[petsc-users] Allocating the diagonal for MatMPIAIJSetPreallocation

Samuel Estes samuelestes91 at gmail.com
Fri Apr 1 11:45:11 CDT 2022

Thanks! This seems like it might be what I need. I'm still a little unclear
on how it works though? My problem is basically that for any given row, I
know the total non-zeros but not how many occur in the diagonal vs
off-diagonal. Without knowledge of the underlying grid, I'm not sure how
there could be a black box utility to figure this out? Am I
misunderstanding how this is used?

On Fri, Apr 1, 2022 at 11:34 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, Apr 1, 2022 at 12:27 PM Samuel Estes <samuelestes91 at gmail.com>
> wrote:
>> Hi,
>> I have a problem in which I know (roughly) the number of non-zero entries
>> for each row of a matrix but I don't have a convenient way of determining
>> whether they belong to the diagonal or off-diagonal part of the parallel
>> matrix. Is there some way I can just allocate the total number of non-zeros
>> in a row regardless of which part they belong to? I'm assuming that this is
>> not possible but I just wanted to check. It seems like it should be
>> possible in principle since the matrix is only split by the rows but the
>> columns of a row are all on the same processor (at least as I understand
>> it). Thanks!
> In serial, the matrix is stored by rows. In parallel, it is split into a
> diagonal and off-diagonal block, so that we can overlap communication and
> computation in the matvec.
> However, we have a convenience structure for figuring this out, called
> MatPreallocator,
> https://petsc.org/main/docs/manualpages/Mat/MATPREALLOCATOR.html
> In my code, I wrote a loop around the code that filled up my matrix, which
> executed twice. On the first pass, I fed in the MatPreallocator matrix.
> When this finished
> you can call
> https://petsc.org/main/docs/manualpages/Mat/MatPreallocatorPreallocate.html#MatPreallocatorPreallocate
> on your system amtrix, then on the second
> pass use the system matrix. This was only a few extra lines of code for
> me. If you want to optimize further, you can have a flag that only computes
> the values on the
> second pass.
>   Thanks,
>       Matt
> Sam
> --
> 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
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
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