[petsc-users] Assembling a finite element matrix in parallel

[Matthew Knepley]

On Sun, Apr 27, 2014 at 4:14 AM, Justin Dong <jsd1 at rice.edu> wrote:

> Hi all,
>
> I'm currently coding a finite element problem in PETSc. I'm computing all
> of the matrices by myself and would prefer to do it that way. I want to
> parallelize the assembly of the global matrices. This is a simplified
> version of the assembly routine (pseudocode):
>
> for (k = 0; k < nelements; ++k)
> {
>     get_index(k,ie,je); /* ie and je are arrays that indicate where to
> place A_local */
>     compute_local_matrix(A_local,...);
>
>     MatSetValues(A_global, nlocal, ie, nlocal, je, A_local, ADD_VALUES);
> }
>
> This is for DG finite elements and I know the matrix easily be assembled
> in parallel. Even on my laptop, this would allow me to significantly speed
> up my code. The only problem is, I'm not sure how to do this in PETSc. I'd
> assume I need to use MatCreateMPIAIJ instead of MatCreateSeqAIJ, but wasn't
> able to find any using tutorials on how I might do this.
>

1) If you just split this loop across processes, it would work immediately.
However, that can be non-optimal in terms
     of communication.

2) PETSc matrices are distributed by contiguous blocks of rows (see manual
section on matrices), so you would like
    those row blocks to correspond roughly to your element blocks.

3) You will also have to preallocate, but that should be the same as you do
now for the sequential case, except you
     check whether a column is inside the diagonal block.

  Thanks,

      Matt


> Sincerely,
> Justin
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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