Hello,
I have a small question and I think the issue lies here. Are these two
function calls equivalent?
ghosted_vector.reinit(
/*locally owned indices*/,
/*ghost indices only*/,
mpi_communicator
);
ghosted_vector.reinit(
/*locally owned indices*/,
/*relevant indices (owned + ghost)*/,
mpi_communicator
);
The program runs as expected for a serial execution. I am using the first
version here and may be that is causing a crash in a parallel execution.
Any reference to a use case of
p::d::Triangulation::global_active_cell_index_partitioner() would be very
helpful :) !
Thanks
On Friday, June 11, 2021 at 11:40:37 AM UTC+5:30 vachanpo...@gmail.com
wrote:
> Hello,
>
> I am having an issue in using DataOut for such vector in a parallel
> process. I am attaching a MWE which captures my problem. I am encountering
> a segmentation fault (signal 11).
>
> #include <deal.II/base/mpi.h>
> #include <deal.II/base/utilities.h>
> #include <deal.II/distributed/tria.h>
> #include <deal.II/grid/tria_accessor.h>
> #include <deal.II/grid/grid_generator.h>
> #include <deal.II/lac/generic_linear_algebra.h>
> #include <deal.II/fe/fe_dgq.h>
> #include <deal.II/fe/mapping_q_generic.h>
> #include <deal.II/dofs/dof_handler.h>
> #include <deal.II/numerics/data_out.h>
>
> #include <fstream>
>
> using namespace dealii;
> namespace LA
> {
> using namespace ::LinearAlgebraPETSc;
> }
>
> int main(int argc, char **argv)
> {
> Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
>
> constexpr int dim = 3;
>
> MPI_Comm mpi_comm(MPI_COMM_WORLD);
>
> parallel::distributed::Triangulation<dim> triang(mpi_comm);
> GridGenerator::subdivided_hyper_cube(triang, 5);
> const std::shared_ptr<const Utilities::MPI::Partitioner> cell_partitioner
> =
> triang.global_active_cell_index_partitioner().lock();
> LA::MPI::Vector vec(cell_partitioner->locally_owned_range(), mpi_comm);
> LA::MPI::Vector gh_vec(
> cell_partitioner->locally_owned_range(),
> cell_partitioner->ghost_indices(),
> mpi_comm
> );
>
> DoFHandler<dim> dof_handler(triang);
> FE_DGQ<dim> fe(2);
> dof_handler.distribute_dofs(fe);
>
> for(auto &cell: dof_handler.active_cell_iterators()){
> if(!cell->is_locally_owned()) continue;
>
> vec[cell->global_active_cell_index()] = cell->global_active_cell_index();
> }
> vec.compress(VectorOperation::insert);
>
> gh_vec = vec;
>
> DataOut<dim> data_out;
> DataOutBase::VtkFlags flags;
> flags.write_higher_order_cells = true;
> data_out.set_flags(flags);
>
> data_out.attach_dof_handler(dof_handler);
>
> data_out.add_data_vector(gh_vec, "x");
>
> data_out.build_patches(
> MappingQGeneric<dim>(2),
> 2,
> DataOut<dim>::CurvedCellRegion::curved_inner_cells
> );
>
> std::ofstream proc_file(
> "output" + Utilities::int_to_string(
> Utilities::MPI::this_mpi_process(mpi_comm),
> 2
> ) + ".vtu"
> );
> data_out.write_vtu(proc_file);
> proc_file.close();
>
> if(Utilities::MPI::this_mpi_process(mpi_comm) == 0){
> std::vector<std::string> filenames;
> for(int i=0; i<Utilities::MPI::n_mpi_processes(mpi_comm); i++){
> filenames.emplace_back(
> "output" + Utilities::int_to_string(i, 2) + ".vtu"
> );
> } // loop over processes
>
> std::ofstream master_file("output.pvtu");
> data_out.write_pvtu_record(master_file, filenames);
> master_file.close();
> }
> return 0;
> }
>
>
> I suspect I am not partitioning the ghosted vector properly hence causing
> a mismatch in what is available and what DataOut wants. Am I missing any
> other step in between?
>
> Thanking in anticipation
>
> On Tue, 8 Jun 2021 at 19:32, vachan potluri <vachanpo...@gmail.com> wrote:
>
>> Thank you :).
>>
>> On Tue, 8 Jun, 2021, 19:24 Wolfgang Bangerth, <bang...@colostate.edu>
>> wrote:
>>
>>> On 6/8/21 4:18 AM, vachanpo...@gmail.com wrote:
>>> > If I want to add such a vector to DataOut, will the regular
>>> > DataOut::add_data_vector() work? Or is something else required to be
>>> done?
>>>
>>> Yes, DataOut::add_data_vector() can take two kinds of vectors:
>>> * Ones that have as many entries as there are DoFs
>>> * Ones that have as many entries as there are active cells
>>>
>>> Best
>>> W.
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Wolfgang Bangerth email: bang...@colostate.edu
>>> www:
>>> http://www.math.colostate.edu/~bangerth/
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
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>>> .
>>>
>>
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