Emerging mathgl-2.1.2 hangs (no CPU, no I/O) just after >>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DHDF4_INCLUDE_DIR=/usr/include -Denable-doc=OFF -Denable-fltk=ON -Denable-gif=ON -Denable-glut=ON -Denable-gsl=ON -Denable-hdf4=OFF -Denable-hdf5_18=ON -Denable-jpeg=ON -Denable-mpi=ON -Denable-octave=OFF -Denable-opengl=ON -Denable-pdf=ON -Denable-png=ON -Denable-qt=ON -Denable-pthread=ON -Denable-python=OFF -Denable-wx=ON -Denable-zlib=ON -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/gentoo_rules.cmake /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2 Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/gentoo_common_config.cmake It might be a cmake error, instead. Thanks for looking into it, Helmut. emerge --info sci-libs/mathgl Portage 2.2.0_alpha161_p9 (default/linux/amd64/13.0/desktop, gcc-4.7.2, glibc-2.16.0, 3.8.4-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.8.4-gentoo-x86_64-AMD_Phenom-tm-_II_X4_955_Processor-with-gentoo-2.2 KiB Mem: 7908764 total, 3031256 free KiB Swap: 1048572 total, 1048572 free Timestamp of tree: Fri, 22 Mar 2013 07:15:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 ccache version 3.1.9 [disabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.4_pre20130317::progress, 3.3.1_pre20130317::progress dev-util/ccache: 3.1.9 dev-util/cmake: 2.8.10.2-r1 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 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, 1.12.6, 1.13.1 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.5.4, 4.6.3, 4.7.2-r1, 4.8.0_pre9999::local sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.8 (virtual/os-headers) sys-libs/glibc: 2.16.0 Repositories: gentoo local sunrise ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-mtune=native -march=native -O2 -msse3 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /var/lib/hsqldb /var/lib/neatx/home" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/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="-mtune=native -march=native -O2 -msse3 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo " LANG="en_US.iso88591" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j4" 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="/usr/local/portage /usr/local/portage/layman/sunrise" SYNC="rsync://rsync.informatik.RWTH-Aachen.de/gentoo-portage" USE="3dnow 3dnowext 3dnowprefetch X a52 aac acl acpi alsa amd64 avahi berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam ffmpeg fftw firefox flac fortran fuse gdbm gfortran gif gimp gnome gpm gtk gtk2 iconv ipv6 jpeg kde lapack lcms libnotify mad mmx mmxext mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly ogg opengl openmp openrc pam pango pcre pdf png policykit ppds qt qt3support qt4 readline sdl session smp spell sqlite sqlite3 sse sse2 sse3 sse4a ssl startup-notification svg tcl tcpd threads tiff tk truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xulrunner xv xvid 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" 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="keyboard mouse evdev wacom" 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_3" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="radeonhd radeon fglrx" 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 ================================================================= Package Settings ================================================================= sci-libs/mathgl-2.0.3 was built with the following: USE="fltk gif glut gsl hdf5 jpeg mpi (multilib) opengl pdf png qt4 threads wxwidgets zlib -doc -double-precision -hdf (-octave) -python -static-libs" LINGUAS="-ru" CFLAGS="-mtune=native -O2 -msse3 -pipe" CXXFLAGS="-mtune=native -O2 -msse3 -pipe"
Same here.
Please attach the entire build log to this bug report.
Created attachment 343092 [details] /var/tmp/portage/sci-libs/mathgl-2.1.2/temp/build.log It still hangs.
Now it hangs still earlier at: >>> Emerging (1 of 11) sci-libs/mathgl-2.1.2 BTW. 'emerge octave' hangs at a similar point: >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-mathematics/octave-3.6.4
See also Bug 462990 and Bug 463220!
Any news? This issue is really nasty, on all of my systems (12 PCs) 'emerge -uvND world' hangs endless at this bug, until I kill manually all "mathgl" processes.
If I mask >=openmpi-1.6.4, reemerge openmpi-1.6.3 the hanging of configure disappears and 'emerge -v1 mathgl' comes until: Scanning dependencies of target _mathgl make[2]: Leaving directory `/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build' make -f lang/CMakeFiles/_mathgl.dir/build.make lang/CMakeFiles/_mathgl.dir/build make[2]: Entering directory `/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build' /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/CMakeFiles [ 29%] Building CXX object lang/CMakeFiles/_mathgl.dir/mathglPYTHON_wrap.cxx.o cd /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/lang && /usr/bin/mpicxx -DNO_COLOR_ARRAY -D_mathgl_EXPORTS -DNDEBUG -march=amdfam10 -O2 -pipe -fPIC -I/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2/include -I/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/include -I/usr/include/python2.7 -o CMakeFiles/_mathgl.dir/mathglPYTHON_wrap.cxx.o -c /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/lang/mathglPYTHON_wrap.cxx /var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build/lang/mathglPYTHON_wrap.cxx:3106:31: fatal error: numpy/arrayobject.h: No such file or directory compilation terminated. make[2]: *** [lang/CMakeFiles/_mathgl.dir/mathglPYTHON_wrap.cxx.o] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-libs/mathgl-2.1.2/work/mathgl-2.1.2_build'
Created attachment 343636 [details] /var/tmp/portage/sci-libs/mathgl-2.1.2/temp/build.log root@impala:/root(47)# emerge --info '=sci-libs/mathgl-2.1.2' Portage 2.1.11.59 (default/linux/amd64/13.0, gcc-4.6.3, glibc-2.17, 3.8.4-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.8.4-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2 KiB Mem: 8165660 total, 645616 free KiB Swap: 50347696 total, 50287764 free Timestamp of tree: Fri, 29 Mar 2013 11:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.3-r3, 3.2.3-r2 dev-util/cmake: 2.8.10.2-r1 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.1 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.6.3, 4.7.2-r1 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.8 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo x11 science sage-on-gentoo sunrise lisp lordvan sabayon 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-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=amdfam10 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /var/lib/hsqldb" CONFIG_PROTECT_MASK="/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/apache2-php5.5/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/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 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -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 xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" 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/science /var/lib/layman/sage-on-gentoo /var/lib/layman/sunrise /var/lib/layman/lisp /var/lib/layman/lordvan /var/lib/layman/sabayon /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 armadillo 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 fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fts3 fuse g3dvl 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 ide imagemagick imap inotify introspection ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kde 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 mod 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 plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rhythmbox 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 sound soup sox speex spell sql sqlite sse sse2 sse4a ssl stlport 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 udisks unicode usb userlocales utempter v4l vaapi vala vdpau video virt-network virtualbox visio vorbis vpx 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" 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="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" OFFICE_IMPLEMENTATION="libreoffice" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON root@impala:/root(48)# emerge -pqv '=sci-libs/mathgl-2.1.2' [ebuild U ] sci-libs/mathgl-2.1.2 [2.0.3] USE="doc fltk gif gsl hdf hdf5 jpeg mpi opengl pdf png python qt4 threads wxwidgets zlib -glut (-octave) -static-libs (-double-precision%)" LINGUAS="ru"
*** This bug has been marked as a duplicate of bug 462990 ***
Hi Jeroen, the bug corresponding to comment 0 is probably a duplicate bug 462990. But what about the bug corresponding to comment 7? This happens with the old openmpi-1.6.3. Should I file a seperate bug report for this?
