[Numpy-discussion] Built Lapack, Atlas from source.... now numpy.linalg.eig() hangs at 100% CPU

Chris Colbert sccolbert@gmail....
Fri Mar 27 09:25:39 CDT 2009


Hey Everyone,

I built Lapack and Atlas from source last night on a C2D running 32-bit
Linux Mint 6.  I ran 'make check' and 'make time' on the lapack build, and
ran the dynamic LU decomp test on atlas. Both packages checked out fine.

Then, I built numpy and scipy against them using the appropriate flags in
site.cfg for the parallel thread atlas libraries. This seems to have worked
properly as numpy.dot() utilizes both cores at 100% on very large arrays. I
have also done id(numpy.dot) and id(numpy.core.multiarray.dot) and verified
that the two ids are different.

So I believe the build went properly. The problem I am having now is that
numpy.linalg.eig (and the eig functions in scipy) hang at 100% CPU and never
returns (no matter the array size). Numpy.test() hung as well, I'm assuming
for this same reason. I have included the configurations below. Any idea
what would cause this?

Thanks!

Chris

Python 2.5.2 (r252:60911, Oct  5 2008, 19:24:49)
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> import scipy
>>> numpy.show_config()
atlas_threads_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    language = f77
    include_dirs = ['/usr/local/atlas/include']

blas_opt_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('NO_ATLAS_INFO', 2)]
    language = c
    include_dirs = ['/usr/local/atlas/include']

atlas_blas_threads_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    language = c
    include_dirs = ['/usr/local/atlas/include']

lapack_opt_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('NO_ATLAS_INFO', 2)]
    language = f77
    include_dirs = ['/usr/local/atlas/include']

lapack_mkl_info:
  NOT AVAILABLE

blas_mkl_info:
  NOT AVAILABLE

mkl_info:
  NOT AVAILABLE

>>> scipy.show_config()
umfpack_info:
  NOT AVAILABLE

atlas_threads_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    language = f77
    include_dirs = ['/usr/local/atlas/include']

blas_opt_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
    language = c
    include_dirs = ['/usr/local/atlas/include']

atlas_blas_threads_info:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    language = c
    include_dirs = ['/usr/local/atlas/include']

lapack_opt_info:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('NO_ATLAS_INFO', 2)]
    language = f77
    include_dirs = ['/usr/local/atlas/include']

lapack_mkl_info:
  NOT AVAILABLE

blas_mkl_info:
  NOT AVAILABLE

mkl_info:
  NOT AVAILABLE
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