0.19 procps_2:3.3.12-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-4 systemd-sysv_231-4 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016g-1 udev_231-4 util-linux_2.28.2-1 x11proto-core-dev_7.0.29-1 x11proto-input-dev_2.3.2-1 x11proto-kb-dev_1.0.7-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Sep 9 03:59:08 2016 UTC
gpgv: using RSA key EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2016-3.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2016.orig.tar.gz
dpkg-source: info: unpacking gromacs_2016-3.debian.tar.xz
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying reproducible-builds.patch
dpkg-source: info: applying doxygen.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying hurd-disable-numa-test.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2016-3+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-b43a0684-d317-4419-8360-3abc2a9abbf5
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2016-3+b1
dpkg-buildpackage: info: source distribution stretch-staging
dpkg-source --before-build gromacs-2016
dpkg-buildpackage: info: host architecture armhf
fakeroot 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 build-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,--as-needed" -DCMAKE_SKIP_RPATH=TRUE -DGMX_X11=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DBUILD_SHARED_LIBS=TRUE)
-- The C compiler identification is GNU 6.1.1
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- 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
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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
-- 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
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- hwloc version:
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.0", minimum required is "1.5")
-- 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
-- Found X11: /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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_r2r_1d in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_r2r_1d 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_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_ - found
-- A library with BLAS API 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 find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- 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,--as-needed" -DCMAKE_SKIP_RPATH=TRUE -DGMX_X11=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DBUILD_SHARED_LIBS=TRUE -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 6.1.1
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- 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:49 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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
-- 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
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- hwloc version:
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.0", minimum required is "1.5")
-- 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
-- Found X11: /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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_r2r_1d in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_r2r_1d 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_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_ - found
-- A library with BLAS API 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 find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- 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,--as-needed" -DCMAKE_SKIP_RPATH=TRUE -DGMX_X11=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=FALSE -DGMX_BUILD_MDRUN_ONLY=TRUE -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 6.1.1
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- 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
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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
-- 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
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- hwloc version:
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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_r2r_1d in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_r2r_1d 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_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_ - found
-- A library with BLAS API 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 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_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- 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,--as-needed" -DCMAKE_SKIP_RPATH=TRUE -DGMX_X11=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=FALSE -DGMX_BUILD_MDRUN_ONLY=TRUE -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 6.1.1
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- 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:49 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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
-- 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
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- hwloc version:
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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_r2r_1d in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_r2r_1d 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_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_ - found
-- A library with BLAS API 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 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_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- 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,--as-needed" -DCMAKE_SKIP_RPATH=TRUE -DGMX_X11=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_DEFAULT_SUFFIX=FALSE -DGMX_X11=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,--as-needed" -DGMX_BUILD_MDRUN_ONLY=TRUE -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 6.1.1
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- 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
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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
-- 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
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- hwloc version:
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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_r2r_1d in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_r2r_1d 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_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_ - found
-- A library with BLAS API 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 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_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- 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,--as-needed" -DCMAKE_SKIP_RPATH=TRUE -DGMX_X11=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_DEFAULT_SUFFIX=FALSE -DGMX_X11=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,--as-needed" -DGMX_BUILD_MDRUN_ONLY=TRUE -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 6.1.1
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- 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:49 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- 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
-- 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
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- hwloc version:
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- 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
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- 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_r2r_1d in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_r2r_1d 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_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_ - found
-- A library with BLAS API 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 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_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_DEPRECATED_REGISTER
-- Performing Test HAS_NO_DEPRECATED_REGISTER - Success
-- 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'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend
make[3]: 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=
make[3]: 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[3]: 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/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_test_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -isystem /<<PKGBUILDDIR>>/src/external/gmock-1.7.0/gtest/include -isystem /<<PKGBUILDDIR>>/src/external/gmock-1.7.0/include -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/mdruncomparisonfixture.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdruncomparisonfixture.cpp
Scanning dependencies of target view_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/md.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.c.cmakein -D VERSION_OUT=utility/baseversion-gen.c -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.c
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=
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -isystem /<<PKGBUILDDIR>>/src/external/gmock-1.7.0/gtest/include -isystem /<<PKGBUILDDIR>>/src/external/gmock-1.7.0/include -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/membed.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -isystem /<<PKGBUILDDIR>>/src/external/gmock-1.7.0/gtest/include -isystem /<<PKGBUILDDIR>>/src/external/gmock-1.7.0/include -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/repl_ex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target mdrun_test_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 1%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/resource-division.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/resource-division.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_box.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/linearalgebra/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/calculate-ewald-splitting-coefficient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/calculate-ewald-splitting-coefficient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/energyhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
/<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:750:1: internal compiler error: in prune_unused_types_walk_loc_descr, at dwarf2out.c:25681
} // namespace gmx
^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
0x3c5547 prune_unused_types_walk_loc_descr
../../src/gcc/dwarf2out.c:25681
0x3c4e87 prune_unused_types_walk_attribs
../../src/gcc/dwarf2out.c:25711
0x3c505b prune_unused_types_walk
../../src/gcc/dwarf2out.c:25911
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3c5003 prune_unused_types_walk
../../src/gcc/dwarf2out.c:25917
0x3d68df prune_unused_types
../../src/gcc/dwarf2out.c:26010
0x3f769f dwarf2out_finish
../../src/gcc/dwarf2out.c:27403
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <file:///usr/share/doc/gcc-6/README.Bugs> for instructions.
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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 -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -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
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp: In member function 'bool gmx::DirectoryEnumerator::Impl::nextFile(std::__cxx11::string*)':
/<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp:201:26: warning: 'int readdir_r(DIR*, dirent*, dirent**)' is deprecated [-Wdeprecated-declarations]
int rc = readdir_r(dirent_handle, direntp_large, &p);
^~~~~~~~~
In file included from /usr/include/features.h:364:0,
from /usr/include/arm-linux-gnueabihf/c++/6/bits/os_defines.h:39,
from /usr/include/arm-linux-gnueabihf/c++/6/bits/c++config.h:495,
from /usr/include/c++/6/string:38,
from /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp:45:
/usr/include/dirent.h:189:12: note: declared here
extern int __REDIRECT (readdir_r,
^
/<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp:201:68: warning: 'int readdir_r(DIR*, dirent*, dirent**)' is deprecated [-Wdeprecated-declarations]
int rc = readdir_r(dirent_handle, direntp_large, &p);
^
In file included from /usr/include/features.h:364:0,
from /usr/include/arm-linux-gnueabihf/c++/6/bits/os_defines.h:39,
from /usr/include/arm-linux-gnueabihf/c++/6/bits/c++config.h:495,
from /usr/include/c++/6/string:38,
from /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp:45:
/usr/include/dirent.h:189:12: note: declared here
extern int __REDIRECT (readdir_r,
^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/qsort_threadsafe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/qsort_threadsafe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dlibgromacs_EXPORTS -isystem /<<PKGBUILDDIR>>/src/external/lmfit -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src/external/thread_mpi/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/build/basic/src/external/tng_io/include -I/<<PKGBUILDDIR>>/src/external/tng_io/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
The bug is not reproducible, so it is likely a hardware or OS problem.
src/gromacs/CMakeFiles/libgromacs.dir/build.make:1655: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o' failed
make[3]: *** [src/gromacs/CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
CMakeFiles/Makefile2:2131: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Makefile:163: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
debian/rules:108: recipe for target 'build-basic' failed
make: *** [build-basic] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2016-10-06T12:03:53Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 1074
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 493
Job: gromacs_2016-3
Machine Architecture: armhf
Package: gromacs
Package-Time: 1626
Source-Version: 2016-3
Space: 0
Status: failed
Version: 2016-3+b1
--------------------------------------------------------------------------------
Finished at 2016-10-06T12:03:53Z
Build needed 00:00:00, 0k disc space