[petsc-users] using petsc tools to solve isolated irregular domains with finite difference
Bishesh Khanal
bisheshkh at gmail.com
Mon Nov 4 10:25:45 CST 2013
On Mon, Nov 4, 2013 at 4:54 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Mon, Nov 4, 2013 at 4:49 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>
>> On Fri, Nov 1, 2013 at 1:30 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Fri, Nov 1, 2013 at 12:08 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>
>>>> On Thu, Oct 31, 2013 at 11:34 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>
>>>>> On Thu, Oct 31, 2013 at 5:02 PM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>>>
>>>>>> On Thu, Oct 31, 2013 at 7:43 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>>
>>>>>>> On Thu, Oct 31, 2013 at 1:25 PM, Bishesh Khanal <bisheshkh at gmail.com
>>>>>>> > wrote:
>>>>>>>
>>>>>>>> I did not call DMCreateMatrix() before when using just dmda (and it
>>>>>>>> is working). In any case, I added a call to DMCreateMatrix() now but still
>>>>>>>> there are problems. Here are the code snippets and the error I get:
>>>>>>>>
>>>>>>>
>>>>>>> Then you were allowing it to be called automatically by PETSc, and
>>>>>>> it would have been this time as well.
>>>>>>>
>>>>>>>
>>>>>>>> //Setting up the section and linking it to DM:
>>>>>>>> ierr = PetscSectionCreate(PETSC_COMM_WORLD, &s);CHKERRQ(ierr);
>>>>>>>> ierr = DMDAGetNumCells(dm, NULL, NULL, NULL, &nC);CHKERRQ(ierr);
>>>>>>>> ierr = PetscSectionSetChart(s, 0, nC);CHKERRQ(ierr);
>>>>>>>> for (PetscInt j = info.ys; j < info.ys+info.ym; ++j) {
>>>>>>>> for (PetscInt i = info.xs; i < info.xs+info.xm; ++i) {
>>>>>>>> PetscInt point;
>>>>>>>> if(isPosInDomain(&testPoisson,i,j,0)) {
>>>>>>>> ierr = DMDAGetCellPoint(dm, i, j, 0,
>>>>>>>> &point);CHKERRQ(ierr);
>>>>>>>> ierr = PetscSectionSetDof(s, point,
>>>>>>>> testPoisson.mDof); // No. of dofs associated with the point.
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>> ierr = PetscSectionSetUp(s);CHKERRQ(ierr);
>>>>>>>> ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
>>>>>>>> ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
>>>>>>>> ierr = DMCreateMatrix(dm,&A);CHKERRQ(ierr);
>>>>>>>>
>>>>>>>> //Set up KSP:
>>>>>>>> ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
>>>>>>>> ierr = KSPSetDM(ksp,dm);CHKERRQ(ierr);
>>>>>>>> ierr =
>>>>>>>> KSPSetComputeOperators(ksp,computeMatrix2dSection,(void*)&testPoisson);CHKERRQ(ierr);
>>>>>>>> ierr =
>>>>>>>> KSPSetComputeRHS(ksp,computeRhs2dSection,(void*)&testPoisson);CHKERRQ(ierr);
>>>>>>>> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
>>>>>>>> ierr = KSPSolve(ksp,NULL,NULL);CHKERRQ(ierr);
>>>>>>>>
>>>>>>>> ------------------------------------------------------
>>>>>>>> The computeMatrix2dSection function has:
>>>>>>>>
>>>>>>>> ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr);
>>>>>>>> ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
>>>>>>>> ierr = DMGetDefaultGlobalSection(da,&gs);CHKERRQ(ierr);
>>>>>>>> for(PetscInt j = info.ys; j<info.ys+info.ym; ++j) {
>>>>>>>> for(PetscInt i = info.xs; i<info.xs+info.xm; ++i) {
>>>>>>>> if (isPosInDomain(ctx,i,j)) {
>>>>>>>> ierr =
>>>>>>>> DMDAGetCellPoint(da,i,j,0,&point);CHKERRQ(ierr);
>>>>>>>> ierr = PetscSectionGetOffset(gs,point,&row);
>>>>>>>> ierr = PetscSectionGetDof(gs,point,&dof);
>>>>>>>> for(PetscInt cDof = 0; cDof < dof; ++cDof) {
>>>>>>>> num = 0;
>>>>>>>> row+=cDof;
>>>>>>>> col[num] = row; //(i,j) position
>>>>>>>> v[num++] = -4;
>>>>>>>> if(isPosInDomain(ctx,i+1,j)) {
>>>>>>>> ierr =
>>>>>>>> DMDAGetCellPoint(da,i+1,j,0,&point);CHKERRQ(ierr);
>>>>>>>> ierr =
>>>>>>>> PetscSectionGetOffset(gs,point,&col[num]);
>>>>>>>> col[num] += cDof;
>>>>>>>> v[num++] = 1;
>>>>>>>> }
>>>>>>>> if(isPosInDomain(ctx,i-1,j)) {
>>>>>>>> ierr =
>>>>>>>> DMDAGetCellPoint(da,i-1,j,0,&point);CHKERRQ(ierr);
>>>>>>>> ierr =
>>>>>>>> PetscSectionGetOffset(gs,point,&col[num]);
>>>>>>>> col[num] += cDof;
>>>>>>>> v[num++] = 1;
>>>>>>>> }
>>>>>>>> if(isPosInDomain(ctx,i,j+1)) {
>>>>>>>> ierr =
>>>>>>>> DMDAGetCellPoint(da,i,j+1,0,&point);CHKERRQ(ierr);
>>>>>>>> ierr =
>>>>>>>> PetscSectionGetOffset(gs,point,&col[num]);
>>>>>>>> col[num] += cDof;
>>>>>>>> v[num++] = 1;
>>>>>>>> }
>>>>>>>> if(isPosInDomain(ctx,i,j-1)) {
>>>>>>>> ierr =
>>>>>>>> DMDAGetCellPoint(da,i,j-1,0,&point);CHKERRQ(ierr);
>>>>>>>> ierr =
>>>>>>>> PetscSectionGetOffset(gs,point,&col[num]);
>>>>>>>> col[num] += cDof;
>>>>>>>> v[num++] = 1;
>>>>>>>> }
>>>>>>>> ierr =
>>>>>>>> MatSetValues(A,1,&row,num,col,v,INSERT_VALUES);CHKERRQ(ierr);
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>> }
>>>>>>>> ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>>>>>>> ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>>>>>>>
>>>>>>>> But this is not working. For e.g. for a 6X6 grid size I get the
>>>>>>>> following error:
>>>>>>>>
>>>>>>>
>>>>>>> Okay, here is how to debug this:
>>>>>>>
>>>>>>> 0) Go to a single scalar equations to make things easier
>>>>>>>
>>>>>>> 1) Use MatView(A, PETSC_VIEWER_STDOUT_WORLD), which should output
>>>>>>> a 36 row matrix with
>>>>>>> the preallocated nonzero pattern, filled with zeros
>>>>>>>
>>>>>>> 2) Make sure this is the pattern you want
>>>>>>>
>>>>>>> 3) Run in the debugger with -start_in_debugger
>>>>>>>
>>>>>>> 4) When you get the error, see
>>>>>>>
>>>>>>> a) If the (i, j) is one that should be setting a value
>>>>>>>
>>>>>>> b) Why this (i, j) was not preallocated
>>>>>>>
>>>>>>
>>>>>> Up to 4 (a), it is correct. There is a problem in the way
>>>>>> DMDAGetCellPoint and PetscSectionGetOffset works in this case scenario. I
>>>>>> will try to explain it below for the case of 4X4 grid.
>>>>>> First case:
>>>>>> If I set the computational domain to be all the points of the dmda
>>>>>> grid, (i.e. isPosInDomain(..,i,j,..) returns true for all i and j in the
>>>>>> dmda grid), the program runs fine and does not give any error.
>>>>>>
>>>>>> Second case:
>>>>>> I want the computational domain to be some part of the whole grid.
>>>>>> There is a problem in this case.
>>>>>> The following test is in a case where,
>>>>>> isPosInDomain(..,i,j,..) returns true ONLY for (i,j) pairs of (2,1)
>>>>>> (1,2) (2,2) (3,2) and (3,2). The grid with its corresponding point number
>>>>>> in the petscsection is shown below:
>>>>>>
>>>>>> 12 13 14 15
>>>>>> 8 9 10 11
>>>>>> 4 5 6 7
>>>>>> 0 1 2 3
>>>>>>
>>>>>> of which 6, 9, 10, 11 and 14 correspond to the (i,j) points that
>>>>>> returns true for isPosInDomain(..,i,j,..)
>>>>>> MatView gives me the 16-row matrix with the star stencil non-zero
>>>>>> structure as expected.
>>>>>> The error I get is: new non-zero at (0,2) caused a malloc.
>>>>>>
>>>>>> This error is for the value of (i,j) = (2,1), i.e. point 6.
>>>>>> The loop to set values in the matrix starts as:
>>>>>> for(PetscInt j = info.ys; j<info.ys+info.ym; ++j) {
>>>>>> for(PetscInt i = info.xs; i<info.xs+info.xm; ++i) {
>>>>>> if (isPosInDomain(ctx,i,j)) {
>>>>>> ierr =
>>>>>> DMDAGetCellPoint(da,i,j,0,&point);CHKERRQ(ierr);
>>>>>> ierr = PetscSectionGetOffset(gs,point,&row);
>>>>>>
>>>>>> Now, what I wanted from the beginning is to create the matrix
>>>>>> containing the rows corresponding to only those points (i,j) which has true
>>>>>> values for isPosInDomain(ctx,i,j), that means in this case 5 row matrix. In
>>>>>> the current test, the first (i,j) that reaches DMDAGetCellPoint is (2,1),
>>>>>> which gives sets point variable to 6.
>>>>>> The line PetscSectionGetOffset(gs,point,&row) sets the value of row
>>>>>> to 0.
>>>>>> So I think this where the inconsistency lies.
>>>>>> MatSetValues(A,1,&row,num,col,v,INSERT_VALUES) expects row variable
>>>>>> and col[] array to correspond to (i,j) based on DMDA, but
>>>>>> PetsSectionGetOffset gives result based on how we masked away some of the
>>>>>> points from dmda grid. Or am I missing something very basic here ?
>>>>>>
>>>>>
>>>>> You are missing something basic. The row is correctly identified as 0,
>>>>> and that means the 2 is
>>>>> point 10.
>>>>>
>>>> The problem must be preallocation. First, you should send the result of
>>>>> MatView().
>>>>>
>>>>
>>>> MatView shows that the preallocation and the matrix created is for the
>>>> full dmda grid which is probably not what we want here, right ? Here is the
>>>> matview result:
>>>>
>>>
>>> Thats right. Did you call
>>>
>>> DMSetDefaultSection(da, s)
>>>
>>> after you made the new section and before you called DMGetMatrix()?
>>>
>> Do you mean before I called DMCreateMatrix() ? I called
>> DMSetDefaultSection(da,s) as below:
>>
>> ...
>> ierr = PetscSectionSetUp(s);CHKERRQ(ierr);
>> ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
>> ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
>> // ierr = DMGetMatrix(dm,&A);CHKERRQ(ierr); //It seems DMGetMatrix is
>> changed to DMCreateMatrix().
>> ierr = DMCreateMatrix(dm,&A);CHKERRQ(ierr);
>> ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
>>
>
> Yes, this is correct. I do exactly this in the example code and it works
> fine. I suspect
> you are not creating the section you think you are. You can send the code
> if you want
> and I will look at it.
>
Thanks, here is the code:
https://github.com/bishesh/petscPoissonIrregular/blob/master/poissonIrregular.cxx
It works for 2D and 3D without using PetscSection. (The choice of using
Petsc_section is on line 68). Using PetsSection currently it implements
only the 2D case with dof = 1. It works when the domain consists of all the
cells of the dmda, it works (to check you can uncomment line 129 in
isPosInDomain(). But it does not when I mask out some of the cells while
creating the petscsection.
>
> Matt
>
>
>> This MatView on A shows (result below) that it still has 16 rows for all
>> DMDA points instead of only those petscsection points for which I set a
>> non-zero dof. Is it what it should not be doing ?
>>
>>> Mat Object: 1 MPI processes
>>>>
>>>> type: seqaij
>>>>
>>>> row 0: (0, 0) (1, 0) (4, 0)
>>>>
>>>> row 1: (0, 0) (1, 0) (2, 0) (5, 0)
>>>>
>>>> row 2: (1, 0) (2, 0) (3, 0) (6, 0)
>>>>
>>>> row 3: (2, 0) (3, 0) (7, 0)
>>>>
>>>> row 4: (0, 0) (4, 0) (5, 0) (8, 0)
>>>>
>>>> row 5: (1, 0) (4, 0) (5, 0) (6, 0) (9, 0)
>>>>
>>>> row 6: (2, 0) (5, 0) (6, 0) (7, 0) (10, 0)
>>>>
>>>> row 7: (3, 0) (6, 0) (7, 0) (11, 0)
>>>>
>>>> row 8: (4, 0) (8, 0) (9, 0) (12, 0)
>>>>
>>>> row 9: (5, 0) (8, 0) (9, 0) (10, 0) (13, 0)
>>>>
>>>> row 10: (6, 0) (9, 0) (10, 0) (11, 0) (14, 0)
>>>>
>>>> row 11: (7, 0) (10, 0) (11, 0) (15, 0)
>>>>
>>>> row 12: (8, 0) (12, 0) (13, 0)
>>>>
>>>> row 13: (9, 0) (12, 0) (13, 0) (14, 0)
>>>>
>>>> row 14: (10, 0) (13, 0) (14, 0) (15, 0)
>>>>
>>>> row 15: (11, 0) (14, 0) (15, 0)
>>>>
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> ------------------------------------
>>>>
>>>> [0]PETSC ERROR: Argument out of range!
>>>>
>>>> [0]PETSC ERROR: New nonzero at (0,2) caused a malloc!
>>>>
>>>>
>>>>
>> For reference here is the code snippet again:
>> ...
>> ierr = PetscSectionCreate(PETSC_COMM_WORLD, &s);CHKERRQ(ierr);
>> ierr = DMDAGetNumCells(dm, NULL, NULL, NULL, &nC);CHKERRQ(ierr);
>> ierr = PetscSectionSetChart(s, 0, nC);CHKERRQ(ierr);
>> for (PetscInt j = info.ys; j < info.ys+info.ym; ++j) {
>> for (PetscInt i = info.xs; i < info.xs+info.xm; ++i) {
>> PetscInt point;
>> if(isPosInDomain(&testPoisson,i,j,0)) {
>> ierr = DMDAGetCellPoint(dm, i, j, 0,
>> &point);CHKERRQ(ierr);
>> ierr = PetscSectionSetDof(s, point, testPoisson.mDof); //
>> No. of dofs associated with the point.
>> }
>> }
>> }
>> ierr = PetscSectionSetUp(s);CHKERRQ(ierr);
>> ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
>> ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
>> ierr = DMCreateMatrix(dm,&A);CHKERRQ(ierr);
>> ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
>>
>> ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
>> ierr = KSPSetDM(ksp,dm);CHKERRQ(ierr);
>>
>> ierr =
>> KSPSetComputeOperators(ksp,computeMatrix2dSection,(void*)&testPoisson);CHKERRQ(ierr);
>> ierr =
>> KSPSetComputeRHS(ksp,computeRhs2dSection,(void*)&testPoisson);CHKERRQ(ierr);
>>
>> ....
>> The function computeMatrix2dSection:
>>
>> #undef __FUNCT__
>> #define __FUNCT__ "computeMatrix2dSection"
>> PetscErrorCode computeMatrix2dSection(KSP ksp, Mat A, Mat B, MatStructure
>> *str, void *context) {
>> PoissonModel *ctx = (PoissonModel*)context;
>> PetscErrorCode ierr;
>> DM da;
>> DMDALocalInfo info;
>> PetscInt row, col[5];
>> PetscInt dof;
>> PetscScalar v[5]; //array to store 5 point stencil for
>> each row
>> PetscInt num; //non-zero position in the current row
>> // PetscScalar dScale = 1; //to scale Dirichlet
>> identity rows if needed
>> PetscSection gs; //Global Section that keeps
>> the grid info and indices
>> PetscInt point; //Current point of the
>> petscSection
>>
>> PetscFunctionBeginUser;
>> ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr);
>> ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
>> ierr = DMGetDefaultGlobalSection(da,&gs);CHKERRQ(ierr);
>> ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr);
>> // ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
>> for(PetscInt j = info.ys; j<info.ys+info.ym; ++j) {
>> for(PetscInt i = info.xs; i<info.xs+info.xm; ++i) {
>> if (isPosInDomain(ctx,i,j)) {
>> ierr = DMDAGetCellPoint(da,i,j,0,&point);CHKERRQ(ierr);
>> ierr = PetscSectionGetOffset(gs,point,&row);
>> ierr = PetscSectionGetDof(gs,point,&dof);
>> for(PetscInt cDof = 0; cDof < ctx->mDof; ++cDof) {
>> num = 0;
>> row+=cDof;
>> col[num] = row; //(i,j) position
>> v[num++] = -4;
>> if(isPosInDomain(ctx,i+1,j)) {
>> ierr =
>> DMDAGetCellPoint(da,i+1,j,0,&point);CHKERRQ(ierr);
>> ierr = PetscSectionGetOffset(gs,point,&col[num]);
>> col[num] += cDof;
>> v[num++] = 1;
>> }
>> if(isPosInDomain(ctx,i-1,j)) {
>> ierr =
>> DMDAGetCellPoint(da,i-1,j,0,&point);CHKERRQ(ierr);
>> ierr = PetscSectionGetOffset(gs,point,&col[num]);
>> col[num] += cDof;
>> v[num++] = 1;
>> }
>> if(isPosInDomain(ctx,i,j+1)) {
>> ierr =
>> DMDAGetCellPoint(da,i,j+1,0,&point);CHKERRQ(ierr);
>> ierr = PetscSectionGetOffset(gs,point,&col[num]);
>> col[num] += cDof;
>> v[num++] = 1;
>> }
>> if(isPosInDomain(ctx,i,j-1)) {
>> ierr =
>> DMDAGetCellPoint(da,i,j-1,0,&point);CHKERRQ(ierr);
>> ierr = PetscSectionGetOffset(gs,point,&col[num]);
>> col[num] += cDof;
>> v[num++] = 1;
>> }
>> ierr =
>> MatSetValues(A,1,&row,num,col,v,INSERT_VALUES);CHKERRQ(ierr);
>> }
>> }
>> }
>> }
>> ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>> ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>>
>>
>>
>>
>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> ------------------------------------
>>>>>>>> [0]PETSC ERROR: Argument out of range!
>>>>>>>> [0]PETSC ERROR: New nonzero at (0,6) caused a malloc!
>>>>>>>> [0]PETSC ERROR:
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: Petsc Development GIT revision:
>>>>>>>> 61e5e40bb2c5bf2423e94b71a15fef47e411b0da GIT Date: 2013-10-25 21:47:45
>>>>>>>> -0500
>>>>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [0]PETSC ERROR:
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: build/poissonIrregular on a arch-linux2-cxx-debug
>>>>>>>> named edwards by bkhanal Thu Oct 31 19:23:58 2013
>>>>>>>> [0]PETSC ERROR: Libraries linked from
>>>>>>>> /home/bkhanal/Documents/softwares/petsc/arch-linux2-cxx-debug/lib
>>>>>>>> [0]PETSC ERROR: Configure run at Sat Oct 26 16:35:15 2013
>>>>>>>> [0]PETSC ERROR: Configure options --download-mpich
>>>>>>>> -download-f-blas-lapack=1 --download-metis --download-parmetis
>>>>>>>> --download-superlu_dist --download-scalapack --download-mumps
>>>>>>>> --download-hypre --with-clanguage=cxx
>>>>>>>> [0]PETSC ERROR:
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: MatSetValues_SeqAIJ() line 413 in
>>>>>>>> src/mat/impls/aij/seq/aij.c
>>>>>>>> [0]PETSC ERROR: MatSetValues() line 1130 in
>>>>>>>> src/mat/interface/matrix.c
>>>>>>>> [0]PETSC ERROR: computeMatrix2dSection() line 318 in
>>>>>>>> /user/bkhanal/home/works/poissonIrregular/poissonIrregular.cxx
>>>>>>>> [0]PETSC ERROR: KSPSetUp() line 228 in
>>>>>>>> src/ksp/ksp/interface/itfunc.c
>>>>>>>> [0]PETSC ERROR: KSPSolve() line 399 in
>>>>>>>> src/ksp/ksp/interface/itfunc.c
>>>>>>>> [0]PETSC ERROR: main() line 598 in
>>>>>>>> /user/bkhanal/home/works/poissonIrregular/poissonIrregular.cxx
>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
>>>>>>>> [unset]: aborting job:
>>>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
>>>>>>>>
>>>>>>>>
>>>>>>>>> Matt
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> However, now since I do not want the rows in the matrix
>>>>>>>>>> corresponding to the points in the grid which do not lie in the
>>>>>>>>>> computational domain. This means the size of the matrix will not
>>>>>>>>>> necessarily equal the total number of cells in DMDA. So in the following
>>>>>>>>>> code:
>>>>>>>>>>
>>>>>>>>>> ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
>>>>>>>>>> ierr = PetscSectionCreate(PETSC_COMM_WORLD, &s);CHKERRQ(ierr);
>>>>>>>>>> ierr = DMDAGetNumCells(dm, NULL, NULL, NULL,
>>>>>>>>>> &nC);CHKERRQ(ierr);
>>>>>>>>>> ierr = PetscSectionSetChart(s, 0, nC);CHKERRQ(ierr);
>>>>>>>>>> for (PetscInt j = info.ys; j < info.ys+info.ym; ++j) {
>>>>>>>>>> for (PetscInt i = info.xs; i < info.xs+info.xm; ++i) {
>>>>>>>>>> PetscInt point;
>>>>>>>>>> if(isPosInDomain(&testPoisson,i,j,0)) {
>>>>>>>>>> ierr = DMDAGetCellPoint(dm, i, j, 0,
>>>>>>>>>> &point);CHKERRQ(ierr);
>>>>>>>>>> ierr = PetscSectionSetDof(s, point,
>>>>>>>>>> testPoisson.mDof); // No. of dofs associated with the point.
>>>>>>>>>> }
>>>>>>>>>>
>>>>>>>>>> }
>>>>>>>>>> }
>>>>>>>>>> ierr = PetscSectionSetUp(s);CHKERRQ(ierr);
>>>>>>>>>> ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
>>>>>>>>>> ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
>>>>>>>>>>
>>>>>>>>>> should I myself compute proper nC (i.e. total no. of points for
>>>>>>>>>> which I want the matrix to have a corresponding row) before calling
>>>>>>>>>> PetscSectionSetChart() or is the masking out of the points inside the loop
>>>>>>>>>> with if(isPosInDomain(&testPoisson,i,j,0)) sufficient ?
>>>>>>>>>> And, when you write:
>>>>>>>>>> PetscSectionGetOffset(gs, p, &ind);
>>>>>>>>>> row = ind < 0 ? -(ind+1) : ind;
>>>>>>>>>>
>>>>>>>>>> it seems you allow the possibility of getting a -ve ind when
>>>>>>>>>> using PetscSectionGetOffset. When would an offset to a particular dof and
>>>>>>>>>> point?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> for(PetscInt j = info.ys; j<info.ys+info.ym; ++j) {
>>>>>>>>>>>> for(PetscInt i = info.xs; i<info.xs+info.xm; ++i) {
>>>>>>>>>>>> num = 0;
>>>>>>>>>>>> /*ierr =
>>>>>>>>>>>> DMDAGetCellPoint(da,i,j,0,&point);CHKERRQ(ierr);*/ /*Get the PetscPoint*/
>>>>>>>>>>>> /*But I did now understand how I would emulate
>>>>>>>>>>>> the row.c and col.c info with PetscSection*/
>>>>>>>>>>>> row.i = i; row.j = j;
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Here you would call
>>>>>>>>>>>
>>>>>>>>>>> ierr = DMDAGetCellPoint(da, i, j, 0, &cell);CHKERRQ(ierr);
>>>>>>>>>>> ierr = PetscSectionGetOffset(da, cell, &row);CHKERRQ(ierr);
>>>>>>>>>>> ierr = PetscSectionGetDof(da, cell, &dof);CHKERRQ(ierr);
>>>>>>>>>>>
>>>>>>>>>>> This means that this cell has global rows = [row, row+dof).
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> col[num].i = i; col[num].j = j;
>>>>>>>>>>>> if (isPosInDomain(ctx,i,j)) { /*put the
>>>>>>>>>>>> operator for only the values for only the points lying in the domain*/
>>>>>>>>>>>> v[num++] = -4;
>>>>>>>>>>>> if(isPosInDomain(ctx,i+1,j)) {
>>>>>>>>>>>> col[num].i = i+1; col[num].j = j;
>>>>>>>>>>>> v[num++] = 1;
>>>>>>>>>>>> }
>>>>>>>>>>>> if(isPosInDomain(ctx,i-1,j)) {
>>>>>>>>>>>> col[num].i = i-1; col[num].j = j;
>>>>>>>>>>>> v[num++] = 1;
>>>>>>>>>>>> }
>>>>>>>>>>>> if(isPosInDomain(ctx,i,j+1)) {
>>>>>>>>>>>> col[num].i = i; col[num].j = j+1;
>>>>>>>>>>>> v[num++] = 1;
>>>>>>>>>>>> }
>>>>>>>>>>>> if(isPosInDomain(ctx,i,j-1)) {
>>>>>>>>>>>> col[num].i = i; col[num].j = j-1;
>>>>>>>>>>>> v[num++] = 1;
>>>>>>>>>>>> }
>>>>>>>>>>>> } else {
>>>>>>>>>>>> v[num++] = dScale; /*set Dirichlet
>>>>>>>>>>>> identity rows for points in the rectangle but outside the computational
>>>>>>>>>>>> domain*/
>>>>>>>>>>>> }
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> You do the same thing for the columns, and then call
>>>>>>>>>>>
>>>>>>>>>>> ierr = MatSetValues(A, dof, rows, num*dof, cols, v,
>>>>>>>>>>> INSERT_VALUES);CHKERRQ(ierr);
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> ierr =
>>>>>>>>>>>> MatSetValuesStencil(A,1,&row,num,col,v,INSERT_VALUES);CHKERRQ(ierr);
>>>>>>>>>>>> }
>>>>>>>>>>>> }
>>>>>>>>>>>> }
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> If not, just put the identity into
>>>>>>>>>>>>>>>>>>>>>>> the rows you do not use on the full cube. It will
>>>>>>>>>>>>>>>>>>>>>>> not hurt scalability or convergence.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> In the case of Poisson with Dirichlet condition this
>>>>>>>>>>>>>>>>>>>>>> might be the case. But is it always true that having identity rows in the
>>>>>>>>>>>>>>>>>>>>>> system matrix will not hurt convergence ? I thought otherwise for the
>>>>>>>>>>>>>>>>>>>>>> following reasons:
>>>>>>>>>>>>>>>>>>>>>> 1) Having read Jed's answer here :
>>>>>>>>>>>>>>>>>>>>>> http://scicomp.stackexchange.com/questions/3426/why-is-pinning-a-point-to-remove-a-null-space-bad/3427#3427
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Jed is talking about a constraint on a the pressure at
>>>>>>>>>>>>>>>>>>>>> a point. This is just decoupling these unknowns from the rest
>>>>>>>>>>>>>>>>>>>>> of the problem.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> 2) Some observation I am getting (but I am still
>>>>>>>>>>>>>>>>>>>>>> doing more experiments to confirm) while solving my staggered-grid 3D
>>>>>>>>>>>>>>>>>>>>>> stokes flow with schur complement and using -pc_type gamg for A00 matrix.
>>>>>>>>>>>>>>>>>>>>>> Putting the identity rows for dirichlet boundaries and for ghost cells
>>>>>>>>>>>>>>>>>>>>>> seemed to have effects on its convergence. I'm hoping once I know how to
>>>>>>>>>>>>>>>>>>>>>> use PetscSection, I can get rid of using ghost cells method for the
>>>>>>>>>>>>>>>>>>>>>> staggered grid and get rid of the identity rows too.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> It can change the exact iteration, but it does not
>>>>>>>>>>>>>>>>>>>>> make the matrix conditioning worse.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Anyway please provide me with some pointers so that
>>>>>>>>>>>>>>>>>>>>>> I can start trying with petscsection on top of a dmda, in the beginning for
>>>>>>>>>>>>>>>>>>>>>> non-staggered case.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>> Bishesh
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Matt
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>> Bishesh
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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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