[SciPy-User] Compiling scipy.sparse.sparsetools extension throws g++ internal error

Agile Aspect agile.aspect@gmail....
Tue Mar 9 15:34:39 CST 2010


On Mon, Mar 8, 2010 at 9:15 PM, David Cournapeau <david@silveregg.co.jp> wrote:
> Diederik van Liere wrote:
>>> Diederik van Liere wrote:
>>
>>>> * *>>* ImportError: /usr/local/lib/python2.6/site-packages/scipy/linalg/clapack.so:*>>* undefined symbol: clapack_sgesv*
>>> what is the output of python setup.py config inside scipy build ?
>>
>> I am not quite sure which output you mean, do you mean the console
>> output or a particular log file? I didn't see any log file in
>> particular.
>
> I meant the console output, yes, to see which BLAS/LAPACK is detected.
>
>> ldd /usr/local/lib/python2.6/site-packages/scipy/lib/lapack/clapack.so
>> libgfortran.so.1 => /usr/lib/libgfortran.so.1 (0x00b96000)
>> libm.so.6 => /lib/libm.so.6 (0x00f41000)
>> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00552000)
>> libc.so.6 => /lib/libc.so.6 (0x00110000)
>> /lib/ld-linux.so.2 (0x00e8f000)
>
> This is indeed suspicious. How did you build your Atlas ? It would be
> useful to have the full build output when building scipy.linalg.
>
>>
>> However, Scipy does find the lapack, blas etc as this snippet from the log
>> shows:
>>
>> atlas_threads_info:
>> Setting PTATLAS=ATLAS
>>   libraries lapack_atlas not found in /usr/local/include
>> numpy.distutils.system_info.atlas_threads_info
>> Setting PTATLAS=ATLAS
>> Setting PTATLAS=ATLAS
>>   FOUND:
>>     libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
>>     library_dirs = ['/usr/local/include']
>>     language = f77
>

You should post your site.cfg which is under

  /usr/local/lib/python2.6/site-packages/numpy/distutils/site.cfg


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