Created attachment 331138 [details] /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/temp/build.log 'emerge gromacs' fails with: ... -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//gpu_utils_generated_memtestG80_core.cu.o.NVCC-depend nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o] Error 1 ... nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o ... -- Generating dependency file: /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//nbnxn_cuda_generated_nbnxn_cuda.cu.o.NVCC-depend make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... nvcc fatal : redefinition of argument 'compiler-bindir' CMake Error at nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.cmake:208 (message): Error generating /var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o make[2]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o] Error 1 make[2]: *** Waiting for unfinished jobs.... ... make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.6_beta1/work/gromacs-4.6_beta1_float' make: *** [all] Error 2 * ERROR: sci-chemistry/gromacs-4.6_beta1 failed (compile phase): * emake failed emerge --info '=sci-chemistry/gromacs-4.6_beta1' fails with: root@impala:/root(80)# emerge --info '=sci-chemistry/gromacs-4.6_beta1' emerge: there are no ebuilds to satisfy "=sci-chemistry/gromacs-4.6_beta1". root@impala:/root(81)# ll /usr/portage/sci-chemistry/gromacs/gromacs-4.6_beta1.ebuild -rw-r--r-- 1 root root 7226 Nov 30 22:08 /usr/portage/sci-chemistry/gromacs/gromacs-4.6_beta1.ebuild root@impala:/root(82)# emerge --info Portage 2.1.11.32 (default/linux/amd64/10.0, gcc-4.6.3, glibc-2.16.0, 3.6.4-gentoo x86_64) ================================================================= System uname: Linux-3.6.4-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2 Timestamp of tree: Sat, 01 Dec 2012 00:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p39 dev-java/java-config: 2.1.12 dev-lang/python: 2.7.3-r2, 3.2.3-r1 dev-util/cmake: 2.8.10.2 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.5 sys-apps/sandbox: 2.6 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.5 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.6.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.16.0 Repositories: gentoo x11 bicatali science sage-on-gentoo dilfridge sunrise lisp java-overlay lordvan x-portage x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-10.3 cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=amdfam10 -O2 -g" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /usr/share/polkit-1/actions /var/lib/hsqldb" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /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="-march=amdfam10 -O2 -g" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news noclean parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LC_ALL="C" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr ru" MAKEOPTS="-j5" 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="/var/lib/layman/x11 /var/lib/layman/bicatali /var/lib/layman/science /var/lib/layman/sage-on-gentoo /var/lib/layman/dilfridge /var/lib/layman/sunrise /var/lib/layman/lisp /var/lib/layman/java-overlay /var/lib/layman/lordvan /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac accessibility acl acpi admin afs alsa amd64 ao apache2 apng applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse g3dvl galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile harness hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag imagemagick imap inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kqemu kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors lua lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript pppd preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets soup sox speex spell sql sqlite sse sse2 sse4a ssl subtitles subversion sudo suexec svg svm swig szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter vaapi vdpau video virtualbox visio vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" 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="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm mdraid 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="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" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON root@impala:/root(83)# emerge -pqv '=sci-chemistry/gromacs-4.6_beta1' [ebuild U ] sci-chemistry/gromacs-4.6_beta1 [4.5.5-r1] USE="X blas cuda%* doc fftw gsl lapack mpi openmp%* single-precision sse2 threads -avx128fma% -avx256% -double-precision -fkernels (-openmm) -power6% -sse41% {-test} -zsh-completion (-altivec%) (-xml%*)"
I have no cuda card, let's see if alexxy can help.
I will take a look on that. Currently I can't see the origin of the first definition of compiler-bindir, only the second which is in our control.
(In reply to comment #2) > I will take a look on that. Currently I can't see the origin of the first > definition of compiler-bindir, only the second which is in our control. It comes from adding -ccbin in gmxManageNvccConfig.cmake: <http://repo.or.cz/w/gromacs.git/blob/HEAD:/cmake/gmxManageNvccConfig.cmake#l97> If you find a general solution to be merged upstream upload it here: https://gerrit.gromacs.org
(In reply to comment #3) > (In reply to comment #2) > > I will take a look on that. Currently I can't see the origin of the first > > definition of compiler-bindir, only the second which is in our control. > > It comes from adding -ccbin in gmxManageNvccConfig.cmake: > <http://repo.or.cz/w/gromacs.git/blob/HEAD:/cmake/gmxManageNvccConfig. > cmake#l97> Thats the second, which we can control. but somehow it got added earlier. I will try to find the source for that.
Got fixed.
