[SciPy-user] Re: linalg.eig on sparse matrices

H Jansen h.jansen at fel.tno.nl
Thu Jan 22 11:33:37 CST 2004


One may want to have a look at pysparse:

http://people.web.psi.ch/geus/pyfemax/pysparse.html

Could this be a candidate for integration with the scipy package?

-Henk


On Wed, 2004-01-21 at 15:14, José Fonseca wrote:
> Nils,
> 
> On Wed, 21 Jan 2004 10:44:54 +0100, Nils Wagner wrote:
> > Hi all,
> >
> > AFAIK, scipy cannot handle sparse matrices in linalg.eig.
> > A first step might be the conversion from sparse to full format. 
> > I am wondering if there is any tool for this task available ?
> 
> If scipy had support for sparse matrix multiplication (scipy has some
> sparse matrix support, but on CVS only AFAIK) then it would be quite
> straightforward using the ARPACK bindings in
> http://jrfonseca.dyndns.org/work/phd/#arpack . Almost a literal
> translation of MATLAB's 'eigs' M-file into Numeric Python would do.
> 
> > Moreover, It would be great, to have eigs (an interface to ARPACK ) in
> > scipy..
> 
> The most import bit is the availability of a generic sparse matrix and
> the implementation of the basic operations (such as matrix
> multiplication, and matrix factorization). 
> 
> ARPACK is doesn't care about the actual sparse matrix format - it only
> wants a matrix-vector multiplication callback (and in some cases the
> vector mutliplication by the matrix inverse). For all purposes the
> matrix may not even exists fully in memory at any time (I actually used
> this once to determine the eigenvalues of a _full_ covariance matrix of
> a random field with millions of elements since it was cheaper to compute
> the matrix elements every time than to store it fully in memory).
> 
> > Any hint would be appreciated.
> 
> You can see at http://mefriss1.swan.ac.uk/svn/python/Sparse.py a real
> usage example. It implements a _very_ basic sparse matrix class (with
> addition, subtraction, and matrix-vector multiplication), and then the
> linear system solver, and a eigenvalue solver. It uses UMFPACK for
> matrix factorization and another C module - spblastk - for matrix-vector
> multiplication which can be a bottleneck.
> 
> And in case you ask about integrating these ARPACK bindings with scipy:
> I don't see much point until scipy provides sparse matrices support, and
> I already have too much on my plate to take such an endeavor (and not
> much immediate interest either). Perhaps you could take this mater in
> your hands instead...
> 
> I hope this helps.
> 
> Jose Fonseca
> 
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-- 
Henk Jansen <h.jansen at fel.tno.nl>
TNO Physics and Electronics Laboratory


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