Bug 308581 – sci-libs/lapack-atlas-3.9.23-r1 has undefined symbols

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Jean-Francis Roy 2010-03-09 04:00:45 UTC]

Upgrading to lapack-atlas-3.9.23-r1 breaks scipy. Trying to use or reinstall scipy result in the following error message:

ImportError: /usr/lib/liblapack.so.0: undefined symbol: ATL_dgelq2


Reproducible: Always

Steps to Reproduce:
1. upgrade to lapack-atlas-3.9.23-r1
2. emerge =sci-libs/scipy-0.7.1



Actual Results:  
ImportError: /usr/lib/liblapack.so.0: undefined symbol: ATL_dgelq2

Expected Results:  
No error...

# emerge --info
Portage 2.2_rc65 (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.9_p20081201-r2, 2.6.33-gentoo x86_64)
=================================================================
System uname: Linux-2.6.33-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_T5600_@_1.83GHz-with-gentoo-2.1.6
Timestamp of tree: Mon, 08 Mar 2010 07:00:01 +0000
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:     4.0_p35
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4-r1
dev-util/cmake:      2.8.0-r2
sys-apps/baselayout: 2.1.6
sys-apps/openrc:     0.6.0
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.19.1-r1
sys-devel/gcc:       4.4.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.29
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config"
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/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-march=core2 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--jobs=3 --load-average=3.0 --with-bdeps y"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_CA.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--sort-common -Wl,--as-needed"
MAKEOPTS="-j3 -l3"
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/sunrise /usr/local/portage/local-overlay"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi alac alsa amd64 berkdb bluetooth branding bzip2 cairo cblas cddb cdr cleartype cli consolekit corefonts cracklib crypt cups cxx dbus dri dts dvd dvdr dvdread eds emboss encode evo faac fam firefox flac fortran gdbm gif gpm gsl gstreamer gtk hal iconv ipv6 jpeg kde lame lapack latex ldap libnotify mad mikmod mmx mng modules mp3 mp4 mpeg msn mudflap multilib ncurses networkmanager nls nptl nptlonly ogg opengl openmp pam pcre pdf perl png ppds pppd pulseaudio python qt3support qt4 quicktime readline reflection sdl semantic-desktop session spell spl sse sse2 ssl startup-notification subversion svg sysfs tcpd thunar tiff truetype type1 unicode usb vorbis wavpack webkit x264 xml xorg xscreensaver 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 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" ELIBC="glibc" INPUT_DEVICES="evdev mouse keyboard joystick synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nouveau" 
Unset:  CPPFLAGS, CTARGET, FFLAGS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Jean-Francis Roy 2010-03-09 04:01:46 UTC]

Created attachment 222769 [details]
build.log from emerging scipy

[Comment 2 Justin Lecher (RETIRED) 2010-03-10 08:15:43 UTC]

This version is masked for some reasons.

[Comment 3 Jean-Francis Roy 2010-03-10 18:22:44 UTC]

Yep it is now. For some reason it wasn't as Portage tried to upgrade to it. Maybe a bad sync (if it's possible) as I didn't play with package.unmask for that package.

Should this bug then be marked as invalid?

[Comment 4 Justin Lecher (RETIRED) 2010-03-10 18:24:31 UTC]

No keep it to remind me to be carefull when doing such tings! :) Actually I don't know what is going wrong. But I will find it out.

[Comment 5 Markus Dittrich (RETIRED) 2010-03-12 02:56:51 UTC]

(In reply to comment #4)
> No keep it to remind me to be carefull when doing such tings! :) Actually I
> don't know what is going wrong. But I will find it out.
> 

One of the seds screws up our ar wrapper (war) resulting in
symbols not being added to the final libs. I've attached a fix
below.

cheers,
Markus

[Comment 6 Markus Dittrich (RETIRED) 2010-03-12 02:57:50 UTC]

Created attachment 223243 [details, diff]
possible fix for missing symbols issue

[Comment 7 Justin Lecher (RETIRED) 2010-03-12 07:30:57 UTC]

Hi markus thanks for the patch. Nevertheless, blas-atlas screws up in case of rising the EAPI. I have to figure out at which points it happens. after that I will unmasked and fix lapack-atlas.

[Comment 8 Markus Dittrich (RETIRED) 2010-03-12 13:47:19 UTC]

(In reply to comment #7)
> Hi markus thanks for the patch. Nevertheless, blas-atlas screws up in case of
> rising the EAPI. I have to figure out at which points it happens. after that I
> will unmasked and fix lapack-atlas.
> 

Both -r1 versions of blas-atlas and lapack-atlas work just fine for me. Initially
the -r1 of blas-atlas was broken as well since it had the same "war" issue than
the lapack-atlas patch above fixes. I am a little puzzled about this since the
version in cvs is good. Maybe some of the mirrors picked up something bad?
In any case the -r1 of blas-atlas that is currently in cvs should work just fine.
Maybe diff against your current version in /usr/portage and see if they differ.

BTW, a very good way to test new blas and lapack-atlas ebuild is to run the test 
suite of itpp which is very comprehensive (I do this every time I do sth to any
of the atlas ebuilds). If it passes your likely in pretty good shape. 

cheers,
Markus 

[Comment 9 Justin Lecher (RETIRED) 2010-03-12 13:56:05 UTC]

There must be something different. I found some major changes in the headers (not just little differences in the estimated timings) and the is additionally the clapack.h installed with blas.atlas, which isn't in the 3.9.23 version.

[Comment 10 Justin Lecher (RETIRED) 2010-04-07 12:47:34 UTC]

*** Bug 313669 has been marked as a duplicate of this bug. ***

[Comment 11 Jean-Francis Roy 2010-04-07 14:41:53 UTC]

Correcting typo on new title ;-)

[Comment 12 Justin Lecher (RETIRED) 2010-04-15 20:13:50 UTC]

Should be fixed, if not please reopen.