[gentoo-science] Re: Sage - Segmentation fault

[gentoo-science] Re: Sage - Segmentation fault

[Christopher Schwan]

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