Gentoo Archives: gentoo-science

From: Christopher Schwan <cschwan@××××××××××××××××××.de>
To: Kamil Radlak <radx3ster@×××××.com>, gentoo-science@l.g.o
Subject: [gentoo-science] Re: Sage - Segmentation fault
Date: Fri, 11 Mar 2011 07:38:06
Message-Id: 201103110837.17982.cschwan@students.uni-mainz.de
Hi Kamil,

thank you for your mail. Did you had a look at

https://github.com/cschwan/sage-on-gentoo/issues#issue/40 ?

The interesting stuff was found out by Martin von Gagern, on January 30, 2011. 
Its turns out that the problem is a bug in glibc, see

https://bugs.gentoo.org/353224

and

http://sources.redhat.com/bugzilla/show_bug.cgi?id=12453

which are hopefully fixed soon.

Cheers,

Christopher

On Thursday 10 March 2011 20:42:45 you wrote:
> Hi Christopher, > i have reproduce exactly same bug with segmentation fault on Sage start > from this thread > http://archives.gentoo.org/gentoo-science/msg_fbdeb9ffce6dd65a98953b648fd31 > 000.xml on amd64 machine. > > I include the backtrace from gdb and emerge info > > Python 2.6.6 (r266:84292, Mar 6 2011, 00:22:21) > [GCC 4.5.2] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > > Program received signal SIGSEGV, Segmentation fault. > 0x00007fffeab74697 in __cxa_allocate_exception () from > /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.2/libstdc++.so.6 > (gdb) bt > #0 0x00007fffeab74697 in __cxa_allocate_exception () > from /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.2/libstdc++.so.6 > #1 0x00007fffcd1ceffe in > GiNaC::function::find_function(std::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&, unsigned int) () > from /usr/lib/libpynac-0.2.so.1 > #2 0x00007fffcc9d6352 in ?? () > from /usr/lib64/python2.6/site-packages/sage/symbolic/function.so > #3 0x00007fffcc9dedc5 in ?? () > from /usr/lib64/python2.6/site-packages/sage/symbolic/function.so > #4 0x00007ffff7aca12c in ?? () from /usr/lib/libpython2.6.so.1.0 > #5 0x00007ffff7a7ea62 in PyObject_Call () from > /usr/lib/libpython2.6.so.1.0 #6 0x00007ffff7b08596 in > PyEval_CallObjectWithKeywords () > from /usr/lib/libpython2.6.so.1.0 > #7 0x00007ffff7a94453 in ?? () from /usr/lib/libpython2.6.so.1.0 > #8 0x00007ffff7a7ea62 in PyObject_Call () from > /usr/lib/libpython2.6.so.1.0 #9 0x00007fffcc9d2f71 in ?? () > from /usr/lib64/python2.6/site-packages/sage/symbolic/function.so > #10 0x00007ffff7aca12c in ?? () from /usr/lib/libpython2.6.so.1.0 > #11 0x00007ffff7a7ea62 in PyObject_Call () from > /usr/lib/libpython2.6.so.1.0 #12 0x00007ffff7b08596 in > PyEval_CallObjectWithKeywords () > from /usr/lib/libpython2.6.so.1.0 > #13 0x00007ffff7a94453 in ?? () from /usr/lib/libpython2.6.so.1.0 > #14 0x00007ffff7a7ea62 in PyObject_Call () from > /usr/lib/libpython2.6.so.1.0 > > > > Portage 2.1.9.42 (default/linux/amd64/10.0/desktop, gcc-4.5.2, > glibc-2.13-r1, 2.6.37-tuxonice x86_64) > ================================================================= > System uname: Linux-2.6.37-tuxonice-x86_64-Intel-R-_Core-TM-_i3_CPU_M_370_@ > _2.40GHz-with-gentoo-2.0.1 > Timestamp of tree: Thu, 10 Mar 2011 17:45:01 +0000 > ccache version 3.1.4 [disabled] > app-shells/bash: 4.2_p7 > dev-java/java-config: 2.1.11-r3 > dev-lang/python: 2.6.6-r2::sage-on-gentoo, 2.7.1-r1, 3.1.3-r1 > dev-util/ccache: 3.1.4 > dev-util/cmake: 2.8.4 > sys-apps/baselayout: 2.0.1-r1 > sys-apps/openrc: 0.7.0 > sys-apps/sandbox: 2.5 > sys-devel/autoconf: 2.13, 2.68 > sys-devel/automake: 1.10.3, 1.11.1 > sys-devel/binutils: 2.21 > sys-devel/gcc: 4.5.2 > sys-devel/gcc-config: 1.4.1 > sys-devel/libtool: 2.4-r1 > sys-devel/make: 3.82 > virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) > ACCEPT_KEYWORDS="amd64 ~amd64" > ACCEPT_LICENSE="*" > CBUILD="x86_64-pc-linux-gnu" > CFLAGS="-march=native -O2 -pipe" > CHOST="x86_64-pc-linux-gnu" > CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt > /usr/share/maven-bin-3.0/conf" > CONFIG_PROTECT_MASK="/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/splash /etc/terminfo /etc/texmf/language.dat.d > /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" > CXXFLAGS="-march=native -O2 -pipe" > DISTDIR="/usr/portage/distfiles" > FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news > parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn > unmerge-logs unmerge-orphans userfetch" > FFLAGS="" > GENTOO_MIRRORS="http://gentoo.mirror.pw.edu.pl/ > ftp://ftp.vectranet.pl/gentoo/" > LANG="pl_PL.UTF-8" > LC_ALL="" > LDFLAGS="-Wl,-O1 -Wl,--as-needed" > LINGUAS="pl" > MAKEOPTS="-j5" > PKGDIR="/usr/portage/packages" > 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="/var/lib/layman/enlightenment-niifaq /var/lib/layman/kde > /var/lib/layman/science /var/lib/layman/sage-on-gentoo > /var/lib/layman/dustin /usr/local/portage" > SYNC="rsync://rsync7.pl.gentoo.org/gentoo-portage" > USE="X a52 aac acl acpi alsa amd64 bash-completion berkdb branding bzip2 > cairo cdr cli consolekit cracklib crypt csharp cups cxx dbus dri dts dvd > dvdr emboss encode exif fam fbsplash firefox flac fortran gdbm gdu gif gpm > gtk handbook i18n iconv intel ipv6 java jpeg latex lcms ldap libnotify lzma > mad mikmod mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl > nptlonly ogg openal opengl openmp pam pango pcre pdf perl png policykit > ppds pppd pulseaudio python qt qt3support qt4 readline scanner sdl session > slang spell sqlite sqlite3 sse sse2 sse3 sse4 ssl ssse3 > startup-notification svg symlink sysfs tcpd threads tiff truetype udev > unicode usb vaapi vim-synxtax vorbis x264 xcb xml xorg 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" > 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 synaptics" KERNEL="linux" > LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb > ncurses text" LINGUAS="pl" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" > USERLAND="GNU" > VIDEO_CARDS="intel" 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