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Bug 324889 - sci-libs/blas-atlas-3.9.* builds but is unusable
Summary: sci-libs/blas-atlas-3.9.* builds but is unusable
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: 372323
  Show dependency tree
 
Reported: 2010-06-20 23:57 UTC by François Bissey
Modified: 2013-01-31 11:08 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
blas-atlas build log (blas-atlas.log.bz2,230.35 KB, application/octet-stream)
2010-06-20 23:58 UTC, François Bissey
Details
lapack-atlas failed build log. (lapack-atlas-3.9.23-r3.log.bz2,5.07 KB, application/octet-stream)
2010-06-20 23:59 UTC, François Bissey
Details
lapack-atlas config log as requested (config.log.bz2,8.20 KB, application/octet-stream)
2010-06-27 23:20 UTC, François Bissey
Details
just in case the result on readelf -s on libatlas.so (readelf-libatlas.txt.bz2,35.67 KB, application/octet-stream)
2010-06-27 23:21 UTC, François Bissey
Details
and readelf -s libblas.so (readelf-libblas.txt.bz2,3.76 KB, application/octet-stream)
2010-06-27 23:21 UTC, François Bissey
Details

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Description François Bissey 2010-06-20 23:57:27 UTC
I have been having this problem for a while now on a ~x86 box (details to follow).
I have this problem with all revisions of 3.9.23 and the latest 3.9.21.
Once blas-atlas is installed lapack-atlas and other applications/libraries using
blas-alas refuse to build, example with lapack-atlas:

checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
configure: error: Cannot find blas libraries

blas-atlas is properly eselected. As it turns out at configuration time
my cpu is identified by ATLAS as supporting sse3 while my cpu most definitely 
doesn't have it! So I am suspecting blas-atlas is built using sse3 instruction
and failing silently to produce proper/usable libraries.


/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r4/work/ATLAS/gentoo-build $ ./xprobe_sse3 
SUCCESS

cat /proc/cpuinfo | grep sse
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe constant_tsc pebs bts pni dtes64 monitor ds_cpl cid
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe constant_tsc pebs bts pni dtes64 monitor ds_cpl cid


 emerge --info blas-atlas
Portage 2.2_rc67 (default/linux/x86/10.0, gcc-4.4.4, glibc-2.11.2-r0, 2.6.33-gentoo-r1 i686)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.33-gentoo-r1-i686-Intel-R-_Pentium-R-_4_CPU_2.80GHz-with-gentoo-2.0.1
Timestamp of tree: Sun, 13 Jun 2010 22:45:03 +0000
app-shells/bash:     4.1_p7
dev-java/java-config: 2.1.11
dev-lang/python:     2.6.5-r99, 3.1.2-r3
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.1-r1
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.7.9-r1, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.4.4
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.34                                                                                                         
ACCEPT_KEYWORDS="x86 ~x86"                                                                                                          
ACCEPT_LICENSE="* -@EULA"                                                                                                           
CBUILD="i686-pc-linux-gnu"                                                                                                          
CFLAGS="-O2 -march=native -pipe"                                                                                                    
CHOST="i686-pc-linux-gnu"                                                                                                           
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"                                                          
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/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"                                                                                                                      
CXXFLAGS="-O2 -march=native -pipe"                                                                                                  
DISTDIR="/usr/portage/distfiles"                                                                                                    
FEATURES="assume-digests collision-protect distlocks fakeroot fixpackages news parallel-fetch preserve-libs protect-owned sandbox sfperms split-elog split-log strict unmerge-logs unmerge-orphans userfetch"                                                           
GENTOO_MIRRORS="ftp://mirror.ihug.co.nz/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo http://gentoo.eliteitminds.com"                                                                                                        
LC_ALL="en_GB.UTF-8"                                                                                                                
LDFLAGS="-Wl,--as-needed"                                                                                                           
LINGUAS="en_GB fr"                                                                                                                  
MAKEOPTS="-j3 VERBOSE=1"                                                                                                            
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/sage-on-gentoo /home/fbissey/Work/overlay"
SYNC="rsync://rsync.au.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext X a52 aac aalib acl acpi alsa amr ao apm asf audiofile berkdb bidi bootsplash branding bzip2 cairo cddb cdf cdparanoia cli composite consolekit cracklib crypt cups curl cxx dbus device-mapper dga dmi dri dts dv dvd dvdr dvdread encode exif expat ffmpeg fftw flac fontconfig foomaticdb fortran fpx fts3 gdbm geoip gif gimpprint glib glitz glut gmp graphviz gs gstreamer gtk gtk2 hal iconv id3tag idn imagemagick imlib imlib2 ipv6 ipython java jbig joystick jpeg jpeg2k kde kdehiddenvisibility kipi kpathsea ladspa lame lapack latex lcms libffi libsamplerate lzo mad mathml matroska mikmod mime mmx mmx2 mmxext mng modules motif mp3 mp4 mpeg mplayer mudflap musicbrainz ncurses netcdf network nls nptl nptlonly ogg openal openexr opengl openmp pcre pdf perl png policykit portaudio posix ppds pppd python qt3support qt4 quicktime readline reflection reiserfs sdl secure-delete semantic-desktop session sndfile sox spell spl sqlite3 sse sse2 ssl startup-notification svg svga sysfs szip t1lib tcl tcltk tcpd tetex tga theora tiff tk truetype unicode usb vcd vnc vorbis wavpack webkit wmf x264 x86 xanim xattr xcb xcomposite xine xinerama xml xorg xpm xsl xv xvid xvmc zeroconf zlib" 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 keyboard mouse joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en_GB fr" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa" 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:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

=================================================================
                        Package Settings
=================================================================

sci-libs/blas-atlas-3.9.23-r4 was built with the following:
USE="-debug -doc" 


a sample build log to follow.
Comment 1 François Bissey 2010-06-20 23:58:38 UTC
Created attachment 236103 [details]
blas-atlas build log

As I said before build and install apparently successfully but is broken.
Comment 2 François Bissey 2010-06-20 23:59:42 UTC
Created attachment 236105 [details]
lapack-atlas failed build log.
Comment 3 François Bissey 2010-06-27 23:20:38 UTC
Created attachment 236763 [details]
lapack-atlas config log as requested
Comment 4 François Bissey 2010-06-27 23:21:33 UTC
Created attachment 236765 [details]
just in case the result on readelf -s on libatlas.so
Comment 5 François Bissey 2010-06-27 23:21:58 UTC
Created attachment 236767 [details]
and readelf -s libblas.so
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2013-01-31 11:08:26 UTC
Dropped all atlas packages from tree.
Please use sci-libs/atlas from sci overlay.
If problem still exist with that package, please reopen the bug or file a new one.