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

Diederik van Liere dvanliere@gmail....
Mon Mar 8 23:06:49 CST 2010


> 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.

The console output does not give any errors as far as I can tell.

Import scipy in python does work.

> Also, the output of ldd on clapack.so may be useful.
The output of ldd looks suspect (I compared it to other posts):

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)

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


How can I prevent starting a new thread every time?

Best,

Diederik
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