[gentoo-science] Cblas, Numpy, Scipy

[gentoo-science] Cblas, Numpy, Scipy

[Bill Dandreta]

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
-- 
gentoo-science@gentoo.org mailing list

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

[Sébastien Fabbro]

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

-- 
gentoo-science@gentoo.org mailing list

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

[Bill Dandreta]

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

[Sébastien Fabbro]

Hi Bill,

Once again, please report on bugs.gentoo.org.

> 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.

You can disable the USE flag lapack if you don't want to rely on
external cblas or lapack libraries on numpy. For scipy, as far as I
know, you need blas/lapack external libraries. If don't want to wait the
full ATLAS full compilation, you can emerge the
{blas,cblas,lapack}-reference. These are not as speed-optimized as
ATLAS, but a lot faster and more robust to build.
Make sure you have a cblas implementation supporting the eselect format,
as required by dev-python/numpy-1.0.1-r1.

> 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


I can't reproduce your failing blas-atlas (which should be at least
blas-atlas-3.7.11-r1 for numpy-1.0.1-r1). It looks it mixes 32 and 64
profiles.
If it persists, once again, please file a bug regarding blas-atlas on
bugs.gentoo.org.

Sébastien
-- 
gentoo-science@gentoo.org mailing list

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

[Bill Dandreta]

Sébastien Fabbro wrote:
>> 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
>>     
>
>
> I can't reproduce your failing blas-atlas (which should be at least
> blas-atlas-3.7.11-r1 for numpy-1.0.1-r1). It looks it mixes 32 and 64
> profiles.
> If it persists, once again, please file a bug regarding blas-atlas on
> bugs.gentoo.org.
>
> Sébastien
>   
Hi Sébastien,

I ran revdep-rebuild and emerged glibc and gcc than blas-atlas compiled OK.

Bill
-- 
gentoo-science@gentoo.org mailing list

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

[Bill Dandreta]

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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.
Hi Sébastien,

I cannot get eselect cblas to work.

I will have to look into it when I get more time.

I had posted my problem in the Gentoo forums before I posted to this 
mailing list. I got a response there that helped me get numpy to 
compile. The post 
<http://forums.gentoo.org/viewtopic.php?p=3936858#3936858> says there is 
a bug in the ebuild.

Bill


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