I tried to implement the example from step 15, but using MPI, so that I can
get a better grasp on how to write such programs. My residual calculation
looks quite similar to the original:
const QGauss<dim> quadrature_formula(fe.degree+1);
FEValues<dim>
fe_values (fe, quadrature_formula,
update_gradients |
update_quadrature_points |
update_JxW_values);
const unsigned int dofs_per_cell = fe.dofs_per_cell;
const unsigned int n_q_points = quadrature_formula.size();
Vector<double> cell_residual (dofs_per_cell);
std::vector<Tensor<1, dim> > gradients(n_q_points);
std::vector<types::global_dof_index> local_dof_indices (dofs_per_cell);
print_status_update(std::string("Starting looping over cells in residual\n"
), false);
for (auto cell = dof_handler.begin_active(); cell!=dof_handler.end(); ++
cell)
{
if(cell->is_locally_owned())
{
cell_residual = 0;
fe_values.reinit (cell);
fe_values.get_function_gradients (evaluation_point,
gradients);
for (unsigned int q_point=0; q_point<n_q_points; ++q_point)
{
const double coeff = 1/std::sqrt(1 +
gradients[q_point] *
gradients[q_point]);
for (unsigned int i = 0; i < dofs_per_cell; ++i)
cell_residual(i) -= (fe_values.shape_grad(i, q_point)
* coeff
* gradients[q_point]
* fe_values.JxW(q_point));
}
cell->get_dof_indices (local_dof_indices);
hanging_node_constraints.distribute_local_to_global(cell_residual,
local_dof_indices, residual);
}
}
residual.compress(VectorOperation::add);//Have to call it after
"distribute_local_to_global
print_status_update(std::string("Setting boundary dofs in residual
calculation\n"), true);
std::vector<bool> boundary_dofs (dof_handler.n_locally_owned_dofs());
DoFTools::extract_boundary_dofs (dof_handler,
ComponentMask(),
boundary_dofs);
print_status_update(std::string("Boundary dofs extracted\n"), true);
print_status_update(std::string("Residual size is " + std::to_string(
residual.size()) + " and boundary dofs size is " + std::to_string(
boundary_dofs.size()) + "\n"), true);
for (unsigned int i=0; i<dof_handler.n_locally_owned_dofs(); ++i)
if (boundary_dofs[i] == true)
residual(i) = 0;
residual.compress(VectorOperation::insert);//Have to call it after setting
the boundary elements
print_status_update(std::string("Returning l2 norm: " + std::to_string(
residual.l2_norm()) + "\n"), true);//Crash here
// At the end of the function, we return the norm of the residual:
return residual.l2_norm();
At the noted line (when trying to access the l2_norm) I get the error
ERROR: Uncaught exception in MPI_InitFinalize on proc 0. Skipping
MPI_Finalize() to avoid a deadlock.
----------------------------------------------------
Exception on processing:
--------------------------------------------------------
An error occurred in line <1774> of file </opt/dealII/include/deal.II/lac/
trilinos_vector.h> in function
dealii::TrilinosWrappers::MPI::Vector::real_type dealii::
TrilinosWrappers::MPI::Vector::l2_norm() const
The violated condition was:
ierr == 0
Additional information:
An error with error number -1 occurred while calling a Trilinos function
--------------------------------------------------------
Aborting!
----------------------------------------------------
ERROR: Uncaught exception in MPI_InitFinalize on proc 1. Skipping
MPI_Finalize() to avoid a deadlock.
----------------------------------------------------
Exception on processing:
--------------------------------------------------------
An error occurred in line <1774> of file </opt/dealII/include/deal.II/lac/
trilinos_vector.h> in function
dealii::TrilinosWrappers::MPI::Vector::real_type dealii::
TrilinosWrappers::MPI::Vector::l2_norm() const
The violated condition was:
ierr == 0
Additional information:
An error with error number -1 occurred while calling a Trilinos function
--------------------------------------------------------
Aborting!
----------------------------------------------------
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
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: [[51822,1],0]
Exit code: 1
--------------------------------------------------------------------------
if running with more than one node (it works fine with one node).
I already know that I have to call l2_norm() in all the nodes I am running
(as stated here:
https://www.dealii.org/8.4.0/doxygen/deal.II/classTrilinosWrappers_1_1MPI_1_1Vector.html),
and that I should call "compress()" before doing so, after I am setting
certain elements in the vector, in order to prevent an MPI error (as
described
here:
https://www.dealii.org/8.4.0/doxygen/deal.II/classTrilinosWrappers_1_1MPI_1_1Vector.html
and
here:
https://www.dealii.org/8.4.0/doxygen/deal.II/classTrilinosWrappers_1_1VectorBase.html#af7b7a23734c0202578e8dd1421e8af5b).
But nevertheless I still get that error. Which point did I forget?
Thanks!
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