[petsc-users] ERROR: Argument out of range!; Local index XX too large XX (max) at 0! with MatSetValuesStencil
Bishesh Khanal
bisheshkh at gmail.com
Fri Jul 5 04:37:06 CDT 2013
On Thu, Jul 4, 2013 at 10:34 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> The j should be tracking the y variable and the i the x variable. See
> for example src/ksp/ksp/examples/tutorials/ex29.c
>
> for (j=ys; j<ys+ym; j++) {
> for (i=xs; i<xs+xm; i++) {
> row.i = i; row.j = j;
>
> Thanks Barry, tracking y variable with i, and x with j was the problem!
Interchanging them worked.
> After you fix this run with a 3 by 4 mesh and check the line number
> printed indicating the problem. Then look at the row and column values for
> that problem and see in the code how it could get out of bounds.
>
I'm afraid I did not understand exactly which line number that gets printed
are you talking about ? Is it this one in the error message ?
[0]PETSC ERROR: main() line 75 in
"unknowndirectory/"/user/bkhanal/home/works/cmake_tuts/petsc_test/examples/FDdmda_test.cxx
where there is a call to the function MatSetValuesStencil ?
Could you please clarify a bit more ?
> Barry
>
> On Jul 4, 2013, at 8:11 AM, Bishesh Khanal <bisheshkh at gmail.com> wrote:
>
> >
> > On Thu, Jul 4, 2013 at 2:59 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Thu, Jul 4, 2013 at 7:32 AM, Bishesh Khanal <bisheshkh at gmail.com>
> wrote:
> > Hi all,
> > I'm trying to use DMCreateMatrix and MatStencil to fill up a matrix that
> results from a finite difference discretization of a PDE (objective is to
> solve the resulting linear system in the form of Ax=b).
> >
> > However there are some errors and I'm not sure about the issue!
> > A short demo:
> > A 2D mXn grid, with two variables at each node (dof=2),
> > so the resulting A would be 2mn X 2mn.
> > Let's say the two variables are vx and vy, and the two associated
> > equations discretized are x-eq and y-eq.
> >
> > Here is the relevant part of the code: (mat1 variable for the A matrix):
> >
> > Just sending the whole code is better. I suspect the logic is wrong for
> selecting the boundary.
> >
> > Matt
> >
> > Thanks, here is the complete code:
> >
> > #include <petscsys.h>
> > #include <petscdmda.h>
> >
> > #undef __FUNCT__
> > #define __FUNCT__ "main"
> > int main(int argc,char **argv)
> > {
> > PetscErrorCode ierr;
> > DM da;
> > PetscInt m=10,n=10;
> >
> > ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
> >
> > /* Create a DMDA and an associated vector */
> > ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE,
> DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,m,n,
> >
> PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr);
> >
> > Mat mat1;
> > ierr = DMCreateMatrix(da,MATMPIAIJ,&mat1); CHKERRQ(ierr);
> > MatStencil row, col[4]; //let's test 4 non-zeros in one row.
> > PetscScalar val[4];
> > PetscScalar coeff = 2.; //just a constant coefficient for testing.
> > PetscInt i,j;
> > DMDALocalInfo info;
> >
> > ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
> >
> > for(i = info.ys; i < info.ys+info.ym; ++i){
> > for(j = info.xs; j < info.xs+info.xm; ++j){
> > row.i = i; row.j = j; //one node at a time
> > if (j == 0 || j == info.mx-1){ //left and right borders
> > //vx(i,j) = 0;
> > row.c = 0;
> > col[0].c = 0; val[0] = 1;
> > col[0].i = i; col[0].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,1,col,val,INSERT_VALUES);CHKERRQ(ierr);
> >
> > //vy: //vy(i,j) - c*vy(i,j+-1) = 0;
> > row.c = 1;
> > col[0].c = 1; val[1] = coeff;
> > col[1].c = 1;
> > col[1].i = i;
> > if(j == 0) //vy(i,j) - c*vy(i,j+1) = 0;
> > col[1].j = j+1;
> > else //vy(i,j) - c*vy(i,j-1) = 0;
> > col[1].j = j-1;
> >
> > ierr =
> MatSetValuesStencil(mat1,1,&row,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
> > }
> > else if (i == 0 || i == info.my-1){ //top and bottom borders
> > //vx: vx(i,j) - c* vx(i+-1,j) = 0;
> > row.c = 0;
> > col[0].c = 0; val[0] = 1;
> > col[0].i = i; col[0].j = j;
> > col[1].c = 0; val[1] = coeff;
> > if (i == 0) //vx(i,j) - c*vx(i+1,j) = 0;
> > col[1].i = i+1;
> > else //vx(i,j) - c*vx(i-1,j) = 0;
> > col[1].i = i-1;
> > col[1].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
> >
> > //vy(i,j) = 0;
> > row.c = 1;
> > col[0].c = 1;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,1,col,val,INSERT_VALUES);CHKERRQ(ierr);
> > }
> > else { //Interior points:
> > row.c = 0;//x-eq
> > col[0].c = 0; val[0] = 2*coeff;
> > col[0].i = i; col[0].j = j+1;
> > col[1].c = 0; val[1] = -val[0] - coeff;
> > col[1].i = i; col[1].j = j;
> > col[2].c = 1; val[2] = 4*coeff;
> > col[2].i = i+1; col[2].j = j;
> > col[3].c = 1; val[3] = 4*coeff;
> > col[3].i = i; col[3].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,4,col,val,INSERT_VALUES);CHKERRQ(ierr);
> >
> > row.c = 1; //y-eq
> > col[0].c = 1; val[0] = 2*coeff;
> > col[0].i = i; col[0].j = j+1;
> > col[1].c = 1; val[1] = -val[0] - coeff;
> > col[1].i = i; col[1].j = j;
> > col[2].c = 0; val[2] = 4*coeff;
> > col[2].i = i+1; col[2].j = j;
> > col[3].c = 0; val[3] = 4*coeff;
> > col[3].i = i; col[3].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,4,col,val,INSERT_VALUES);CHKERRQ(ierr);
> > }
> > }
> > }
> >
> > MatAssemblyBegin(mat1,MAT_FINAL_ASSEMBLY);
> > MatAssemblyEnd(mat1,MAT_FINAL_ASSEMBLY);
> > ierr =
> MatSetOption(mat1,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
> > ierr = PetscObjectSetName((PetscObject)mat1,"mat1");CHKERRQ(ierr);
> >
> > /* clean up and exit */
> > ierr = DMDestroy(&da);CHKERRQ(ierr);
> > ierr = MatDestroy(&mat1);
> > ierr = PetscFinalize();
> > return 0;
> > }
> >
> >
> >
> >
> > PetscInt m = 10, n=10;
> > ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE,
> DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,m,n,
> >
> PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr);
> >
> > Mat mat1;
> > ierr = DMCreateMatrix(da,MATMPIAIJ,&mat1); CHKERRQ(ierr);
> > MatStencil row, col[4]; //let's test 4 non-zeros in one row.
> > PetscScalar val[4];
> > PetscScalar coeff = 2.; //just a constant coefficient for testing.
> > PetscInt i,j;
> > DMDALocalInfo info;
> > ierr = DMDAGetLocalInfo(da,&info); CHKERRQ(ierr);
> > //Now fill up the matrix:
> > for(i = info.ys; i < info.ys+info.ym; ++i){
> > for(j = info.xs; j < info.xs+info.xm; ++j){
> > row.i = i; row.j = j; //one node at a time
> > if (j == 0 || j == info.mx-1){ //left and right borders
> > //vx(i,j) = 0;
> > row.c = 0;
> > col[0].c = 0; val[0] = 1;
> > col[0].i = i; col[0].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,1,col,val,INSERT_VALUES);CHKERRQ(ierr);
> >
> > //vy: //vy(i,j) - c*vy(i,j+-1) = 0;
> > row.c = 1;
> > col[0].c = 1; val[1] = coeff;
> > col[1].c = 1;
> > col[1].i = i;
> > if(j == 0) //vy(i,j) - c*vy(i,j+1) = 0;
> > col[1].j = j+1;
> > else //vy(i,j) - c*vy(i,j-1) = 0;
> > col[1].j = j-1;
> >
> > ierr =
> MatSetValuesStencil(mat1,1,&row,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
> > }
> > else if (i == 0 || i == info.my-1){ //top and bottom borders
> > //vx: vx(i,j) - c* vx(i+-1,j) = 0;
> > row.c = 0;
> > col[0].c = 0; val[0] = 1;
> > col[0].i = i; col[0].j = j;
> > col[1].c = 0; val[1] = coeff;
> > if (i == 0) //vx(i,j) - c*vx(i+1,j) = 0;
> > col[1].i = i+1;
> > else //vx(i,j) - c*vx(i-1,j) = 0;
> > col[1].i = i-1;
> > col[1].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
> >
> > //vy(i,j) = 0;
> > row.c = 1;
> > col[0].c = 1;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,1,col,val,INSERT_VALUES);CHKERRQ(ierr);
> > }
> > else { //Interior points:
> > row.c = 0;//x-eq
> > col[0].c = 0; val[0] = 2*coeff;
> > col[0].i = i; col[0].j = j+1;
> > col[1].c = 0; val[1] = -val[0] - coeff;
> > col[1].i = i; col[1].j = j;
> > col[2].c = 1; val[2] = 4*coeff;
> > col[2].i = i+1; col[2].j = j;
> > col[3].c = 1; val[3] = 4*coeff;
> > col[3].i = i; col[3].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,4,col,val,INSERT_VALUES);CHKERRQ(ierr);
> >
> > row.c = 1; //y-eq
> > col[0].c = 1; val[0] = 2*coeff;
> > col[0].i = i; col[0].j = j+1;
> > col[1].c = 1; val[1] = -val[0] - coeff;
> > col[1].i = i; col[1].j = j;
> > col[2].c = 0; val[2] = 4*coeff;
> > col[2].i = i+1; col[2].j = j;
> > col[3].c = 0; val[3] = 4*coeff;
> > col[3].i = i; col[3].j = j;
> > ierr =
> MatSetValuesStencil(mat1,1,&row,4,col,val,INSERT_VALUES);CHKERRQ(ierr);
> > }
> > }
> > }
> >
> > MatAssemblyBegin(mat1,MAT_FINAL_ASSEMBLY);
> > MatAssemblyEnd(mat1,MAT_FINAL_ASSEMBLY);
> >
> > However I get the following error when run with 2 processors.
> > [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > [0]PETSC ERROR: Argument out of range!
> > [0]PETSC ERROR: Local index 120 too large 120 (max) at 0!
> > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Release Version 3.4.1, Jun, 10, 2013
> > [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: examples/FDdmda_test on a arch-linux2-cxx-debug named
> edwards by bkhanal Thu Jul 4 14:20:11 2013
> > [0]PETSC ERROR: Libraries linked from
> /home/bkhanal/Documents/softwares/petsc-3.4.1/arch-linux2-cxx-debug/lib
> > [0]PETSC ERROR: Configure run at Wed Jun 19 11:04:51 2013
> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=g77
> --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1
> -with-clanguage=cxx --download-hypre=1
> > [0]PETSC ERROR:
> ------------------------------------------------------------------------
> > [0]PETSC ERROR: ISLocalToGlobalMappingApply() line 444 in
> /home/bkhanal/Documents/softwares/petsc-3.4.1/src/vec/is/utils/isltog.c
> > [0]PETSC ERROR: MatSetValuesLocal() line 1967 in
> /home/bkhanal/Documents/softwares/petsc-3.4.1/src/mat/interface/matrix.c
> > [0]PETSC ERROR: MatSetValuesStencil() line 1339 in
> /home/bkhanal/Documents/softwares/petsc-3.4.1/src/mat/interface/matrix.c
> > [0]PETSC ERROR: main() line 75 in
> "unknowndirectory/"/user/bkhanal/home/works/cmake_tuts/petsc_test/examples/FDdmda_test.cxx
> > application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
> > [cli_0]: aborting job:
> > application called MPI_Abort(MPI_COMM_WORLD, 63) - process 0
> >
> >
> ===================================================================================
> > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> > = EXIT CODE: 63
> > = CLEANING UP REMAINING PROCESSES
> > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> >
> ===================================================================================
> >
> > I do not understand how the index (i,j) are out of range when set to
> corresponding fields in row and col variables. What could be the possible
> problem ? And any suggestions on the way to debug this sort of issues ?
> >
> > 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
> >
>
>
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