Bug 273206 – dev-python/numpy-1.3.0 fails to emerge with MKL and USE="lapack"

• Product: Gentoo Linux
• Status: RESOLVED TEST-REQUEST

[Description Flo Gravo 2009-06-08 14:16:31 UTC]

Emerging dev-python/numpy-1.3.0 fail at numpy.distutils.system_info.atlas_threads_info

Reproducible: Always

Steps to Reproduce:
1. Install intel MKL like described in http://www.gentoo.org/proj/en/science/blas-lapack.xml
2. Enable lapack USE flag
3. emerge dev-python/numpy

Actual Results:  
Output: 
  FOUND:
    libraries = []
    library_dirs = ['/usr/lib64']
    language = c
    define_macros = [('NO_ATLAS_INFO', 2)]

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Traceback (most recent call last):
  File "setup.py", line 172, in <module>
    setup_package()
  File "setup.py", line 165, in setup_package
    configuration=configuration )
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/core.py", line 150, in setup
    config = configuration()
  File "setup.py", line 128, in configuration
    config.add_subpackage('numpy')
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/misc_util.py", line 852, in add_subpackage
    caller_level = 2)
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/misc_util.py", line 835, in get_subpackage
    caller_level = caller_level + 1)
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/misc_util.py", line 782, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "numpy/setup.py", line 14, in configuration
    config.add_subpackage('linalg')
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/misc_util.py", line 852, in add_subpackage
    caller_level = 2)
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/misc_util.py", line 835, in get_subpackage
    caller_level = caller_level + 1)
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/misc_util.py", line 782, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "numpy/linalg/setup.py", line 12, in configuration
    lapack_info = get_info('lapack_opt',0) # and {}
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/system_info.py", line 303, in get_info
    return cl().get_info(notfound_action)
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/system_info.py", line 448, in get_info
    self.calc_info()
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/system_info.py", line 1264, in calc_info
    atlas_info = get_info('atlas_threads')
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/system_info.py", line 303, in get_info
    return cl().get_info(notfound_action)
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/system_info.py", line 448, in get_info
    self.calc_info()
  File "/var/tmp/portage/dev-python/numpy-1.3.0/work/numpy-1.3.0/numpy/distutils/system_info.py", line 973, in calc_info
    lapack_name = lapack['libraries'][0]

IndexError: list index out of range
 * 
 * ERROR: dev-python/numpy-1.3.0 failed.
 * Call stack:
 *               ebuild.sh, line   49:  Called src_compile
 *             environment, line 2891:  Called distutils_src_compile 'config_fc' '--noopt' '--noarch'
 *             environment, line  834:  Called die
 * The specific snippet of code:
 *       ${python} setup.py build "$@" || die "compilation failed"
 *  The die message:
 *   compilation failed
 * 
 * If you need support, post the topmost build error, and the call stack if relevant.
 * A complete build log is located at '/var/tmp/portage/dev-python/numpy-1.3.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/numpy-1.3.0/temp/environment'.
 * 

>>> Failed to emerge dev-python/numpy-1.3.0, Log file:

>>>  '/var/tmp/portage/dev-python/numpy-1.3.0/temp/build.log'


# emerge --info
Portage 2.2_rc33 (default/linux/amd64/2008.0/desktop, gcc-4.4.0, glibc-2.9_p20081201-r2, 2.6.29-gentoo-r5 x86_64)
=================================================================
System uname: Linux-2.6.29-gentoo-r5-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T9550_@_2.66GHz-with-gentoo-2.0.0
Timestamp of tree: Sun, 07 Jun 2009 05:30:01 +0000
app-shells/bash:     4.0_p24
dev-java/java-config: 2.1.8
dev-lang/python:     2.6.2-r1
dev-util/cmake:      2.6.4
sys-apps/baselayout: 2.0.0-r2
sys-apps/openrc:     0.4.2-r1
sys-apps/sandbox:    2.0
sys-devel/autoconf:  2.13, 2.63-r1
sys-devel/automake:  1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.19.1-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.29
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -O2 -pipe -msse4.1"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /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 -msse4.1"
DISTDIR="/usr/portage/distfiles"
FEATURES="collision-protect distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/      http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/      http://de-mirror.org/distro/gentoo/      http://ftp.snt.utwente.nl/pub/os/linux/gentoo/      http://mirror.ovh.net/gentoo-distfiles/"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Wl,-z,-combreloc"
LINGUAS="en en_US de"
MAKEOPTS="-j3"
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"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="16bit 7zip X a52 aac ace acpi aim alsa amazon amd64 audiofile autoipd avahi bash-completion berkdb bidi binary-drivers bitdefender blas bluetooth bonjour bzip2 cairo cblas cdaudio cdda cddb cdio cdr cg cgi chm cleartype cli config_wizard consolekit contrast corefonts cpudetection cracklib crypt css cuda cups cupsddk custom-cpuopts cvs cxx daap dbus dga dhcpcd dirac dnotify dri dts dv dvb dvd dvdr dvdread dvi emboss encode exif fame fat ffmpeg fftw firefox flac foomaticdb fortran freetype ftp gcj gdbm gif gimp git glade glib glibc-omitfp glitz gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphite gs gsm gstreamer gtk gzip hal hdri hfs icecast iconv icq id3 id3tag idea imagemagick imap inotify ioctl ipod irc irda isdnlog jabber java java6 javascript jfs jingle joystick jpeg jpeg2k kerberos kickoff kpathsea kvm lame lapack laptop lasi lastfmradio latex latex3 ldap libffi libnotify live lj lm_sensors lzma lzo mad matroska mdnsresponder-compat meanwhile metric midi mime mjpeg mmx mmxext mng modplug mozdevelop mozilla mozsha1 mp2 mp3 mp3rtp mp3tunes mp4 mp4live mpeg mpeg2 msn mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses nepomuk network networkmanager nls nptl nptlonly nsplugin ntfs ntp nvidia offensive ogg openal openexr opengl openmp pam pango pcmcia pcre pdf perl php pidgin plotutils pmu png policykit postscript ppds pppd prediction projectm pulseaudio python qt3support quicktime quotas rar raw readline realmedia reflection replytolist rhythmbox rss rtf rtsp samba sasl scanner schroedinger science scrobbler sdl sdl-image semantic-desktop session sftp shaders slp smp sourceview speex spell spl sse sse2 sse3 sse4a ssl ssse3 startup-notification stream subversion svg symlink tagwriting tcpd tex tex4ht tga theora threads thunderbird tiff timezone tracker truetype tta twolame type1 udev unicode usb v4l v4l2 vcd vcdx vim-syntax vim-with-x vlc vlm voice vorbis wav wavpack wifi wma wmf wmp wps x264 xcb xcomposite xetex xforms xfs xft xhtml xine xinerama xml xmp xorg xpm xprint xrandr xscreensaver xslt xulrunner xv xvid xvmc yahoo zeroconf zip zlib" ALSA_CARDS="hda-intel" 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" APACHE2_MPMS="prefork" CAMERAS="agfa_cl20 casio_qv dimagev dimera3500 kodak_dc120 kodak_dc210 kodak_dc240      kodak_dc3200 kodak_ez200 konica_qm150 panasonic_coolshot panasonic_dc1000      panasonic_dc1580 panasonic_l859 polaroid_pdc320 polaroid_pdc640 polaroid_pdc700      ricoh_g3 sipix_blink sipix_blink2 sipix_web2 sony_dscf1 sony_dscf55 toshiba_pdrm11      adc65 aox barbie canon clicksmart310 digigr8 digita directory enigma13 fuji gsmart300      hp215 iclick jamcam jd11 konica largan lg_gsm mars mustek pccam300 pccam600 ptp2 ricoh      samsung sierra smal sonix soundvision spca50x sq905 stv0674 stv0680 sx330z template" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US de" USERLAND="GNU" VIDEO_CARDS="nvidia"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

[Comment 1 Flo Gravo 2009-06-08 14:17:57 UTC]

Created attachment 193898 [details]
/var/tmp/portage/dev-python/numpy-1.3.0/temp/build.log

[Comment 2 Mathias Weigt 2009-09-06 09:26:27 UTC]

(In reply to comment #1)
> Created an attachment (id=193898) [edit]
> /var/tmp/portage/dev-python/numpy-1.3.0/temp/build.log
> 

Fails here too (1.3.0-r1 also9), without MKL!!!! and USE="lapack".

Will this get now some attention?

[Comment 3 Mathias Weigt 2009-09-07 16:41:56 UTC]

(In reply to comment #2)
> (In reply to comment #1)
> > Created an attachment (id=193898) [edit]
> > /var/tmp/portage/dev-python/numpy-1.3.0/temp/build.log
> > 
> 
> Fails here too (1.3.0-r1 also9), without MKL!!!! and USE="lapack".

Please forget my comment as I'm obviously an idiot: Someone changed my CFLAGS (to something weird containing -ffast-math) after changing back and recompiling python numpy compiles fine (with and without USE="lapack").

[Comment 4 Sébastien Fabbro (RETIRED) 2010-06-04 15:41:44 UTC]

*** Bug 321737 has been marked as a duplicate of this bug. ***

[Comment 5 Joel Berendzen 2010-11-30 15:38:29 UTC]

Bump, please.  Still true with numpy 1.5.0-r2 and 1.5.1.  I must uninstall mkl for numpy to build.  I would like to be able to use mkl with numpy.

[Comment 6 Justin Lecher (RETIRED) 2010-11-30 16:33:01 UTC]

Works her, could please attach /usr/lib64/pkgconfig/blas.pc?

[Comment 7 José María Fernández González 2011-02-20 21:09:06 UTC]

On a Gentoo x86 installation with Intel mkl 10.0.5.025 I have got numpy emerged with:

LIBRARY_PATH=/opt/intel/mkl/10.0.5.025/lib/32 emerge -avq1 numpy

so the gcc finds in the linking stage the libraries pointed by /usr/lib/libblas.so, which is a symlink to /opt/intel/mkl/10.0.5.025/lib/32/libmkl.so, which is indeed an ld script:

GROUP (libmkl_intel.so libmkl_intel_thread.so libmkl_core.so)

[Comment 8 Justin Lecher (RETIRED) 2012-12-07 08:30:13 UTC]

What about latest numpy and mkl?