[SciPy-user] undefined symbol: clapack_sgesv

David Cournapeau david@ar.media.kyoto-u.ac...
Sat Feb 9 05:55:15 CST 2008


Stefan van der Walt wrote:
> Hi all,
>
> I am having some trouble compiling and running scipy (latest SVN).
> When I try to import scipy.linalg, I see
>
> ImportError: /home/stefan/lib/python2.5/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv
>
> I then investigated clapack_sgesv with ldd:
>
> $ ldd /home/stefan/lib/python2.5/site-packages/scipy/linalg/clapack.so
>         linux-gate.so.1 =>  (0xffffe000)
>         libf77blas.so.3 => /usr/lib/sse2/libf77blas.so.3 (0xb79e3000)
>         libcblas.so.3 => /usr/lib/sse2/libcblas.so.3 (0xb74d5000)
>         libatlas.so.3 => /usr/lib/sse2/libatlas.so.3 (0xb6f2c000)
>         liblapack.so.3 => /usr/lib/atlas/sse2/liblapack.so.3 (0xb68dc000)
>         libg2c.so.0 => /usr/lib/libg2c.so.0 (0xb68b5000)
>         libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb6890000)
>         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb6885000)
>         libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb6736000)
>         libblas.so.3 => /usr/lib/atlas/sse2/libblas.so.3 (0xb6159000)
>         /lib/ld-linux.so.2 (0x80000000)
>
> And
>
> $ nm /usr/lib/atlas/sse2/liblapack.a | grep clapack_sgesv
> clapack_sgesv.o:
> 00000000 T clapack_sgesv
Not that it should matter since it looks like you are using atlas 
packaged by debian, but what does ldd says for liblapack.so ?
>
> I believe I am missing something obvious, and I hope someone can point
> it out.  I also tried modifying my site.cfg to include
>
> [blas_opt]
> libraries = ptf77blas, ptcblas, lapack_atlas
>
> [lapack_opt]
> libraries = lapack-3, ptf77blas, ptcblas, lapack_atlas
>
> (the scipy.cfg example says [atlas] is deprecated)
>
> but it doesn't look like anything is linked against lapack_atlas.
You don't care about that, because debian packages atlas in a clever 
way: libblas.so and liblapack.so are drop-in replacements for netlib 
blas and lapack, but with ATLAS as an implementation.

cheers,

David


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