}
+namespace
+{
+#ifdef DEAL_II_WITH_HDF5
+ /**
+ * Helper function to actually perform the HDF5 output.
+ */
+ template <int dim, int spacedim>
+ void
+ do_write_hdf5(const std::vector<DataOutBase::Patch<dim, spacedim>> &patches,
+ const DataOutBase::DataOutFilter &data_filter,
+ const bool write_mesh_file,
+ const std::string & mesh_filename,
+ const std::string & solution_filename,
+ const MPI_Comm & comm)
+ {
+ hid_t h5_mesh_file_id = -1, h5_solution_file_id, file_plist_id, plist_id;
+ hid_t node_dataspace, node_dataset, node_file_dataspace,
+ node_memory_dataspace;
+ hid_t cell_dataspace, cell_dataset, cell_file_dataspace,
+ cell_memory_dataspace;
+ hid_t pt_data_dataspace, pt_data_dataset, pt_data_file_dataspace,
+ pt_data_memory_dataspace;
+ herr_t status;
+ std::uint64_t local_node_cell_count[2];
+ hsize_t count[2], offset[2], node_ds_dim[2], cell_ds_dim[2];
+ std::vector<double> node_data_vec;
+ std::vector<unsigned int> cell_data_vec;
+
+
+
+ local_node_cell_count[0] = data_filter.n_nodes();
+ local_node_cell_count[1] = data_filter.n_cells();
+
+ // Create file access properties
+ file_plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ AssertThrow(file_plist_id != -1, ExcIO());
+ // If MPI is enabled *and* HDF5 is parallel, we can do parallel output
+# ifdef DEAL_II_WITH_MPI
+# ifdef H5_HAVE_PARALLEL
+ // Set the access to use the specified MPI_Comm object
+ status = H5Pset_fapl_mpio(file_plist_id, comm, MPI_INFO_NULL);
+ AssertThrow(status >= 0, ExcIO());
+# endif
+# endif
+
+ // Compute the global total number of nodes/cells and determine the offset
+ // of the data for this process
+
+ std::uint64_t global_node_cell_count[2] = {0, 0};
+ std::uint64_t global_node_cell_offsets[2] = {0, 0};
+
+# ifdef DEAL_II_WITH_MPI
+ int ierr = MPI_Allreduce(local_node_cell_count,
+ global_node_cell_count,
+ 2,
+ MPI_UINT64_T,
+ MPI_SUM,
+ comm);
+ AssertThrowMPI(ierr);
+ ierr = MPI_Exscan(local_node_cell_count,
+ global_node_cell_offsets,
+ 2,
+ MPI_UINT64_T,
+ MPI_SUM,
+ comm);
+ AssertThrowMPI(ierr);
+# else
+ global_node_cell_count[0] = local_node_cell_count[0];
+ global_node_cell_count[1] = local_node_cell_count[1];
+ global_node_cell_offsets[0] = global_node_cell_offsets[1] = 0;
+# endif
+
+ // Create the property list for a collective write
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ AssertThrow(plist_id >= 0, ExcIO());
+# ifdef DEAL_II_WITH_MPI
+# ifdef H5_HAVE_PARALLEL
+ status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+ AssertThrow(status >= 0, ExcIO());
+# endif
+# endif
+
+ if (write_mesh_file)
+ {
+ // Overwrite any existing files (change this to an option?)
+ h5_mesh_file_id = H5Fcreate(mesh_filename.c_str(),
+ H5F_ACC_TRUNC,
+ H5P_DEFAULT,
+ file_plist_id);
+ AssertThrow(h5_mesh_file_id >= 0, ExcIO());
+
+ // Create the dataspace for the nodes and cells. HDF5 only supports 2-
+ // or 3-dimensional coordinates
+ node_ds_dim[0] = global_node_cell_count[0];
+ node_ds_dim[1] = (spacedim < 2) ? 2 : spacedim;
+ node_dataspace = H5Screate_simple(2, node_ds_dim, nullptr);
+ AssertThrow(node_dataspace >= 0, ExcIO());
+
+ cell_ds_dim[0] = global_node_cell_count[1];
+ cell_ds_dim[1] = patches[0].reference_cell.n_vertices();
+ cell_dataspace = H5Screate_simple(2, cell_ds_dim, nullptr);
+ AssertThrow(cell_dataspace >= 0, ExcIO());
+
+ // Create the dataset for the nodes and cells
+# if H5Gcreate_vers == 1
+ node_dataset = H5Dcreate(h5_mesh_file_id,
+ "nodes",
+ H5T_NATIVE_DOUBLE,
+ node_dataspace,
+ H5P_DEFAULT);
+# else
+ node_dataset = H5Dcreate(h5_mesh_file_id,
+ "nodes",
+ H5T_NATIVE_DOUBLE,
+ node_dataspace,
+ H5P_DEFAULT,
+ H5P_DEFAULT,
+ H5P_DEFAULT);
+# endif
+ AssertThrow(node_dataset >= 0, ExcIO());
+# if H5Gcreate_vers == 1
+ cell_dataset = H5Dcreate(h5_mesh_file_id,
+ "cells",
+ H5T_NATIVE_UINT,
+ cell_dataspace,
+ H5P_DEFAULT);
+# else
+ cell_dataset = H5Dcreate(h5_mesh_file_id,
+ "cells",
+ H5T_NATIVE_UINT,
+ cell_dataspace,
+ H5P_DEFAULT,
+ H5P_DEFAULT,
+ H5P_DEFAULT);
+# endif
+ AssertThrow(cell_dataset >= 0, ExcIO());
+
+ // Close the node and cell dataspaces since we're done with them
+ status = H5Sclose(node_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(cell_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Create the data subset we'll use to read from memory. HDF5 only
+ // supports 2- or 3-dimensional coordinates
+ count[0] = local_node_cell_count[0];
+ count[1] = (spacedim < 2) ? 2 : spacedim;
+
+ offset[0] = global_node_cell_offsets[0];
+ offset[1] = 0;
+
+ node_memory_dataspace = H5Screate_simple(2, count, nullptr);
+ AssertThrow(node_memory_dataspace >= 0, ExcIO());
+
+ // Select the hyperslab in the file
+ node_file_dataspace = H5Dget_space(node_dataset);
+ AssertThrow(node_file_dataspace >= 0, ExcIO());
+ status = H5Sselect_hyperslab(
+ node_file_dataspace, H5S_SELECT_SET, offset, nullptr, count, nullptr);
+ AssertThrow(status >= 0, ExcIO());
+
+ // And repeat for cells
+ count[0] = local_node_cell_count[1];
+ count[1] = patches[0].reference_cell.n_vertices();
+ offset[0] = global_node_cell_offsets[1];
+ offset[1] = 0;
+ cell_memory_dataspace = H5Screate_simple(2, count, nullptr);
+ AssertThrow(cell_memory_dataspace >= 0, ExcIO());
+
+ cell_file_dataspace = H5Dget_space(cell_dataset);
+ AssertThrow(cell_file_dataspace >= 0, ExcIO());
+ status = H5Sselect_hyperslab(
+ cell_file_dataspace, H5S_SELECT_SET, offset, nullptr, count, nullptr);
+ AssertThrow(status >= 0, ExcIO());
+
+ // And finally, write the node data
+ data_filter.fill_node_data(node_data_vec);
+ status = H5Dwrite(node_dataset,
+ H5T_NATIVE_DOUBLE,
+ node_memory_dataspace,
+ node_file_dataspace,
+ plist_id,
+ node_data_vec.data());
+ AssertThrow(status >= 0, ExcIO());
+ node_data_vec.clear();
+
+ // And the cell data
+ data_filter.fill_cell_data(global_node_cell_offsets[0], cell_data_vec);
+ status = H5Dwrite(cell_dataset,
+ H5T_NATIVE_UINT,
+ cell_memory_dataspace,
+ cell_file_dataspace,
+ plist_id,
+ cell_data_vec.data());
+ AssertThrow(status >= 0, ExcIO());
+ cell_data_vec.clear();
+
+ // Close the file dataspaces
+ status = H5Sclose(node_file_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(cell_file_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the memory dataspaces
+ status = H5Sclose(node_memory_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(cell_memory_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the datasets
+ status = H5Dclose(node_dataset);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Dclose(cell_dataset);
+ AssertThrow(status >= 0, ExcIO());
+
+ // If the filenames are different, we need to close the mesh file
+ if (mesh_filename != solution_filename)
+ {
+ status = H5Fclose(h5_mesh_file_id);
+ AssertThrow(status >= 0, ExcIO());
+ }
+ }
+
+ // If the filenames are identical, continue with the same file
+ if (mesh_filename == solution_filename && write_mesh_file)
+ {
+ h5_solution_file_id = h5_mesh_file_id;
+ }
+ else
+ {
+ // Otherwise we need to open a new file
+ h5_solution_file_id = H5Fcreate(solution_filename.c_str(),
+ H5F_ACC_TRUNC,
+ H5P_DEFAULT,
+ file_plist_id);
+ AssertThrow(h5_solution_file_id >= 0, ExcIO());
+ }
+
+ // when writing, first write out all vector data, then handle the scalar
+ // data sets that have been left over
+ unsigned int i;
+ std::string vector_name;
+ for (i = 0; i < data_filter.n_data_sets(); ++i)
+ {
+ // Allocate space for the point data
+ // Must be either 1D or 3D
+ const unsigned int pt_data_vector_dim = data_filter.get_data_set_dim(i);
+ vector_name = data_filter.get_data_set_name(i);
+
+ // Create the dataspace for the point data
+ node_ds_dim[0] = global_node_cell_count[0];
+ node_ds_dim[1] = pt_data_vector_dim;
+ pt_data_dataspace = H5Screate_simple(2, node_ds_dim, nullptr);
+ AssertThrow(pt_data_dataspace >= 0, ExcIO());
+
+# if H5Gcreate_vers == 1
+ pt_data_dataset = H5Dcreate(h5_solution_file_id,
+ vector_name.c_str(),
+ H5T_NATIVE_DOUBLE,
+ pt_data_dataspace,
+ H5P_DEFAULT);
+# else
+ pt_data_dataset = H5Dcreate(h5_solution_file_id,
+ vector_name.c_str(),
+ H5T_NATIVE_DOUBLE,
+ pt_data_dataspace,
+ H5P_DEFAULT,
+ H5P_DEFAULT,
+ H5P_DEFAULT);
+# endif
+ AssertThrow(pt_data_dataset >= 0, ExcIO());
+
+ // Create the data subset we'll use to read from memory
+ count[0] = local_node_cell_count[0];
+ count[1] = pt_data_vector_dim;
+ offset[0] = global_node_cell_offsets[0];
+ offset[1] = 0;
+ pt_data_memory_dataspace = H5Screate_simple(2, count, nullptr);
+ AssertThrow(pt_data_memory_dataspace >= 0, ExcIO());
+
+ // Select the hyperslab in the file
+ pt_data_file_dataspace = H5Dget_space(pt_data_dataset);
+ AssertThrow(pt_data_file_dataspace >= 0, ExcIO());
+ status = H5Sselect_hyperslab(pt_data_file_dataspace,
+ H5S_SELECT_SET,
+ offset,
+ nullptr,
+ count,
+ nullptr);
+ AssertThrow(status >= 0, ExcIO());
+
+ // And finally, write the data
+ status = H5Dwrite(pt_data_dataset,
+ H5T_NATIVE_DOUBLE,
+ pt_data_memory_dataspace,
+ pt_data_file_dataspace,
+ plist_id,
+ data_filter.get_data_set(i));
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the dataspaces
+ status = H5Sclose(pt_data_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(pt_data_memory_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ status = H5Sclose(pt_data_file_dataspace);
+ AssertThrow(status >= 0, ExcIO());
+ // Close the dataset
+ status = H5Dclose(pt_data_dataset);
+ AssertThrow(status >= 0, ExcIO());
+ }
+
+ // Close the file property list
+ status = H5Pclose(file_plist_id);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the parallel access
+ status = H5Pclose(plist_id);
+ AssertThrow(status >= 0, ExcIO());
+
+ // Close the file
+ status = H5Fclose(h5_solution_file_id);
+ AssertThrow(status >= 0, ExcIO());
+ }
+#endif
+} // namespace
template <int dim, int spacedim>
void
(void)comm;
AssertThrow(false, ExcMessage("HDF5 support is disabled."));
#else
-# ifndef DEAL_II_WITH_MPI
- (void)comm;
-# endif
- // verify that there are indeed patches to be written out. most of the times,
- // people just forget to call build_patches when there are no patches, so a
- // warning is in order. that said, the assertion is disabled if we support MPI
- // since then it can happen that on the coarsest mesh, a processor simply has
- // no cells it actually owns, and in that case it is legit if there are no
- // patches
- Assert(patches.size() > 0, ExcNoPatches());
+ const unsigned int n_ranks = Utilities::MPI::n_mpi_processes(comm);
+ (void)n_ranks;
- hid_t h5_mesh_file_id = -1, h5_solution_file_id, file_plist_id, plist_id;
- hid_t node_dataspace, node_dataset, node_file_dataspace,
- node_memory_dataspace;
- hid_t cell_dataspace, cell_dataset, cell_file_dataspace,
- cell_memory_dataspace;
- hid_t pt_data_dataspace, pt_data_dataset, pt_data_file_dataspace,
- pt_data_memory_dataspace;
- herr_t status;
- std::uint64_t local_node_cell_count[2];
- hsize_t count[2], offset[2], node_ds_dim[2], cell_ds_dim[2];
- std::vector<double> node_data_vec;
- std::vector<unsigned int> cell_data_vec;
-
- // If HDF5 is not parallel and we're using multiple processes, abort
+ // If HDF5 is not parallel and we're using multiple processes, abort:
# ifndef H5_HAVE_PARALLEL
-# ifdef DEAL_II_WITH_MPI
- int world_size = Utilities::MPI::n_mpi_processes(comm);
AssertThrow(
- world_size <= 1,
+ n_ranks <= 1,
ExcMessage(
"Serial HDF5 output on multiple processes is not yet supported."));
-# endif
-# endif
-
- local_node_cell_count[0] = data_filter.n_nodes();
- local_node_cell_count[1] = data_filter.n_cells();
-
- // Create file access properties
- file_plist_id = H5Pcreate(H5P_FILE_ACCESS);
- AssertThrow(file_plist_id != -1, ExcIO());
- // If MPI is enabled *and* HDF5 is parallel, we can do parallel output
-# ifdef DEAL_II_WITH_MPI
-# ifdef H5_HAVE_PARALLEL
- // Set the access to use the specified MPI_Comm object
- status = H5Pset_fapl_mpio(file_plist_id, comm, MPI_INFO_NULL);
- AssertThrow(status >= 0, ExcIO());
-# endif
-# endif
-
- // Compute the global total number of nodes/cells and determine the offset of
- // the data for this process
-
- std::uint64_t global_node_cell_count[2] = {0, 0};
- std::uint64_t global_node_cell_offsets[2] = {0, 0};
-
-# ifdef DEAL_II_WITH_MPI
- ierr = MPI_Allreduce(local_node_cell_count,
- global_node_cell_count,
- 2,
- MPI_UINT64_T,
- MPI_SUM,
- comm);
- AssertThrowMPI(ierr);
- ierr = MPI_Exscan(local_node_cell_count,
- global_node_cell_offsets,
- 2,
- MPI_UINT64_T,
- MPI_SUM,
- comm);
- AssertThrowMPI(ierr);
-# else
- global_node_cell_count[0] = local_node_cell_count[0];
- global_node_cell_count[1] = local_node_cell_count[1];
- global_node_cell_offsets[0] = global_node_cell_offsets[1] = 0;
# endif
- // Create the property list for a collective write
- plist_id = H5Pcreate(H5P_DATASET_XFER);
- AssertThrow(plist_id >= 0, ExcIO());
-# ifdef DEAL_II_WITH_MPI
-# ifdef H5_HAVE_PARALLEL
- status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
- AssertThrow(status >= 0, ExcIO());
-# endif
-# endif
-
- if (write_mesh_file)
- {
- // Overwrite any existing files (change this to an option?)
- h5_mesh_file_id = H5Fcreate(mesh_filename.c_str(),
- H5F_ACC_TRUNC,
- H5P_DEFAULT,
- file_plist_id);
- AssertThrow(h5_mesh_file_id >= 0, ExcIO());
-
- // Create the dataspace for the nodes and cells. HDF5 only supports 2- or
- // 3-dimensional coordinates
- node_ds_dim[0] = global_node_cell_count[0];
- node_ds_dim[1] = (spacedim < 2) ? 2 : spacedim;
- node_dataspace = H5Screate_simple(2, node_ds_dim, nullptr);
- AssertThrow(node_dataspace >= 0, ExcIO());
-
- cell_ds_dim[0] = global_node_cell_count[1];
- cell_ds_dim[1] = patches[0].reference_cell.n_vertices();
- cell_dataspace = H5Screate_simple(2, cell_ds_dim, nullptr);
- AssertThrow(cell_dataspace >= 0, ExcIO());
-
- // Create the dataset for the nodes and cells
-# if H5Gcreate_vers == 1
- node_dataset = H5Dcreate(h5_mesh_file_id,
- "nodes",
- H5T_NATIVE_DOUBLE,
- node_dataspace,
- H5P_DEFAULT);
-# else
- node_dataset = H5Dcreate(h5_mesh_file_id,
- "nodes",
- H5T_NATIVE_DOUBLE,
- node_dataspace,
- H5P_DEFAULT,
- H5P_DEFAULT,
- H5P_DEFAULT);
-# endif
- AssertThrow(node_dataset >= 0, ExcIO());
-# if H5Gcreate_vers == 1
- cell_dataset = H5Dcreate(
- h5_mesh_file_id, "cells", H5T_NATIVE_UINT, cell_dataspace, H5P_DEFAULT);
-# else
- cell_dataset = H5Dcreate(h5_mesh_file_id,
- "cells",
- H5T_NATIVE_UINT,
- cell_dataspace,
- H5P_DEFAULT,
- H5P_DEFAULT,
- H5P_DEFAULT);
-# endif
- AssertThrow(cell_dataset >= 0, ExcIO());
-
- // Close the node and cell dataspaces since we're done with them
- status = H5Sclose(node_dataspace);
- AssertThrow(status >= 0, ExcIO());
- status = H5Sclose(cell_dataspace);
- AssertThrow(status >= 0, ExcIO());
-
- // Create the data subset we'll use to read from memory. HDF5 only
- // supports 2- or 3-dimensional coordinates
- count[0] = local_node_cell_count[0];
- count[1] = (spacedim < 2) ? 2 : spacedim;
-
- offset[0] = global_node_cell_offsets[0];
- offset[1] = 0;
-
- node_memory_dataspace = H5Screate_simple(2, count, nullptr);
- AssertThrow(node_memory_dataspace >= 0, ExcIO());
-
- // Select the hyperslab in the file
- node_file_dataspace = H5Dget_space(node_dataset);
- AssertThrow(node_file_dataspace >= 0, ExcIO());
- status = H5Sselect_hyperslab(
- node_file_dataspace, H5S_SELECT_SET, offset, nullptr, count, nullptr);
- AssertThrow(status >= 0, ExcIO());
-
- // And repeat for cells
- count[0] = local_node_cell_count[1];
- count[1] = patches[0].reference_cell.n_vertices();
- offset[0] = global_node_cell_offsets[1];
- offset[1] = 0;
- cell_memory_dataspace = H5Screate_simple(2, count, nullptr);
- AssertThrow(cell_memory_dataspace >= 0, ExcIO());
-
- cell_file_dataspace = H5Dget_space(cell_dataset);
- AssertThrow(cell_file_dataspace >= 0, ExcIO());
- status = H5Sselect_hyperslab(
- cell_file_dataspace, H5S_SELECT_SET, offset, nullptr, count, nullptr);
- AssertThrow(status >= 0, ExcIO());
-
- // And finally, write the node data
- data_filter.fill_node_data(node_data_vec);
- status = H5Dwrite(node_dataset,
- H5T_NATIVE_DOUBLE,
- node_memory_dataspace,
- node_file_dataspace,
- plist_id,
- node_data_vec.data());
- AssertThrow(status >= 0, ExcIO());
- node_data_vec.clear();
-
- // And the cell data
- data_filter.fill_cell_data(global_node_cell_offsets[0], cell_data_vec);
- status = H5Dwrite(cell_dataset,
- H5T_NATIVE_UINT,
- cell_memory_dataspace,
- cell_file_dataspace,
- plist_id,
- cell_data_vec.data());
- AssertThrow(status >= 0, ExcIO());
- cell_data_vec.clear();
-
- // Close the file dataspaces
- status = H5Sclose(node_file_dataspace);
- AssertThrow(status >= 0, ExcIO());
- status = H5Sclose(cell_file_dataspace);
- AssertThrow(status >= 0, ExcIO());
-
- // Close the memory dataspaces
- status = H5Sclose(node_memory_dataspace);
- AssertThrow(status >= 0, ExcIO());
- status = H5Sclose(cell_memory_dataspace);
- AssertThrow(status >= 0, ExcIO());
-
- // Close the datasets
- status = H5Dclose(node_dataset);
- AssertThrow(status >= 0, ExcIO());
- status = H5Dclose(cell_dataset);
- AssertThrow(status >= 0, ExcIO());
-
- // If the filenames are different, we need to close the mesh file
- if (mesh_filename != solution_filename)
- {
- status = H5Fclose(h5_mesh_file_id);
- AssertThrow(status >= 0, ExcIO());
- }
- }
-
- // If the filenames are identical, continue with the same file
- if (mesh_filename == solution_filename && write_mesh_file)
- {
- h5_solution_file_id = h5_mesh_file_id;
- }
- else
- {
- // Otherwise we need to open a new file
- h5_solution_file_id = H5Fcreate(solution_filename.c_str(),
- H5F_ACC_TRUNC,
- H5P_DEFAULT,
- file_plist_id);
- AssertThrow(h5_solution_file_id >= 0, ExcIO());
- }
+ // Verify that there are indeed patches to be written out. most of the times,
+ // people just forget to call build_patches when there are no patches, so a
+ // warning is in order. That said, the assertion is disabled if we run with
+ // more than one MPI rank,
+ // since then it can happen that, on coarse meshes, a processor simply has
+ // no cells it actually owns, and in that case it is legit if there are no
+ // patches.
+ Assert((patches.size() > 0) || (n_ranks > 1), ExcNoPatches());
+
+ // The HDF5 routines perform a bunch of collective calls that expect all
+ // ranks to participate. One ranks without any patches we are missing
+ // critical information, so rather than broadcasting that information, just
+ // create a new communicator that only contains ranks with cells and
+ // use that to perform the write operations:
+ const bool have_patches = (patches.size() > 0);
+ MPI_Comm split_comm;
+ {
+ const int key = Utilities::MPI::this_mpi_process(comm);
+ const int color = (have_patches ? 1 : 0);
+ const int ierr = MPI_Comm_split(comm, color, key, &split_comm);
+ AssertThrowMPI(ierr);
+ }
- // when writing, first write out all vector data, then handle the scalar data
- // sets that have been left over
- unsigned int i;
- std::string vector_name;
- for (i = 0; i < data_filter.n_data_sets(); ++i)
+ if (have_patches)
{
- // Allocate space for the point data
- // Must be either 1D or 3D
- const unsigned int pt_data_vector_dim = data_filter.get_data_set_dim(i);
- vector_name = data_filter.get_data_set_name(i);
-
- // Create the dataspace for the point data
- node_ds_dim[0] = global_node_cell_count[0];
- node_ds_dim[1] = pt_data_vector_dim;
- pt_data_dataspace = H5Screate_simple(2, node_ds_dim, nullptr);
- AssertThrow(pt_data_dataspace >= 0, ExcIO());
-
-# if H5Gcreate_vers == 1
- pt_data_dataset = H5Dcreate(h5_solution_file_id,
- vector_name.c_str(),
- H5T_NATIVE_DOUBLE,
- pt_data_dataspace,
- H5P_DEFAULT);
-# else
- pt_data_dataset = H5Dcreate(h5_solution_file_id,
- vector_name.c_str(),
- H5T_NATIVE_DOUBLE,
- pt_data_dataspace,
- H5P_DEFAULT,
- H5P_DEFAULT,
- H5P_DEFAULT);
-# endif
- AssertThrow(pt_data_dataset >= 0, ExcIO());
-
- // Create the data subset we'll use to read from memory
- count[0] = local_node_cell_count[0];
- count[1] = pt_data_vector_dim;
- offset[0] = global_node_cell_offsets[0];
- offset[1] = 0;
- pt_data_memory_dataspace = H5Screate_simple(2, count, nullptr);
- AssertThrow(pt_data_memory_dataspace >= 0, ExcIO());
-
- // Select the hyperslab in the file
- pt_data_file_dataspace = H5Dget_space(pt_data_dataset);
- AssertThrow(pt_data_file_dataspace >= 0, ExcIO());
- status = H5Sselect_hyperslab(pt_data_file_dataspace,
- H5S_SELECT_SET,
- offset,
- nullptr,
- count,
- nullptr);
- AssertThrow(status >= 0, ExcIO());
-
- // And finally, write the data
- status = H5Dwrite(pt_data_dataset,
- H5T_NATIVE_DOUBLE,
- pt_data_memory_dataspace,
- pt_data_file_dataspace,
- plist_id,
- data_filter.get_data_set(i));
- AssertThrow(status >= 0, ExcIO());
-
- // Close the dataspaces
- status = H5Sclose(pt_data_dataspace);
- AssertThrow(status >= 0, ExcIO());
- status = H5Sclose(pt_data_memory_dataspace);
- AssertThrow(status >= 0, ExcIO());
- status = H5Sclose(pt_data_file_dataspace);
- AssertThrow(status >= 0, ExcIO());
- // Close the dataset
- status = H5Dclose(pt_data_dataset);
- AssertThrow(status >= 0, ExcIO());
+ do_write_hdf5<dim, spacedim>(patches,
+ data_filter,
+ write_mesh_file,
+ mesh_filename,
+ solution_filename,
+ split_comm);
}
- // Close the file property list
- status = H5Pclose(file_plist_id);
- AssertThrow(status >= 0, ExcIO());
-
- // Close the parallel access
- status = H5Pclose(plist_id);
- AssertThrow(status >= 0, ExcIO());
+ ierr = MPI_Comm_free(&split_comm);
+ AssertThrowMPI(ierr);
- // Close the file
- status = H5Fclose(h5_solution_file_id);
- AssertThrow(status >= 0, ExcIO());
#endif
}
projects / dealii.git / commitdiff