Bug 584902 – dev-python/matplotlib (1.4.3, 1.5.1) segmentation fault when calling pyplot.show()

• Product: Gentoo Linux
• Status: RESOLVED INVALID

[Description lumbrius 2016-06-03 07:13:08 UTC]

Created attachment 436254 [details]
strace log

In matplotlib, segmentation fault happens whenever pyplot.show() is called.
It happens with both qt and gtk aggregators.

Prifole set is
default/linux/amd64/13.0/desktop/plasma
DE is plasma-desktop-5.5.5-r1


How it happens:
mpl-test.py 

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
if __name__ == '__main__':
    plt.plot(range(0,3),range(0,3))
    plt.show()



python2.7 mpl-test.py 
Segmentation fault

python3.4 mpl-test.py 
Segmentation fault

emerge --info
Portage 2.2.28 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-4.9.3, glibc-2.22-r4, 4.4.6-gentoo x86_64)
=================================================================
System uname: Linux-4.4.6-gentoo-x86_64-Intel-R-_Core-TM-_i5-6300HQ_CPU_@_2.30GHz-with-gentoo-2.2
KiB Mem:     8048508 total,   5869488 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 02 Jun 2016 09:00:01 +0000
sh bash 4.3_p42-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/cmake:           3.3.1-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.19.1::gentoo
sys-apps/sandbox:         2.10-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r4::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

science
    location: /var/lib/layman/science
    masters: gentoo
    priority: 0

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -fno-stack-protector -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -fno-stack-protector -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 preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="ru_RU.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif glamor gpm gtk iconv ipv6 jpeg kde kipi lcms ldap libnotify mad mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds qml qt3support qt4 qt5 readline sdl seccomp semantic-desktop session spell sse sse2 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis widgets wxwidgets x264 xattr xcb xcomposite xinerama xml xscreensaver xv xvid zlib" ABI_X86="64 32" 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" 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 author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 fma3 mmx mmxext mpx popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 ublox ubx" GRUB_PLATFORMS="efi-64" 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

Strace output in attachment

[Comment 1 lumbrius 2016-06-03 20:01:55 UTC]

Most probably it is bug in lapack-reference

core dump backtrace

#0  0x00002adcef2fe0e0 in dcopy_ () from /usr/lib64/libblas.so.3
#1  0x00002adcf0256caa in ?? ()
#2  0x0000000000000002 in ?? ()
#3  0x00007ffca8b4fe2c in ?? ()
#4  0x00007ffca8b4fe28 in ?? ()
#5  0x00007ffca8b4fe24 in ?? ()
#6  0x00002adcf46c60f8 in ?? ()
#7  0x0000000000000000 in ?? ()

after emerging numpy with '-lapack' no segmentation fault.