[SciPy-user] undefined symbol: clapack_sgesv

Stefan van der Walt stefan@sun.ac...
Fri Feb 8 19:20:58 CST 2008


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

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.

Any ideas?

Regards
Stéfan


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