[petsc-users] Calculate only the diagonal elements for matrix matrix multiplications

[ehsan sadrfaridpour]

Thanks a lot.

Best,
Ehsan

On Wed, Jun 22, 2016 at 5:01 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>    Say you want to compute the diagonal of A * B where A and B are PETSc
> SeqAIJ matrices. If we use "MATLAB" notation A(i,:) to represent the ith
> row of A and B(:,j) to represent the nth column of B then you are
> computing  for each i A(i,:) * B(:,i) that is the ith row of A with the ith
> column of B.
>
>    PETSc SeqAIJ matrices are stored "by row" and for each row is stored
> the column indices of the nonzeros (sorted) and the numerical values for
> those columns. If the nonzero structure of B is not related to the non-zero
> structure of A then computing the diagonal is a set of "sparse" vector
> vector products. Generic sparse vector vector products are never super
> efficient and to make matters worse with SeqAIJ we don't have stored
> directly the columns of B (only the rows)
>
>   If you look at MatMatMult_SeqAIJ_SeqAIJ() you will see we have SIX
> implementations using different approaches to try to get reasonable
> performance of the sparse matrix-matrix product. So if this computation of
> the diagonal is an important kernel in your code (and takes significant
> time) then you have some work cut out for you to write the appropriate code
> using the SeqAIJ data structure directly. We don't provide anything out of
> the box for this computation. I suggest looking at the various approaches
> for sparse matrix matrix product and see what one looks reasonable to
> specialize to compute just the diagonal portion.
>
>   Barry
>
>
> > On Jun 22, 2016, at 3:41 PM, ehsan sadrfaridpour <it.sadr at gmail.com>
> wrote:
> >
> > Now, they are sparse (AIJ) and sequential. But I will upgrade the code
> to parallel later.
> >
> >
> > On Wed, Jun 22, 2016 at 4:34 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> >    Matrix A and B, sparse or dense, parallel or sequential?
> >
> >
> > > On Jun 22, 2016, at 3:27 PM, ehsan sadrfaridpour <it.sadr at gmail.com>
> wrote:
> > >
> > > Hi,
> > > I need the diagonal elements from result of multiplying matrix A, B
> together.
> > > I can get by multiplying the 2 matrices and then call MatGetDiagonal.
> > > However, I only need the values on the diagonal and the rest of the
> elements are useless for me.
> > > As the size of matrices increase, I am afraid it affect the
> performance.
> > >
> > > So, I am looking for another method that only calculates the diagonal
> of multiplication and not the rest of elements.
> > > If there is not such a method for matrix, how can I use the vector's
> operations to reach the same results?
> > >
> > >
> > > Best,
> > > Ehsan
> >
> >
>
>
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