114885 2005-12-08 08:56 0000 dev-python/numeric: singular_value_decomposition hangs when built with gcc 3.4.4-r1 2007-02-07 17:24:33 0000 1 1 1 Unclassified Gentoo Linux Unspecified unspecified All Linux RESOLVED FIXED P2 critical --- 1 schiotz@fysik.dtu.dk python@gentoo.org bicatali@gentoo.org schiotz@fysik.dtu.dk 2005-12-08 08:56:09 0000 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 schiotz@fysik.dtu.dk 2005-12-08 08:56:42 0000 Created an attachment (id=74315) Test script. schiotz@fysik.dtu.dk 2005-12-12 01:48:25 0000 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 jak137@o2.pl 2005-12-19 14:39:51 0000 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. bicatali@gentoo.org 2006-06-07 10:23:25 0000 (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. schiotz@fysik.dtu.dk 2006-10-24 07:08:08 0000 I agree with comment #4. I just wanted to add, that the bug is also present when compiling with GCC 4.1.1. /Jakob bicatali@gentoo.org 2007-02-07 17:24:33 0000 fixed in >=dev-python/numeric-24.2-r1, now in cvs. Thanks for testing! 74315 2005-12-08 08:56 0000 Test script. testcase.py text/plain ZnJvbSBOdW1lcmljIGltcG9ydCAqCmltcG9ydCBMaW5lYXJBbGdlYnJhCgpwYXIgPSBbNC44ODEy MDcxMiwgLTAuMDczMjk1Nzk5OTk5OTk5OTk0LCAtMC4wODg4Mzg3NjAwMDAwMDAwMDMsIDAuMzAy MzA4NDMwMDAwMDAwMDIsIC0wLjk5MzkxMDM5OTk5OTk5OTk3LCAwLjk5NTgxNDA1OTk5OTk5OTk1 LCAtMC42NDc5MTYzMTAwMDAwMDAwNSwgMC4zOTA5MjUyMTAwMDAwMDAwMiwgLTAuMzcyMTg0NjIw MDAwMDAwMDIsIDAuMjI0NDM2NTAwMDAwMDAwMDEsIC0wLjExNzYyNzc3MDAwMDAwMDAxLCAwLjA4 OTI5NzkyMDAwMDAwMDAwMywgLTAuMDM1MzY4NjYwMDAwMDAwMDAzLCAwLjAxNjA0NTMxLCAtMC4w Mjc3MDk1Njk5OTk5OTk5OTksIDAuMCwgMC4wLCAwLjAsIDAuMCwgMC4wLCAwLjAsIDAuMCwgMC4w LCAwLjAsIDAuMCwgMC4wLCAwLjAsIDAuMCwgLTAuMzM4NjIxMDI5OTk5OTk5OTksIC0wLjMxNTgx MTQzLCAwLjAsIDAuMCwgMC4wLCAwLjAsIDAuMCwgMC4wLCAwLjAsIDAuMCwgMC4wLCAwLjBdCgpk ZWYgRXhwbShhbHBoYSx4KToKICAgIHJDdXQgPSA0Ljg1CiAgICB3aXRoaW5jdXRvZmZyYWRpdXMg PSBsZXNzX2VxdWFsKHgsckN1dCkKICAgIHJldHVybiAoZXhwKC1hbHBoYSp4KS0oYWxwaGEqKHJD dXQteCkrMSkqZXhwKC1hbHBoYSpyQ3V0KSkqd2l0aGluY3V0b2ZmcmFkaXVzCgpkZWYgRGVuc2l0 eShsYXQsYWxwaGEpOgogICAgcmV0dXJuIDgqRXhwbShhbHBoYSxsYXQqc3FydCgzLjApLzIuMCkr NipFeHBtKGFscGhhLGxhdCkrMTIqRXhwbShhbHBoYSxsYXQqc3FydCgyLjApKQoKZGVmIExhdHRp Y2VDb25zdGFudChyaG8sYyk6CiAgICByZXR1cm4gY1swXSArIGNbMV0qbG9nKHJobykrY1syXSpy aG8qbG9nKHJobykrY1szXSpyaG8qKjIqbG9nKHJobykrY1s0XSpyaG8qKjMqbG9nKHJobykgKyBy aG8qY1s1XSArIDEvcmhvKmNbNl0gKyAxL3JobyoqMipjWzddCiAgICAKYWxwaGEgPSA0Ljg4MTIw NzEyClkgPSBbXQpBID0gW10Kbm9ybSA9IERlbnNpdHkoMy4xODcyLGFscGhhKQpmb3IgbGF0IGlu IGFyYW5nZSgyLjksMy41MSwwLjEpOgogICAgWS5hcHBlbmQobGF0KQogICAgcmhvID0gRGVuc2l0 eShsYXQsYWxwaGEpL25vcm0KICAgIEEuYXBwZW5kKFtdKQogICAgZm9yIGkgaW4gcmFuZ2UoOCk6 CiAgICAgICAgYyA9IHplcm9zKCg4LCkpCiAgICAgICAgY1tpXSA9IDEKICAgICAgICBBWy0xXS5h cHBlbmQoTGF0dGljZUNvbnN0YW50KHJobyxjKSkKZm9yIGxhdCBpbiBhcmFuZ2UoMy4xMiwzLjIz LDAuMDEpOgogICAgWS5hcHBlbmQobGF0KQogICAgcmhvID0gRGVuc2l0eShsYXQsYWxwaGEpL25v cm0KICAgIEEuYXBwZW5kKFtdKQogICAgZm9yIGkgaW4gcmFuZ2UoOCk6CiAgICAgICAgYyA9IHpl cm9zKCg4LCkpCiAgICAgICAgY1tpXSA9IDEKICAgICAgICBBWy0xXS5hcHBlbmQoTGF0dGljZUNv bnN0YW50KHJobyxjKSkKWSA9IGFycmF5KFkpCkEgPSBhcnJheShBKQoKcHJpbnQgWQpwcmludCBB ClUsdyxWID0gTGluZWFyQWxnZWJyYS5zaW5ndWxhcl92YWx1ZV9kZWNvbXBvc2l0aW9uKEEpCg==