[SciPy-User] Undefined symbol: clapack_sgesv when doing import in Python

Diederik van Liere dvanliere@gmail....
Thu Mar 11 12:10:14 CST 2010


>> ImportError:
/usr/local/lib/python2.6/site-packages/scipy/linalg/clapack.so:
>> undefined symbol: clapack_sgesv


> You should use nm to check for the symbol in your ATLAS libraries to
> see if it's really missing or if numpy just can't find it.

> Try

> nm -A  /usr/local/atlas/lib/lib*.so | grep clapack_sgesv

> or just

> nm liblapack.so | grep clapack_sgesv

This is my output:
liblapack.a:clapack_sgesv.o:00000000 r .LC0
liblapack.a:clapack_sgesv.o:00000000 r .LC1
liblapack.a:clapack_sgesv.o:0000002c r .LC2
liblapack.a:clapack_sgesv.o:0000005c r .LC3
liblapack.a:clapack_sgesv.o:00000090 r .LC4
liblapack.a:clapack_sgesv.o:000000b8 r .LC5
liblapack.a:clapack_sgesv.o:         U ATL_sgetrf
liblapack.a:clapack_sgesv.o:         U ATL_sgetrs
liblapack.a:clapack_sgesv.o:         U _GLOBAL_OFFSET_TABLE_
liblapack.a:clapack_sgesv.o:00000000 T __i686.get_pc_thunk.bx
liblapack.a:clapack_sgesv.o:         U cblas_xerbla
liblapack.a:clapack_sgesv.o:00000000 T clapack_sgesv

I don't have .so files, I have .a files, could that be an issue? So it looks
that ATLAS is properly compiled, right?

> If the symbol is defined in your ATLAS libraries, then you should post
> your site.cfg from numpy.

My site.cfg from numpy reads:

[DEFAULT]
library_dirs = /usr/local/atlas/lib/
include_dirs = /usr/local/atlas/include/

[blas_opt]
libraries = lapack, f77blas, cblas, atlas

[lapack_opt]
libraries = lapack, f77blas, cblas, atlas


Thanks so much for your patience and help.
Best,

Diederik
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