[petsc-users] The matrix allocated by calling MatMPIAIJSetProallocation() was flushed out after calling DMMGSetSNESLocal()
Xuefei (Rebecca) Yuan
xyuan at lbl.gov
Sat Jan 21 12:19:54 CST 2012
Hello,
After I was not able to get rid of the zeros in the matrix by
>> ierr = MatSetOption(jacobian, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr);
I would like to create the matrix by the following routine:
ierr = MatCreate(PETSC_COMM_WORLD, &jacobian);CHKERRQ(ierr);
ierr = MatSetType(jacobian, MATMPIAIJ);CHKERRQ(ierr);
ierr = MatSetSizes(jacobian, PETSC_DECIDE, PETSC_DECIDE, (PetscInt)(info.mx*info.my*4), (PetscInt)(info.mx*info.my*4));CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(jacobian, 11, PETSC_NULL, 18, PETSC_NULL);CHKERRQ(ierr);
instead of using
ierr = DMGetMatrix(DMMGGetDM(dmmg), MATAIJ, &jacobian);CHKERRQ(ierr);
to save the memory. However, I found that the routine DMGetMatrix() was still called inside DMMGSetSNESLocal(), therefore, the matrix I created was useless:
*********************************************
Breakpoint 2, main (argc=3, argv=0x7fff5fbff770) at twcartffxmhd.c:255
255 ierr = MatCreate(PETSC_COMM_WORLD, &jacobian);CHKERRQ(ierr);
(gdb) n
256 ierr = MatSetType(jacobian, MATMPIAIJ);CHKERRQ(ierr);
(gdb)
257 ierr = MatSetSizes(jacobian, PETSC_DECIDE, PETSC_DECIDE, (PetscInt)(info.mx*info.my*4), (PetscInt)(info.mx*info.my*4));CHKERRQ(ierr);
(gdb)
258 ierr = MatMPIAIJSetPreallocation(jacobian, 11, PETSC_NULL, 18, PETSC_NULL);CHKERRQ(ierr);
(gdb)
Breakpoint 3, main (argc=3, argv=0x7fff5fbff770) at twcartffxmhd.c:260
260 ierr = DMMGSetSNESLocal(dmmg, FormFunctionLocal, FormJacobianLocal,0,0);CHKERRQ(ierr);
(gdb) s
DMMGSetSNESLocal_Private (dmmg=0x102004480, function=0x100016ba9 <FormFunctionLocal>, jacobian=0x100050e83 <FormJacobianLocal>, ad_function=0, admf_function=0) at damgsnes.c:932
932 PetscInt i,nlevels = dmmg[0]->nlevels;
(gdb) n
934 PetscErrorCode (*computejacobian)(SNES,Vec,Mat*,Mat*,MatStructure*,void*) = 0;
(gdb) s
937 PetscFunctionBegin;
(gdb) n
938 if (jacobian) computejacobian = DMMGComputeJacobian;
(gdb)
942 CHKMEMQ;
(gdb)
943 ierr = PetscObjectGetCookie((PetscObject) dmmg[0]->dm,&cookie);CHKERRQ(ierr);
(gdb)
944 if (cookie == DM_COOKIE) {
(gdb)
948 ierr = PetscOptionsHasName(PETSC_NULL, "-dmmg_form_function_ghost", &flag);CHKERRQ(ierr);
(gdb)
949 if (flag) {
(gdb)
952 ierr = DMMGSetSNES(dmmg,DMMGFormFunction,computejacobian);CHKERRQ(ierr);
(gdb)
Matrix Object:
type=seqaij, rows=100, cols=100
total: nonzeros=5776, allocated nonzeros=5776
using I-node routines: found 25 nodes, limit used is 5
954 for (i=0; i<nlevels; i++) {
(gdb) b twcartffxmhd.c:280
Breakpoint 4 at 0x100004032: file twcartffxmhd.c, line 282.
(gdb) c
Continuing.
Matrix Object:
type=mpiaij, rows=100, cols=100
total: nonzeros=0, allocated nonzeros=2900
using I-node (on process 0) routines: found 20 nodes, limit used is 5
*********************************************
The final matrix after FormJacobianlLocal() call still have 5776 nonzeros:
% Size = 100 100
2 % Nonzeros = 5776
3 zzz = zeros(5776,3);
Is there a way that I can pass the matrix created via line 255-258 to FormJacobianLocal()?
Thanks very much!
Cheers,
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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