[petsc-users] efficiency of MatSetValues

[Margarita Satraki]

Great, thanks for your help!

Margarita

On 3 February 2012 23:27, Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, Feb 3, 2012 at 5:05 PM, Margarita Satraki <
> margarita.satraki at gmail.com> wrote:
>
>> Does the same happen with MatDuplicate? It overwrites the
>> MatSeqAIJSetPreallocation?
>>
>
> Yes.
>
>
>> In this case, can I redefine the nonzero places?
>>
>
> No.
>
>
>> I need it for the case of creating the preconditioner by changing the
>> jacobian slightly.
>>
>
> The right way to do this is just fully allocate the preconditioner. We
> have benchmarked
> this hundreds of times, and it is negligible.
>
>   Thanks,
>
>      Matt
>
>
>> Margarita
>>
>> On 3 February 2012 22:58, Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> 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
>>>
>>
>>
>
>
> --
> 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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