This probably is an ebuild error, as it works out of the box if I build gromacs manually.. The error given is nvcc fatal : redefinition of argument 'compiler-bindir' I join the build log... Reproducible: Always Steps to Reproduce: 1. USE="cuda" emerge gromacs Actual Results: build failes as discribed above.. Expected Results: build should succeed... haschka@warpcore ~ $ emerge --info Portage 2.1.11.62 (default/linux/amd64/13.0, gcc-4.6.3, glibc-2.15-r3, 3.8.13-gentoo x86_64) ================================================================= System uname: Linux-3.8.13-gentoo-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16123636 total, 13868872 free KiB Swap: 30427132 total, 30427132 free Timestamp of tree: Tue, 28 May 2013 06:00:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p45 dev-lang/python: 2.7.3-r3, 3.2.3-r2 dev-util/cmake: 2.8.10.2-r2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.6.3 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.7 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -fomit-frame-pointer -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=native -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -march=native -fomit-frame-pointer -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -march=native -fomit-frame-pointer -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j9" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --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="" SYNC="rsync://192.168.0.2/gentoo-portage" USE="X acl alsa amd64 avx avx256 berkdb bzip2 cli cracklib crypt cuda cxx dbus dri fontconfig fortran g3dvl gdbm gif gpm iconv jpeg mmx modules mudflap multilib ncurses nls nptl opencl opengl openmp pam pcre png readline session smp sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 tcpd threads tiff truetype unicode vaapi vdpau xft xvmc zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" 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" 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 ubx" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia intel i965" 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" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 349422 [details] build.log
The problem is probably found here.. -DCUDA_HOST_COMPILER_OPTIONS=-O2 -v --compiler-bindir=\"/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3\" or in the ebuild where it says -DCUDA_HOST_COMPILER_OPTIONS="${NVCCFLAGS}" (line 185) which by default seems to produce the line above on my machine.. which doesn't work. But trying to set export NVCCFLAGS="-O2" or export NVCCFLAGS="" prior emerging did fail either.. ( in both cases --compiler-bindir is set as shown above.. )
Actually it worked before those changes... i will try to get the old ebuild.. http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.1.ebuild?r1=1.1&r2=1.2
FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-4.6.1/work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory /var/tmp/portage/sci-chemistry/gromacs-4.6.1/work/gromacs-4.6.1_float/src/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-4.6.1/work/gromacs-4.6.1_float/src/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-4.6.1/work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P /var/tmp/portage/sci-chemistry/gromacs-4.6.1/work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6.1/work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o FAILED: cd .../work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir && /usr/bin/cmake -E make_directory .../work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//. && /usr/bin/cmake -D verbose:BOOL=OFF -D build_configuration:STRING=Gentoo -D generated_file:STRING=.../gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o -D generated_cubin_file:STRING=.../work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o.cubin.txt -P .../work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_gpu_utils.cu.o.cmake nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:208 (message): Error generating .../work/gromacs-4.6.1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
I currently don't have access to my cuda system, so I leave it to Justin. @justin: Gromacs' cuda detection is custom, so I guess the flags are duplicated in ${WORKDIR}/cmake/gmxManageNvccConfig.cmake !
Should be fixed in 4.6.2
Over here it works as expected in 4.6.2 - Thanks!
*** Bug 472260 has been marked as a duplicate of this bug. ***
This one isn't so easy. I will try to find a solution soonish.
Is this fixed with nvidia-toolkit-5.5?
*** Bug 486224 has been marked as a duplicate of this bug. ***
With cuda 5.5 it should be fixed
