ExcMessage("XDMF only supports 2 or 3 space dimensions."));
local_node_cell_count[0] = data_filter.n_nodes();
- local_node_cell_count[1] = data_filter.n_cells();
+ // n_cells returns an invalid unsigned int if the object is empty:
+ local_node_cell_count[1] =
+ (data_filter.n_nodes() > 0) ? data_filter.n_cells() : 0;
+
// And compute the global total
#ifdef DEAL_II_WITH_MPI
global_node_cell_count[1] = local_node_cell_count[1];
#endif
- // Output the XDMF file only on the root process
- if (myrank == 0)
+ // The implementation is a bit complicated because we are supposed to return
+ // the correct data on rank 0 and an empty object on all other ranks but all
+ // information (for example the attributes) are only available on ranks that
+ // have any cells.
+ // We will identify the smallest rank that has data and then communicate
+ // from this rank to rank 0 (if they are different ranks).
+
+ const bool have_data = (data_filter.n_nodes() > 0);
+ MPI_Comm split_comm;
+ {
+ const int key = myrank;
+ const int color = (have_data ? 1 : 0);
+ const int ierr = MPI_Comm_split(comm, color, key, &split_comm);
+ AssertThrowMPI(ierr);
+ }
+
+ const bool am_i_first_rank_with_data =
+ have_data && (Utilities::MPI::this_mpi_process(split_comm) == 0);
+
+ ierr = MPI_Comm_free(&split_comm);
+ AssertThrowMPI(ierr);
+
+ const int tag = 47381;
+
+ // Output the XDMF file only on the root process of all ranks with data:
+ if (am_i_first_rank_with_data)
{
const auto &patches = get_patches();
Assert(patches.size() > 0, DataOutBase::ExcNoPatches());
+
// We currently don't support writing mixed meshes:
#ifdef DEBUG
for (const auto &patch : patches)
ExcNotImplemented());
#endif
-
- XDMFEntry entry(h5_mesh_filename,
+ XDMFEntry entry(h5_mesh_filename,
h5_solution_filename,
cur_time,
global_node_cell_count[0],
dim,
spacedim,
patches[0].reference_cell);
- unsigned int n_data_sets = data_filter.n_data_sets();
+ const unsigned int n_data_sets = data_filter.n_data_sets();
- // The vector names generated here must match those generated in the HDF5
- // file
- unsigned int i;
- for (i = 0; i < n_data_sets; ++i)
+ // The vector names generated here must match those generated in
+ // the HDF5 file
+ for (unsigned int i = 0; i < n_data_sets; ++i)
{
entry.add_attribute(data_filter.get_data_set_name(i),
data_filter.get_data_set_dim(i));
}
- return entry;
+ if (myrank != 0)
+ {
+ // send to rank 0
+ const std::vector<char> buffer = Utilities::pack(entry, false);
+ ierr = MPI_Send(buffer.data(), buffer.size(), MPI_CHAR, 0, tag, comm);
+ AssertThrowMPI(ierr);
+
+ return {};
+ }
+ else
+ return entry;
}
- else
+
+ if (myrank == 0 && !am_i_first_rank_with_data)
{
- return {};
+ // receive the XDMF data on rank 0 if we don't have it...
+
+ MPI_Status status;
+ int ierr = MPI_Probe(MPI_ANY_SOURCE, tag, comm, &status);
+ AssertThrowMPI(ierr);
+
+ int len;
+ ierr = MPI_Get_count(&status, MPI_BYTE, &len);
+ AssertThrowMPI(ierr);
+
+ std::vector<char> buffer(len);
+ ierr = MPI_Recv(buffer.data(),
+ len,
+ MPI_BYTE,
+ status.MPI_SOURCE,
+ tag,
+ comm,
+ MPI_STATUS_IGNORE);
+ AssertThrowMPI(ierr);
+
+ return Utilities::unpack<XDMFEntry>(buffer, false);
}
+
+ // default case for any other rank is to return an empty object
+ return {};
}
template <int dim, int spacedim>
//
// ---------------------------------------------------------------------
-// test parallel DataOut with HDF5
+// test parallel DataOut with HDF5 + xdmf
//
// When running with 3 MPI ranks, one of the ranks will have 0
// cells. This tests a corner case that used to fail because the code
{
parallel::distributed::Triangulation<dim> tria(MPI_COMM_WORLD);
std::vector<unsigned int> repetitions(dim, 1);
- repetitions[0] = 2; // 2x1x1 cells
+ repetitions[0] = 1; // 2x1x1 cells
Point<dim> p1;
Point<dim> p2;
for (int i = 0; i < dim; ++i)
DataOutBase::DataOutFilter data_filter(
DataOutBase::DataOutFilterFlags(false, false));
data_out.write_filtered_data(data_filter);
+ deallog << "n_cells on my rank: " << data_filter.n_cells() << std::endl;
data_out.write_hdf5_parallel(data_filter, "out.h5", MPI_COMM_WORLD);
+ std::vector<XDMFEntry> xdmf_entries;
+ xdmf_entries.push_back(
+ data_out.create_xdmf_entry(data_filter, "out.h5", 0, MPI_COMM_WORLD));
+
+ data_out.write_xdmf_file(xdmf_entries, "out.xdmf", MPI_COMM_WORLD);
+
if (Utilities::MPI::this_mpi_process(MPI_COMM_WORLD) == 0)
{
+ cat_file("out.xdmf");
+
// Sadly hdf5 is binary and we can not use hd5dump because it might
// not be in the path.
std::ifstream f("out.h5");
+DEAL:0::n_cells on my rank: 4
+<?xml version="1.0" ?>
+<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
+<Xdmf Version="2.0">
+ <Domain>
+ <Grid Name="CellTime" GridType="Collection" CollectionType="Temporal">
+ <Grid Name="mesh" GridType="Uniform">
+ <Time Value="0"/>
+ <Geometry GeometryType="XY">
+ <DataItem Dimensions="16 2" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/nodes
+ </DataItem>
+ </Geometry>
+ <Topology TopologyType="Quadrilateral" NumberOfElements="4">
+ <DataItem Dimensions="4 4" NumberType="UInt" Format="HDF">
+ out.h5:/cells
+ </DataItem>
+ </Topology>
+ <Attribute Name="bla" AttributeType="Scalar" Center="Node">
+ <DataItem Dimensions="16 1" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/bla
+ </DataItem>
+ </Attribute>
+ </Grid>
+ </Grid>
+ </Domain>
+</Xdmf>
+
DEAL:0::ok
+DEAL:0::n_cells on my rank: 8
+<?xml version="1.0" ?>
+<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
+<Xdmf Version="2.0">
+ <Domain>
+ <Grid Name="CellTime" GridType="Collection" CollectionType="Temporal">
+ <Grid Name="mesh" GridType="Uniform">
+ <Time Value="0"/>
+ <Geometry GeometryType="XYZ">
+ <DataItem Dimensions="64 3" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/nodes
+ </DataItem>
+ </Geometry>
+ <Topology TopologyType="Hexahedron" NumberOfElements="8">
+ <DataItem Dimensions="8 8" NumberType="UInt" Format="HDF">
+ out.h5:/cells
+ </DataItem>
+ </Topology>
+ <Attribute Name="bla" AttributeType="Scalar" Center="Node">
+ <DataItem Dimensions="64 1" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/bla
+ </DataItem>
+ </Attribute>
+ </Grid>
+ </Grid>
+ </Domain>
+</Xdmf>
+
DEAL:0::ok
+DEAL:1::n_cells on my rank: 4294967295
+DEAL:1::n_cells on my rank: 4294967295
+DEAL:0::n_cells on my rank: 4294967295
+<?xml version="1.0" ?>
+<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
+<Xdmf Version="2.0">
+ <Domain>
+ <Grid Name="CellTime" GridType="Collection" CollectionType="Temporal">
+ <Grid Name="mesh" GridType="Uniform">
+ <Time Value="0"/>
+ <Geometry GeometryType="XY">
+ <DataItem Dimensions="16 2" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/nodes
+ </DataItem>
+ </Geometry>
+ <Topology TopologyType="Quadrilateral" NumberOfElements="4">
+ <DataItem Dimensions="4 4" NumberType="UInt" Format="HDF">
+ out.h5:/cells
+ </DataItem>
+ </Topology>
+ <Attribute Name="bla" AttributeType="Scalar" Center="Node">
+ <DataItem Dimensions="16 1" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/bla
+ </DataItem>
+ </Attribute>
+ </Grid>
+ </Grid>
+ </Domain>
+</Xdmf>
+
DEAL:0::ok
+DEAL:0::n_cells on my rank: 4294967295
+<?xml version="1.0" ?>
+<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
+<Xdmf Version="2.0">
+ <Domain>
+ <Grid Name="CellTime" GridType="Collection" CollectionType="Temporal">
+ <Grid Name="mesh" GridType="Uniform">
+ <Time Value="0"/>
+ <Geometry GeometryType="XYZ">
+ <DataItem Dimensions="64 3" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/nodes
+ </DataItem>
+ </Geometry>
+ <Topology TopologyType="Hexahedron" NumberOfElements="8">
+ <DataItem Dimensions="8 8" NumberType="UInt" Format="HDF">
+ out.h5:/cells
+ </DataItem>
+ </Topology>
+ <Attribute Name="bla" AttributeType="Scalar" Center="Node">
+ <DataItem Dimensions="64 1" NumberType="Float" Precision="8" Format="HDF">
+ out.h5:/bla
+ </DataItem>
+ </Attribute>
+ </Grid>
+ </Grid>
+ </Domain>
+</Xdmf>
+
DEAL:0::ok
+DEAL:1::n_cells on my rank: 4294967295
+DEAL:1::n_cells on my rank: 8
+
+
+DEAL:2::n_cells on my rank: 4
+DEAL:2::n_cells on my rank: 4294967295
const unsigned int dim = 2;
const unsigned int spacedim = 3;
- XDMFEntry entry1(
- mesh_filename, solution_filename, time, nodes, cells, dim, spacedim);
+ XDMFEntry entry1(mesh_filename,
+ solution_filename,
+ time,
+ nodes,
+ cells,
+ dim,
+ spacedim,
+ ReferenceCells::Quadrilateral);
XDMFEntry entry2;
// save data to archive
projects / dealii.git / commitdiff