[petsc-users] How to simplify the nonzero structure of the jacobian matrix.
Xuefei (Rebecca) Yuan
xyuan at lbl.gov
Fri Jan 20 19:32:27 CST 2012
I have replace INSERT_VALUES by ADD_VALUES,
ierr = MatSetValuesStencil(jacobian, 1, &row, 6, col, v, ADD_VALUES);CHKERRQ(ierr);
but still cannot get rid of those zeros...
Cheers,
R
On Jan 20, 2012, at 5:28 PM, Xuefei (Rebecca) Yuan wrote:
> I did use
>
> ierr = MatSetValuesStencil(jacobian, 1, &row, 13, column, value, INSERT_VALUES);CHKERRQ(ierr);
>
>
> so it is INSERT_VALUES.
>
> Let me try to use ADD_VALUES instead of INSERT_VALUES, and see if this will make any difference.
>
> Thanks,
>
> R
>
>
>
> On Jan 20, 2012, at 5:23 PM, Matthew Knepley wrote:
>
>> On Fri, Jan 20, 2012 at 7:07 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov> wrote:
>> Here is the output:
>>
>>
>>
>>
>>
>> On Jan 20, 2012, at 5:01 PM, Matthew Knepley wrote:
>>
>>> On Fri, Jan 20, 2012 at 6:55 PM, Xuefei (Rebecca) Yuan <xyuan at lbl.gov> wrote:
>>> Hello Matt,
>>>
>>> I tried several times for 3.1-p8 and dev version by putting MatSetOption
>>>
>>> Are you sure your entries are exactly 0.0?
>>
>>
>> Are you using ADD_VALUES?
>>
>> http://petsc.cs.iit.edu/petsc/petsc-dev/file/783e93230143/src/mat/impls/aij/seq/aij.c#l310
>>
>> Matt
>>
>>> Matt
>>>
>>> 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
>>>
>>>
>>>
>>>
>>> --
>>> 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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