[petsc-users] MatFDColorCreate takes really big portion of the total time

[Bao Kai]

Sorry, I failed in attaching file.

Kai

On 6/26/12, Bao Kai <paeanball at gmail.com> wrote:
> Hi, Barry,
>
> Parallel on a bluegene/P machine.
>
> Attached please find the result information. The log_summary output is
> at the bottom of the file.
>
>
> BTW: how to respond in the mailing list directly? I always have to
> copy the message in my mailbox to reply.
>
> Best Regards,
> Kai
>
>
>
>  Parallel or sequential?
>
>    Barry
>
> Please send entire -log_summary output
>
> On Jun 26, 2012, at 2:22 PM, Bao Kai wrote:
>
>> Hi, all,
>>
>> I use the SNES in petsc-3.2 to solve my problem. The problem is a 3-D
>> finite difference problem with structured grid.
>>
>> I use MatFDColorCreate to generate the Jacobian matrix. I just found
>> that when the size of problem is big, MatFDColorCreate takes really
>> long time.  The following results is the summary with size of the mesh
>> to be 1000^3. 90% of the time is costed in MatFDColorCreate.
>>
>>    237 MatGetOrdering         1 1.0 1.3502e-03 1.1 0.00e+00 0.0
>> 0.0e+00 0.0e+00 2.0e+00  0  0  0  0  0   0  0  0  0  0     0
>>    238 MatZeroEntries        39 1.0 9.2822e-02 1.2 0.00e+00 0.0
>> 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
>>    239 MatFDColorCreate      10 1.0 3.2863e+03 1.0 0.00e+00 0.0
>> 1.6e+07 5.0e+02 6.8e+02 90  0  0  0  3  90  0  0  0  3     0
>>    240 MatFDColorApply       20 1.0 2.5288e+01 1.0 3.54e+07 1.1
>> 4.6e+08 2.0e+03 8.0e+01  1  0  5  5  0   1  0  5  5  0 42708
>>    241 MatFDColorFunc       560 1.0 9.5386e+00 1.3 0.00e+00 0.0
>> 4.5e+08 2.0e+03 0.0e+00  0  0  5  5  0   0  0  5  5  0     0
>>
>> And the following the code I use.
>>
>>    262        call DMGetMatrix(solv%da, MATAIJ, solv%jac,ierr)
>>    263        call
>> DMGetColoring(solv%da,IS_COLORING_GLOBAL,MATAIJ,iscoloring,ierr)
>>    264        call
>> MatFDColoringCreate(solv%jac,iscoloring,matfdcoloring,ierr)
>>    265        call
>> MatFDColoringSetFunction(matfdcoloring,FormFunction,equ,ierr)
>>    266        call MatFDColoringSetFromOptions(matfdcoloring,ierr)
>>    267        call SNESSetJacobian(solv%snes, solv%jac,
>> solv%jac,SNESDefaultComputeJacobianColor, matfdcoloring, ierr)
>>    268        call ISColoringDestroy(iscoloring,ierr)
>>
>> I am wondering if there is anything I can do to improve this problem.
>>
>> Thank you very much.
>>
>> Best Regards,
>> Kai
>
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