Undefined symbol: clapack_sgesv when doing import in Python
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
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 -fPIC 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: [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
Looks good. -- Enjoy global warming while it lasts.
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