[Numpy-discussion] atlas not found, why?

T J tjhnson@gmail....
Fri Nov 7 03:58:32 CST 2008


On Fri, Nov 7, 2008 at 1:26 AM, David Cournapeau
<david@ar.media.kyoto-u.ac.jp> wrote:
> David Cournapeau wrote:
>>
>> Ok, I took a brief look at this: I forgot that Ubuntu and Debian added
>> an aditional library suffix to libraries depending on gfortran ABI. I
>> added support for this in numpy.distutils - which was looking for
>> libraries explicitly; could you retry *without* a site.cfg ? It
>> should work, now,
>>
>
> And it won't, because I am afraid the Ubuntu atlas package is broken in
> 8.10... They use the gfortran  ABI, but they built the fortran wrappers
> with g77, according to ATL_buildinfo.
>
> https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/295051
>
> I would strongly advise using atlas on Ubuntu 8.10 until this bug is
> solved: it means any numpy/scipy code using linear algebra is
> potentially broken (segfault, wrong results).
>

Intended:
   '''I would strongly advise *against* using atlas on Ubuntu 8.10.'''   :-)

That the fortran wrappers were compiled using g77 is also apparent via
what is printed out during setup when ATLAS is detected:

gcc -pthread _configtest.o -L/usr/lib/atlas -llapack -lblas -o _configtest
ATLAS version 3.6.0 built by root on Fri Jan  9 15:57:20 UTC 2004:
   UNAME    : Linux intech67 2.4.20 #1 SMP Fri Jan 10 18:29:51 EST
2003 i686 GNU/Linux
   INSTFLG  :
   MMDEF    : /fix/g/camm/atlas3-3.6.0/CONFIG/ARCHS/P4SSE2/gcc/gemm
   ARCHDEF  : /fix/g/camm/atlas3-3.6.0/CONFIG/ARCHS/P4SSE2/gcc/misc
   F2CDEFS  : -DAdd__ -DStringSunStyle
   CACHEEDGE: 1048576
   F77      : /usr/bin/g77, version GNU Fortran (GCC) 3.3.3 20031229
(prerelease) (Debian)
   F77FLAGS : -fomit-frame-pointer -O
   CC       : /usr/bin/gcc, version gcc (GCC) 3.3.3 20031229
(prerelease) (Debian)
   CC FLAGS : -fomit-frame-pointer -O3 -funroll-all-loops
   MCC      : /usr/bin/gcc, version gcc (GCC) 3.3.3 20031229
(prerelease) (Debian)
   MCCFLAGS : -fomit-frame-pointer -O
success!

And the problem with this, as you've mentioned before, is that g77 and
gfortran are not abi compatible.  But isn't this issue separate from
the autodetection of atlas without a site.cfg?  With r5986, atlas is
still only detected if I declare ATLAS:

$ ATLAS=/usr/lib python setup.py build

versus

$ unset ATLAS; python setup.py build


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