diff --git a/Applications/Utils/FileConverter/PVD2XDMF.cpp b/Applications/Utils/FileConverter/PVD2XDMF.cpp
index f581c5cbac6c9694895116bf094cd10d5d917df4..2f99ff70acc2ea13006b5bd9fd3615de7a117935 100644
--- a/Applications/Utils/FileConverter/PVD2XDMF.cpp
+++ b/Applications/Utils/FileConverter/PVD2XDMF.cpp
@@ -190,7 +190,8 @@ int main(int argc, char* argv[])
mesh_xdmf_hdf_writer = std::make_unique<MeshLib::IO::XdmfHdfWriter>(
std::vector{std::cref(*main_mesh)}, output_file_path,
0 /*timestep*/, time, variable_output_names,
- true /*output_file.compression*/, 1 /*output_file.n_files*/);
+ true /*output_file.compression*/, 1 /*output_file.n_files*/,
+ 1048576 /*chunk_size_bytes*/);
}
for (std::size_t timestep = 1; timestep < timeseries.size(); ++timestep)
diff --git a/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md b/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md
index 2043711a7a77bcb4ca95a5845138c5bfb9b6761d..a7ba20e050d1eef345e39650d24661e405750dab 100644
--- a/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md
+++ b/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md
@@ -1,2 +1,2 @@
Group of parameters when XDMF/HDF writer is used.
-Type of output in time_loop must be XDMF
+Type of output must be XDMF
diff --git a/Documentation/ProjectFile/prj/time_loop/output/hdf/t_chunk_size_bytes.md b/Documentation/ProjectFile/prj/time_loop/output/hdf/t_chunk_size_bytes.md
new file mode 100644
index 0000000000000000000000000000000000000000..c15129e7db1e053faa9025d4aa2d601ac3e6f2a1
--- /dev/null
+++ b/Documentation/ProjectFile/prj/time_loop/output/hdf/t_chunk_size_bytes.md
@@ -0,0 +1 @@
+\copydoc ProcessLib::OutputXDMFHDF5Format::chunk_size_bytes
diff --git a/MeshLib/IO/XDMF/HdfData.cpp b/MeshLib/IO/XDMF/HdfData.cpp
index 333d7b71b8e3970c3242cc742c3d50949817c237..d14d334b06da6ac190afd67c58ba2e19bf347874 100644
--- a/MeshLib/IO/XDMF/HdfData.cpp
+++ b/MeshLib/IO/XDMF/HdfData.cpp
@@ -45,21 +45,34 @@ static hid_t meshPropertyType2HdfType(MeshPropertyDataType const ogs_data_type)
HdfData::HdfData(void const* data_start, std::size_t const size_partitioned_dim,
std::size_t const size_tuple, std::string const& name,
MeshPropertyDataType const mesh_property_data_type,
- unsigned int const n_files)
+ unsigned int const n_files,
+ unsigned int const chunk_size_bytes)
: data_start(data_start), name(name)
{
+ data_type = meshPropertyType2HdfType(mesh_property_data_type);
+
auto const& partition_info =
getPartitionInfo(size_partitioned_dim, n_files);
auto const& offset_partitioned_dim = partition_info.local_offset;
offsets = {offset_partitioned_dim, 0};
- std::size_t unified_length = partition_info.local_length;
+ std::size_t const unified_length = partition_info.local_length;
+ int const type_size = H5Tget_size(data_type);
+ std::size_t const space =
+ (chunk_size_bytes > 0)
+ ? std::min(std::size_t(std::lround(float(chunk_size_bytes) /
+ (size_tuple * type_size) +
+ 0.5)),
+ partition_info.global_length)
+ : partition_info.longest_local_length;
- chunk_space =
- (size_tuple > 1)
- ? std::vector<Hdf5DimType>{partition_info.longest_local_length,
- size_tuple}
- : std::vector<Hdf5DimType>{partition_info.longest_local_length};
+ if (chunk_size_bytes > 0 && space == partition_info.global_length)
+ {
+ INFO("HDF5: Using a single chunk for dataset {:s} .", name);
+ }
+
+ chunk_space = (size_tuple > 1) ? std::vector<Hdf5DimType>{space, size_tuple}
+ : std::vector<Hdf5DimType>{space};
data_space = (size_tuple > 1)
? std::vector<Hdf5DimType>{unified_length, size_tuple}
@@ -69,8 +82,6 @@ HdfData::HdfData(void const* data_start, std::size_t const size_partitioned_dim,
? std::vector<Hdf5DimType>{partition_info.global_length, size_tuple}
: std::vector<Hdf5DimType>{partition_info.global_length};
- data_type = meshPropertyType2HdfType(mesh_property_data_type);
-
DBUG(
"HDF: dataset name: {:s}, offset: {:d}, data_space: {:d}, chunk_space "
"{:d}, file_space: {:d}, tuples: {:d}",
diff --git a/MeshLib/IO/XDMF/HdfData.h b/MeshLib/IO/XDMF/HdfData.h
index 6be7b77c2cbe2ce3a826aa208c547bd4ab455275..dee2d9c0d486b628519bbf58308ea27cef46262c 100644
--- a/MeshLib/IO/XDMF/HdfData.h
+++ b/MeshLib/IO/XDMF/HdfData.h
@@ -27,7 +27,8 @@ struct HdfData final
{
HdfData(void const* data_start, std::size_t size_partitioned_dim,
std::size_t size_tuple, std::string const& name,
- MeshPropertyDataType mesh_property_data_type, unsigned int n_files);
+ MeshPropertyDataType mesh_property_data_type, unsigned int n_files,
+ unsigned int chunk_size_bytes);
void const* data_start;
std::vector<Hdf5DimType> data_space;
std::vector<Hdf5DimType> offsets;
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
index e88fcd5114c1b9bf86e587ee90e7de2fa7474fe8..6509e0d5d0a7aac1d198077bed3ee36bd5186c9a 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
@@ -67,7 +67,8 @@ XdmfHdfWriter::XdmfHdfWriter(
std::filesystem::path const& filepath, unsigned long long const time_step,
double const initial_time,
std::set<std::string> const& variable_output_names,
- bool const use_compression, unsigned int const n_files)
+ bool const use_compression, unsigned int const n_files,
+ unsigned int const chunk_size_bytes)
{
// ogs meshes to vector of Xdmf/HDF meshes (we keep Xdmf and HDF together
// because XDMF depends on HDF) to meta
@@ -81,12 +82,12 @@ XdmfHdfWriter::XdmfHdfWriter(
// Transform the data to be written into a format conforming with the rules
// of xdmf topology and geometry
auto const transform_ogs_mesh_data_to_xdmf_conforming_data =
- [&n_files](auto const& mesh)
+ [&n_files, &chunk_size_bytes](auto const& mesh)
{
auto flattened_geometry_values = transformToXDMFGeometry(mesh);
// actually this line is only needed to calculate the offset
- XdmfHdfData const& geometry =
- transformGeometry(mesh, flattened_geometry_values.data(), n_files);
+ XdmfHdfData const& geometry = transformGeometry(
+ mesh, flattened_geometry_values.data(), n_files, chunk_size_bytes);
auto const flattened_topology_values =
transformToXDMFTopology(mesh, geometry.hdf.offsets[0]);
return std::make_unique<TransformedMeshData>(
@@ -96,8 +97,8 @@ XdmfHdfWriter::XdmfHdfWriter(
// create metadata for transformed data and original ogs mesh data
auto const transform_to_meta_data =
- [&transform_ogs_mesh_data_to_xdmf_conforming_data,
- &n_files](auto const& mesh)
+ [&transform_ogs_mesh_data_to_xdmf_conforming_data, &n_files,
+ &chunk_size_bytes](auto const& mesh)
{
// important: transformed data must survive and be unique, raw pointer
// to its memory!
@@ -105,10 +106,12 @@ XdmfHdfWriter::XdmfHdfWriter(
transform_ogs_mesh_data_to_xdmf_conforming_data(mesh);
auto const geometry = transformGeometry(
mesh, xdmf_conforming_data->flattened_geometry_values.data(),
- n_files);
- auto const topology = transformTopology(
- xdmf_conforming_data->flattened_topology_values, n_files);
- auto const attributes = transformAttributes(mesh, n_files);
+ n_files, chunk_size_bytes);
+ auto const topology =
+ transformTopology(xdmf_conforming_data->flattened_topology_values,
+ n_files, chunk_size_bytes);
+ auto const attributes =
+ transformAttributes(mesh, n_files, chunk_size_bytes);
return XdmfHdfMesh{std::move(geometry), std::move(topology),
std::move(attributes), mesh.get().getName(),
std::move(xdmf_conforming_data)};
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.h b/MeshLib/IO/XDMF/XdmfHdfWriter.h
index 03a98f2c08ca1b632c7a77a3406bea8da693f3ac..542d69d69e05185ecb146c100941624be6d529d7 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.h
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.h
@@ -35,12 +35,15 @@ public:
* @param use_compression if true, zlib compression in HDFWriter component
* is used
* @param n_files number of hdf5 output files
+ * @param chunk_size_bytes Data will be split into chunks. The parameter
+ * specifies the size (in bytes) of the largest chunk.
*/
XdmfHdfWriter(
std::vector<std::reference_wrapper<const MeshLib::Mesh>> const& meshes,
std::filesystem::path const& filepath, unsigned long long time_step,
double initial_time, std::set<std::string> const& variable_output_names,
- bool use_compression, unsigned int n_files);
+ bool use_compression, unsigned int n_files,
+ unsigned int chunk_size_bytes);
/**
* \brief Adds data for either lazy (xdmf) or eager (hdf) writing algorithm
diff --git a/MeshLib/IO/XDMF/mpi/fileIO.cpp b/MeshLib/IO/XDMF/mpi/fileIO.cpp
index b42fbf50ada8a4a1900d5a0f52744f77be9288b2..f3cb4f852b572f1a736cf4019490c448d5d4dcd0 100644
--- a/MeshLib/IO/XDMF/mpi/fileIO.cpp
+++ b/MeshLib/IO/XDMF/mpi/fileIO.cpp
@@ -44,6 +44,8 @@ hid_t createFile(std::filesystem::path const& filepath,
hid_t const plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, comm, info);
+ H5Pset_coll_metadata_write(plist_id, true);
+
std::filesystem::path const partition_filename =
partitionFilename(filepath, communicator.color);
hid_t file = H5Fcreate(partition_filename.string().c_str(), H5F_ACC_TRUNC,
diff --git a/MeshLib/IO/XDMF/transformData.cpp b/MeshLib/IO/XDMF/transformData.cpp
index 7e4e6b2a5ff190fe4e007f56266c7ce4a210aa80..4d5abd6c97c8c79e8b43fece9ec4343c92a314b1 100644
--- a/MeshLib/IO/XDMF/transformData.cpp
+++ b/MeshLib/IO/XDMF/transformData.cpp
@@ -71,7 +71,7 @@ constexpr auto cellTypeOGS2XDMF(MeshLib::CellType const& cell_type)
std::optional<XdmfHdfData> transformAttribute(
std::pair<std::string, PropertyVectorBase*> const& property_pair,
- unsigned int const n_files)
+ unsigned int const n_files, unsigned int const chunk_size_bytes)
{
// 3 data that will be captured and written by lambda f below
MeshPropertyDataType data_type = MeshPropertyDataType::unknown;
@@ -189,8 +189,8 @@ std::optional<XdmfHdfData> transformAttribute(
std::string const& name = property_base->getPropertyName();
- HdfData hdf = {data_ptr, num_of_tuples, ui_global_components,
- name, data_type, n_files};
+ HdfData hdf = {data_ptr, num_of_tuples, ui_global_components, name,
+ data_type, n_files, chunk_size_bytes};
XdmfData xdmf = {num_of_tuples, ui_global_components, data_type,
name, mesh_item_type, 0,
@@ -199,8 +199,9 @@ std::optional<XdmfHdfData> transformAttribute(
return XdmfHdfData{std::move(hdf), std::move(xdmf)};
}
-std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh,
- unsigned int const n_files)
+std::vector<XdmfHdfData> transformAttributes(
+ MeshLib::Mesh const& mesh, unsigned int const n_files,
+ unsigned int const chunk_size_bytes)
{
MeshLib::Properties const& properties = mesh.getProperties();
@@ -220,7 +221,10 @@ std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh,
}
if (auto const attribute = transformAttribute(
- std::pair(std::string(name), property_base), n_files))
+
+ std::pair(std::string(name), property_base), n_files,
+ chunk_size_bytes))
+
{
attributes.push_back(attribute.value());
}
@@ -248,9 +252,9 @@ std::vector<double> transformToXDMFGeometry(MeshLib::Mesh const& mesh)
return values;
}
-XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh,
- double const* data_ptr,
- unsigned int const n_files)
+XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh, double const* data_ptr,
+ unsigned int const n_files,
+ unsigned int const chunk_size_bytes)
{
std::string const name = "geometry";
std::vector<MeshLib::Node*> const& nodes = mesh.getNodes();
@@ -263,7 +267,8 @@ XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh,
point_size,
name,
MeshPropertyDataType::float64,
- n_files};
+ n_files,
+ chunk_size_bytes};
XdmfData const xdmf = {
partition_dim, point_size, MeshPropertyDataType::float64,
name, std::nullopt, 2,
@@ -300,12 +305,13 @@ std::vector<int> transformToXDMFTopology(MeshLib::Mesh const& mesh,
}
XdmfHdfData transformTopology(std::vector<int> const& values,
- unsigned int const n_files)
+ unsigned int const n_files,
+ unsigned int const chunk_size_bytes)
{
std::string const name = "topology";
HdfData const hdf = {
- values.data(), values.size(), 1, name, MeshPropertyDataType::int32,
- n_files};
+ values.data(), values.size(), 1, name, MeshPropertyDataType::int32,
+ n_files, chunk_size_bytes};
XdmfData const xdmf = {
values.size(), 1, MeshPropertyDataType::int32, name, std::nullopt, 3,
n_files};
diff --git a/MeshLib/IO/XDMF/transformData.h b/MeshLib/IO/XDMF/transformData.h
index 13cf818deabf609a7c14fbdb00914f77ecf5c8c9..463e26022761012e6107b7e016cfcd36405b2721 100644
--- a/MeshLib/IO/XDMF/transformData.h
+++ b/MeshLib/IO/XDMF/transformData.h
@@ -28,29 +28,38 @@ namespace MeshLib::IO
* \param mesh OGS mesh can be mesh or partitionedMesh
* \param n_files specifies the number of files. If greater than 1 it groups the
* data of each process to n_files
- * \return vector of meta data
+ * @param chunk_size_bytes Data will be split into chunks. The parameter
+ * specifies the size (in bytes) of the largest chunk.
+ * @return vector of meta data
*/
std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh,
- unsigned int n_files);
+ unsigned int n_files,
+ unsigned int chunk_size_bytes);
/**
* \brief Create meta data for geometry used for hdf5 and xdmf
* \param mesh OGS mesh can be mesh or partitionedMesh
* \param data_ptr Memory location of geometry values.
* \param n_files specifies the number of files. If greater than 1 it groups the
* data of each process to n_files
+ * \param chunk_size_bytes Data will be split into chunks. The parameter
+ * specifies the size (in bytes) of the largest chunk.
* \return Geometry meta data
*/
XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh, double const* data_ptr,
- unsigned int n_files);
+ unsigned int n_files,
+ unsigned int chunk_size_bytes);
/**
* \brief Create meta data for topology used for HDF5 and XDMF
* \param values actual topology values to get size and memory location
* \param n_files specifies the number of files. If greater than 1 it groups the
* data of each process to n_files
+ * \param chunk_size_bytes Data will be split into chunks. The parameter
+ * specifies the size (in bytes) of the largest chunk.
* \return Topology meta data
*/
XdmfHdfData transformTopology(std::vector<int> const& values,
- unsigned int n_files);
+ unsigned int n_files,
+ unsigned int chunk_size_bytes);
/**
* \brief Copies all node points into a new vector. Contiguous data used for
* writing. Conform with XDMF standard in
diff --git a/MeshLib/IO/writeMeshToFile.cpp b/MeshLib/IO/writeMeshToFile.cpp
index 0fca1a97fefce31ca9ab9b635fce8986b4543903..0016be32eeeed59ca058ca1ea4d5630cf9561049 100644
--- a/MeshLib/IO/writeMeshToFile.cpp
+++ b/MeshLib/IO/writeMeshToFile.cpp
@@ -51,7 +51,7 @@ int writeMeshToFile(const MeshLib::Mesh& mesh,
const std::reference_wrapper<const MeshLib::Mesh> mr = mesh;
meshes.push_back(mr);
MeshLib::IO::XdmfHdfWriter(std::move(meshes), file_path, 0, 0.0,
- variable_output_names, true, 1);
+ variable_output_names, true, 1, 1048576);
return 0;
}
ERR("writeMeshToFile(): Unknown file extension '{:s}'. Can not write file "
diff --git a/ProcessLib/Output/CreateOutput.cpp b/ProcessLib/Output/CreateOutput.cpp
index d5bf7d59a9f9dc76bd3ec638dd443dd5bcb9a8fd..90268f8c22ba8bacd7dc84504d20ad13165d5699 100644
--- a/ProcessLib/Output/CreateOutput.cpp
+++ b/ProcessLib/Output/CreateOutput.cpp
@@ -61,7 +61,8 @@ namespace ProcessLib
std::unique_ptr<OutputFormat> createOutputFormat(
std::string const& output_directory, OutputType const output_type,
std::string prefix, std::string suffix, std::string const& data_mode,
- bool const compress_output, unsigned int const number_of_files)
+ bool const compress_output, unsigned int const number_of_files,
+ unsigned int const chunk_size_bytes)
{
switch (output_type)
{
@@ -72,7 +73,7 @@ std::unique_ptr<OutputFormat> createOutputFormat(
case OutputType::xdmf:
return std::make_unique<OutputXDMFHDF5Format>(
output_directory, std::move(prefix), std::move(suffix),
- compress_output, number_of_files);
+ compress_output, number_of_files, chunk_size_bytes);
default:
OGS_FATAL(
"No supported file type provided. Read '{}' from "
@@ -87,7 +88,7 @@ Output createOutput(OutputConfig&& oc, std::string const& output_directory,
auto output_format = createOutputFormat(
output_directory, oc.output_type, std::move(oc.prefix),
std::move(oc.suffix), oc.data_mode, oc.compress_output,
- oc.number_of_files);
+ oc.number_of_files, oc.chunk_size_bytes);
OutputDataSpecification output_data_specification{
std::move(oc.output_variables), std::move(oc.fixed_output_times),
diff --git a/ProcessLib/Output/CreateOutputConfig.cpp b/ProcessLib/Output/CreateOutputConfig.cpp
index 17242d76f44785e0df1d049d7a13ed9a10679746..f120c1e8c8201781e3d372b871bdc797b04f5324 100644
--- a/ProcessLib/Output/CreateOutputConfig.cpp
+++ b/ProcessLib/Output/CreateOutputConfig.cpp
@@ -130,6 +130,16 @@ OutputConfig createOutputConfig(
}
return 1;
}();
+ output_config.chunk_size_bytes = [&hdf]() -> unsigned int
+ {
+ if (hdf)
+ {
+ //! \ogs_file_param{prj__time_loop__output__hdf__chunk_size_bytes}
+ return hdf->getConfigParameter<unsigned int>("chunk_size_bytes");
+ }
+ return 1048576; // default chunk size in bytes according to
+ // https://www.hdfgroup.org/2022/10/improve-hdf5-performance-using-caching/
+ }();
output_config.data_mode =
//! \ogs_file_param{prj__time_loop__output__data_mode}
diff --git a/ProcessLib/Output/OutputConfig.h b/ProcessLib/Output/OutputConfig.h
index 6b1953dabb928a8ed03255365115b4993c57e640..e11a0cdb091f59357d111502327bdb5caa302cc1 100644
--- a/ProcessLib/Output/OutputConfig.h
+++ b/ProcessLib/Output/OutputConfig.h
@@ -38,6 +38,7 @@ struct OutputConfig
std::string suffix;
bool compress_output;
unsigned int number_of_files;
+ unsigned int chunk_size_bytes;
std::string data_mode;
/// A list of repeat/step-count pairs. If the list is empty, and no
/// fixed_output_times were specified, a default pair 1/1 will be inserted
diff --git a/ProcessLib/Output/OutputFormat.cpp b/ProcessLib/Output/OutputFormat.cpp
index 7c54cda07f2bcb06b2795336635f7f94cd3bf6c0..7ccac641221eb359479f7e2341d8a9c9bb283401 100644
--- a/ProcessLib/Output/OutputFormat.cpp
+++ b/ProcessLib/Output/OutputFormat.cpp
@@ -122,7 +122,8 @@ void OutputXDMFHDF5Format::outputMeshXdmf(
iteration);
std::filesystem::path path(BaseLib::joinPaths(directory, name));
mesh_xdmf_hdf_writer = std::make_unique<MeshLib::IO::XdmfHdfWriter>(
- meshes, path, timestep, t, output_variables, compression, n_files);
+ meshes, path, timestep, t, output_variables, compression, n_files,
+ chunk_size_bytes);
}
else
{
diff --git a/ProcessLib/Output/OutputFormat.h b/ProcessLib/Output/OutputFormat.h
index 2111b9424d20235204fd3b3ba3c4980c4758f3ee..f351c6d8e3d95a9e4ca41b4a05c4b972625681ff 100644
--- a/ProcessLib/Output/OutputFormat.h
+++ b/ProcessLib/Output/OutputFormat.h
@@ -95,10 +95,12 @@ struct OutputXDMFHDF5Format final : public OutputFormat
{
OutputXDMFHDF5Format(std::string const& directory, std::string prefix,
std::string suffix, bool const compression,
- unsigned int const n_files)
+ unsigned int const n_files,
+ unsigned int const chunk_size_bytes)
: OutputFormat(directory, std::move(prefix), std::move(suffix),
compression),
- n_files(n_files)
+ n_files(n_files),
+ chunk_size_bytes(chunk_size_bytes)
{
}
@@ -117,6 +119,8 @@ struct OutputXDMFHDF5Format final : public OutputFormat
mutable std::unique_ptr<MeshLib::IO::XdmfHdfWriter> mesh_xdmf_hdf_writer;
//! Specifies the number of hdf5 output files.
unsigned int n_files;
+ //! Specifies the chunks size in bytes per hdf5 output file.
+ unsigned int const chunk_size_bytes;
void outputMeshXdmf(
std::set<std::string> const& output_variables,
diff --git a/Tests/Data/EllipticPETSc/cube_1e3.include b/Tests/Data/EllipticPETSc/cube_1e3.include
new file mode 100644
index 0000000000000000000000000000000000000000..e85244dce8b0afd69ad380d82066eeae3f9152da
--- /dev/null
+++ b/Tests/Data/EllipticPETSc/cube_1e3.include
@@ -0,0 +1,96 @@
+
+<mesh>cube_1x1x1_hex_1e3.vtu</mesh>
+<geometry>cube_1x1x1.gml</geometry>
+<processes>
+ <process>
+ <name>GW23</name>
+ <type>STEADY_STATE_DIFFUSION</type>
+ <integration_order>2</integration_order>
+ <process_variables>
+ <process_variable>pressure</process_variable>
+ </process_variables>
+ <secondary_variables>
+ <secondary_variable internal_name="darcy_velocity" output_name="v" />
+ </secondary_variables>
+ </process>
+</processes>
+<media>
+ <medium id="0">
+ <phases />
+ <properties>
+ <property>
+ <name>diffusion</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>reference_temperature</name>
+ <type>Constant</type>
+ <value>293.15</value>
+ </property>
+ </properties>
+ </medium>
+</media>
+<parameters>
+ <parameter>
+ <name>p0</name>
+ <type>Constant</type>
+ <value>0</value>
+ </parameter>
+ <parameter>
+ <name>p_Dirichlet_left</name>
+ <type>Constant</type>
+ <value>1</value>
+ </parameter>
+ <parameter>
+ <name>p_Dirichlet_right</name>
+ <type>Constant</type>
+ <value>-1</value>
+ </parameter>
+</parameters>
+<process_variables>
+ <process_variable>
+ <name>pressure</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>p0</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <geometrical_set>cube_1x1x1_geometry</geometrical_set>
+ <geometry>left</geometry>
+ <type>Dirichlet</type>
+ <parameter>p_Dirichlet_left</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <geometrical_set>cube_1x1x1_geometry</geometrical_set>
+ <geometry>right</geometry>
+ <type>Dirichlet</type>
+ <parameter>p_Dirichlet_right</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+</process_variables>
+<nonlinear_solvers>
+ <nonlinear_solver>
+ <name>basic_picard</name>
+ <type>Picard</type>
+ <max_iter>10</max_iter>
+ <linear_solver>general_linear_solver</linear_solver>
+ </nonlinear_solver>
+</nonlinear_solvers>
+<linear_solvers>
+ <linear_solver>
+ <name>general_linear_solver</name>
+ <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
+ <eigen>
+ <solver_type>CG</solver_type>
+ <precon_type>DIAGONAL</precon_type>
+ <max_iteration_step>10000</max_iteration_step>
+ <error_tolerance>1e-16</error_tolerance>
+ </eigen>
+ <petsc>
+ <prefix>gw</prefix>
+ <parameters>-gw_ksp_type bcgs -gw_pc_type mg -gw_ksp_rtol 1.e-16 -gw_ksp_max_it 10000</parameters>
+ </petsc>
+ </linear_solver>
+</linear_solvers>
\ No newline at end of file
diff --git a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np2.prj b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np2.prj
index 4a82534b0a7fd94f6f17adf8a3d1cbda893eeae7..537de1e64197a22b0c465f4ff3f3e035f8387657 100644
--- a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np2.prj
+++ b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np2.prj
@@ -1,68 +1,7 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<OpenGeoSysProject>
- <mesh>cube_1x1x1_hex_1e3.vtu</mesh>
- <geometry>cube_1x1x1.gml</geometry>
- <processes>
- <process>
- <name>GW23</name>
- <type>STEADY_STATE_DIFFUSION</type>
- <integration_order>2</integration_order>
- <process_variables>
- <process_variable>pressure</process_variable>
- </process_variables>
- <secondary_variables>
- <secondary_variable internal_name="darcy_velocity" output_name="v"/>
- </secondary_variables>
- </process>
- </processes>
- <media>
- <medium id="0">
- <phases/>
- <properties>
- <property>
- <name>diffusion</name>
- <type>Constant</type>
- <value>1</value>
- </property>
- <property>
- <name>reference_temperature</name>
- <type>Constant</type>
- <value>293.15</value>
- </property>
- </properties>
- </medium>
- </media>
<time_loop>
- <processes>
- <process ref="GW23">
- <nonlinear_solver>basic_picard</nonlinear_solver>
- <convergence_criterion>
- <type>DeltaX</type>
- <norm_type>NORM2</norm_type>
- <abstol>1.e-6</abstol>
- </convergence_criterion>
- <time_discretization>
- <type>BackwardEuler</type>
- </time_discretization>
- <time_stepping>
- <type>FixedTimeStepping</type>
- <t_initial>0.0</t_initial>
- <t_end>1e-1</t_end>
- <timesteps>
- <!-- Testing precision of the time step value output. -->
- <pair>
- <repeat>1</repeat>
- <!-- 0.1 - 1e-15 -->
- <delta_t>.099999999999999</delta_t>
- </pair>
- <pair>
- <repeat>1</repeat>
- <delta_t>1e-1</delta_t>
- </pair>
- </timesteps>
- </time_stepping>
- </process>
- </processes>
+ <include file="steady_state_diffusion.include"/>
<output>
<type>XDMF</type>
<prefix>cube_1e3_np2</prefix>
@@ -79,67 +18,5 @@
</timesteps>
</output>
</time_loop>
- <parameters>
- <parameter>
- <name>p0</name>
- <type>Constant</type>
- <value>0</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_left</name>
- <type>Constant</type>
- <value>1</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_right</name>
- <type>Constant</type>
- <value>-1</value>
- </parameter>
- </parameters>
- <process_variables>
- <process_variable>
- <name>pressure</name>
- <components>1</components>
- <order>1</order>
- <initial_condition>p0</initial_condition>
- <boundary_conditions>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>left</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_left</parameter>
- </boundary_condition>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>right</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_right</parameter>
- </boundary_condition>
- </boundary_conditions>
- </process_variable>
- </process_variables>
- <nonlinear_solvers>
- <nonlinear_solver>
- <name>basic_picard</name>
- <type>Picard</type>
- <max_iter>10</max_iter>
- <linear_solver>general_linear_solver</linear_solver>
- </nonlinear_solver>
- </nonlinear_solvers>
- <linear_solvers>
- <linear_solver>
- <name>general_linear_solver</name>
- <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
- <eigen>
- <solver_type>CG</solver_type>
- <precon_type>DIAGONAL</precon_type>
- <max_iteration_step>10000</max_iteration_step>
- <error_tolerance>1e-16</error_tolerance>
- </eigen>
- <petsc>
- <prefix>gw</prefix>
- <parameters>-gw_ksp_type bcgs -gw_pc_type mg -gw_ksp_rtol 1.e-16 -gw_ksp_max_it 10000</parameters>
- </petsc>
- </linear_solver>
- </linear_solvers>
-</OpenGeoSysProject>
+ <include file="cube_1e3.include"/>
+</OpenGeoSysProject>
\ No newline at end of file
diff --git a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj
index eea6db0a3d6c15afa314da9c5a36c5b1ae76b3f4..768a35f1a42b194ffd4843f9279808498b2def7e 100644
--- a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj
+++ b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj
@@ -1,62 +1,7 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<OpenGeoSysProject>
- <mesh>cube_1x1x1_hex_1e3.vtu</mesh>
- <geometry>cube_1x1x1.gml</geometry>
- <processes>
- <process>
- <name>GW23</name>
- <type>STEADY_STATE_DIFFUSION</type>
- <integration_order>2</integration_order>
- <process_variables>
- <process_variable>pressure</process_variable>
- </process_variables>
- <secondary_variables>
- <secondary_variable internal_name="darcy_velocity" output_name="v"/>
- </secondary_variables>
- </process>
- </processes>
- <media>
- <medium id="0">
- <phases/>
- <properties>
- <property>
- <name>diffusion</name>
- <type>Constant</type>
- <value>1</value>
- </property>
- <property>
- <name>reference_temperature</name>
- <type>Constant</type>
- <value>293.15</value>
- </property>
- </properties>
- </medium>
- </media>
<time_loop>
- <processes>
- <process ref="GW23">
- <nonlinear_solver>basic_picard</nonlinear_solver>
- <convergence_criterion>
- <type>DeltaX</type>
- <norm_type>NORM2</norm_type>
- <abstol>1.e-6</abstol>
- </convergence_criterion>
- <time_discretization>
- <type>BackwardEuler</type>
- </time_discretization>
- <time_stepping>
- <type>FixedTimeStepping</type>
- <t_initial>0.0</t_initial>
- <t_end>1e-1</t_end>
- <timesteps>
- <pair>
- <repeat>1</repeat>
- <delta_t>1e-1</delta_t>
- </pair>
- </timesteps>
- </time_stepping>
- </process>
- </processes>
+ <include file="steady_state_diffusion.include"/>
<output>
<type>XDMF</type>
<prefix>cube_1e3_np3</prefix>
@@ -67,70 +12,9 @@
<suffix>_ts_{:timestep}_t_{:time}</suffix>
<hdf>
<number_of_files>1</number_of_files>
+ <chunk_size_bytes>1048576</chunk_size_bytes>
</hdf>
</output>
</time_loop>
- <parameters>
- <parameter>
- <name>p0</name>
- <type>Constant</type>
- <value>0</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_left</name>
- <type>Constant</type>
- <value>1</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_right</name>
- <type>Constant</type>
- <value>-1</value>
- </parameter>
- </parameters>
- <process_variables>
- <process_variable>
- <name>pressure</name>
- <components>1</components>
- <order>1</order>
- <initial_condition>p0</initial_condition>
- <boundary_conditions>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>left</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_left</parameter>
- </boundary_condition>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>right</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_right</parameter>
- </boundary_condition>
- </boundary_conditions>
- </process_variable>
- </process_variables>
- <nonlinear_solvers>
- <nonlinear_solver>
- <name>basic_picard</name>
- <type>Picard</type>
- <max_iter>10</max_iter>
- <linear_solver>general_linear_solver</linear_solver>
- </nonlinear_solver>
- </nonlinear_solvers>
- <linear_solvers>
- <linear_solver>
- <name>general_linear_solver</name>
- <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
- <eigen>
- <solver_type>CG</solver_type>
- <precon_type>DIAGONAL</precon_type>
- <max_iteration_step>10000</max_iteration_step>
- <error_tolerance>1e-16</error_tolerance>
- </eigen>
- <petsc>
- <prefix>gw</prefix>
- <parameters>-gw_ksp_type bcgs -gw_pc_type mg -gw_ksp_rtol 1.e-16 -gw_ksp_max_it 10000</parameters>
- </petsc>
- </linear_solver>
- </linear_solvers>
+ <include file="cube_1e3.include"/>
</OpenGeoSysProject>
diff --git a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_2files.prj b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_2files.prj
index 87ec030106216b19566d3a48d806574172f2d129..44484628f9c52e5ba84e04858cafb1e390400549 100644
--- a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_2files.prj
+++ b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_2files.prj
@@ -1,62 +1,7 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<OpenGeoSysProject>
- <mesh>cube_1x1x1_hex_1e3.vtu</mesh>
- <geometry>cube_1x1x1.gml</geometry>
- <processes>
- <process>
- <name>GW23</name>
- <type>STEADY_STATE_DIFFUSION</type>
- <integration_order>2</integration_order>
- <process_variables>
- <process_variable>pressure</process_variable>
- </process_variables>
- <secondary_variables>
- <secondary_variable internal_name="darcy_velocity" output_name="v"/>
- </secondary_variables>
- </process>
- </processes>
- <media>
- <medium id="0">
- <phases/>
- <properties>
- <property>
- <name>diffusion</name>
- <type>Constant</type>
- <value>1</value>
- </property>
- <property>
- <name>reference_temperature</name>
- <type>Constant</type>
- <value>293.15</value>
- </property>
- </properties>
- </medium>
- </media>
<time_loop>
- <processes>
- <process ref="GW23">
- <nonlinear_solver>basic_picard</nonlinear_solver>
- <convergence_criterion>
- <type>DeltaX</type>
- <norm_type>NORM2</norm_type>
- <abstol>1.e-6</abstol>
- </convergence_criterion>
- <time_discretization>
- <type>BackwardEuler</type>
- </time_discretization>
- <time_stepping>
- <type>FixedTimeStepping</type>
- <t_initial>0.0</t_initial>
- <t_end>1e-1</t_end>
- <timesteps>
- <pair>
- <repeat>1</repeat>
- <delta_t>1e-1</delta_t>
- </pair>
- </timesteps>
- </time_stepping>
- </process>
- </processes>
+ <include file="steady_state_diffusion.include"/>
<output>
<type>XDMF</type>
<prefix>cube_1e3_np3</prefix>
@@ -67,70 +12,10 @@
<suffix>_ts_{:timestep}_t_{:time}</suffix>
<hdf>
<number_of_files>2</number_of_files>
+ <chunk_size_bytes>1048576</chunk_size_bytes>
</hdf>
</output>
</time_loop>
- <parameters>
- <parameter>
- <name>p0</name>
- <type>Constant</type>
- <value>0</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_left</name>
- <type>Constant</type>
- <value>1</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_right</name>
- <type>Constant</type>
- <value>-1</value>
- </parameter>
- </parameters>
- <process_variables>
- <process_variable>
- <name>pressure</name>
- <components>1</components>
- <order>1</order>
- <initial_condition>p0</initial_condition>
- <boundary_conditions>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>left</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_left</parameter>
- </boundary_condition>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>right</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_right</parameter>
- </boundary_condition>
- </boundary_conditions>
- </process_variable>
- </process_variables>
- <nonlinear_solvers>
- <nonlinear_solver>
- <name>basic_picard</name>
- <type>Picard</type>
- <max_iter>10</max_iter>
- <linear_solver>general_linear_solver</linear_solver>
- </nonlinear_solver>
- </nonlinear_solvers>
- <linear_solvers>
- <linear_solver>
- <name>general_linear_solver</name>
- <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
- <eigen>
- <solver_type>CG</solver_type>
- <precon_type>DIAGONAL</precon_type>
- <max_iteration_step>10000</max_iteration_step>
- <error_tolerance>1e-16</error_tolerance>
- </eigen>
- <petsc>
- <prefix>gw</prefix>
- <parameters>-gw_ksp_type bcgs -gw_pc_type mg -gw_ksp_rtol 1.e-16 -gw_ksp_max_it 10000</parameters>
- </petsc>
- </linear_solver>
- </linear_solvers>
-</OpenGeoSysProject>
+
+ <include file="cube_1e3.include"/>
+</OpenGeoSysProject>
\ No newline at end of file
diff --git a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_3files.prj b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_3files.prj
index 470bf91b822936486ec30670edeeb4568b940537..5e7c13203127c8bf0fcb77d86daad3fabdaad3e8 100644
--- a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_3files.prj
+++ b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3_3files.prj
@@ -1,62 +1,7 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<OpenGeoSysProject>
- <mesh>cube_1x1x1_hex_1e3.vtu</mesh>
- <geometry>cube_1x1x1.gml</geometry>
- <processes>
- <process>
- <name>GW23</name>
- <type>STEADY_STATE_DIFFUSION</type>
- <integration_order>2</integration_order>
- <process_variables>
- <process_variable>pressure</process_variable>
- </process_variables>
- <secondary_variables>
- <secondary_variable internal_name="darcy_velocity" output_name="v"/>
- </secondary_variables>
- </process>
- </processes>
- <media>
- <medium id="0">
- <phases/>
- <properties>
- <property>
- <name>diffusion</name>
- <type>Constant</type>
- <value>1</value>
- </property>
- <property>
- <name>reference_temperature</name>
- <type>Constant</type>
- <value>293.15</value>
- </property>
- </properties>
- </medium>
- </media>
<time_loop>
- <processes>
- <process ref="GW23">
- <nonlinear_solver>basic_picard</nonlinear_solver>
- <convergence_criterion>
- <type>DeltaX</type>
- <norm_type>NORM2</norm_type>
- <abstol>1.e-6</abstol>
- </convergence_criterion>
- <time_discretization>
- <type>BackwardEuler</type>
- </time_discretization>
- <time_stepping>
- <type>FixedTimeStepping</type>
- <t_initial>0.0</t_initial>
- <t_end>1e-1</t_end>
- <timesteps>
- <pair>
- <repeat>1</repeat>
- <delta_t>1e-1</delta_t>
- </pair>
- </timesteps>
- </time_stepping>
- </process>
- </processes>
+ <include file="steady_state_diffusion.include"/>
<output>
<type>XDMF</type>
<prefix>cube_1e3_np3</prefix>
@@ -67,70 +12,9 @@
<suffix>_ts_{:timestep}_t_{:time}</suffix>
<hdf>
<number_of_files>3</number_of_files>
+ <chunk_size_bytes>1048576</chunk_size_bytes>
</hdf>
</output>
</time_loop>
- <parameters>
- <parameter>
- <name>p0</name>
- <type>Constant</type>
- <value>0</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_left</name>
- <type>Constant</type>
- <value>1</value>
- </parameter>
- <parameter>
- <name>p_Dirichlet_right</name>
- <type>Constant</type>
- <value>-1</value>
- </parameter>
- </parameters>
- <process_variables>
- <process_variable>
- <name>pressure</name>
- <components>1</components>
- <order>1</order>
- <initial_condition>p0</initial_condition>
- <boundary_conditions>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>left</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_left</parameter>
- </boundary_condition>
- <boundary_condition>
- <geometrical_set>cube_1x1x1_geometry</geometrical_set>
- <geometry>right</geometry>
- <type>Dirichlet</type>
- <parameter>p_Dirichlet_right</parameter>
- </boundary_condition>
- </boundary_conditions>
- </process_variable>
- </process_variables>
- <nonlinear_solvers>
- <nonlinear_solver>
- <name>basic_picard</name>
- <type>Picard</type>
- <max_iter>10</max_iter>
- <linear_solver>general_linear_solver</linear_solver>
- </nonlinear_solver>
- </nonlinear_solvers>
- <linear_solvers>
- <linear_solver>
- <name>general_linear_solver</name>
- <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
- <eigen>
- <solver_type>CG</solver_type>
- <precon_type>DIAGONAL</precon_type>
- <max_iteration_step>10000</max_iteration_step>
- <error_tolerance>1e-16</error_tolerance>
- </eigen>
- <petsc>
- <prefix>gw</prefix>
- <parameters>-gw_ksp_type bcgs -gw_pc_type mg -gw_ksp_rtol 1.e-16 -gw_ksp_max_it 10000</parameters>
- </petsc>
- </linear_solver>
- </linear_solvers>
+ <include file="cube_1e3.include"/>
</OpenGeoSysProject>
diff --git a/Tests/Data/EllipticPETSc/steady_state_diffusion.include b/Tests/Data/EllipticPETSc/steady_state_diffusion.include
new file mode 100644
index 0000000000000000000000000000000000000000..4227bc402f6ee3cede8c1cd6a2e7fe218b4b9aeb
--- /dev/null
+++ b/Tests/Data/EllipticPETSc/steady_state_diffusion.include
@@ -0,0 +1,24 @@
+<processes>
+ <process ref="GW23">
+ <nonlinear_solver>basic_picard</nonlinear_solver>
+ <convergence_criterion>
+ <type>DeltaX</type>
+ <norm_type>NORM2</norm_type>
+ <abstol>1.e-6</abstol>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0.0</t_initial>
+ <t_end>1e-1</t_end>
+ <timesteps>
+ <pair>
+ <repeat>1</repeat>
+ <delta_t>1e-1</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+</processes>
\ No newline at end of file
diff --git a/Tests/Data/Parabolic/LiquidFlow/SimpleSynthetics/XDMF/FunctionParameterTest_XDMF.prj b/Tests/Data/Parabolic/LiquidFlow/SimpleSynthetics/XDMF/FunctionParameterTest_XDMF.prj
index 7753f7d2465a4dc136e10d026001cf907c427e72..dd6cadc47cffb0f20ee4efc6c464e3ea8aa7b78a 100644
--- a/Tests/Data/Parabolic/LiquidFlow/SimpleSynthetics/XDMF/FunctionParameterTest_XDMF.prj
+++ b/Tests/Data/Parabolic/LiquidFlow/SimpleSynthetics/XDMF/FunctionParameterTest_XDMF.prj
@@ -141,6 +141,10 @@ boundary meshes will be written as well -->
<each_steps>1</each_steps>
</pair>
</timesteps>
+ <hdf>
+ <chunk_size_bytes>123456</chunk_size_bytes>
+ <number_of_files>1</number_of_files>
+ </hdf>
<output_iteration_results>false</output_iteration_results>
<variables>
<variable> pressure </variable>