sci-libs/arpack fails to detect blas libraries from sci-libs/atlas merge of sci-libs/arpack crashes with: configure: error: Cannot find BLAS libraries USE flags: USE="-doc -examples -mpi -static-libs" bug is present in stable 0.96-r3 and last 3.1.3-r1 (I suppose in all others too) Reproducible: Always Steps to Reproduce: 1. emerge sci-libs/atlas 2. eselect blas set atlas 3. emerge -1 arpack || echo 'Fail :(' Vela ~ # eix -Ic atlas [I] sci-libs/atlas [1] (3.10.1-r1@01/19/2014): Automatically Tuned Linear Algebra Software [1] "science" /var/lib/layman/science Vela ~ # eselect blas list Available providers for blas: [1] atlas * Vela ~ # emerge --info Portage 2.2.7 (default/linux/amd64/13.0/desktop, gcc-4.7.3, glibc-2.17, 3.2.54-gentoo x86_64) ================================================================= System uname: Linux-3.2.54-gentoo-x86_64-Intel-R-_Core-TM-_i3_CPU_M_330_@_2.13GHz-with-gentoo-2.2 KiB Mem: 5907944 total, 3578168 free KiB Swap: 0 total, 0 free Timestamp of tree: Sat, 18 Jan 2014 20:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.5-r3, 3.3.2-r2 dev-util/cmake: 2.8.11.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.12.6, 1.13.4 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.7.3-r1 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.9 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo science octave ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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 -pipe -march=native" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--autounmask-write=y" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://trumpetti.atm.tut.fi/gentoo" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/octave" USE="X a52 aac acl acpi alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cpudetection cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gpm gtk iconv ipv6 jpeg lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds qt3support qt4 readline sdl session spell sse sse2 sse3 sse4_1 ssl ssse3 startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xv xvid zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DRACUT_MODULES="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 ublox ubx" INPUT_DEVICES="evdev keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="ru en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="intel" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
Do you have /usr/lib64/libblas.so present?
(In reply to Justin Lecher from comment #1) > Do you have /usr/lib64/libblas.so present? Oops, I didnt have it. Made symlink /usr/lib64/libblas.so -> /usr/lib64/libptf77blas.so manually and all works. I'm sorry for bad report then :(.
(In reply to lumbrius from comment #2) > Oops, I didnt have it. > Made symlink /usr/lib64/libblas.so -> /usr/lib64/libptf77blas.so manually > and all works. > Having it is wrong. it should work without.
Could you please attach a build.log with /usr/lib64/libblas.so removed?
Created attachment 368282 [details] arpack-3.1.3-r1 build log there it is
Created attachment 368284 [details] config log
There is still a libatlas from an old install in /usr/lib64: /usr/lib64/libatlas.so.3: undefined reference to `pthread_mutex_trylock' /usr/lib64/libatlas.so.3: undefined reference to `pthread_attr_setaffinity_np' /usr/lib64/libatlas.so.3: undefined reference to `ATL_DecAtomicCount' /usr/lib64/libatlas.so.3: undefined reference to `pthread_create' /usr/lib64/libatlas.so.3: undefined reference to `ATL_ResetAtomicCount' /usr/lib64/libatlas.so.3: undefined reference to `ATL_FreeAtomicCount' /usr/lib64/libatlas.so.3: undefined reference to `ATL_SetAtomicCount' /usr/lib64/libatlas.so.3: undefined reference to `pthread_join' You need to remove that too.
Actually I am wrong libatlas is ok to be there. But your threaded atlas is missing some symbols. Did you emerge atlas with the thread useflag?
OK got it too. It looks like even if you compile atlas without threads, the symbols for threaded atlas are still put in libatlas: ldd -r /usr/lib64/libatlas.so.3 linux-vdso.so.1 (0x00007fffbcb4c000) libm.so.6 => /lib64/libm.so.6 (0x00007fbde01a0000) libc.so.6 => /lib64/libc.so.6 (0x00007fbddfdf3000) /lib64/ld-linux-x86-64.so.2 (0x00007fbde0da2000) undefined symbol: ATL_DecAtomicCount (/usr/lib64/libatlas.so.3) undefined symbol: ATL_ResetAtomicCount (/usr/lib64/libatlas.so.3) undefined symbol: pthread_mutex_trylock (/usr/lib64/libatlas.so.3) undefined symbol: pthread_join (/usr/lib64/libatlas.so.3) undefined symbol: pthread_create (/usr/lib64/libatlas.so.3) undefined symbol: pthread_attr_setaffinity_np (/usr/lib64/libatlas.so.3) undefined symbol: ATL_FreeAtomicCount (/usr/lib64/libatlas.so.3) undefined symbol: ATL_SetAtomicCount (/usr/lib64/libatlas.so.3) so people with hardware supporting threading and building atlas without threads all get that, at least.
Yes, alas was emerged without threads. With threads enabled, arpack compiles fine.
No longer in sci overlay
