Bug 114885 – dev-python/numeric: singular_value_decomposition hangs when built with gcc 3.4.4-r1

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Jakob Schiotz 2005-12-08 08:56:09 UTC]

GCC 3.4.4-r1 just went stable, but it looks like the
singular_value_decomposition function in dev-python/numeric breaks with this
compiler.

The attached test script illustrates the problem.  It should run to completion,
but hangs in singular_value_decomposition.  I have extracted this from a program
that worked a few days ago, but after rebuilding everything with the new gcc it
hangs.

My CFLAGS are CFLAGS="-O2 -march=pentium4 -fomit-frame-pointer -pipe"



Reproducible: Always
Steps to Reproduce:
1. Run the attached Python script
2.
3.

Actual Results:  
It hangs.



demokrit ~ # gcc-config -c
i686-pc-linux-gnu-3.4.4
demokrit ~ # etcat -v gcc
[ Results for search key           : gcc ]
[ Candidate applications found : 17 ]

 Only printing found installed programs.

*  sys-devel/gcc :
        [M  ] 2.95.3-r9 (2.95)
        [M  ] 3.1.1-r2 (3.1)
        [M  ] 3.2.2 (3.2)
        [M  ] 3.2.3-r4 (3.2)
        [M  ] 3.3.2-r7 (3.3)
        [   ] 3.3.5-r1 (3.3)
        [   ] 3.3.5.20050130-r1 (3.3)
        [M~ ] 3.3.5.20050130-r2 (3.3)
        [  I] 3.3.6 (3.3)
        [M~ ] 3.4.1-r3 (3.4)
        [M~ ] 3.4.3-r1 (3.4)
        [M~ ] 3.4.3.20050110-r2 (3.4)
        [  I] 3.4.4-r1 (3.4)
        [M  ] 3.4.5 (3.4)
        [M  ] 4.0.1 (4.0)
        [M  ] 4.0.2-r1 (4.0)
        [M  ] 4.1.0_beta20051202 (4.1)
demokrit ~ # emerge info
Portage 2.0.51.22-r3 (default-linux/x86/2005.0, gcc-3.4.4, glibc-2.3.5-r2,
2.6.14-gentoo-r2 i686)
=================================================================
System uname: 2.6.14-gentoo-r2 i686 Mobile Intel(R) Pentium(R) 4 - M CPU 2.00GHz
Gentoo Base System version 1.6.13
dev-lang/python:     2.3.5-r2, 2.4.2
sys-apps/sandbox:    1.2.12
sys-devel/autoconf:  2.13, 2.59-r6
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1
sys-devel/binutils:  2.16.1
sys-devel/libtool:   1.5.20
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=pentium4 -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env
/usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config
/usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config
/usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/
/usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/
/usr/share/texmf/xdvi/ /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d"
CXXFLAGS="-O2 -march=pentium4 -fomit-frame-pointer -pipe"
DISTDIR="/var/portage/distfiles"
FEATURES="autoconfig distlocks fixpackages sandbox sfperms strict"
GENTOO_MIRRORS="http://trumpetti.atm.tut.fi/gentoo/
ftp://trumpetti.atm.tut.fi/gentoo/ ftp://ftp.rhnet.is/pub/gentoo/
ftp://gd.tuwien.ac.at/opsys/linux/gentoo/"
LINGUAS="dk"
MAKEOPTS="-j2"
PKGDIR="/var/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/home/schiotz/development/CamposEbuilds/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="x86 X Xaw3d acpi alsa atlas audiofile avi berkdb bitmap-fonts bzip2 cdr
crypt cups curl dga dvd eds emacs emboss encode exif expat fam ffmpeg flac
font-server foomaticdb fortran gd gdbm gif glut gpm gstreamer gtk gtk2 idn
imagemagick imap imlib java jpeg kde kdeenablefinal kdexdeltas lcms libg++
libwww mad maildir mbox mikmod mime mng motif mozilla mp3 mpeg mule ncurses
netcdf nls nptl ogg oggvorbis opengl oss pam pcmcia pcre pdflib perl png pnp
ppds python qt quicktime readline real scanner sdl smime spell sse sse2 ssl
tcltk tcpd tetex tiff truetype truetype-fonts trusted type1-fonts udev usb
vorbis win32codecs wxwindows xine xml2 xmms xv xvid zlib linguas_dk userland_GNU
kernel_linux elibc_glibc"
Unset:  ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS

[Comment 1 Jakob Schiotz 2005-12-08 08:56:42 UTC]

Created attachment 74315 [details]
Test script.

[Comment 2 Jakob Schiotz 2005-12-12 01:48:25 UTC]

I did some more testing.  The fomit-frame-pointer flag has no effect, it still
hangs when I remove it.  But recompiling numeric with i686-pc-linux-gnu-3.3.6
fixes the problem.  I will keep the old compiler around just for the purpose of
compiling numeric.

This bug is assigned to the python herd, but it is of course possible that it is
a GCC problem.

/Jakob

[Comment 3 Jaroslaw Kalinowski 2005-12-19 14:39:51 UTC]

Other solution would be to fix numeric ebuilds to use syatem lapack for LinearAlgebra module. It has been discussed (http://bugs.gentoo.org/show_bug.cgi?id=81520) but unfortunately it seems that no ebuilds were added to portage as a result. I have numeric-23.8 compiled with gcc-3.4.4, linked with lapack-atlas-3.6.0 and no problems with your script.

[Comment 4 Sébastien Fabbro (RETIRED) 2006-06-07 10:23:25 UTC]

(In reply to comment #3)
> Other solution would be to fix numeric ebuilds to use syatem lapack for
> LinearAlgebra module. 

I did an ebuild for numeric-24.2 that links with blas/lapack, in the Gentoo Scientific overlay: http://gentooscience.org.

[Comment 5 Jakob Schiotz 2006-10-24 07:08:08 UTC]

I agree with comment #4.

I just wanted to add, that the bug is also present when compiling with GCC 4.1.1.

/Jakob

[Comment 6 Sébastien Fabbro (RETIRED) 2007-02-07 17:24:33 UTC]

fixed in >=dev-python/numeric-24.2-r1, now in cvs. Thanks for testing!