Here is a minimal self contained example that produces the error.
On Thu, Sep 18, 2025 at 8:16 AM 'Wolfgang Bangerth' via deal.II User Group <
[email protected]> wrote:
> On 9/16/25 22:56, Jalil Khan wrote:
> > Here is how I call my data_out object to write HDF5,
> >
> > |DataOutBase::DataOutFilter
> > data_filter(DataOutBase::DataOutFilterFlags(true,true));
> > data_out.write_filtered_data(data_filter);
> > data_out.write_hdf5_parallel(data_filter, write_mesh_file,
> mesh_filename,
> > solution_filename, mpi_comm);|
>
> Jalil:
> Can you make this into a self-contained testcase that illustrates the
> problem?
> Best
> W.
>
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Regards,
JRK
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#include <deal.II/base/utilities.h>
#include <deal.II/base/mpi.h>
#include <deal.II/distributed/tria.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/fe_system.h>
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/lac/la_parallel_vector.h>
#include <deal.II/numerics/data_out.h>
#include <deal.II/numerics/data_out_dof_data.h>
#include <deal.II/dofs/dof_tools.h>
#include <random>
#include <iostream>
#include <fstream>
#include <cstdlib>
using namespace dealii;
static const int dim = 3;
static const int degree = 4;
typedef LinearAlgebra::distributed::Vector<double> PVector;
typedef parallel::distributed::Triangulation<dim> PTriangulation;
//------------------------------------------------------------------------------
int main(int argc, char **argv)
{
Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
PTriangulation triangulation(MPI_COMM_WORLD);
GridGenerator::hyper_cube(triangulation, 0.0, 1.0);
triangulation.refine_global(7); // 2^7 x degree(4) approx 512
DoFHandler<dim> dof_handler(triangulation);
const FESystem<dim> fe(FE_Q<dim>(degree), dim+2);
dof_handler.clear();
dof_handler.distribute_dofs(fe);
const auto& locally_owned_dofs = dof_handler.locally_owned_dofs();
IndexSet locally_relevant_dofs = DoFTools::extract_locally_relevant_dofs(dof_handler);
PVector solution;
solution.reinit(locally_owned_dofs, locally_relevant_dofs, MPI_COMM_WORLD);
// Fill random values into solution
std::mt19937 rng(42);
std::uniform_real_distribution<double> dist(0.0, 1.0);
for(auto i : solution.locally_owned_elements())
solution[i] = dist(rng);
solution.compress(VectorOperation::insert);
solution.update_ghost_values();
solution *= 0.1234;
const bool write_mesh_file = true;
std::string mesh_filename = "mesh.h5";
std::string solution_filename = "vars.h5";
DataOut<dim> data_out;
data_out.add_data_vector(dof_handler, solution, "solution");
data_out.build_patches(fe.degree);
DataOutBase::DataOutFilter data_filter(DataOutBase::DataOutFilterFlags(true, true));
data_out.write_filtered_data(data_filter);
data_out.write_hdf5_parallel(data_filter,
write_mesh_file,
mesh_filename,
solution_filename,
MPI_COMM_WORLD);
XDMFEntry new_xdmf_entry = data_out.create_xdmf_entry(data_filter,
mesh_filename,
solution_filename,
0.0,
MPI_COMM_WORLD);
std::vector<XDMFEntry> xdmf_entries;
xdmf_entries.push_back(new_xdmf_entry);
data_out.write_xdmf_file(xdmf_entries, "solution.xdmf", MPI_COMM_WORLD);
return 0;
}
