[SciPy-user] undefined symbol: clapack_sgesv
David Cournapeau
david at ar.media.kyoto-u.ac.jp
Sat Feb 9 06:55:15 EST 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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