[petsc-users] converting scipy sparse CSR matrix to petcs matrix with mpi

[John Travers]

On 28 Aug 2013, at 14:58, Jed Brown <jedbrown at mcs.anl.gov> wrote:
> John Travers <jtravs at gmail.com> writes:
> 
>> Hi,
>> 
>> I currently generate PETSc matrices from scipy.sparse CSR format matrices as follows (where A is a scipy sparse CSR matrix):
>> 
>> pA = PETSc.Mat().createAIJ(size=A.shape, csr=(A.indptr, A.indices, A.data)) 
>> 
>> This work correctly on sequential runs, but if I run under MPI I get an error which I presume to be caused by the fact that all of my MPI processes try to simultaneously create this matrix, rather than splitting it? Eg. for 4 processes I get:
> 
> Yeah, the size of the passed CSR part doesn't match the local size of
> the matrix.  I think that given a range [rstart,rend), you can pass
> 
>  csr=(A.indptr[rstart:rend] - A.indptr[rstart],
>       A.indices[A.indptr[rstart]:A.indptr[rend]],
>       A.data[A.indptr[rstart]:A.indptr[rend]])
> 

Thanks, this works (except it should be A.indptr[rstart:rend+1] in the first line I think).

> More simply, you can just create the matrix and loop over rows calling
> MatSetValues, but you have to do half of the spec above to set the
> number of nonzeros per row if you want it to be fast.
> 
> Do you have to start with redundantly-computed scipy matrices?  (That'll
> be a scalability bottleneck.  It's usually important to distribute
> computation of the matrix entries unless you're only trying to use a few
> cores.)

Well, not in the long run, but at the moment that code is debugged and working and I only wanted to try the slepc solvers first.