[petsc-users] Problem with Preallocating

[Matthew Knepley]

Can you send a small example? This looks like it should work.

   Matt

On Wed, Oct 29, 2014 at 8:00 AM, Florian Lindner <mailinglists at xgm.de>
wrote:

> Hello,
>
> I try to preallocate a sparse matrix like it was recommended in another
> posting, but get an error which kind of surprises me. Somehow I think it
> might be related to the order of assembly calls...
>
> My code creates the matrix:
>
>   MatSetType(_matrixC.matrix, MATSBAIJ);
>   MatSetSizes(_matrixC.matrix, PETSC_DECIDE, PETSC_DECIDE, n, n);
>   MatSetOption(_matrixC.matrix, MAT_SYMMETRY_ETERNAL, PETSC_TRUE);
>
> Than I enter a loop to get the number of elements per row.  The entire
> code is a bit too long, but right before the SetPreallocaiton I do:
>
>   for (int r = 0; r < n; r++) {
>     cout << "Preallocated row " << r << " with " << nnz[r]  << "
> elements." << endl;
>   }
>
> which results in the output:
>
> Matrix Size = 9
> Preallocated row 0 with 9 elements.
> Preallocated row 1 with 8 elements.
> Preallocated row 2 with 7 elements.
> Preallocated row 3 with 6 elements.
> Preallocated row 4 with 5 elements.
> Preallocated row 5 with 4 elements.
> Preallocated row 6 with 1 elements.
> Preallocated row 7 with 1 elements.
> Preallocated row 8 with 1 elements.
>
> at least in rows 0 to 5 it's a dense upper triangular matrix (incl. main
> diagonal).
>
>   ierr = MatSeqSBAIJSetPreallocation(_matrixC.matrix, 1, PETSC_DEFAULT,
> nnz);
>
> Now more or less the same loops as above with MatSetValues call for each
> row.
>
> Since the KSPSolver requires that the diagonal is set, even if it's merely
> with zeros I do:
>
>   _matrixC.assemble(MAT_FLUSH_ASSEMBLY)  // my helper function, but I'm
> sure you get the point ;-)
>   petsc::Vector zeros(_matrixC);
>   MatDiagonalSet(_matrixC.matrix, zeros.vector, ADD_VALUES);
>   ierr = MatAssemblyBegin(_matrixC.matrix, MAT_FINAL_ASSEMBLY);
> CHKERRV(ierr);
>   [ some more code ]
>   ierr = MatAssemblyEnd(_matrixC.matrix, MAT_FINAL_ASSEMBLY);
> CHKERRV(ierr);
>
> But when I run the code I get an error message:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: New nonzero at (0,0) 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 3.5.2, unknown
> [0]PETSC ERROR: ./petBench on a arch-linux2-c-debug named helium by
> lindnefn Wed Oct 29 13:48:49 2014
> [0]PETSC ERROR: Configure options --with-debugging=1
> [0]PETSC ERROR: #1 MatSetValues_SeqSBAIJ() line 977 in
> /data2/scratch/lindner/petsc/src/mat/impls/sbaij/seq/sbaij.c
> [0]PETSC ERROR: #2 MatSetValues() line 1135 in
> /data2/scratch/lindner/petsc/src/mat/interface/matrix.c
> [0]PETSC ERROR: #3 MatDiagonalSet_Default() line 203 in
> /data2/scratch/lindner/petsc/src/mat/utils/axpy.c
> [0]PETSC ERROR: #4 MatDiagonalSet() line 241 in
> /data2/scratch/lindner/petsc/src/mat/utils/axpy.c
>
> I'm surprised that I get this error message since I do have preallocated 9
> elements and I do not understand why inserting an element at (0, 0) could
> be a problem / needing a malloc. Has the preallocation got lost somewhere?
>
> Thanks once again....
>
> Florian
>



-- 
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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