[petsc-users] How to simplify the nonzero structure of the jacobian matrix.

[Matthew Knepley]

On Fri, Jan 20, 2012 at 6:28 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov>wrote:

> Hello Matt,
>
> I have changed the code as
>
>         ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES,
> PETSC_TRUE);CHKERRQ(ierr);
>         ierr = MatAssemblyBegin(jacobian,
> MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>         ierr = MatAssemblyEnd(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>

You have to set it before you start setting values, so we know to ignore
them.

   Matt


> but still get the same result as before, the matrix still has 5776
> nonzeros:
>
> % Size = 100 100
>    2 % Nonzeros = 5776
>    3 zzz = zeros(5776,3);
>
> Then I switch the order as
>
>         ierr = MatAssemblyBegin(jacobian,
> MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>         ierr = MatAssemblyEnd(jacobian, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>         ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES,
> PETSC_TRUE);CHKERRQ(ierr);
>
> nothing changed.
>
> The version is 3.1-p8.
>
> Thanks very much!
>
> Best regards,
>
> Rebecca
>
>
>
>
> On Jan 20, 2012, at 4:09 PM, Matthew Knepley wrote:
>
> On Fri, Jan 20, 2012 at 6:02 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov>wrote:
>
>> Hello all,
>>
>> This is a test for np=1 case of the nonzero structure of the jacobian
>> matrix. The jacobian matrix is created via
>>
>> ierr =
>> DMDACreate2d(comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,
>> parameters.mxfield, parameters.myfield, PETSC_DECIDE, PETSC_DECIDE, 4, 2,
>> 0, 0, &da);CHKERRQ(ierr);
>>
>> ierr = DMCreateMatrix(DMMGGetDM(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr);
>>
>> After creation of the jacobian matrix,
>>
>>                ierr = MatAssemblyBegin(jacobian,
>> MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>                ierr = MatAssemblyEnd(jacobian,
>> MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>
>>                PetscViewer viewer;
>>                char fileName[120];
>>                sprintf(fileName,
>> "jacobian_after_creation.m");CHKERRQ(ierr);
>>
>>                FILE * fp;
>>
>>                ierr =
>> PetscViewerASCIIOpen(PETSC_COMM_WORLD,fileName,&viewer);CHKERRQ(ierr);
>>                ierr =
>> PetscViewerSetFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
>>                ierr = MatView (jacobian, viewer); CHKERRQ (ierr);
>>                ierr = PetscFOpen(PETSC_COMM_WORLD,fileName,"a",&fp);
>> CHKERRQ(ierr);
>>                ierr =
>> PetscViewerASCIIPrintf(viewer,"spy((spconvert(zzz)));\n");CHKERRQ(ierr);
>>                ierr = PetscFClose(PETSC_COMM_WORLD,fp);CHKERRQ(ierr);
>>                PetscViewerDestroy(&viewer);
>>
>> I took a look at the structure of the jacobian by storing it in the
>> matlab format, the matrix has 5776 nonzeros entries, however, those values
>> are all zeros at the moment as I have not insert or add any values into it
>> yet, the structure shows: (the following figure shows a global replacement
>> of 0.0 by 1.0 for those 5776 numbers)
>>
>>
>>
>>
>> Inside the FormJacobianLocal() function, I have selected the index to
>> pass to the nonzero values to jacobian, for example,
>>
>>  ierr = MatSetValuesStencil(jacobian, 1, &row, 6, col, v,
>> INSERT_VALUES);CHKERRQ(ierr);
>>
>> where
>>
>>                    col[0].i = column[4].i;
>>                    col[1].i = column[5].i;
>>                    col[2].i = column[6].i;
>>                    col[3].i = column[9].i;
>>                    col[4].i = column[10].i;
>>                    col[5].i = column[12].i;
>>
>>
>>                    col[0].j = column[4].j;
>>                    col[1].j = column[5].j;
>>                    col[2].j = column[6].j;
>>                    col[3].j = column[9].j;
>>                    col[4].j = column[10].j;
>>                    col[5].j = column[12].j;
>>
>>                    col[0].c = column[4].c;
>>                    col[1].c = column[5].c;
>>                    col[2].c = column[6].c;
>>                    col[3].c = column[9].c;
>>                    col[4].c = column[10].c;
>>                    col[5].c = column[12].c;
>>
>>                    v[0] = value[4];
>>                    v[1] = value[5];
>>                    v[2] = value[6];
>>                    v[3] = value[9];
>>                    v[4] = value[10];
>>                    v[5] = value[12];
>>
>> and did not pass the zero entries into the jacobian matrix. However,
>>  after inserting or adding all values to the matrix, by the same routine
>> above to take a look at the jacobian matrix in matlab format, the matrix
>> still has 5776 nonzeros, in which 1075 numbers are nonzeros, and the other
>> 4701 numbers are all zeros. The spy() gives
>>
>>
>>
>>
>> for the true nonzero structures.
>>
>> But the ksp_view will give the nonzeros number as 5776, instead of 1075:
>>
>>  linear system matrix = precond matrix:
>>  Matrix Object:  Mat_0x84000000_1   1 MPI processes
>>    type: seqaij
>>    rows=100, cols=100
>>    total: nonzeros=5776, allocated nonzeros=5776
>>
>> It is a waste of memory to have all those values of zeros been stored in
>> the jacobian.
>>
>> Is there anyway to get rid of those zero values in jacobian and has the
>> only nonzero numbers stored in jacobian? In such a case, the ksp_view will
>> tell that total:  nonzeros=1075.
>>
>
> MatSetOption(MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);
>
>    Matt
>
>
>> Thanks very much!
>>
>> Have a nice weekend!
>>
>> Cheers,
>>
>> Rebecca
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> 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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