[Numpy-discussion] wired error message in scipy.sparse.eigen function: Segmentation fault
David Cournapeau
david at silveregg.co.jp
Thu Jan 28 01:11:25 EST 2010
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.
In the short term, you may want to do without arpack support in scipy.
In the longer term, I intend to improve support for sparse matrices
linear algebra, as it is needed for my new job.
> Now I switch to use numpy.linalg.eigvals, but it is slower than
> scipy.sparse.linalg.eigen.arpack module.
If you have a reasonable ATLAS install, scipy.linalg.eigvals should
actually be quite fast. Sparse eigenvalues solver are much slower than
full ones in general as long as:
- your matrices are tiny (with tiny defined here as the plain matrix
requiring one order of magnitude less memory than the total available
memory, so something like matrices with ~ 1e7/1e8 entries on current
desktop computers)
- you need more than a few eigenvalues, or not just the
biggest/smallest ones
cheers,
David
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