Dear Timo,
Regarding using MappingQEulerian class in parallel, I did what you said for
the vector type template argument. It works when I run the code on my own
machine but I got the following error when I run it on cluster:
An error occurred in line <1480> of file
</shared/hpc/deal.ii-candi/deal.II-v8.4.1/include/deal.II/base/index_set.h>
in function
dealii::IndexSet::size_type
dealii::IndexSet::index_within_set(dealii::IndexSet::size_type) const
The violated condition was:
is_element(n) == true
The name and call sequence of the exception was:
ExcIndexNotPresent (n)
Additional Information:
The global index 0 is not an element of this set.
Stacktrace:
-----------
#0 ./parallel_large-strain_PT: dealii::IndexSet::index_within_set(unsigned
int) const
#1 /shared/hpc/deal.ii-candi/deal.II-v8.4.1/lib/libdeal_II.g.so.8.4.1:
dealii::PETScWrappers::internal::VectorReference::operator double() const
#2 ./parallel_large-strain_PT: PhaseField::Solid<3>::output_results() const
#3 ./parallel_large-strain_PT: PhaseField::Solid<3>::run()
#4 ./parallel_large-strain_PT: main
--------------------------------------------------------
Following is my out_put object. problem is related to the MappingQEulerian
since when I uncomment it (the red lines) I don't get error.
template <int dim>
void Solid<dim>::output_results() const
{
DataOut<dim> data_out;
std::vector<std::string> displacement_names;
switch (dim)
{
case 1:
displacement_names.push_back ("displacement");
break;
case 2:
displacement_names.push_back ("x_displacement");
displacement_names.push_back ("y_displacement");
break;
case 3:
displacement_names.push_back ("x_displacement");
displacement_names.push_back ("y_displacement");
displacement_names.push_back ("z_displacement");
break;
default:
Assert (false, ExcNotImplemented());
}
data_out.add_data_vector (dof_handler, solution, displacement_names);
data_out.add_data_vector (dof_handler_eta, solution_eta,
"order_parameter");
LA::MPI::Vector soln ;
soln.reinit(locally_owned_dofs,mpi_communicator);
for (unsigned int i = 0; i < soln.size(); ++i)
soln(i) = solution(i);
MappingQEulerian<dim, LA::MPI::Vector > q_mapping(degree, dof_handler,
soln);
Vector<float> subdomain (triangulation.n_active_cells());
for (unsigned int i=0; i<subdomain.size(); ++i)
subdomain(i) = triangulation.locally_owned_subdomain();
data_out.add_data_vector (subdomain, "subdomain");
data_out.build_patches(q_mapping, degree);
const unsigned int cycle = time.get_timestep();
const std::string filename = ("solution-" +
Utilities::int_to_string (cycle, 2) +
"." +
Utilities::int_to_string
(triangulation.locally_owned_subdomain(),
4));
std::ofstream output ((filename + ".vtu").c_str());
data_out.write_vtu (output);
if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0)
{
std::vector<std::string> filenames;
for (unsigned int i=0;
i<Utilities::MPI::n_mpi_processes(mpi_communicator);
++i)
filenames.push_back ("solution-" +
Utilities::int_to_string (cycle, 2) +
"." +
Utilities::int_to_string (i, 4) +
".vtu");
std::ofstream master_output (("solution-" +
Utilities::int_to_string (cycle, 2) +
".pvtu").c_str());
data_out.write_pvtu_record (master_output, filenames);
}
}
}
It would be appreciated if you could give me any clue to resolve the error.
Thanks,
Hamed
On Sunday, October 16, 2016 at 7:58:40 AM UTC-5, Timo Heister wrote:
>
> > "To enable the use of the MappingQ1Eulerian class also in the context of
> > parallel codes using the PETSc wrapper classes, the type of the vector
> can
> > be specified as template parameter EulerVectorType Not specifying this
> > template argument in applications using the PETSc vector classes leads
> to
> > the construction of a copy of the vector which is not accessible
> > afterwards!"
> > I can't understatnd what it means and what changes I should make.
>
> The class MappingQ1Eulerian has a template argument for the vector
> type. You need to set this to be a parallel vector (like
> PETScWrappers::MPI::Vector).
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
>
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