when emerging scilab-4.1 on amd64, I seem to get a large number of missing symbols in /usr/lib64/libcblas.so and /usr/lib64/liblapack.so. Checking the given files confirms that the symbols are undefined. Reproducible: Always Steps to Reproduce: 1.emerge scilab 2. 3. Actual Results: make[1]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/ocaml' linking /var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/libs/xsci.a(x_misc.o): In function `SysErrorM x_misc.c:(.text+0x113): warning: `sys_errlist' is deprecated; use `strerror' or `strerror_r' instead x_misc.c:(.text+0x106): warning: `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead /var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/libs/system.a(scicurdir.o): In function `scig scicurdir.c:(.text+0x24): warning: the `getwd' function is dangerous and should not be used. /var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/libs/os_specific.a(link.o): In function `Crea link.c:(.text+0x491): warning: the use of `mktemp' is dangerous, better use `mkstemp' /usr/lib64/liblapack.so: undefined reference to `cblas_dswap' /usr/lib64/liblapack.so: undefined reference to `cblas_ssyrk' /usr/lib64/liblapack.so: undefined reference to `cblas_icamax' /usr/lib64/libcblas.so: undefined reference to `do_lio' /usr/lib64/libcblas.so: undefined reference to `e_wsle' /usr/lib64/liblapack.so: undefined reference to `cblas_isamax' /usr/lib64/liblapack.so: undefined reference to `cblas_izamax' /usr/lib64/liblapack.so: undefined reference to `cblas_dsyrk' /usr/lib64/libcblas.so: undefined reference to `e_wsfe' /usr/lib64/libcblas.so: undefined reference to `z_abs' /usr/lib64/liblapack.so: undefined reference to `cblas_cgemm' /usr/lib64/liblapack.so: undefined reference to `cblas_strsm' /usr/lib64/libcblas.so: undefined reference to `c_sqrt' /usr/lib64/liblapack.so: undefined reference to `cblas_cscal' /usr/lib64/liblapack.so: undefined reference to `cblas_dtrsm' /usr/lib64/liblapack.so: undefined reference to `cblas_dtrmm' /usr/lib64/libcblas.so: undefined reference to `s_cmp' /usr/lib64/libcblas.so: undefined reference to `z_exp' /usr/lib64/liblapack.so: undefined reference to `cblas_dgemm' /usr/lib64/liblapack.so: undefined reference to `cblas_zherk' /usr/lib64/libcblas.so: undefined reference to `e_rsfi' /usr/lib64/liblapack.so: undefined reference to `cblas_cherk' /usr/lib64/liblapack.so: undefined reference to `cblas_ztrmm' /usr/lib64/libcblas.so: undefined reference to `c_exp' /usr/lib64/liblapack.so: undefined reference to `cblas_sscal' /usr/lib64/libcblas.so: undefined reference to `i_indx' /usr/lib64/liblapack.so: undefined reference to `cblas_ztrsm' /usr/lib64/liblapack.so: undefined reference to `cblas_cswap' /usr/lib64/liblapack.so: undefined reference to `cblas_sgemm' /usr/lib64/libcblas.so: undefined reference to `s_rsfi' /usr/lib64/libcblas.so: undefined reference to `do_fio' /usr/lib64/libcblas.so: undefined reference to `z_sqrt' /usr/lib64/libcblas.so: undefined reference to `e_wsfi' /usr/lib64/libcblas.so: undefined reference to `s_cat' /usr/lib64/liblapack.so: undefined reference to `cblas_ctrmm' /usr/lib64/libcblas.so: undefined reference to `s_stop' /usr/lib64/libcblas.so: undefined reference to `s_wsfi' /usr/lib64/liblapack.so: undefined reference to `cblas_strmm' Expected Results: no linking errors, and a successful install [ebuild U ] sci-mathematics/scilab-4.1 [2.7-r3] USE="Xaw3d%* ocaml%* tk%* -debug% -gtk -java% (-X%*) (-ifc%) (-tcltk%)" 0 kB emerge --info Portage 2.1.2.3 (default-linux/amd64/2006.1, gcc-4.1.2, glibc-2.5-r1, 2.6.18-gentoo-r1 x86_64) ================================================================= System uname: 2.6.18-gentoo-r1 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ Gentoo Base System release 1.12.10 Timestamp of tree: Sat, 14 Apr 2007 03:20:01 +0000 dev-java/java-config: 1.3.7, 2.0.31-r5 dev-lang/python: 2.4.4 dev-python/pycrypto: 2.0.1-r5 sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.61 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.17 sys-devel/gcc-config: 1.3.15-r1 sys-devel/libtool: 1.5.23b virtual/os-headers: 2.6.20-r2 ACCEPT_KEYWORDS="amd64 ~amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=athlon64 -O3 -pipe -fomit-frame-pointer -fgcse-las -fgcse-sm" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://gentoo.llarian.net/ http://gentoo.mirrors.pair.com" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/stuart-server /usr/portage/local/layman/sunrise /usr/portage/local/layman/chtekk-syscp /usr/portage/local/layman/science /usr/portage/local/layman/mozilla /usr/portage/local/layman/emacs /usr/portage/local/layman/stuart-desktop /usr/portage/local/layman/haskell /usr/portage/local/layman/pro-audio /usr/portage/local/layman/common-lisp /usr/portage/local/layman/xeffects /usr/portage/local/layman/wschlich-testing /usr/portage/local/layman/wschlich /usr/portage/local/layman/wrobel /usr/local/portage" SYNC="rsync://192.168.0.1/gentoo-portage" USE="64bit X aac aalib aiglx alsa amd64 auctex bcmath berkdb binary-drivers bitmap-fonts blas blender-game cairo cblas cdrw cli clisp clock-screen cluster colordiff cracklib crosscompile crypt cups directfb divx dmx dri dvd esd ffmpeg fftw figlet firefox flac fortran fortran95 fping gcj gcl gd gdbm gimp ginac glgd glut gmedia gmp gpm graphviz gs guile iconv imagemagick ipv6 isdnlog jack key-screen lame lapack ldb libcaca libedit libg++ mad mastroka matroska midi mp3 mp4 mpe-sdk mpeg mplayer mupad-noscilab musepack nas ncurses netboot netjack network nis nls nptl nptlonly nvidia objc objc++ objc-gc ocaml octave offensive ogg opengl pam pcre perl ppds pppd python qhull readline realmedia reflection sbcl screen scsh sdl search-screen server session shorten slang smp spl ssl tcpd tetex theora threads truetype-fonts type1-fonts unicode usb vorbis wavpack wmp x11vnc x264 xfs xorg zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Hi Marty, What cblas/lapack are you using on your system and could you please post the output of ldd /usr/lib64/libcblas.so ldd /usr/lib64/liblapack.so Could you please recompile both of them using CFLAGS/FFLAGS="-march=athlon64 -O2 -pipe" and try again. Thanks, Markus
(In reply to comment #1) > Hi Marty, > > What cblas/lapack are you using on your system When I was attempting to compile scilab, I was using acml for both. > and could you please > post the output of > ldd /usr/lib64/libcblas.so libacml_mv.so => /usr/lib/libacml_mv.so (0x00002ad1c1dd7000) libc.so.6 => /lib/libc.so.6 (0x00002ad1c1f07000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) > ldd /usr/lib64/liblapack.so libacml_mv.so => /usr/lib/libacml_mv.so (0x00002b44e5552000) libc.so.6 => /lib/libc.so.6 (0x00002b44e5682000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) Seeing that they were both linked to libacml, I tried switching both settings to atlas. It gave similar link errors with /usr/lib/libacml.so. unmerging acml resulted in the following error (scilab doesn't depend on acml. This shouldn't happen.) Since acml isn't compiled, I can't imagine that changing CFLAGS would have any effect. Not that I think it will have any affect, I'm currently recompiling every blas/lapack implementation with sane use flags. I'll post the results when that's done in a few hours. Here are the results of running ldd on all of the .so's from acml. A side note, there's a new acml out. I'll try making an ebuild for it. libacml_mv.so => /usr/lib/libacml_mv.so (0x00002ac586918000) libc.so.6 => /lib/libc.so.6 (0x00002ac586a48000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) libc.so.6 => /lib/libc.so.6 (0x00002b86eff7a000) /lib64/ld-linux-x86-64.so.2 (0x0000555555554000) Creating html help files /var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/bin/scilab -l eng \ -nwni -e "xmltohtml([],[],'html-rev.xsl');quit" -args -nouserstartup /var/tmp/portage/sci-mathematics/scilab-4.1/work/scilab-4.1/bin/scilex: error while loading shared libraries: libacml.so: cannot open shared object file: No such file or directory
(In reply to comment #2) > to atlas. It gave similar link errors with /usr/lib/libacml.so. unmerging > acml resulted in the following error (scilab doesn't depend on acml. This > shouldn't happen.) Since acml isn't compiled, I can't imagine that changing scilab depends on virtual/blas and virtual/lapack which acml provides, hence there is not problem here. Your issue is due to acml not scilab as far as I can tell and if recompiling/installing doesn't help we should probably file this as an acml bug so the developer in charge of acml can have a look. Thanks, Markus
Has this problem been solved or is it still an issue? Thanks, Markus
I get something similar with scilab-4.1.2: again, a linker error. The exact error is ### SNIPPET ### make[3]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/pvm3/pvmgs/LINUX' done building group server and library make[2]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/pvm3' make[1]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/pvm3' linking gfortran: /usr/lib/liblapack.so: No such file or directory make: *** [bin/scilex] Error 1 ### END SNIPPET ### I must say that this happens on a system that had emerge -uDN world and revdep-rebuild run on it and then repeated. Reproducible: always Steps: emerge scilab Portage says I should provide this: GENTOO_VM=sun-jdk-1.6 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.04" JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="" Plus, emerge --info: Portage 2.1.4 (default-linux/x86/2007.0/desktop, gcc-4.2.2, glibc-2.7-r1, 2.6.24-gentoo i686) ================================================================= System uname: 2.6.24-gentoo i686 Intel(R) Pentium(R) 4 CPU 3.20GHz Timestamp of tree: Thu, 31 Jan 2008 02:00:01 +0000 app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.4 dev-lang/python: 2.5.1-r5 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.24 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -pipe -finline-functions" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -march=pentium4 -pipe -finline-functions" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="" FEATURES="distlocks fixpackages metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://ftp.belnet.be/mirror/rsync.gentoo.org/gentoo/ http://gentoo.mirror.icd.hu/ http://www.gigaload.org/gentoo.org/ http://ftp.easynet.nl/mirror/gentoo/ http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo" LANG="en_US" LC_ALL="en_US.utf8" LINGUAS="en sl" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/xeffects /usr/portage/local/layman/d /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac aalib acl acpi alsa asf bash-completion berkdb bidi bitmap-fonts browserplugin bzip2 cairo ccache cddb cdr cdrom cjk cli cracklib crypt css cups curl dba dbus directfb divx4linux dlloader dri dts dvd dvdr dvdread eds encode evo fam fame fbcon ffmpeg firefox flac fortran freetype ftp gd gdbm gif gimpprint gkrellm glx gpm gstreamer gtk gtk2 hal iconv imap isdnlog jack java javascript jikes jpeg kde kdeenablefinal kdexdeltas kerberos ldap libcaca live logitech-mouse mad maildir matroska midi mikmod mime mmap mmx mmxext mozilla mp3 mp4 mpeg mplayer mtrr mudflap musepack musicbrainz nas ncurses nls no-old-linux nptl nptlonly nsplugin nvidia ogg oggvorbis opengl openmp opera pam pcre pdf perl pic png pppd python qt qt3 qt3support qt4 quicktime readline reflection sblive screen sdl session skins sndfile spell spl sse sse2 ssl stream subtitles subversion svg tcpd tga theora threads tiff truetype truetype-fonts type1-fonts unicode usb utf8 vcd vim-syntax vorbis win32codecs wmf x x86 xcomposite xml xml2 xorg xpm xv xvid zlib" ALSA_CARDS="emu10k1" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter 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 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" APACHE2_MPMS="worker" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en sl" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ### END EMERGE --INFO ###
Please try using eselect lapack list to list all available lapack packages on your system and then eselect lapack set <some lapack package> to select one of them. There should now be a symbolic link /usr/lib/liblapack.so and scilab should compile. Thanks, Markus
Has this issue been resolved or does it persist? Thanks, Markus
Have 4.1.2 happily installed (which means it compiled)... eix says: Installed versions: 4.1.2(09:33:42 PM 01/31/2008)(gtk java -Xaw3d -debug -elibc_FreeBSD -ocaml) Guess upstream fixed it... Cheers, G
Great, thanks! Closing this one then .... cheers, Markus
