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

Agile Aspect agile.aspect@gmail....
Fri Mar 12 10:28:32 CST 2010

On Thu, Mar 11, 2010 at 10:10 AM, Diederik van Liere
<dvanliere@gmail.com> wrote:
>>> 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?

I presume it has to be shared (it's never worked for me otherwise.)

It looks like it might not have been compiled with


which is necessary to build shared libraries.

If you built the libraries from source, you should be able to

   make shared
   make ptshared

which would included the -fPIC compile option and create the shared
libraries for you.

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

Looks good.

      Enjoy global warming while it lasts.

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