[petsc-users] questions about matrix preallocation

[Dominik Szczerba]

On Thu, Nov 24, 2011 at 2:36 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:
> On Thu, Nov 24, 2011 at 07:33, Dominik Szczerba <dominik at itis.ethz.ch>
> wrote:
>>
>> MatCreateMPIAIJ(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, NTOT,
>> NTOT, 500, PETSC_NULL, 500, PETSC_NULL, &A);
>>
>> (with 500 a big overshoot)
>>
>> then I do in a loop:
>>
>> 1. ierr = MatMPIAIJSetPreallocation(A, 500, PETSC_NULL, 500,
>> PETSC_NULL); CHKERRQ(ierr);
>> 2. ierr = MatZeroEntries(A); CHKERRQ(ierr);
>>
>> Line 1. does not matter the first time in the loop, info.mallocs is
>> always 0, but if it is commented out, info.mallocs is non-zero the
>> second time loop is executed.
>> So I am confused, is the preallocation in MatCreateMPIAIJ not
>> sufficient? Does it need to be refreshed?
>
> You must be changing the number of nonzeros in each iteration of the loop.

Yes, that is true, but 1) within the overshot preallocation margin 2)
I do it at each execution of the loop, so I do not see why only the
second time there are mallocs. I display mallocs directly before
KSPSolve().

> I suggest assembling all possible entries (even the ones that happen to be
> zero) in the first assembly. Then there will be space and you can reuse the
> data structure.

This will require a bigger change in my code. Is always calling
MatMPIAIJSetPreallocation a bad (inefficient) alternative?

Thanks
Dominik