[Numpy-discussion] wired error message in scipy.sparse.eigen function: Segmentation fault
David Cournapeau
cournape@gmail....
Fri Feb 5 01:22:57 CST 2010
On Thu, Jan 28, 2010 at 3:11 PM, David Cournapeau <david@silveregg.co.jp> wrote:
> Jankins wrote:
>> Yes. I am using scipy.sparse.linalg.eigen.arpack.
>>
>> The exact output is:
>>
>> /usr/local/lib/python2.6/dist-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so
>
> I need the output of ldd on this file, actually, i.e the output of "ldd
> /usr/local/lib/python2.6/dist-packages/scipy/sparse/linalg/eigen/arpack/_arpack.so".
> It should output the libraries actually loaded by the OS.
>
>> In fact, the matrix is from a directed graph with about 18,000 nodes and
>> 41,000 edges. Actually, this matrix is the smallest one I used.
>
> Is it available somewhere ? 41000 edges should make the matrix very
> sparse. I first thought that your problem may be some buggy ATLAS, but
> the current arpack interface (the one used by sparse.linalg.eigen) is
> also quite buggy in my experience, though I could not reproduce it.
> Having a matrix which consistently reproduce the bug would be very useful.
Ok, I took a look at it, and unfortunately, it is indeed most likely
an ATLAS problem. I get crashes when scipy is linked against Atlas
(v3.8.3), but if I link against plain BLAS/LAPACK, I don't get any
crash anymore (and valgrind does not complain).
I will try with a recent development from atlas,
cheers,
David
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