[petsc-users] PETSc set off-diagonal matrix pre-allocation

[Andrew Ho]

I have a 3x6 matrix, and I want to set it to (just as an example):

0 0 0 1 1 1
0 0 0 1 1 1
0 0 0 1 1 1

>From what I can tell, according to the documentation the MPIAIJ sparsity of
this matrix is:

d_nnz = [0, 0, 0]
o_nnz = [3, 3, 3]

However, when I do this, I get the following error:

[0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: New nonzero at (0,3) caused a malloc
> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn
> off this check
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.7.5, unknown
> [0]PETSC ERROR: ./ex3 on a arch-linux2-c-opt Tue Feb 14 04:23:56 2017
> [0]PETSC ERROR: Configure options --with-debugging=0 --COPTFLAGS="-O3
> -march=native" --CXXOPTFLAGS="-O3 -march=native" --FOPTFLAGS="-O3
> -march=native"
> [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 582 in
> petsc/src/mat/impls/aij/mpi/mpiaij.c
> [0]PETSC ERROR: #2 MatSetValues() line 1190 in
> petsc/src/mat/interface/matrix.c
> [0]PETSC ERROR: #3 main() line 36 in ex3.c
> [0]PETSC ERROR: No PETSc Option Table entries
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------


Here's a working test code:

#include <petsc.h>
> #include <mpi.h>
> int main(int argc, char** argv)
> {
>   PetscErrorCode err;
>   err = PetscInitialize(&argc, &argv, NULL, "help");
>   CHKERRQ(err);
>   // create a sparse AIJ matrix distributed across MPI
>   PetscInt global_width = 6;
>   PetscInt global_height = 3;
>   Mat A;
>   err = MatCreate(MPI_COMM_WORLD, &A);
>   CHKERRQ(err);
>   err = MatSetType(A, MATMPIAIJ);
>   CHKERRQ(err);
>   // setup pre-allocation for matrix space
>   {
>     err =
>       MatSetSizes(A, global_height, PETSC_DECIDE, global_height,
> global_width);
>     CHKERRQ(err);
>     PetscInt d_nnz[] = {0, 0, 0};
>     PetscInt o_nnz[] = {3, 3, 3};
>     err = MatMPIAIJSetPreallocation(A, 0, d_nnz, 0, o_nnz);
>     CHKERRQ(err);
>   }
>   err = MatSetUp(A);
>   CHKERRQ(err);
>   // set values inside the matrix
>   for (PetscInt row = 0; row < global_height; ++row)
>   {
>     for (PetscInt col = global_height; col < global_width; ++col)
>     {
>       err = MatSetValue(A, row, col, 1, INSERT_VALUES);
>       CHKERRQ(err);
>     }
>   }
>   err = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
>   CHKERRQ(err);
>   err = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
>   CHKERRQ(err);
>   err = MatView(A, PETSC_VIEWER_STDOUT_WORLD);
>   CHKERRQ(err);
>   // free memory
>   err = MatDestroy(&A);
>   CHKERRQ(err);
>   // cleanup any internal PETSc data at end of program
>   err = PetscFinalize();
>   CHKERRQ(err);
> }


Am I mis-understanding what the d_nnz and o_nnz parameter are supposed to
mean?
-- 
Andrew Ho
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