Hello Matt,
I tried several times for 3.1-p8 and dev version by putting MatSetOption
1) right after creation of the matrix:
#ifdef petscDev
ierr = DMCreateMatrix(DMMGGetDM(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr);
#else
ierr = DAGetMatrix(DMMGGetDA(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr);
#endif
ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES,
PETSC_TRUE);CHKERRQ(ierr);
2) at the beginning of the FormJacobianLocal() routine:
PetscFunctionBegin;
ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES,
PETSC_TRUE);CHKERRQ(ierr);
3) before calling MatAssemblyBegin() in FormJacobianLocal() routine:
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);
None of those works. What is wrong here?
Thanks,
R
On Jan 20, 2012, at 4:32 PM, Matthew Knepley wrote:
> 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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