Dear All,
I am doing a radiation transport problem, which has multiple individual
equations (number determined by the number of directions we input). As the
number of directions is arbitrary, I put the sparsematries are contained in
std::vectors as raw pointers (using LA namespace to stand for PETScWrappers)
std::vector<LA::MPI::SparseMatrix*> sys_mats;
When initializing:
for (unsigned int i=0; i<n_dir; ++i)
{
sys_mats.push_back (new LA::MPI::SparseMatrix*);
sys_mats[i]->reinit (locally_owned_dofs,
locally_owned_dofs,
dsp,
mpi_communicator);
}
When assembling:
for (; cell!=endc; ++cell)
{
if (cell->is_locally_owned())
{
std::vector<FullMatrix<double> > local_mats
// do local matrix and boundary term assembly for all directions in one
cell
cell->get_dof_indices (local_dof_indices);
// Map local matrices to global matrices for all directions
for (unsigned int i=0; i<n_dir; ++i)
{
sys_mats[i]->add (local_dof_indices,
local_mats [ i ]);
}
}
}
Then we compress:
for (unsigned int i=0; i<n_dir; ++i)
{
sys_mats[i]->compress (VectorOperation::add);
pcout << "we have compressed Dir " << i << std::endl;
}
Now, I got the error: compressing can go through direction 0 but not 1 with
the error at the end of this post.
Any ideas how to fix it?
Thanks in advance!
Weixiong
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: Inserting a new nonzero at global row/column (6, 15) into
matrix
[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, unknown
[0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 613 in
/usr/local/src/d2-parallel-package/petsc/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: #2 MatAssemblyEnd_MPIAIJ() line 731 in
/usr/local/src/d2-parallel-package/petsc/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: #3 MatAssemblyEnd() line 5098 in
/usr/local/src/d2-parallel-package/petsc/src/mat/interface/matrix.c
ERROR: Uncaught exception in MPI_InitFinalize on proc 0. Skipping
MPI_Finalize() to avoid a deadlock.
----------------------------------------------------
Exception on processing:
--------------------------------------------------------
An error occurred in line <263> of file
<../source/lac/petsc_matrix_base.cc> in function
void dealii::PETScWrappers::MatrixBase::compress(const
VectorOperation::values)
The violated condition was:
ierr == 0
The name and call sequence of the exception was:
ExcPETScError(ierr)
Additional Information:
An error with error number 63 occurred while calling a PETSc function
--------------------------------------------------------
Aborting!
----------------------------------------------------
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 59.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors
[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[1]PETSC ERROR: to get more information on the crash.
[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Signal received
[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, unknown
[1]PETSC ERROR: dg-ep-proto on a uly named my_hostname by GrillCheese Tue
Jun 6 01:18:23 2017
[1]PETSC ERROR: Configure options --with-make-np=8 --with-debugging=0
--prefix=/Applications/deal.II.app/Contents/Resources/opt/petsc-3e25e16
--with-mpi-dir=/Applications/deal.II.app/Contents/Resources/opt/openmpi-1.10.2
--with-sundials-dir=/Applications/deal.II.app/Contents/Resources/opt/sundials-6b7e4b6
--with-shared-libraries
--with-external-packages-dir=/Users/heltai/d2-parallel-package/petsc-external
--download-parmetis --download-metis --download-hypre --download-mumps
--download-scalapack --download-superlu --download-superlu_dist
--download-hdf5
[1]PETSC ERROR: #1 User provided function() line 0 in unknown file
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[50193,1],0]
Exit code: 1
--------------------------------------------------------------------------
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