Linking vmd_LINUX ... /opt/cuda/lib/libcudart.so: undefined reference to `std::__detail::_List_node_base::_M_unhook()@GLIBCXX_3.4.15' /opt/cuda/lib/libcudart.so: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)@GLIBCXX_3.4.15' collect2: ld returned 1 exit status make: *** [vmd_LINUX] Error 1 I guess nvidia-cuda-toolkit needs a newer glibc. Portage 2.2.0_alpha151 (default/linux/x86/10.0/desktop, gcc-4.5.4, glibc-2.15-r3, 3.5.7-gentoo i686) ================================================================= System uname: Linux-3.5.7-gentoo-i686-Intel-R-_Atom-TM-_CPU_330_@_1.60GHz-with-gentoo-2.1 Timestamp of tree: Tue, 15 Jan 2013 15:45:01 +0000 ld GNU ld (GNU Binutils) 2.22 ccache version 3.1.8 [enabled] app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.3-r2, 3.2.3 dev-util/ccache: 3.1.8 dev-util/cmake: 2.8.9 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.1-r1 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, 1.11.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.4, 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: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo location: /usr/portage sync: rsync://rsync.us.gentoo.org/gentoo-portage priority: -1000 cj-overlay location: /var/lib/layman/cj-overlay masters: gentoo priority: 0 science location: /var/lib/layman/science masters: gentoo priority: 1 Installed sets: @kernels ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA @EULA" ACCEPT_PROPERTIES="*" ALSA_CARDS="hda-intel" 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" ARCH="x86" AUTOCLEAN="yes" BOOTSTRAP_USE="cxx unicode" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" CBUILD="i686-pc-linux-gnu" CCACHE_DIR="/var/tmp/ccache" CCACHE_SIZE="40G" CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" CG_COMPILER_EXE="/opt/bin/cgc" CG_INC_PATH="/opt/nvidia-cg-toolkit/include" CG_LIB_PATH="/opt/nvidia-cg-toolkit/lib" CHOST="i686-pc-linux-gnu" CLEAN_DELAY="5" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" COLLISION_IGNORE="/lib/modules/* *.py[co] *$py.class" COLORTERM="Terminal" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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="-march=native -O2 -pipe -fomit-frame-pointer" DISPLAY=":0.0" DISTDIR="/usr/portage/distfiles" EDITOR="/usr/bin/vi" ELIBC="glibc" EMERGE_DEFAULT_OPTS="--verbose --with-bdeps y --jobs=5 --load-average=5 --autounmask-write" EMERGE_WARNING_DELAY="10" EPREFIX="" EROOT="/" FCFLAGS="-O2 -march=i686 -pipe" FEATURES="assume-digests binpkg-logs ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FETCHCOMMAND="wget -t 3 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" FETCHCOMMAND_RSYNC="rsync -avP "${URI}" "${DISTDIR}/${FILE}"" FETCHCOMMAND_SFTP="bash -c "x=\${2#sftp://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port=22 ; exec sftp -P \${port} \"\${host}:/\${x#*/}\" \"\$1\"" sftp "${DISTDIR}/${FILE}" "${URI}"" FETCHCOMMAND_SSH="bash -c "x=\${2#ssh://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port=22 ; exec rsync --rsh=\"ssh -p\${port}\" -avP \"\${host}:/\${x#*/}\" \"\$1\"" rsync "${DISTDIR}/${FILE}" "${URI}"" FFLAGS="-O2 -march=i686 -pipe" FLTK_DOCDIR="/usr/share/doc/fltk-1.3.0-r1/html" GCC_SPECS="" GDK_USE_XFT="1" GENTOO_MIRRORS="http://mirror.iawnet.sandia.gov/gentoo/ http://gentoo.llarian.net/ http://gentoo.mirrors.hoobly.com/" 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" GRUB_PLATFORMS="" GSETTINGS_BACKEND="gconf" HG="/usr/bin/hg" HOME="/root" INFOPATH="/usr/share/info:/usr/share/gcc-data/i686-pc-linux-gnu/4.5.4/info:/usr/share/binutils-data/i686-pc-linux-gnu/2.22/info:/usr/share/info/emacs-24" INPUT_DEVICES="evdev" IUSE_IMPLICIT="prefix" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LC_CTYPE="de_DE.utf8" LDFLAGS="-Wl,-O2 -Wl,--as-needed" LESS="-R -M --shift 5" LESSOPEN="|lesspipe %s" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en de" LOGNAME="root" LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:" MAIL="/var/mail/root" MAKEOPTS="-j5" MANPATH="/usr/local/share/man:/usr/share/man:/usr/share/gcc-data/i686-pc-linux-gnu/4.5.4/man:/usr/share/binutils-data/i686-pc-linux-gnu/2.22/man:/etc/java-config/system-vm/man/" MULTIOSDIRS="../lib" NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" NVCC_FLAGS="-gencode;arch=compute_11,code=sm_11;-use_fast_math" OPENCL_PROFILE="nvidia" OPENGL_PROFILE="nvidia" PAGER="/usr/bin/less" PATH="/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/opt/bin:/opt/cuda/bin" PHP_TARGETS="php5-3" PKGDIR="/usr/portage/packages" PORTAGE_ARCHLIST="ppc sparc64-freebsd ppc-openbsd x86-openbsd ppc64 x86-winnt x86-fbsd ppc-aix alpha arm x86-freebsd s390 amd64 arm-linux x86-macos x64-openbsd ia64-hpux hppa x86-netbsd ppc64-linux x86-cygwin amd64-linux ia64-linux x86 sparc-solaris x64-freebsd sparc64-solaris x86-linux x64-macos sparc m68k-mint ia64 mips ppc-macos x86-interix hppa-hpux amd64-fbsd x64-solaris m68k sh x86-solaris sparc-fbsd" PORTAGE_BIN_PATH="/usr/lib/portage/bin" PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png" PORTAGE_CONFIGROOT="/" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ELOG_CLASSES="warn error" PORTAGE_ELOG_MAILFROM="portage@localhost" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_ELOG_SYSTEM="save" PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5" PORTAGE_FETCH_RESUME_MIN_SIZE="350K" PORTAGE_GID="250" PORTAGE_GPG_SIGNING_COMMAND="gpg --sign --digest-algo SHA256 --clearsign --yes --default-key "${PORTAGE_GPG_KEY}" --homedir "${PORTAGE_GPG_DIR}" "${FILE}"" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_NICENESS="19" PORTAGE_OVERRIDE_EPREFIX="" PORTAGE_PYM_PATH="/usr/lib/portage/pym" 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_RSYNC_RETRIES="-1" PORTAGE_SYNC_STALE="30" PORTAGE_TMPDIR="/var/tmp" PORTAGE_VERBOSE="1" PORTAGE_WORKDIR_MODE="0755" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/cj-overlay /var/lib/layman/science" PORT_LOGDIR_CLEAN="find "${PORT_LOGDIR}" -type f ! -name "summary.log*" -mtime +7 -delete" PRELINK_PATH_MASK="/usr/lib/libfreebl3.so:/usr/lib/libnssdbm3.so:/usr/lib/libsoftokn3.so" PROFILE_ONLY_VARIABLES="ARCH ELIBC IUSE_IMPLICIT KERNEL USERLAND USE_EXPAND_IMPLICIT USE_EXPAND_UNPREFIXED USE_EXPAND_VALUES_ARCH USE_EXPAND_VALUES_ELIBC USE_EXPAND_VALUES_KERNEL USE_EXPAND_VALUES_USERLAND" PYTHONDOCS_2_7="/usr/share/doc/python-docs-2.7.2/html/library" PYTHONDOCS_3_2="/usr/share/doc/python-docs-3.2.2/html/library" PYTHONDONTWRITEBYTECODE="1" PYTHONPATH="/usr/lib/portage/pym" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QT_GRAPHICSSYSTEM="raster" RESUMECOMMAND="wget -c -t 3 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}"" RESUMECOMMAND_RSYNC="rsync -avP "${URI}" "${DISTDIR}/${FILE}"" RESUMECOMMAND_SSH="bash -c "x=\${2#ssh://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port=22 ; exec rsync --rsh=\"ssh -p\${port}\" -avP \"\${host}:/\${x#*/}\" \"\$1\"" rsync "${DISTDIR}/${FILE}" "${URI}"" ROOT="/" ROOTPATH="/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/4.5.4:/opt/nvidia-cg-toolkit/bin:/opt/cuda/bin" RPMDIR="/usr/portage/rpm" RUBYOPT="-rauto_gem" RUBY_TARGETS="ruby18 ruby19" SHELL="/bin/bash" SUDO_COMMAND="/usr/bin/emerge --info" SUDO_GID="100" SUDO_UID="1000" SUDO_USER="christoph" SYNC="rsync://rsync.us.gentoo.org/gentoo-portage" TERM="xterm" UNINSTALL_IGNORE="/lib/modules/*" USE="X a52 aac aalib acl acpi alsa apm audiofile bash-completion berkdb bluetooth branding bzip2 cairo cdda cddb cdr cli consolekit cracklib crypt cscope css cuda cups curl cvs cxx dbus djvu doc dri dts dvd dvdr emboss encode examples exif fam fbcon ffmpeg fftw firefox flac fontconfig fortran gallium gd gdbm gif gmp gnuplot gnutls gpm gstreamer gtk hal hdf5 iconv ieee1394 imagemagick ipv6 java java6 jbig jpeg jpeg2k lame latex lcms ldap libnotify lua mad mmx mng modules mozilla mp3 mp4 mpeg mudflap ncurses networkmanager nls nptl nsplugin ogg opencl openexr opengl openmp packages pam pango pcmcia pcre pdf perl plotutils png policykit postscript ppds pppd qt3support qt4 quicktime readline ruby samba sdl session smp sndfile spell sse sse2 ssl startup-notification subversion svg syslog szip taglib tcl tcpd theora threads tiff tk truetype udev udisks unicode upower usb v4l v4l2 vcd vim-syntax vorbis win32codecs wxwidgets x264 x86 xcb xine xml xulrunner xv xvid zlib" ALSA_CARDS="hda-intel" 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" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en de" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia" 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" USER="root" USERLAND="GNU" USERNAME="root" USE_EXPAND="ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CALLIGRA_FEATURES CAMERAS COLLECTD_PLUGINS CROSSCOMPILE_OPTS CURL_SSL DRACUT_MODULES DVB_CARDS ELIBC ENLIGHTENMENT_MODULES FCDSL_CARDS FFTOOLS FOO2ZJS_DEVICES FRITZCAPI_CARDS GPSD_PROTOCOLS GRUB_PLATFORMS INPUT_DEVICES KERNEL LCD_DEVICES LIBREOFFICE_EXTENSIONS LINGUAS LIRC_DEVICES MISDN_CARDS NETBEANS_MODULES NGINX_MODULES_HTTP NGINX_MODULES_MAIL OFED_DRIVERS OPENMPI_FABRICS OPENMPI_OFED_FEATURES OPENMPI_RM PHP_TARGETS PYTHON_SINGLE_TARGET PYTHON_TARGETS QEMU_SOFTMMU_TARGETS QEMU_USER_TARGETS RUBY_TARGETS SANE_BACKENDS USERLAND VIDEO_CARDS VOICEMAIL_STORAGE XFCE_PLUGINS XTABLES_ADDONS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_EXPAND_IMPLICIT="ARCH ELIBC KERNEL USERLAND" USE_EXPAND_UNPREFIXED="ARCH" USE_EXPAND_VALUES_ARCH="alpha amd64 amd64-fbsd amd64-linux arm arm-linux hppa hppa-hpux ia64 ia64-hpux ia64-linux m68k m68k-mint mips ppc ppc64 ppc64-linux ppc-aix ppc-macos ppc-openbsd s390 sh sparc sparc64-freebsd sparc64-solaris sparc-fbsd sparc-solaris x64-freebsd x64-macos x64-openbsd x64-solaris x86 x86-cygwin x86-fbsd x86-freebsd x86-interix x86-linux x86-macos x86-netbsd x86-openbsd x86-solaris x86-winnt" USE_EXPAND_VALUES_ELIBC="AIX Cygwin Darwin FreeBSD glibc HPUX Interix mintlib NetBSD OpenBSD SunOS uclibc Winnt" USE_EXPAND_VALUES_KERNEL="AIX Cygwin Darwin FreeBSD freemint HPUX Interix linux NetBSD OpenBSD SunOS Winnt" USE_EXPAND_VALUES_USERLAND="BSD GNU" USE_ORDER="env:pkg:conf:defaults:pkginternal:repo:env.d" VIDEO_CARDS="nvidia" XAUTHORITY="/home/christoph/.Xauthority" XDG_CONFIG_DIRS="/etc/xdg" XDG_DATA_DIRS="/usr/local/share:/usr/share" 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"
+ 16 Jan 2013; Justin Lecher <jlec@gentoo.org> + nvidia-cuda-toolkit-5.0.35.ebuild: + Drop old version of gcc which do not provide GLIBCXX_3.4.15;depend on cxx + support in gcc +
Please remerge nvidia-cuda-toolkit.
(In reply to comment #2) > Please remerge nvidia-cuda-toolkit. sys-devel/gcc:4.6[cxx] was already installed, but not selected as vmd has gcc:4.[45] in CDEPEND. I think, with the new cuda class that is not needed anymore as cuda-config keeps track of the supported gcc version, right? Concerning nvidia-cuda-toolkit-5.0.35.ebuild, shouldn't cuda_supported_gcc in src_prepare be set to 4.6 now?
(In reply to comment #3) > (In reply to comment #2) > > Please remerge nvidia-cuda-toolkit. > sys-devel/gcc:4.6[cxx] was already installed, but not selected as vmd has > gcc:4.[45] in CDEPEND. > > I think, with the new cuda class that is not needed anymore as cuda-config > keeps track of the supported gcc version, right? > > Concerning nvidia-cuda-toolkit-5.0.35.ebuild, shouldn't cuda_supported_gcc > in src_prepare be set to 4.6 now? You are right. I only fix the dep and didn't set the support version. And we need both as cuda-config is need by the cuda.eclass to find the support version of the current installation. +*nvidia-cuda-toolkit-5.0.35-r1 (16 Jan 2013) + + 16 Jan 2013; Justin Lecher <jlec@gentoo.org> + -nvidia-cuda-toolkit-5.0.35.ebuild, +nvidia-cuda-toolkit-5.0.35-r1.ebuild: + Correct support gcc version, #452386 +
