Dear PETSc developers
I got an error with MatZeroRowsColumns, which said there was one missing
diagonal entries
This is the full log message that I got:
Mat Object: 2 MPI processes
type: mpiaij
rows=41064, cols=41064, bs=4
total: nonzeros=5.66069e+06, allocated nonzeros=1.28112e+07
total number of mallocs used during MatSetValues calls =0
using I-node (on process 0) routines: found 5647 nodes, limit used is 5
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Matrix is missing diagonal entry in row 7
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
[0]PETSC ERROR: python on a arch-linux2-cxx-opt named bermuda by hbui2 Wed
Jan 13 10:27:42 2016
[0]PETSC ERROR: Configure options --with-shared-libraries
--with-debugging=0 --with-pic --with-clanguage=cxx
--download-fblas-lapack=yes --download-ptscotch=yes --download-metis=yes
--download-parmetis=yes --download-scalapack=yes --download-mumps=yes
--download-hypre=yes --download-ml=yes --download-klu=yes
--download-pastix=yes --with-mpi-dir=/opt/openmpi-1.10.1_thread-multiple
--prefix=/home/hbui/opt/petsc-3.6.3
[0]PETSC ERROR: #1 MatZeroRowsColumns_SeqAIJ() line 1901 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: #2 MatZeroRowsColumns() line 5476 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/interface/matrix.c
[0]PETSC ERROR: #3 MatZeroRowsColumns_MPIAIJ() line 908 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: #4 MatZeroRowsColumns() line 5476 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/interface/matrix.c
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Object is in wrong state
[1]PETSC ERROR: Matrix is missing diagonal entry in row 7
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[1]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015
[1]PETSC ERROR: python on a arch-linux2-cxx-opt named bermuda by hbui2 Wed
Jan 13 10:27:42 2016
[1]PETSC ERROR: Configure options --with-shared-libraries
--with-debugging=0 --with-pic --with-clanguage=cxx
--download-fblas-lapack=yes --download-ptscotch=yes --download-metis=yes
--download-parmetis=yes --download-scalapack=yes --download-mumps=yes
--download-hypre=yes --download-ml=yes --download-klu=yes
--download-pastix=yes --with-mpi-dir=/opt/openmpi-1.10.1_thread-multiple
--prefix=/home/hbui/opt/petsc-3.6.3
[1]PETSC ERROR: #1 MatZeroRowsColumns_SeqAIJ() line 1901 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/impls/aij/seq/aij.c
[1]PETSC ERROR: #2 MatZeroRowsColumns() line 5476 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/interface/matrix.c
[1]PETSC ERROR: #3 MatZeroRowsColumns_MPIAIJ() line 908 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: #4 MatZeroRowsColumns() line 5476 in
/media/NEW_HOME/sw2/petsc-3.6.3/src/mat/interface/matrix.c
The problem is, before calling MatZeroRowsColumns, I searched for zero rows
and set the respective diagonal:
PetscInt Istart, Iend;
MatGetOwnershipRange(rA.Get(), &Istart, &Iend);
// loop through each row in the current partition
for(PetscInt row = Istart; row < Iend; ++row)
{
int ncols;
const PetscInt* cols;
const PetscScalar* vals;
MatGetRow(rA.Get(), row, &ncols, &cols, &vals);
PetscScalar row_norm = 0.0;
for(int i = 0; i < ncols; ++i)
{
PetscScalar val = vals[i];
row_norm += pow(val, 2);
}
row_norm = sqrt(row_norm);
if(row_norm == 0.0)
{
for(int i = 0; i < ncols; ++i)
{
PetscInt col = cols[i];
if(col == row)
{
MatSetValue(rA.Get(), row, col, 1.0, INSERT_VALUES);
}
}
}
MatRestoreRow(rA.Get(), row, &ncols, &cols, &vals);
}
// cached the modification
MatAssemblyBegin(rA.Get(), MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(rA.Get(), MAT_FINAL_ASSEMBLY);
This should set all the missing diagonal for missing rows. But I could not
figure out why the error message above happen. Any ideas?
Regards
Giang
