'emerge -uvDN atlas' fails with: ... BEGIN BASIC KERNEL TESTS: Kernel dmvn_C.c(900000) passes basic test DONE BASIC KERNEL TESTS: BEGIN L1-BLOCKED TUNING 900001:dmvn_C.c (M=2300, N=2000, lda=2303) gets 177.03 MFLOPS 1make[3]: *** [res/dMVNK.sum] Segmentation fault make[3]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.49/work/ATLAS_shared/tune/blas/gemv' make[2]: *** [/var/tmp/portage/sci-libs/atlas-3.9.49/work/ATLAS_shared/tune/blas/gemv/res/dMVNK.sum] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/atlas-3.9.49/work/ATLAS_shared/bin' ERROR 914 DURING MVNTUNE!!. CHECK INSTALL_LOG/dMVNTUNE.LOG FOR DETAILS. Perhaps it is related to Bug 382547, even if the error output is not identical. Reproducible: Always root@inspironM12:/root(15)# emerge --info =sci-libs/atlas-3.9.49 Portage 2.1.10.15 (default/linux/x86/10.0/desktop, gcc-4.5.3, glibc-2.13-r4, 3.0.3-gentoo i686) ================================================================= System Settings ================================================================= System uname: Linux-3.0.3-gentoo-i686-Intel-R-_Atom-TM-_CPU_Z520_@_1.33GHz-with-gentoo-2.0.3 Timestamp of tree: Tue, 13 Sep 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: 0.9.3-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 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/dconf /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 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 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 mplayer mtp mudflap 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 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 tools truetype udev unicode usb userlocales utempter v4l2 vaapi virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 x86 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" 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:/root(16)# emerge -pqv =sci-libs/atlas-3.9.49 [ebuild U ] sci-libs/atlas-3.9.49 [3.9.47] USE="doc fortran lapack threads -static-libs"
Created attachment 286303 [details] /var/tmp/portage/sci-libs/atlas-3.9.49/work/ATLAS_shared/bin/INSTALL_LOG/dMVNTUNE.LOG
Created attachment 286305 [details] gzipped /var/tmp/portage/sci-libs/atlas-3.9.49/temp/build.log
This issue blocks several packages: root@inspironM12:/root(8)# emerge -pvuND world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-libs/atlas-3.9.49 [3.9.47] USE="doc fortran lapack threads -static-libs" 0 kB [1] [ebuild N ] sci-libs/umfpack-5.5.1 USE="doc -metis -static-libs" 0 kB [0] [ebuild N ] sci-libs/cholmod-1.7.3 USE="doc supernodal -metis -minimal -static-libs" 0 kB [0] [ebuild N ] sci-libs/arpack-96-r3 USE="doc examples mpi -static-libs" 0 kB [0] [ebuild N ] sci-chemistry/apbs-1.3-r1 USE="arpack doc openmp python tools -fetk -mpi" 0 kB [0] [ebuild U ] sci-visualization/veusz-1.13 [1.12] USE="doc examples fits" 0 kB [0] [ebuild N ] sci-chemistry/pdb2pqr-1.7.0-r1 USE="doc examples pdb2pka -opal" 0 kB [0] [ebuild N ] sci-mathematics/octave-3.4.0-r2 USE="curl doc fftw readline sparse zlib -test" 0 kB [0] Is there any workaround? Regards
(In reply to comment #3) > This issue blocks several packages: > > root@inspironM12:/root(8)# emerge -pvuND world > > These are the packages that would be merged, in order: > > Calculating dependencies... done! <snip> > > Is there any workaround? > > Regards What about eselecting another blas/cblas/lapack. Why can't you use 3.8.4? I said it in other forums before 3.9.xx is buggy anyway (dgemm dgemv seem to give bad stuff in some cases)
Thanks Francois for the hint. After masking >sci-libs/atlas-3.8.4 I could emerge atlas and the depending packages.
Still present in 3.10.0?
gone long time ago
