[petsc-users] How to simplify the nonzero structure of the jacobian matrix.
Jed Brown
jedbrown at mcs.anl.gov
Mon Jan 23 15:55:38 CST 2012
-dm_preallocate_only
http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/DM/DMSetMatrixPreallocateOnly.html
On Mon, Jan 23, 2012 at 15:52, Xuefei (Rebecca) Yuan <xyuan at lbl.gov> wrote:
> Hello all,
>
> There is one example that has used the
>
> ierr = MatSetOption(*B,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
>
> in /src/mat/examples/tutorials/ex12.c,
>
> and this option works for this case because the matrix B is created via
>
> ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n+1,n+1,0,cnt,B);CHKERRQ(ierr);
>
> and the values are inserted by
>
> ierr = MatSetValues(*B,1,&i,aij->i[i+1] - aij->i[i],aij->j +
> aij->i[i],aij->a + aij->i[i],INSERT_VALUES);CHKERRQ(ierr);
>
>
> However, the option MAT_IGNORE_ZERO_ENTRIES does not work for the matrix
> if it is generated via
>
> ierr = DMCreateMatrix(DMMGGetDM(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr);
>
> no matter if MatSetValues() or MatSetValuesStencil() is used.
>
> In the other word, if the matrix is generated based on the stencil
> information, the zero entries cannot be ignored even if the option is
> called before inserting/adding values.
>
> Is there anyway that can get rid of those zeros in the matrix generated
> based on the stencil information?
>
>
> Thanks very much!
>
> Best regards,
>
> Rebecca
>
>
>
>
>
> 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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