[petsc-users] Problem with Preallocating

[Florian Lindner]

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