Bug 171087 – sci-mathematics/octave segfaults when compiled with 'hdf5' useflag

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Ben Schwartz 2007-03-15 21:01:17 UTC]

Octave dies and segfaults on execution of any nontrivial code iff compiled with +hdf5. Compiled -hdf5, octave runs fine.

Reproducible: Always

Steps to Reproduce:
1. USE="hdf5" emerge octave
2. B0rked.
3. USE="-hdf5" emerge octave
4. Works.
5. USE="hdf5" emerge octave
6. B0rked again.

Actual Results:  
octave:1> rand()
ans = 0.32615
octave:2> sqrt(2)
panic: Segmentation fault -- stopping myself...
attempting to save variables to `octave-core'...
save to `octave-core' complete
Segmentation fault

Expected Results:  
print out 1.414...

bens@bemasc ~ $ emerge --info
Portage 2.1.2.2 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.5-r0, 2.6.19-gentoo-r5 i686)
=================================================================
System uname: 2.6.19-gentoo-r5 i686 Genuine Intel(R) CPU           L2400  @ 1.66GHz
Gentoo Base System release 1.12.9
Timestamp of tree: Sat, 10 Mar 2007 20:20:01 +0000
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled]
ccache version 2.4 [enabled]
dev-java/java-config: 1.3.7, 2.0.31
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r6
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-march=prescott -O2 -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-O2 -mcpu=i686 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig ccache confcache distlocks metadata-transfer parallel-fetch sandbox sfperms strict userfetch userpriv usersandbox"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LANG="en_US.UTF-8"
LINGUAS="en_US en es"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage"
USE="3ds X X509 a52 aac acpi aiglx aim alsa amr amrr aotuv asf avahi bash-completion beagle berkdb bitmap-fonts blas bluetooth bootsplash branding bzip2 cairo ccache cdda cddb cdparanoia cdr cjk cli cpudetection cracklib crosscompile crypt cups dbus directfb dmi dmx doc dri dts dv dvd dvdr dvdread dvi eds emacs emboss encode esd exif fam fbcon fbsplash ffmpeg fftw firefox flac flash fortran ftp gb gcj gdbm gif gimp ginac glitz glut gnome gnuplot gphoto2 gpm gps grammar gstreamer gtk guile gzip hal hardenedphp hdaps hddtemp i8x0 iconv icq ieee1394 imagemagick imap imlib ipv6 irc isdnlog jabber jack java javascript jbig jpeg jpeg2k kdeenablefinal kerberos ladspa lapack lash lcms ldap libg++ libnotify lirc live mad matroska midi mikmod mime ming mjpeg mmap mmx mmxext mng mod mono mozsvg mp3 mp4 mpeg musepack nautilus ncurses nls nptl nptlonly nsplugin ntfs offensive ogg opengl oscar pam pcre pda pdf perl plotutils png ppds pppd python quicktime readline real realmedia reflection rtc sdl session shorten smp speex spell spl sse sse-filters sse2 ssl svg tcpd tetex tga theora threads thunderbird tiff timidity toolkit-scroll-bars truetype truetype-fonts type1-fonts unicode usb vcd videos vorbis wifi win32codecs wma wmf x264 x86 xanim xine xinerama xml xorg xpm xv xvid xvmc yv12 zip zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en_US en es" USERLAND="GNU" VIDEO_CARDS="i810 vesa"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

Also, I have hdf5 installed:
[ebuild   R   ] sci-libs/hdf5-1.6.4  USE="ssl threads zlib -debug -hlapi -mpi -static -szip" 0 kB

[Comment 1 Ben Schwartz 2007-03-15 21:02:10 UTC]

Created attachment 113401 [details]
core dump from octave

This core dump is probably of no use.

[Comment 2 Ben Schwartz 2007-03-15 21:06:07 UTC]

Created attachment 113403 [details]
Stack trace

This stack strace (from strace) shows octave's response to 'sqrt(2)' in interactive mode. Only the last 50 lines or so are likely to be relevant.

[Comment 3 Ben Schwartz 2007-03-15 21:17:55 UTC]

I forgot to mention the version:
sci-mathematics/octave-2.1.73

[Comment 4 Ben Schwartz 2007-03-15 23:18:56 UTC]

Recompiling octave-forge after changing octave's useflags fixes the problem.

I wish portage knew enough to automatically recompile octave-forge in this case.

[Comment 5 Markus Dittrich (RETIRED) 2007-03-16 12:43:55 UTC]

(In reply to comment #4)
> Recompiling octave-forge after changing octave's useflags fixes the problem.
> 
> I wish portage knew enough to automatically recompile octave-forge in this
> case.
> 

Thanks for the note! I guess the best we could do would be to add a 
comment in octave's pkg_postinst(). I'll see if I can reproduce this issue
on my dev boxes and will add a warning if it is reproducible.

Thanks,
Markus