[petsc-users] Problem with MPI, MatAXPY and SAME_NONZERO_PATTERN
Klaus Kaiser
kaiser at igpm.rwth-aachen.de
Mon Mar 30 05:18:39 CDT 2015
Hallo Metthew,
at the weekend I updated petsc to the newest release version 3.5.2 and I
still got this strange behavior.
Best
Klaus
On 03/27/2015 05:07 PM, Klaus Kaiser wrote:
> Hallo Matthew,
>
> here is a short example I used for 8 cores:
>
> int d_nnz[3];
> int o_nnz[3];
> d_nnz[0] = 3; d_nnz[1] = 3; d_nnz[2] = 3;
> o_nnz[0] = 6; o_nnz[1] = 6; o_nnz[2] = 6;
> ierr = MatCreateBAIJ(PETSC_COMM_WORLD, 3, 9, 9, 72, 72, 0, d_nnz,
> 0, o_nnz,&A);
> ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
> ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);
> ierr = MatSetOption(A,MAT_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);
> ierr = MatCreateBAIJ(PETSC_COMM_WORLD, 3, 9, 9, 72, 72, 0, d_nnz,
> 0, o_nnz,&Ah);
> ierr = MatCreateBAIJ(PETSC_COMM_WORLD, 3, 9, 9, 72, 72, 0, d_nnz,
> 0, o_nnz,&At);
>
> std::vector<double> insert(3*3*3*3, 1.0);
> for(int i=0;i<8;++i)
> {
> int rows[3] = {i,i+1,i+3};
> int cols[3] = {i,i+1,i+3};
>
> MatSetValuesBlocked(A, 3, rows, 3, cols, &insert[0], ADD_VALUES);
> }
>
> MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
> MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
> MatDuplicate(A,MAT_COPY_VALUES,&Ah);
> MatDuplicate(A,MAT_COPY_VALUES,&At);
> MatAssemblyBegin(Ah,MAT_FINAL_ASSEMBLY);
> MatAssemblyEnd(Ah,MAT_FINAL_ASSEMBLY);
> MatAssemblyBegin(At,MAT_FINAL_ASSEMBLY);
> MatAssemblyEnd(At,MAT_FINAL_ASSEMBLY);
>
> MatAXPY(Ah,1.,At,SAME_NONZERO_PATTERN);
> MatAXPY(A,1.,Ah,SAME_NONZERO_PATTERN);
>
> MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
> MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
>
> The result is, that only some values are computed correctly.
>
> Best and Thank you a lot
>
> Klaus
>
>
>
> On 03/27/2015 04:26 PM, Matthew Knepley wrote:
>> On Fri, Mar 27, 2015 at 10:16 AM, Klaus Kaiser
>> <kaiser at igpm.rwth-aachen.de <mailto:kaiser at igpm.rwth-aachen.de>> wrote:
>>
>> Hallo Matthew,
>>
>> thanks for your fast response. With "no beside the nonzero
>> structure" I meant, that I do not create a different non-zero
>> structure while I'm adding values to my matrices.
>>
>> I also tried MAT_COPY_VALUES and the result was the same.
>>
>>
>> Please send the small example and we will figure out what is going wrong.
>>
>> Thanks,
>>
>> Matt
>>
>> I do not get a error message but the resulting matrix is wrong.
>> Here I have a short example. The first 9 rows and first 3 colomn
>> of the matrices Ah, At and Ah+At on the first processor (of 8):
>>
>> Ah:
>> 0: 60.3553 -0.249975 2.77556e-17
>> 1: 0 60.3553 0
>> 2: 0 0 60.3553
>> 3: 17.6777 0.374962 0.124987
>> 4: 0 17.6777 0
>> 5: 0 0 17.6777
>> 6: -7.32233 -0.124987 0.374962
>> 7: 0 -7.32233 0
>> 8: 0 0 -7.32233
>>
>>
>> At:
>> 0: 0 0 0
>> 1: 2500 0 0
>> 2: -4.54747e-13 0 0
>> 3: 0 0 0
>> 4: 1250 0 0
>> 5: 1250 0 0
>> 6: 0 0 0
>> 7: 1250 0 0
>> 8: 3750 0 0
>>
>> Ah+At
>> 0: 60.3553 -0.249975 2.77556e-17
>> 1: 2500 60.3553 0
>> 2: -4.54747e-13 0 60.3553
>> 3: 17.6777 0.374962 0.124987
>> 4: 0 17.6777 0
>> 5: 0 0 17.6777
>> 6: -7.32233 -0.124987 0.374962
>> 7: 0 -7.32233 0
>> 8: 0 0 -7.32233
>>
>> you can see the first 3 rows of the resulting matrix looks
>> exactly like what I would expect, but the last 6 rows only
>> consists of the values of Ah. When you would also look on the
>> matrix A and A+Ah+At you would also see, that values where both
>> matrices have an nonzero entry are not sum correctly.
>>
>> Best
>>
>> Klaus
>>
>> On 03/27/2015 03:59 PM, Matthew Knepley wrote:
>>> On Fri, Mar 27, 2015 at 9:48 AM, Klaus Kaiser
>>> <kaiser at igpm.rwth-aachen.de <mailto:kaiser at igpm.rwth-aachen.de>>
>>> wrote:
>>>
>>> Hallo,
>>>
>>> I have a strange behavior in my code concerning the function
>>> MatAXPY. I create 3 different Matrices
>>>
>>> ierr = MatCreateBAIJ(PETSC_COMM_WORLD, block_size,
>>> local_size, local_size, system_size, system_size, 0, d_nnz,
>>> 0, o_nnz,&A);
>>> ierr =
>>> MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
>>> ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);
>>> ierr =
>>> MatSetOption(A,MAT_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);
>>>
>>> ierr = MatCreateBAIJ(PETSC_COMM_WORLD, block_size,
>>> local_size, local_size, system_size, system_size, 0, d_nnz,
>>> 0, o_nnz,&At);
>>> ierr =
>>> MatSetOption(At,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
>>> ierr = MatSetOption(At,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);
>>> ierr =
>>> MatSetOption(At,MAT_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);
>>>
>>> ierr = MatCreateBAIJ(PETSC_COMM_WORLD, block_size,
>>> local_size, local_size, system_size, system_size, 0, d_nnz,
>>> 0, o_nnz,&Ah);
>>> ierr =
>>> MatSetOption(Ah,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
>>> ierr = MatSetOption(Ah,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);
>>> ierr =
>>> MatSetOption(Ah,MAT_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);
>>>
>>>
>>> These creations are superfluous since you use MatDuplicate() below.
>>>
>>> and want to sum these three matrixes with different factors.
>>> First I fill the Matrix A with some values, and duplicate
>>> the structure of A to the other two matrices:
>>>
>>> MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
>>> MatDuplicate(A,MAT_DO_NOT_COPY_VALUES,&Ah);
>>> MatDuplicate(A,MAT_DO_NOT_COPY_VALUES,&At);
>>> MatAssemblyBegin(Ah,MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(Ah,MAT_FINAL_ASSEMBLY);
>>> MatAssemblyBegin(At,MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(At,MAT_FINAL_ASSEMBLY);
>>>
>>>
>>> After this I fill the matrices At and Ah with some other
>>> values, which are not beside the non zero structure (I also
>>> tried with just copying the Matrix A). Now after another
>>> MatAssembly
>>>
>>>
>>> I do not understand "no beside the nonzero structure". Do you
>>> mean that the nonzero structure is the same?
>>>
>>> Can you first test with MAT_COPY_VALUES?
>>>
>>> I want to add these Matrices in the form A+c*(Ah+d*At):
>>>
>>>
>>> MatAXPY(Ah,c,At,SAME_NONZERO_PATTERN);
>>> MatAXPY(A,d,Ah,SAME_NONZERO_PATTERN);
>>>
>>> When I run the method with mpi and one core everything works
>>> fine. Starting the same method with more cores, the sum of
>>> the matrices fails. It seems like some values are added
>>>
>>>
>>> Please send the full output of a failure when you use
>>> MAT_COPY_VALUES on 2 procs.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>> correctly and many values are missed. Using
>>> DIFFERENT_NONZERO_STRUCTURE leads to the right behavior in
>>> the multi-core case, but is very slow. I checked with a
>>> viewer if all matrices have the same nonzero structure and
>>> this is the case.
>>>
>>> Does anyone know why this fails, or do I have made any wrong
>>> thoughts?
>>>
>>> I'm corrently working with a petsc version (Petsc Release
>>> Version 3.3.0, Patch 5, Sat Dec 1 15:10:41 CST 2012), I
>>> looked into the changelogs up to the current version and did
>>> not find any note about MatAXPY or MatAYPX.
>>>
>>>
>>> Best and Thanks a lot for your help
>>>
>>> Klaus
>>>
>>>
>>>
>>>
>>> --
>>> 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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