Bug 380723 – sci-libs/clapack-3.2.1-r6 fails to configure because BLAS libraries are not found

• Product: Gentoo Linux
• Status: RESOLVED INVALID

[Description Juergen Rose 2011-08-26 07:51:08 UTC]

'emerge clapack' fails with:>>> Emerging (1 of 17) sci-libs/clapack-3.2.1-r6
 * clapack-3.2.1-CMAKE.tgz RMD160 SHA1 SHA256 size ;-) ...                                                                                                                                     [ ok ]
>>> Unpacking source...
>>> Unpacking clapack-3.2.1-CMAKE.tgz to /var/tmp/portage/sci-libs/clapack-3.2.1-r6/work
>>> Source unpacked in /var/tmp/portage/sci-libs/clapack-3.2.1-r6/work
>>> Preparing source in /var/tmp/portage/sci-libs/clapack-3.2.1-r6/work/clapack-3.2.1-CMAKE ...
 * Applying clapack-3.2.1-fix_include_file.patch ...                                                                                                                                           [ ok ]
 * Applying clapack-3.2.1-noblasf2c.patch ...                                                                                                                                                  [ ok ]
 * Applying clapack-3.2.1-hang.patch ...                                                                                                                                                       [ ok ]
 * Applying clapack-3.2.1-findblas-r6.patch ...                                                                                                                                                [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/clapack-3.2.1-r6/work/clapack-3.2.1-CMAKE ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-libs/clapack-3.2.1-r6/work/clapack-3.2.1_build"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-libs/clapack-3.2.1-r6/temp/gentoo_common_config.cmake -DCMAKE_INSTALL_PREFIX=/usr -DENABLE_TESTS=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-libs/clapack-3.2.1-r6/temp/gentoo_rules.cmake  /var/tmp/portage/sci-libs/clapack-3.2.1-r6/work/clapack-3.2.1-CMAKE
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-libs/clapack-3.2.1-r6/temp/gentoo_common_config.cmake
Re-run cmake no build system arguments
-- The C compiler identification is GNU
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- checking for module 'blas'
--   package 'blas' not found
CMake Error at CMakeLists.txt:53 (message):
  --> BLAS libraries needed but not found.


-- Configuring incomplete, errors occurred!
 * ERROR: sci-libs/clapack-3.2.1-r6 failed (configure phase):


atlas-3.9.47 is installed:
root@grizzly:/usr/src(35)# qlist -Iv atlas
sci-libs/atlas-3.9.47


Reproducible: Always




rose@grizzly:/home/rose(1)$ emerge --info
Portage 2.1.10.11 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.13-r4, 3.0.3 x86_64)
=================================================================
System uname: Linux-3.0.3-x86_64-AMD_Athlon-tm-_64_Processor_3200+-with-gentoo-2.0.3
Timestamp of tree: Thu, 25 Aug 2011 10:30:01 +0000
app-shells/bash:          4.2_p10
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r2, 3.2-r2
dev-util/cmake:           2.8.5-r2::science
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.0.3
sys-apps/openrc:          0.8.3-r1
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.1-r1
sys-devel/binutils:       2.21.1-r1
sys-devel/gcc:            4.5.3-r1
sys-devel/gcc-config:     1.4.1-r1
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r1
sys-kernel/linux-headers: 2.6.39 (virtual/os-headers)
sys-libs/glibc:           2.13-r4
Repositories: gentoo java-overlay lordvan science x11 sunrise arcon local x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=k8"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /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/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/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"
CXXFLAGS="-O2 -march=k8"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -march=k8"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ "
LANG="de_DE.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j1"
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/java-overlay /var/lib/layman/lordvan /var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/arcon /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago garmin gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kde kdrive kerberos kpathsea ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" ALSA_CARDS="intel8x0" 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="tda10046 saa7134" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" LIRC_DEVICES="hauppauge_dvb" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

rose

[Comment 1 Justin Lecher (RETIRED) 2011-08-26 13:02:15 UTC]

Same here. Full builg.log.
Whatdoes pkg-config --libs blas say? Are all those libs in place?

[Comment 2 Juergen Rose 2011-08-27 07:38:54 UTC]

root@grizzly:/usr/src(41)# pkg-config --libs blas 
Package blas was not found in the pkg-config search path.
Perhaps you should add the directory containing `blas.pc'
to the PKG_CONFIG_PATH environment variable
No package 'blas' found

[Comment 3 Juergen Rose 2011-08-27 07:39:29 UTC]

Created attachment 284777 [details]
/var/tmp/portage/sci-libs/clapack-3.2.1-r6/temp/build.log

[Comment 4 Juergen Rose 2011-08-27 07:41:09 UTC]

root@grizzly:/usr/src(43)# qlist atlas
/etc/env.d/alternatives/blas/atlas/_importance
/etc/env.d/alternatives/cblas/atlas/_importance
/etc/env.d/alternatives/lapack/atlas/_importance
/usr/lib64/pkgconfig/atlas-clapack.pc
/usr/lib64/pkgconfig/atlas-blas.pc
/usr/lib64/pkgconfig/atlas-cblas.pc
/usr/lib64/pkgconfig/atlas-lapack.pc
/usr/lib64/libatlas.so.3
/usr/lib64/libatlcblas.so.3
/usr/lib64/libatlclapack.so.3
/usr/lib64/libatlclapack.so
/usr/lib64/libf77blas.so.3
/usr/lib64/libatlas.so
/usr/lib64/libf77blas.so
/usr/lib64/libatlcblas.so
/usr/lib64/libatllapack.so.3
/usr/share/doc/atlas-3.9.47/cblas.pdf
...
/usr/include/atlas/atlas_ptalias3.h
/etc/env.d/alternatives/blas/atlas/usr/lib64/pkgconfig/blas.pc
/etc/env.d/alternatives/cblas/atlas/usr/lib64/pkgconfig/cblas.pc
/etc/env.d/alternatives/cblas/atlas/usr/include/cblas.h
/etc/env.d/alternatives/lapack/atlas/usr/lib64/pkgconfig/lapack.pc
/usr/lib64/libatllapack.so

[Comment 5 Juergen Rose 2011-08-27 07:56:18 UTC]

I still tried 'strace -o strace-pkg-config.log -f pkg-config --libs blas' grizzly and on a system where blas is detected. On the system where blas is detected there are the following links:


root@impala:/root(28)# ll /usr/lib64/pkgconfig/blas.pc
lrwxrwxrwx 1 root root 73 Aug  7 14:02 /usr/lib64/pkgconfig/blas.pc -> ../../../etc/env.d/alternatives/blas/_current/usr/lib64/pkgconfig/blas.pc
root@impala:/root(30)# ll /etc/env.d/alternatives/blas/_current/usr/lib64/pkgconfig/blas.pc
lrwxrwxrwx 1 root root 57 Aug  7 14:02 /etc/env.d/alternatives/blas/_current/usr/lib64/pkgconfig/blas.pc -> ../../../../../../../../usr/lib64/pkgconfig/atlas-blas.pc
root@impala:/root(31)# ll  /etc/env.d/alternatives/blas/_current
lrwxrwxrwx 1 root root 5 Aug  7 14:02 /etc/env.d/alternatives/blas/_current -> atlas/


These links are missing on grizzly:

root@grizzly:/usr/src(51)# ll /usr/lib64/pkgconfig/blas.pc
/bin/ls: cannot access /usr/lib64/pkgconfig/blas.pc: No such file or directory
root@grizzly:/usr/src(52)# ll /etc/env.d/alternatives/blas/_current/usr/lib64/pkgconfig/blas.pc
/bin/ls: cannot access /etc/env.d/alternatives/blas/_current/usr/lib64/pkgconfig/blas.pc: No such file or directory
root@grizzly:/usr/src(53)# ll  /etc/env.d/alternatives/blas/_current
/bin/ls: cannot access /etc/env.d/alternatives/blas/_current: No such file or directory

[Comment 6 Justin Lecher (RETIRED) 2011-08-27 10:25:54 UTC]

It seems something went wrong with your atlas installation. mine has all those .pc files. Please try to reemerge atlas and try again.

[Comment 7 Juergen Rose 2011-08-27 23:05:04 UTC]

Some hours later after reemerging atlas 'pkg-config --libs blas' says:

root@grizzly:/usr/src(62)#  pkg-config --libs blas 
-lf77blas -lm -latlas  

Thanks Justin.

[Comment 8 Justin Lecher (RETIRED) 2011-08-27 23:09:30 UTC]

Okay then, good to hear.

[Comment 9 Juergen Rose 2011-08-28 00:45:08 UTC]

nd 'emerge sci-libs/clapack-3.2.1-r6' works too.