Re: [gentoo-science] Cblas, Numpy, Scipy

[Bill Dandreta <wjdandreta@att.net>]

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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
>>     
>
>   


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