[petsc-users] efficiency of MatSetValues

[Matthew Knepley]

On Fri, Feb 3, 2012 at 4:46 PM, Margarita Satraki <
margarita.satraki at gmail.com> wrote:

> Hi Jed,
>
> Thanks for the reply.
> I've defined 2 nonzeros per row so it should consider them to be in the
> correct place (1 for diagonal and 1 for the 1st off diagonal). I do not
> want to delete anything, just experiment with inserting new entries. This
> is a simple example to demonstrate my problem with a more complicated code
> of nonlinear elasticity.


Assembly of a matrix compresses it, throwing away extra allocated places
that were not used.

   Matt



> Margarita
>
>
> On 3 February 2012 22:41, Jed Brown <jedbrown at mcs.anl.gov> wrote:
>
>> On Sat, Feb 4, 2012 at 01:35, Margarita Satraki <
>> margarita.satraki at gmail.com> wrote:
>>
>>> It seems that only the 1st case gives good results in the sense that by
>>> increasing the size of the matrix you increase the time needed by
>>> MatSetValues linearly. Both the 2nd and the 3rd case give similar results,
>>> much worse than the 1st. I understand that the 1st case has the advantage
>>> because of accurate memory allocation but shouldn't the 2ndcase be better
>>> than the 3rd since it at least defines the number of nonzeros per row so it
>>> again allocates memory more accurately?
>>
>>
>> Those nonzeros are in the wrong place and PETSc does not know that you
>> want to "delete" the old entries.
>>
>> Just preallocate the correct number of nonzeros and it will be fast,
>> don't bother with copying in a "similar" matrix.
>>
>
>


-- 
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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