| Summary: | sci-libs/scipy-0.8 segfaults | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Paulo da Silva <psdasilva> |
| Component: | [OLD] Unspecified | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED WORKSFORME | ||
| Severity: | normal | CC: | bugs |
| Priority: | High | ||
| Version: | unspecified | ||
| Hardware: | AMD64 | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
Try python -v ; help("modules") and see if its a specific library that crashes it.
(In reply to comment #1) > Try python -v ; help("modules") and see if its a specific library that crashes > it. > Below what I got. I reemerged scipy. No success. The sequence import scipy; help("modules") works. # /usr/lib64/python2.6/site-packages/scipy/fftpack/__init__.pyc matches /usr/lib64/python2.6/site-packages/scipy/fftpack/__init__.py import scipy.fftpack # precompiled from /usr/lib64/python2.6/site-packages/scipy/fftpack/__init__.pyc # /usr/lib64/python2.6/site-packages/scipy/fftpack/fftpack_version.pyc matches /usr/lib64/python2.6/site-packages/scipy/fftpack/fftpack_version.py import scipy.fftpack.fftpack_version # precompiled from /usr/lib64/python2.6/site-packages/scipy/fftpack/fftpack_version.pyc # /usr/lib64/python2.6/site-packages/scipy/fftpack/basic.pyc matches /usr/lib64/python2.6/site-packages/scipy/fftpack/basic.py import scipy.fftpack.basic # precompiled from /usr/lib64/python2.6/site-packages/scipy/fftpack/basic.pyc dlopen("/usr/lib64/python2.6/site-packages/scipy/fftpack/_fftpack.so", 102); Segmentation fault What version of scipy? Please try rebuilding it (In reply to comment #3) > What version of scipy? Please try rebuilding it > The version is 0.8.0. What do you mean by "rebuilding it"? I wrote I already reemerged it. Anything else I can do? (In reply to comment #4) > (In reply to comment #3) > > What version of scipy? Please try rebuilding it > > > > The version is 0.8.0. > > What do you mean by "rebuilding it"? I wrote I already reemerged it. Anything > else I can do? Sorry, I somehow missed that you actually reemerged it. I just tried building scipy and tried with python 2.6.6 and python 2.7 - weren't able to reproduce. Next step will be backporting to 2.6.5. If you could try updating to 2.6.6 (in unstable), that would be helpful. (In reply to comment #5) > (In reply to comment #4) > > (In reply to comment #3) > If you could > try updating to 2.6.6 (in unstable), that would be helpful. > I emerged python-2.6.6-r1 and scipy (again). The same symptoms! Seg fault. If I import scipy then help("modules") works as expected. Has anyone in the sci herd been able to reproduce this? I'm at a loss here :( i was able to replicate a while ago but it seems gone now. probably something fishy going on in the dlopen so i will close it for now, feel free to reopen |
I am having a seg fault when I type help("modules"). I don't know if there are any other implications. I already reemerged python (this version) and ran python-updater. No success. Here is what happens: $ python Python 2.6.5 (release26-maint, Nov 9 2010, 03:26:26) [GCC 4.4.4] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> help("modules") Please wait a moment while I gather a list of all available modules... CXX is installed. The support files you need are in the PYTHON/etc/CXX directory. The include files are in the distutils include path already. Just refer to them as "CXX/CXX_Objects.h", etc. Segmentation fault Reproducible: Always Expected Results: A list of available modules. Portage 2.2.0_alpha3 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.4, glibc-2.11.2-r3, 2.6.35-gentoo-r12 x86_64) ================================================================= System uname: Linux-2.6.35-gentoo-r12-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7700_@_2.40GHz-with-gentoo-1.12.14 Timestamp of tree: Mon, 08 Nov 2010 22:15:02 +0000 distcc 3.1 x86_64-pc-linux-gnu [enabled] ccache version 2.4 [enabled] app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11 dev-lang/python: 2.6.5-r3, 3.1.2-r4 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 1.12.14-r1 sys-apps/sandbox: 2.3-r1 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.8.5-r3, 1.9.6-r2, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.4-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.30-r1 (sys-kernel/linux-headers) Repositories: gentoo psergio ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 googleearth AdobeFlash-10.1 skype-eula" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" DISTDIR="/GentooPalma/PKGS/distfiles" FEATURES="assume-digests binpkg-logs ccache distcc distlocks fixlafiles fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="pt_PT.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="pt pt_PT pt_BR en" MAKEOPTS="-j9" PKGDIR="/GentooPalma/PKGS/packages64" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac acpi alsa amd64 apm arts audiofile berkdb bidi bluetooth bzip2 cairo cdparanoia cdr cli consolekit cracklib crypt css cups curl cxx dbus dga doc dri dts dvd dvdr dvdread eds embedded emboss encode exif fam fbcon ffmpeg firefox flac foomaticdb fortran gdbm gif gphoto2 gpm gstreamer gtk hal iconv imagemagick imlib ipv6 java java5 java6 jpeg kde lcms libnotify libwww mad midi mikmod mmx mng modules motif mozilla mp3 mp4 mpeg mplayer msn mudflap multilib musepack mysql nas ncurses net nls nptl nptlonly nsplugin nvidia ogg opengl openmp pam pango pcmcia pcre pdf perl pic png ppds pppd python qt3support qt4 quicktime readline rtc scanner sdl session snmp socks5 speex spell sqlite sqlite3 sse sse2 ssl startup-notification subversion svg sysfs tcl tcpd tetex threads tiff tk truetype unicode usb userlocales v4l v4l2 vcd videos vorbis webkit wifi wxwindows x264 xcb xcomposite xine xml xorg xprint xulrunner xv xvid zlib" 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 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" 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 synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="pt pt_PT pt_BR en" PHP_TARGETS="php5-2" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa fbdev" 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, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS