As already reported in Bug 376185 the installation of sci-libs/cholmod-1.7.3-r1 and sci-libs/umfpack-5.5.1 fails on ATOM CPU system after sci-libs/atlas-3.9.46 was installed. Now I found that 'emerge arpack' fails with: ... checking for sgemm_ in -lf77blas -lm -latlas ... no checking if sgemm_ is being linked in already... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -lblas... no checking for sgemm_ in -lmkl... no checking for sgemm_ in -framework vecLib... 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 !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/arpack-96-r3/work/ARPACK/config.log * ERROR: sci-libs/arpack-96-r3 failed (configure phase): In config.log I find again: ... configure:14958: checking for ATL_xerbla in -latlas configure:14991: i686-pc-linux-gnu-gcc -o conftest -O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe -Wl,-O1 -Wl,--as-needed conftest.c -latlas -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.2 -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../../i686-pc-linux-gnu/lib -L/usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../.. -lgfortran -lm >&5 /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_thread_free' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_join_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_free_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_wait_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_signal_tree' /usr/lib/gcc/i686-pc-linux-gnu/4.5.2/../../../libatlas.so: undefined reference to `ATL_thread_init' collect2: ld returned 1 exit status ... Reproducible: Always
Created attachment 281799 [details] /var/tmp/portage/sci-libs/arpack-96-r3/work/ARPACK/config.log
Created attachment 281821 [details] /var/tmp/portage/sci-libs/umfpack-5.5.1/work/UMFPACK/config.log
sci-libs/superlu-4.1-r1 fails to emerge with the same symptoms: ... checking for sgemm_ in -lf77blas -lm -latlas ... no checking if sgemm_ is being linked in already... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -lblas... no checking for sgemm_ in -lmkl... no checking for sgemm_ in -framework vecLib... 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
Created attachment 281823 [details] /var/tmp/portage/sci-libs/superlu-4.1-r1/work/SuperLU_4.1/config.log
Created attachment 281829 [details] /var/tmp/portage/sci-libs/cholmod-1.7.3-r1/work/CHOLMOD/config.log
Also veusz-1.12-r1 has a problem with libatlas.so.3. Emerge veusz fails with: ... >>> Emerging (1 of 2) sci-visualization/veusz-1.12-r1 * veusz-1.12.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking veusz-1.12.tar.gz to /var/tmp/portage/sci-visualization/veusz-1.12-r1/work >>> Source unpacked in /var/tmp/portage/sci-visualization/veusz-1.12-r1/work >>> Preparing source in /var/tmp/portage/sci-visualization/veusz-1.12-r1/work/veusz-1.12 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-visualization/veusz-1.12-r1/work/veusz-1.12 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-visualization/veusz-1.12-r1/work/veusz-1.12 ... * Building of sci-visualization/veusz-1.12-r1 with CPython 2.7... python2.7 setup.py build -b build-2.7 Traceback (most recent call last): File "setup.py", line 29, in <module> import numpy File "/usr/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module> import add_newdocs File "/usr/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module> from numpy.lib import add_newdoc File "/usr/lib/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module> from polynomial import * File "/usr/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module> from numpy.linalg import eigvals, lstsq File "/usr/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module> from linalg import * File "/usr/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module> from numpy.linalg import lapack_lite ImportError: /usr/lib/libatlas.so.3: undefined symbol: ATL_thread_free * ERROR: sci-visualization/veusz-1.12-r1 failed (compile phase):
root@inspironM12:/usr/local/portage/sci-libs(92)# emerge --info =sci-visualization/veusz-1.12-r1 Portage 2.1.10.9 (default/linux/x86/10.0/desktop, gcc-4.5.2, glibc-2.13-r4, 2.6.39-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-2.6.39-gentoo-i686-Intel-R-_Atom-TM-_CPU_Z520_@_1.33GHz-with-gentoo-2.0.3 Timestamp of tree: Tue, 02 Aug 2011 02:00:01 +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 sys-devel/gcc: 4.5.2 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 2.6.38 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo java-overlay science x11 bicatali x-portage x-cpan g-octave ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=core2 -mtune=generic -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" 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=core2 -mtune=generic -fomit-frame-pointer -pipe" 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="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.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/science /var/lib/layman/x11 /var/lib/layman/bicatali /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d a52 aac abiword acl acpi admin afs alsa ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus declarative dell 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 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 hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kvm ladspa lame lapack laptop 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 mpi-threads mplayer mtp mudflap musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia 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 samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl ssse3 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 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 x86 xattr xcb xemacs xext 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="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" 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 jruby" USERLAND="GNU" VIDEO_CARDS="psb intel 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
root@inspironM12:/usr/local/portage/sci-libs(93)# emerge -pqv =sci-visualization/veusz-1.12-r1 [ebuild U ] sci-visualization/veusz-1.12-r1 [1.12] USE="doc examples fits"
Created attachment 281831 [details] /var/tmp/portage/sci-visualization/veusz-1.12-r1/temp/build.log
All packages that fails for you are from bicatali overlay?
No, only atlas-3.9.46 and cholmod-1.7.3-r1 is from the bicatali overlay. The other packages are from the normal portage tree: rose@inspironM12:/home/rose(1)$ emerge -pvD sci-libs/atlas sci-libs/arpack sci-libs/umfpack sci-libs/cholmod sci-visualization/veusz These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/atlas-3.9.46 USE="doc fortran lapack threads -static-libs" 0 kB [1] [ebuild N ] sci-libs/arpack-96-r3 USE="doc examples mpi -static-libs" 0 kB [0] [ebuild N ] sci-libs/umfpack-5.5.1 USE="doc -metis -static-libs" 0 kB [0] [ebuild N ] sci-libs/cholmod-1.7.3-r1 USE="doc supernodal -metis -minimal -static-libs" 0 kB [1] [ebuild U ] sci-visualization/veusz-1.12-r1 [1.12] USE="doc examples fits" 0 kB [0] Total: 5 packages (1 upgrade, 3 new, 1 reinstall), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/bicatali Perhaps the installed libatlas is in any way not complete. Please notice what I already mentioned in Bug 376185. I find that the size of /usr/lib/libatlas.so.3 on the system with the ATOM CPU is with 3258008 Bytes has almost the size of library on an i686 Intel P4 system (3287640 Bytes), but less than the half of the size on a system with an Core(TM)2 CPU (6961488 Bytes). Is this to expect? I already emerged twice atlas-3.9.46 on the system with the ATOM CPU and have not observed any error. What could I else do? Should I emerge atlas-3.9.46 with the nostrip FEATURE?
There was no need of posting all of these logs when you see that the error is the same. Instead, could you post the build log for sci-libs/atlas-3.9.46? Your libatlas.so does seem incomplete.
OK, I will reemerge atlas-3.9.46 with FEATURES="fixpackages nostrip noclean". But we have to wait the last both times it needed more than 15 hours.
Created attachment 281935 [details] bzip2ed /var/tmp/portage/sci-libs/atlas-3.9.46/temp/build.log
If I analyse now /usr/lib/libatlas.so.3 for some functions, I find: root@inspironM12:/usr/local/portage/sci-libs(116)# nm /usr/lib/libatlas.so.3 | grep ATL_thread 002beed0 T ATL_thread_exit U ATL_thread_free U ATL_thread_init 002beef0 T ATL_thread_join 002bec50 T ATL_thread_start 002be8b0 T ATL_thread_yield root@inspironM12:/usr/local/portage/sci-libs(117)# nm /usr/lib/libatlas.so.3 | grep ATL_join U ATL_join_tree root@inspironM12:/usr/local/portage/sci-libs(118)# nm /usr/lib/libatlas.so.3 | grep ATL_free U ATL_free_tree root@inspironM12:/usr/local/portage/sci-libs(119)# nm /usr/lib/libatlas.so.3 | grep ATL_wait U ATL_wait_tree root@inspironM12:/usr/local/portage/sci-libs(120)# nm /usr/lib/libatlas.so.3 | grep ATL_signal U ATL_signal_tree I suppose that capital U means undefined.
On an Intel Quad Core where I don't have any problems with regard to libatlas I get the following results with respect to the missing symbols: root@moose:/root(43)# cat /proc/cpuinfo | grep "model name" model name : Intel(R) Core(TM)2 Quad CPU Q9650 @ 3.00GHz model name : Intel(R) Core(TM)2 Quad CPU Q9650 @ 3.00GHz model name : Intel(R) Core(TM)2 Quad CPU Q9650 @ 3.00GHz model name : Intel(R) Core(TM)2 Quad CPU Q9650 @ 3.00GHz root@moose:/root(44)# nm /usr/lib/libatlas.so.3 | grep ATL_thread 00000000006396e0 T ATL_thread_exit 00000000006396f0 T ATL_thread_join 00000000006394b0 T ATL_thread_start 0000000000639200 T ATL_thread_yield root@moose:/root(45)# nm /usr/lib/libatlas.so.3 | grep ATL_free root@moose:/root(46)# nm /usr/lib/libatlas.so.3 | grep ATL_wait root@moose:/root(47)# nm /usr/lib/libatlas.so.3 | grep ATL_signal root@moose:/root(48)#
I just found, that I still had the mpi-threads USE flag activated in /etc/make.conf, which made difficulties already in the past on other system. So I removed that flag and will emerge again world and atlas and report the results.
atlas does not use mpi, so mpi-threads should not matter. the problem is your ATOM processor not being recognized from the default atlas config. in your log, you can see in the beggining of your log: Architecture configured as UNKNOWNx86 (26) ERROR: enum fam=3, chip=2, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 then atlas goes on onto trying to get a grasp of your system. you should report upstream. it looks like it is linked to http://sourceforge.net/tracker/?func=detail&aid=3375778&group_id=23725&atid=379483 or http://sourceforge.net/tracker/?func=detail&aid=3301697&group_id=23725&atid=379483
I sent it as Ticket #21016 to http://sourceforge.net/tracker.
It is at http://sourceforge.net/apps/trac/sourceforge/ticket/21016
The link in Comment 19 and 20 was on the wrong tracker. The right link should be: https://sourceforge.net/tracker/?func=detail&atid=379483&aid=3385926&group_id=23725
*** Bug 376685 has been marked as a duplicate of this bug. ***
I have attached a patch that fixes things for me. I've also submitted the patch upstream, we'll see if it gets picked up (see https://sourceforge.net/tracker/?func=detail&aid=3301697&group_id=23725&atid=379483)
Created attachment 286999 [details, diff] patch to Make.miptblas
no more.
