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

David Cournapeau david@silveregg.co...
Mon Mar 8 23:15:46 CST 2010


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

I don't know if this linked to our issue, but this PTATLAS=ATLAS seems a 
bit strange, I don't remember having seen it.

> How can I prevent starting a new thread every time?

It is a setting in your email client - are you using email or something 
else to post ?

David


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