[Numpy-discussion] wired error message in scipy.sparse.eigen function: Segmentation fault

Bruce Southey bsouthey at gmail.com
Thu Jan 28 09:46:43 EST 2010

On Thu, Jan 28, 2010 at 12:11 AM, David Cournapeau
<david at 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.
> 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

You are using Atlas version 3.6, perhaps you should upgrade to a more
recent version (3.8.x)?

What version of numpy are you using?
Where did Atlas etc come from?

Did you install both numpy and scipy from scratch (preferably built at
the same time against the same library versions)?
Sometimes removing everything and then rebuilding or reinstalling
everything from scratch can help

Perhaps less of a concern, but since your OS is 32-bit, is everything
32-bit and do you have sufficient memory for the system to run your

After that, the array and code in question is need.


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