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Bug 505480 - sci-chemistry/gromacs-5.0_beta1 fails boost/assert.hpp:102:47: error: ‘noinline’ was not declared in this scope
Summary: sci-chemistry/gromacs-5.0_beta1 fails boost/assert.hpp:102:47: error: ‘noinli...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL: http://redmine.gromacs.org/issues/1468
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-03-23 19:05 UTC by Justin Lecher (RETIRED)
Modified: 2014-04-08 08:19 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
gromacs-5.0_beta1:20140323-171811.log (gromacs-5.0_beta1:20140323-171811.log,60.75 KB, text/plain)
2014-03-23 19:05 UTC, Justin Lecher (RETIRED)
Details

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Description Justin Lecher (RETIRED) gentoo-dev 2014-03-23 19:05:09 UTC
AILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//cuda_tools_generated_cudautils.cu.o.cmake
/usr/include/boost/assert.hpp:102:47: error: ‘noinline’ was not declared in this scope
           BOOST_NOINLINE void assertion_failed_msg(CharT const * expr, char const * msg, char const * function,
                                               ^
CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:261 (message):
  Error generating file
  /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o


FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o -D generated_cubin_file:STRING=/var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-5.0_beta1/work/gromacs-5.0_beta1_float/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake
/usr/include/boost/assert.hpp:102:47: error: ‘noinline’ was not declared in this scope
           BOOST_NOINLINE void assertion_failed_msg(CharT const * expr, char const * msg, char const * function,
                                               ^


$ einfo =sci-chemistry/gromacs-5.0_beta1
Portage 2.2.8-r1 (default/linux/amd64/13.0, gcc-4.8.2, glibc-2.19, 3.13.6-lh-nvidia x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.13.6-lh-nvidia-x86_64-Intel-R-_Core-TM-_i7-2600_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16344408 total,   2850396 free
KiB Swap:    3987452 total,   3902700 free
Timestamp of tree: Sat, 22 Mar 2014 08:00:01 +0000
ld GNU ld (GNU Binutils) 2.24
ccache version 3.1.9 [enabled]
app-shells/bash:          4.2_p45-r1
dev-java/java-config:     2.2.0
dev-lang/python:          2.6.9, 2.7.6, 3.2.5-r3, 3.3.4
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.10.3, 1.11.6, 1.13.4, 1.14.1
sys-devel/binutils:       2.24-r2
sys-devel/gcc:            4.4.7, 4.5.4, 4.6.4, 4.7.3-r1, 4.8.2-r1
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.13 (virtual/os-headers)
sys-libs/glibc:           2.19
Repositories: gentoo sunrise bicatali betagarden dummy Neurogeek science Raspberry-Pi-Overlay last-hope g-ctan
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -ftracer   -march=native -mtune=native -frecord-gcc-switches -g -Wimplicit-function-declaration"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib/systemd/system /usr/share/eselect/ /usr/share/gnupg/qualified.txt /usr/share/nano/ /var/lib/hsqldb /var/spool/munin-async/.ssh"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -ftracer   -march=native -mtune=native -frecord-gcc-switches -g -Wenum-compare"
DISTDIR="/var/cache/portage/distfiles"
EMERGE_DEFAULT_OPTS=" -vt --keep-going --autounmask-write --autounmask --quiet-build=n"
FCFLAGS="-O2 -pipe -ftracer   -march=native -mtune=native -frecord-gcc-switches -g"
FEATURES="assume-digests binpkg-logs buildsyspkg ccache cgroup collision-protect compressdebug distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news noinfo parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms sign split-log splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -ftracer   -march=native -mtune=native -frecord-gcc-switches -g"
GENTOO_MIRRORS=" /mnt/tmpfs/ http://gentoo.j-schmitz.net/mirror/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo/"
LANG="en_GB.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common"
MAKEOPTS="-j12 -l9"
PKGDIR="/var/cache/portage/packages"
PORTAGE_COMPRESS="xz"
PORTAGE_COMPRESS_FLAGS="-z -e -9 -v"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_EXTRA_OPTS="--omit-dir-times"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/local/overlays/sunrise-reviewed /local/overlays/bicatali /local/overlays/betagarden /local/overlays/dummy /local/overlays/neurogeek /local/overlays/sci /local/overlays/gen2pi /local/overlays/lh-overlay /local/overlays/g-ctan"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X acl alsa amd64 avx bash-completion berkdb branding bzip2 cairo caps cli cracklib crypt cxx dbus dri fortran gdbm gif gmp gnome gnome-keyring gstreamer gtk iconv icu ipv6 jpeg jpeg2k mmx mmxext modules ncurses network-cron nls nptl nsplugin numa opengl openmp pam pcre pgo png pulseaudio qt3support raw readline session smp sse sse2 sse2_4way sse2check sse3 sse4 sse41 sse4_1 sse4_2 sse4a ssl ssse3 startup-notification systemd tcpd threads tiff truetype unicode vaapi vdpau xattr xinerama zlib" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DRACUT_MODULES="plymouth" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer pdfimport scripting-javascript wiki-publisher nlpsolver" LINGUAS="en" NGINX_MODULES_HTTP="access auth_basic autoindex browser charset empty_gif fastcgi geo gzip limit_conn limit_req map memcached proxy referer rewrite scgi split_clients ssi upstream_ip_hash userid uwsgi stub_status" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_6 python2_7 python3_2 python3_3 pypy2_0" QEMU_SOFTMMU_TARGETS="i386 x86_64 arm armeb" QEMU_USER_TARGETS="i386 x86_64 arm armeb" RUBY_TARGETS="ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia nouveau" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
USE_PYTHON="2.6 2.7 3.2 3.3 2.7-pypy-2.0"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND

=================================================================
                        Package Settings
=================================================================

sci-chemistry/gromacs-5.0_beta1 was built with the following:
USE="X blas cuda doc fftw lapack offensive openmp single-precision sse2 sse4_1 threads -avx128fma -avx256 -double-precision -gsl -mkl -mpi -test -zsh-completion"
CFLAGS="-g -march=native -mtune=native -Wimplicit-function-declaration -O3"
CXXFLAGS="-g -march=native -mtune=native -Wenum-compare -O3"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common -Wl,-O1 -Wl,--hash-style=gnu -Wl,--sort-common"
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2014-03-23 19:05:47 UTC
Created attachment 373340 [details]
gromacs-5.0_beta1:20140323-171811.log

build.log
Comment 2 Christoph Junghans (RETIRED) gentoo-dev 2014-03-31 15:40:56 UTC
@jlec: could you try gromacs-9999 (soon to be 5.0_rc1), it should be fixed in there.
Comment 3 Alexey Shvetsov archtester gentoo-dev 2014-04-08 08:19:35 UTC
Should be fixed with 5.0_rc1