Hi Sébastien,
I was trying to use acml to avoid compiling blas-atlas (it takes about 2
hours and I don't really need it right now. Also numpy and scipy are not
supposed to require it.
Note: This is on a new installation, some binaries came from the Gentoo
2006.1 stage3 tarball.
I tried compiling atlas, with the following error:
"libgfortran.so: could not read symbols: File in wrong format"
Here is the output from emerge:
gcc -shared .libs/libatlas.la-3.o -lpthread
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/32/libgfortran.so -Wl,-soname
-Wl,libatlas.so.0 -o .libs/libatlas.so.0.0.0
/usr/lib/gcc/x86_64-pc-linux-gnu/4.1.1/32/libgfortran.so: could not read
symbols: File in wrong format
collect2: ld returned 1 exit status
libtool: install: `libatlas.la' is not a valid libtool archive
Try `libtool --help --mode=install' for more information.
make[1]: *** [libatlas.so] Error 1
make[1]: Leaving directory
`/var/tmp/portage/sci-libs/blas-atlas-3.7.11/work/ATLAS'
make: *** [shared-strip] Error 2
!!! ERROR: sci-libs/blas-atlas-3.7.11 failed.
Call stack:
ebuild.sh, line 1614: Called dyn_compile
ebuild.sh, line 971: Called qa_call 'src_compile'
environment, line 3741: Called src_compile
blas-atlas-3.7.11.ebuild, line 132: Called die
Here is output from emerge --info:
plum ~ # emerge --info
Portage 2.1.2-r9 (default-linux/amd64/2006.1, gcc-4.1.1, glibc-2.5-r0,
2.6.19-gentoo-r5 x86_64)
=================================================================
System uname: 2.6.19-gentoo-r5 x86_64 AMD Athlon(tm) 64 Processor 3000+
Gentoo Base System version 1.12.1
Timestamp of tree: Sun, 25 Feb 2007 01:00:08 +0000
dev-lang/python: 2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox: 1.2.17
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: 2.16.1-r3
sys-devel/gcc-config: 1.3.14
sys-devel/libtool: 1.5.22
virtual/os-headers: 2.6.17-r1
ACCEPT_KEYWORDS="amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=athlon64 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo"
CXXFLAGS="-march=athlon64 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.datapipe.net/gentoo
ftp://mirror.datapipe.net/gentoo http://gentoo.mirrors.tds.net/gentoo
http://64.158.56.55 ftp://gentoo.mirrors.tds.net/gentoo";
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times
--compress --force --whole-file --delete --delete-after --stats
--timeout=300 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /usr/local/sci"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 apache2 berkdb bitmap-fonts cli cracklib crypt cups doc dri
dvdread fortran gdbm gpm iconv ipv6 isdnlog libg++ midi mysql ncurses
nls nptl nptlonly pam pcre perl ppds pppd python readline reflection
session spl ssl tcpd truetype-fonts type1-fonts unicode usb wxwindows
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="fglrx
radeon vesa fbdev"
Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL,
LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS
Bill
Sébastien Fabbro wrote:
Hi Bill,
You should report on bugs.gentoo.org.
First make sure you synced your portage tree.
Then see which cblas you have chosen with eselect show cblas.
If it shows reference, atlas or threaded-atlas, and you still cannot get
numpy to compile, then file a bug on the site above with en emerge
--info, and I will see what I can do. acml needs more work, and is not
yet supported by the ebuilds.
Sebastien
Bill Dandreta wrote:
I cannot get Numpy, Scipy to compile. Cblas error.
Compiling source in
/var/tmp/portage/dev-python/numpy-1.0.1-r1/work/numpy-1.0.1 ...
!!! Error: Can't load module cblas
* You need to set cblas to atlas or reference. Do:
* eselect cblas set <impl>
* where <impl> is atlas, threaded-atlas or reference
!!! ERROR: dev-python/numpy-1.0.1-r1 failed.
Call stack:
ebuild.sh, line 1614: Called dyn_compile
ebuild.sh, line 971: Called qa_call 'src_compile'
environment, line 3970: Called src_compile
numpy-1.0.1-r1.ebuild, line 123: Called numpy_configure
numpy-1.0.1-r1.ebuild, line 38: Called die
eselect cblas set <anything>
gives:
!!! Error: Can't load module cblas
Killed
After:
emerge -av eselect-cblas
Compiling source in
/var/tmp/portage/dev-python/numpy-1.0.1-r1/work/numpy-1.0.1 ...
* You need to set cblas to atlas or reference. Do:
* eselect cblas set <impl>
* where <impl> is atlas, threaded-atlas or reference
!!! ERROR: dev-python/numpy-1.0.1-r1 failed.
Call stack:
ebuild.sh, line 1614: Called dyn_compile
ebuild.sh, line 971: Called qa_call 'src_compile'
environment, line 3970: Called src_compile
numpy-1.0.1-r1.ebuild, line 123: Called numpy_configure
numpy-1.0.1-r1.ebuild, line 38: Called die
!!! setup failed
!!! If you need support, post the topmost build error, and the call
stack if relevant.
!!! A complete build log is located at
'/var/tmp/portage/dev-python/numpy-1.0.1-r1/temp/build.log'.
I tried setting cblas to acml but I cannot get it to work.
Any suggestions??
Bill
