diff --git a/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md b/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md
new file mode 100644
index 0000000000000000000000000000000000000000..2043711a7a77bcb4ca95a5845138c5bfb9b6761d
--- /dev/null
+++ b/Documentation/ProjectFile/prj/time_loop/output/hdf/i_hdf.md
@@ -0,0 +1,2 @@
+Group of parameters when XDMF/HDF writer is used.
+Type of output in time_loop must be XDMF
diff --git a/Documentation/ProjectFile/prj/time_loop/output/hdf/t_number_of_files.md b/Documentation/ProjectFile/prj/time_loop/output/hdf/t_number_of_files.md
new file mode 100644
index 0000000000000000000000000000000000000000..662f4178c831d66745976513dc56e3a36f240376
--- /dev/null
+++ b/Documentation/ProjectFile/prj/time_loop/output/hdf/t_number_of_files.md
@@ -0,0 +1 @@
+\copydoc ProcessLib::Output::_n_files
diff --git a/MeshLib/IO/XDMF/HdfData.cpp b/MeshLib/IO/XDMF/HdfData.cpp
index 76b3ce2da9a83ebb5fec5a0b5361317ede20ae23..dc0b6272af6f1332a5375ed02ec7b2cfd4ec1eee 100644
--- a/MeshLib/IO/XDMF/HdfData.cpp
+++ b/MeshLib/IO/XDMF/HdfData.cpp
@@ -42,10 +42,12 @@ 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)
+ MeshPropertyDataType const mesh_property_data_type,
+ unsigned int const num_of_files)
: data_start(data_start), name(name)
{
- auto const& partition_info = getPartitionInfo(size_partitioned_dim);
+ auto const& partition_info =
+ getPartitionInfo(size_partitioned_dim, num_of_files);
auto const& offset_partitioned_dim = partition_info.local_offset;
offsets = {offset_partitioned_dim, 0};
diff --git a/MeshLib/IO/XDMF/HdfData.h b/MeshLib/IO/XDMF/HdfData.h
index 50f6eb17a5be138b362bf03d8b5ddac378b0c0a5..bc41db110b2f0d10a0b5b0fcb9b409c3f2d72f82 100644
--- a/MeshLib/IO/XDMF/HdfData.h
+++ b/MeshLib/IO/XDMF/HdfData.h
@@ -25,7 +25,8 @@ 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);
+ MeshPropertyDataType mesh_property_data_type,
+ unsigned int num_of_files);
void const* data_start;
std::vector<Hdf5DimType> data_space;
std::vector<Hdf5DimType> offsets;
diff --git a/MeshLib/IO/XDMF/HdfWriter.cpp b/MeshLib/IO/XDMF/HdfWriter.cpp
index 4723120c8a5b8d871fe8d94644bd0531cc5894af..a4ba35cb9c8f6b7bb606396ac49799107c502464 100644
--- a/MeshLib/IO/XDMF/HdfWriter.cpp
+++ b/MeshLib/IO/XDMF/HdfWriter.cpp
@@ -213,9 +213,10 @@ HdfWriter::HdfWriter(std::vector<MeshHdfData> meshes,
unsigned long long const initial_step,
std::filesystem::path const& filepath,
bool const use_compression,
- bool const is_file_manager)
+ bool const is_file_manager,
+ unsigned int const num_of_files)
: _hdf5_filepath(filepath),
- _file(createFile(filepath)),
+ _file(createFile(filepath, num_of_files)),
_meshes_group(
H5Gcreate2(_file, "/meshes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)),
_step_times{0}, // ToDo need to be initial time
diff --git a/MeshLib/IO/XDMF/HdfWriter.h b/MeshLib/IO/XDMF/HdfWriter.h
index 97c8707850a552134f3efd4092502089933e88ee..a58c1f4bd4dca35ac1ee4f5033112d231418ddc2 100644
--- a/MeshLib/IO/XDMF/HdfWriter.h
+++ b/MeshLib/IO/XDMF/HdfWriter.h
@@ -43,13 +43,15 @@ public:
* @param filepath absolute or relative filepath to the hdf5 file
* @param use_compression if true gzip compression is enabled
* @param is_file_manager True if process (in parallel execution) is
+ * @param num_of_files Number of outputfiles
* File_Manager
*/
HdfWriter(std::vector<MeshHdfData> meshes,
unsigned long long initial_step,
std::filesystem::path const& filepath,
bool use_compression,
- bool is_file_manager);
+ bool is_file_manager,
+ unsigned int num_of_files);
/**
* \brief Writes attributes. The data
* itself is hold by a structure outside of this class. The writer assumes
diff --git a/MeshLib/IO/XDMF/XdmfData.cpp b/MeshLib/IO/XDMF/XdmfData.cpp
index 432895df556c906536ff1bd612fdfb0065b8eb04..f2e2b3c9eef39c19e8153cb39e652e434b02f5e2 100644
--- a/MeshLib/IO/XDMF/XdmfData.cpp
+++ b/MeshLib/IO/XDMF/XdmfData.cpp
@@ -23,7 +23,8 @@ XdmfData::XdmfData(std::size_t const size_partitioned_dim,
MeshPropertyDataType const mesh_property_data_type,
std::string const& name,
std::optional<MeshLib::MeshItemType> const attribute_center,
- unsigned int const index)
+ unsigned int const index,
+ unsigned int const num_of_files)
: starts(
[&size_tuple]()
{
@@ -53,7 +54,7 @@ XdmfData::XdmfData(std::size_t const size_partitioned_dim,
attribute_center(attribute_center),
index(index)
{
- auto partition_info = getPartitionInfo(size_partitioned_dim);
+ auto partition_info = getPartitionInfo(size_partitioned_dim, num_of_files);
// TODO (tm) XdmfLib does not support 64 bit data types so far
assert(partition_info.local_length <
std::numeric_limits<unsigned int>::max());
diff --git a/MeshLib/IO/XDMF/XdmfData.h b/MeshLib/IO/XDMF/XdmfData.h
index 5d256f248120b5ec1c44d2f5839b0e824126164e..d3a96f11d261c8294273b24ad06735195e3f03bc 100644
--- a/MeshLib/IO/XDMF/XdmfData.h
+++ b/MeshLib/IO/XDMF/XdmfData.h
@@ -46,13 +46,15 @@ struct XdmfData final
* @param index The position of the DataItem parents in a grid
* (representing a single step). Convention is: 1=Time, 2=
* Geometry, 3=Topology, 4>=Attribute
+ * @param num_of_files If greater than 1 it groups the data of each process.
+ * The num_of_files specifies the number of groups
*
*/
XdmfData(std::size_t size_partitioned_dim, std::size_t size_tuple,
MeshPropertyDataType mesh_property_data_type,
std::string const& name,
std::optional<MeshLib::MeshItemType> attribute_center,
- unsigned int const index);
+ unsigned int const index, unsigned int num_of_files);
// a hyperslab is defined by starts and strides see
// https://www.xdmf.org/index.php/XDMF_Model_and_Format#HyperSlab
std::vector<XdmfDimType> starts;
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
index 3d3e1381d1606a2dd14105044aea8cc0cfb25910..265a639422550ce3f4938d67c8dd7ba2894e9d12 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.cpp
@@ -39,7 +39,7 @@ 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)
+ bool const use_compression, unsigned int const num_of_files)
{
// ogs meshes to vector of Xdmf/HDF meshes (we keep Xdmf and HDF together
// because XDMF depends on HDF) to meta
@@ -79,12 +79,12 @@ 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 =
- [](auto const& mesh)
+ [&num_of_files](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());
+ XdmfHdfData const& geometry = transformGeometry(
+ mesh, flattened_geometry_values.data(), num_of_files);
auto const flattened_topology_values =
transformToXDMFTopology(mesh, geometry.hdf.offsets[0]);
return std::make_unique<TransformedMeshData>(
@@ -94,17 +94,19 @@ 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](auto const& mesh)
+ [&transform_ogs_mesh_data_to_xdmf_conforming_data,
+ &num_of_files](auto const& mesh)
{
// important: transformed data must survive and be unique, raw pointer
// to its memory!
std::unique_ptr<TransformedMeshData> xdmf_conforming_data =
transform_ogs_mesh_data_to_xdmf_conforming_data(mesh);
auto const geometry = transformGeometry(
- mesh, xdmf_conforming_data->flattened_geometry_values.data());
- auto const topology =
- transformTopology(xdmf_conforming_data->flattened_topology_values);
- auto const attributes = transformAttributes(mesh);
+ mesh, xdmf_conforming_data->flattened_geometry_values.data(),
+ num_of_files);
+ auto const topology = transformTopology(
+ xdmf_conforming_data->flattened_topology_values, num_of_files);
+ auto const attributes = transformAttributes(mesh, num_of_files);
return XdmfHdfMesh{std::move(geometry), std::move(topology),
std::move(attributes), mesh.get().getName(),
std::move(xdmf_conforming_data)};
@@ -157,7 +159,7 @@ XdmfHdfWriter::XdmfHdfWriter(
auto const is_file_manager = isFileManager();
_hdf_writer = std::make_unique<HdfWriter>(std::move(hdf_meshes), time_step,
hdf_filepath, use_compression,
- is_file_manager);
+ is_file_manager, num_of_files);
// --------------- XDMF ---------------------
// The light data is only written by just one process
@@ -174,7 +176,8 @@ XdmfHdfWriter::XdmfHdfWriter(
{
std::string const xdmf_name = metamesh.name;
std::filesystem::path const xdmf_filepath =
- filepath.parent_path() / (xdmf_name + ".xdmf");
+ filepath.parent_path() /
+ (filepath.stem().string() + "_" + xdmf_name + ".xdmf");
std::vector<XdmfData> xdmf_attributes;
std::transform(metamesh.attributes.begin(), metamesh.attributes.end(),
diff --git a/MeshLib/IO/XDMF/XdmfHdfWriter.h b/MeshLib/IO/XDMF/XdmfHdfWriter.h
index 69d8b8e233fbaff0327339a7ef4bf85300876506..bdb3b884ec3c1bd733dc6421422095ce09712c6c 100644
--- a/MeshLib/IO/XDMF/XdmfHdfWriter.h
+++ b/MeshLib/IO/XDMF/XdmfHdfWriter.h
@@ -36,12 +36,13 @@ public:
* that change over time
* @param use_compression if true, zlib compression in HDFWriter component
* is used
+ * @param num_of_files number of hdf5 output files
*/
XdmfHdfWriter(
std::vector<std::reference_wrapper<const MeshLib::Mesh>> 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);
+ bool use_compression, unsigned int num_of_files);
/**
* \brief Adds data for either lazy (xdmf) or eager (hdf) writing algorithm
diff --git a/MeshLib/IO/XDMF/fileIO.h b/MeshLib/IO/XDMF/fileIO.h
index 1fe20cd1e448ec02edd7133f43fa6c67445a95a9..1e03fafa175c1b474b831faed32ca5ad24914925 100644
--- a/MeshLib/IO/XDMF/fileIO.h
+++ b/MeshLib/IO/XDMF/fileIO.h
@@ -18,7 +18,9 @@
namespace MeshLib::IO
{
-int64_t createFile(std::filesystem::path const& filepath);
-int64_t openHDF5File(std::filesystem::path const& filepath);
+int64_t createFile(std::filesystem::path const& filepath,
+ unsigned int num_of_files);
+int64_t openHDF5File(std::filesystem::path const& filepath,
+ unsigned int num_of_files);
int64_t createHDF5TransferPolicy();
} // namespace MeshLib::IO
diff --git a/MeshLib/IO/XDMF/mpi/fileIO.cpp b/MeshLib/IO/XDMF/mpi/fileIO.cpp
index 6b3215f61c10c9102097272b97a4f808a7fac051..6e1343056508108386a98ec75991c00d82cd470b 100644
--- a/MeshLib/IO/XDMF/mpi/fileIO.cpp
+++ b/MeshLib/IO/XDMF/mpi/fileIO.cpp
@@ -17,24 +17,47 @@
#include <mpi.h>
#include "BaseLib/Logging.h"
+#include "getCommunicator.h"
+using namespace std::string_literals;
namespace MeshLib::IO
{
-hid_t createFile(std::filesystem::path const& filepath)
+std::filesystem::path partitionFilename(
+ std::filesystem::path const& basic_filepath, int file_group)
{
- MPI_Comm comm = MPI_COMM_WORLD;
- MPI_Info info = MPI_INFO_NULL;
+ std::string const filename = (file_group > 0)
+ ? basic_filepath.stem().string() + "_"s +
+ std::to_string(file_group) +
+ basic_filepath.extension().string()
+ : basic_filepath.filename().string();
+ std::filesystem::path const filepathwithextension =
+ basic_filepath.parent_path() / filename;
+ DBUG("HDF Filepath: {:s}.", filepathwithextension.string());
+ return filepathwithextension;
+};
+
+hid_t createFile(std::filesystem::path const& filepath,
+ unsigned int const num_of_files)
+{
+ auto const communicator = getCommunicator(num_of_files);
+ MPI_Comm const comm = communicator.mpi_communicator;
+ MPI_Info const info = MPI_INFO_NULL;
hid_t const plist_id = H5Pcreate(H5P_FILE_ACCESS);
+
H5Pset_fapl_mpio(plist_id, comm, info);
- hid_t file = H5Fcreate(filepath.string().c_str(), H5F_ACC_TRUNC,
+ std::filesystem::path const partition_filename =
+ partitionFilename(filepath, communicator.color);
+ hid_t file = H5Fcreate(partition_filename.string().c_str(), H5F_ACC_TRUNC,
H5P_DEFAULT, plist_id);
H5Pclose(plist_id);
+
return file;
}
-hid_t openHDF5File(std::filesystem::path const& filepath)
+hid_t openHDF5File(std::filesystem::path const& filepath,
+ unsigned int const num_of_files)
{
- MPI_Comm comm = MPI_COMM_WORLD;
+ MPI_Comm const comm = getCommunicator(num_of_files).mpi_communicator;
MPI_Info info = MPI_INFO_NULL;
hid_t const plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, comm, info);
diff --git a/MeshLib/IO/XDMF/mpi/getCommunicator.cpp b/MeshLib/IO/XDMF/mpi/getCommunicator.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c6ac67395e772e63d9c29308e7be8336a80f759c
--- /dev/null
+++ b/MeshLib/IO/XDMF/mpi/getCommunicator.cpp
@@ -0,0 +1,55 @@
+/**
+ * \file
+ * \author Tobias Meisel
+ * \date 2020-12-08
+ * \brief Function specific to execution with MPI, never include directly!!
+ * \copyright
+ * Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
+ * Distributed under a Modified BSD License.
+ * See accompanying file LICENSE.txt or
+ * http://www.opengeosys.org/project/license
+ *
+ */
+
+#include "getCommunicator.h"
+
+#include <hdf5.h>
+#include <math.h>
+#include <mpi.h>
+
+#include <cassert>
+
+#include "BaseLib/Logging.h"
+#include "MeshLib/IO/XDMF/fileIO.h"
+
+using namespace std::string_literals;
+
+namespace MeshLib::IO
+{
+int getGroupIndex(int const input_index, int const input_size,
+ int const new_group_size)
+{
+ // A grouping algorithm that determines the number of groups and return the
+ // group idx of the specified input_index
+ assert(input_size >= new_group_size);
+ int const minimal_output_group_size =
+ std::lround(input_size / new_group_size);
+ int const maximal_output_group_size = (input_size % new_group_size)
+ ? minimal_output_group_size + 1
+ : minimal_output_group_size;
+ return std::lround(input_index / maximal_output_group_size);
+};
+
+FileCommunicator getCommunicator(unsigned int const num_of_files)
+{
+ int num_procs;
+ MPI_Comm_size(MPI_COMM_WORLD, &num_procs);
+ int rank_id;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank_id);
+ int file_group_id = getGroupIndex(rank_id, num_procs, num_of_files);
+ MPI_Comm new_communicator;
+ MPI_Comm_split(MPI_COMM_WORLD, file_group_id, rank_id, &new_communicator);
+ return FileCommunicator{std::move(new_communicator),
+ std::move(file_group_id), ""};
+}
+} // namespace MeshLib::IO
\ No newline at end of file
diff --git a/MeshLib/IO/XDMF/mpi/getCommunicator.h b/MeshLib/IO/XDMF/mpi/getCommunicator.h
new file mode 100644
index 0000000000000000000000000000000000000000..416b59ec2a62e0f0c40703bca0e042ea8c67375b
--- /dev/null
+++ b/MeshLib/IO/XDMF/mpi/getCommunicator.h
@@ -0,0 +1,16 @@
+#pragma once
+
+#include <mpi.h>
+
+#include <filesystem>
+
+namespace MeshLib::IO
+{
+struct FileCommunicator final
+{
+ MPI_Comm mpi_communicator;
+ int color;
+ std::filesystem::path output_filename;
+};
+FileCommunicator getCommunicator(unsigned int num_of_files);
+} // namespace MeshLib::IO
\ No newline at end of file
diff --git a/MeshLib/IO/XDMF/mpi/partition.cpp b/MeshLib/IO/XDMF/mpi/partition.cpp
index a398f6a5f383d3d3fb75b65723bc2fa148fe535e..67e0e5791faa1d01260ce9e9711cd704261f5664 100644
--- a/MeshLib/IO/XDMF/mpi/partition.cpp
+++ b/MeshLib/IO/XDMF/mpi/partition.cpp
@@ -15,11 +15,11 @@
#include <mpi.h>
-#include <deque>
#include <numeric>
#include "BaseLib/Logging.h"
#include "MeshLib/IO/XDMF/fileIO.h"
+#include "getCommunicator.h"
namespace MeshLib::IO
{
@@ -30,9 +30,10 @@ bool isFileManager()
return mpi_rank == 0;
}
-PartitionInfo getPartitionInfo(std::size_t const size)
+PartitionInfo getPartitionInfo(std::size_t const size,
+ unsigned int const num_of_files)
{
- MPI_Comm const mpi_comm = MPI_COMM_WORLD;
+ MPI_Comm const mpi_comm = getCommunicator(num_of_files).mpi_communicator;
int mpi_size;
int mpi_rank;
MPI_Comm_size(mpi_comm, &mpi_size);
diff --git a/MeshLib/IO/XDMF/partition.h b/MeshLib/IO/XDMF/partition.h
index a343c590fe9d969397fe3790783a5b4fae4f6bae..afb2cb8134d91eda895581513af5ef5988c0a7de 100644
--- a/MeshLib/IO/XDMF/partition.h
+++ b/MeshLib/IO/XDMF/partition.h
@@ -24,6 +24,7 @@ struct PartitionInfo
std::size_t global_length;
};
-PartitionInfo getPartitionInfo(std::size_t const size);
+PartitionInfo getPartitionInfo(std::size_t const size,
+ unsigned int const num_of_files);
bool isFileManager();
} // namespace MeshLib::IO
diff --git a/MeshLib/IO/XDMF/posix/fileIO.cpp b/MeshLib/IO/XDMF/posix/fileIO.cpp
index 2f7d081a8417d82729a41a5e0bb161e593a1fd6c..a9c3ad6b6fdd083bade4be547e096007e463f260 100644
--- a/MeshLib/IO/XDMF/posix/fileIO.cpp
+++ b/MeshLib/IO/XDMF/posix/fileIO.cpp
@@ -16,7 +16,7 @@
#include <hdf5.h>
namespace MeshLib::IO
{
-int64_t createFile(std::filesystem::path const& filepath)
+int64_t createFile(std::filesystem::path const& filepath, unsigned int)
{
return H5Fcreate(filepath.string().c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
diff --git a/MeshLib/IO/XDMF/posix/partition.cpp b/MeshLib/IO/XDMF/posix/partition.cpp
index 2fe296585719e16226f4358d4837835e82baff92..15796288e1e1cd06bad2ece80a36b9713ecce6d8 100644
--- a/MeshLib/IO/XDMF/posix/partition.cpp
+++ b/MeshLib/IO/XDMF/posix/partition.cpp
@@ -17,7 +17,7 @@ bool isFileManager()
return true;
}
-PartitionInfo getPartitionInfo(std::size_t const size)
+PartitionInfo getPartitionInfo(std::size_t const size, unsigned int)
{
// local_offset, local_length, longest_local_length, global_number_process
return {0, size, size, size};
diff --git a/MeshLib/IO/XDMF/transformData.cpp b/MeshLib/IO/XDMF/transformData.cpp
index cd07b709a27ac7058db884c36d67e3d544e1ccf5..c2bb18dfee53cbd48a6d32567d71c5164207ac89 100644
--- a/MeshLib/IO/XDMF/transformData.cpp
+++ b/MeshLib/IO/XDMF/transformData.cpp
@@ -70,7 +70,8 @@ constexpr auto cellTypeOGS2XDMF(MeshLib::CellType const& cell_type)
}
std::optional<XdmfHdfData> transformAttribute(
- std::pair<std::string, PropertyVectorBase*> const& property_pair)
+ std::pair<std::string, PropertyVectorBase*> const& property_pair,
+ unsigned int const num_of_files)
{
// 3 data that will be captured and written by lambda f below
MeshPropertyDataType data_type = MeshPropertyDataType::unknown;
@@ -190,16 +191,18 @@ std::optional<XdmfHdfData> transformAttribute(
std::string const& name = property_base->getPropertyName();
- HdfData hdf = {data_ptr, num_of_tuples, ui_global_components, name,
- data_type};
+ HdfData hdf = {data_ptr, num_of_tuples, ui_global_components,
+ name, data_type, num_of_files};
XdmfData xdmf = {num_of_tuples, ui_global_components, data_type,
- name, mesh_item_type, 0};
+ name, mesh_item_type, 0,
+ num_of_files};
return XdmfHdfData{std::move(hdf), std::move(xdmf)};
}
-std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh)
+std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh,
+ unsigned int const num_of_files)
{
MeshLib::Properties const& properties = mesh.getProperties();
@@ -213,8 +216,8 @@ std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh)
continue;
}
- if (auto const attribute =
- transformAttribute(std::pair(name, property_base)))
+ if (auto const attribute = transformAttribute(
+ std::pair(name, property_base), num_of_files))
{
attributes.push_back(attribute.value());
}
@@ -242,7 +245,9 @@ std::vector<double> transformToXDMFGeometry(MeshLib::Mesh const& mesh)
return values;
}
-XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh, double const* data_ptr)
+XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh,
+ double const* data_ptr,
+ unsigned int const num_of_files)
{
std::string const name = "geometry";
std::vector<MeshLib::Node*> const& nodes = mesh.getNodes();
@@ -250,11 +255,16 @@ XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh, double const* data_ptr)
int const point_size = 3;
auto const& partition_dim = nodes.size();
- HdfData const hdf = {data_ptr, partition_dim, point_size, name,
- MeshPropertyDataType::float64};
+ HdfData const hdf = {data_ptr,
+ partition_dim,
+ point_size,
+ name,
+ MeshPropertyDataType::float64,
+ num_of_files};
XdmfData const xdmf = {
partition_dim, point_size, MeshPropertyDataType::float64,
- name, std::nullopt, 2};
+ name, std::nullopt, 2,
+ num_of_files};
return XdmfHdfData{std::move(hdf), std::move(xdmf)};
}
@@ -286,13 +296,16 @@ std::vector<int> transformToXDMFTopology(MeshLib::Mesh const& mesh,
return values;
}
-XdmfHdfData transformTopology(std::vector<int> const& values)
+XdmfHdfData transformTopology(std::vector<int> const& values,
+ unsigned int const num_of_files)
{
std::string const name = "topology";
- HdfData const hdf = {values.data(), values.size(), 1, name,
- MeshPropertyDataType::int32};
- XdmfData const xdmf = {values.size(), 1, MeshPropertyDataType::int32, name,
- std::nullopt, 3};
+ HdfData const hdf = {
+ values.data(), values.size(), 1, name, MeshPropertyDataType::int32,
+ num_of_files};
+ XdmfData const xdmf = {
+ values.size(), 1, MeshPropertyDataType::int32, name, std::nullopt, 3,
+ num_of_files};
return XdmfHdfData{std::move(hdf), std::move(xdmf)};
}
diff --git a/MeshLib/IO/XDMF/transformData.h b/MeshLib/IO/XDMF/transformData.h
index 16284421061aae9e1222594528f55b1344a47e0f..8c0e789cd5f839cde13b59c20dee588deb2caa1a 100644
--- a/MeshLib/IO/XDMF/transformData.h
+++ b/MeshLib/IO/XDMF/transformData.h
@@ -26,23 +26,31 @@ namespace MeshLib::IO
/**
* \brief Create meta data for attributes used for hdf5 and xdmf
* @param mesh OGS mesh can be mesh or partitionedMesh
+ * @param num_of_files If greater than 1 it groups the data of each process. The
+ * num_of_files specifies the number of groups
* @return vector of meta data
*/
-std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh);
+std::vector<XdmfHdfData> transformAttributes(MeshLib::Mesh const& mesh,
+ unsigned int num_of_files);
/**
* \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 num_of_files If greater than 1 it groups the data of each process. The
+ * num_of_files specifies the number of groups
* @return Geometry meta data
*/
-XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh,
- double const* data_ptr);
+XdmfHdfData transformGeometry(MeshLib::Mesh const& mesh, double const* data_ptr,
+ unsigned int num_of_files);
/**
* \brief Create meta data for topology used for HDF5 and XDMF
* @param values actual topology values to get size and memory location
+ * @param num_of_files If greater than 1 it groups the data of each process. The
+ * num_of_files specifies the number of groups
* @return Topology meta data
*/
-XdmfHdfData transformTopology(std::vector<int> const& values);
+XdmfHdfData transformTopology(std::vector<int> const& values,
+ unsigned int num_of_files);
/**
* \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 36b0ef47815aee160fc0458641ff204eecfb9fa9..bf170fca3263d1fb1ffca50647422d9548c24135 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);
+ variable_output_names, true, 1);
return 0;
}
ERR("writeMeshToFile(): Unknown file extension '{:s}'. Can not write file "
diff --git a/ProcessLib/LiquidFlow/Tests.cmake b/ProcessLib/LiquidFlow/Tests.cmake
index 401fc4ae88a0f54188f46c0f8fde178e99fd8a45..5f06a0792dc390902be5d89b58966f72eb636c9f 100644
--- a/ProcessLib/LiquidFlow/Tests.cmake
+++ b/ProcessLib/LiquidFlow/Tests.cmake
@@ -483,16 +483,16 @@ AddTest(
TESTER xdmfdiff
REQUIREMENTS NOT OGS_USE_MPI
DIFF_DATA
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf pressure pressure 1e-7 1e-13
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf HydraulicFlow HydraulicFlow 1e-7 1e-13
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf MaterialIDs MaterialIDs 1e-7 1e-13
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf v v 1e-7 1e-13
- square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_right_boundary.xdmf pressure pressure 1e-7 1e-13
- square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_right_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
- square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_right_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
- square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_left_boundary.xdmf pressure pressure 1e-7 1e-13
- square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_left_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
- square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_left_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf pressure pressure 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf HydraulicFlow HydraulicFlow 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf MaterialIDs MaterialIDs 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf v v 1e-7 1e-13
+ square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_right_boundary.xdmf pressure pressure 1e-7 1e-13
+ square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_right_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
+ square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_right_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
+ square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_left_boundary.xdmf pressure pressure 1e-7 1e-13
+ square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_left_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
+ square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_left_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
)
AddTest(
@@ -504,16 +504,16 @@ AddTest(
TESTER xdmfdiff
REQUIREMENTS NOT OGS_USE_MPI
DIFF_DATA
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf pressure pressure 1e-7 1e-13
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf HydraulicFlow HydraulicFlow 1e-7 1e-13
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf MaterialIDs MaterialIDs 1e-7 1e-13
- square_5x5_tris_32.xdmf square_5x5_tris_32.xdmf v v 1e-7 1e-13
- square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_right_boundary.xdmf pressure pressure 1e-7 1e-13
- square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_right_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
- square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_right_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
- square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_left_boundary.xdmf pressure pressure 1e-7 1e-13
- square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_left_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
- square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_left_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf pressure pressure 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf HydraulicFlow HydraulicFlow 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf MaterialIDs MaterialIDs 1e-7 1e-13
+ square_5x5_tris_32.xdmf square_5x5_tris_32_square_5x5_tris_32.xdmf v v 1e-7 1e-13
+ square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_right_boundary.xdmf pressure pressure 1e-7 1e-13
+ square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_right_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
+ square_5x5_tris_32_right_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_right_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
+ square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_left_boundary.xdmf pressure pressure 1e-7 1e-13
+ square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_left_boundary.xdmf bulk_element_ids bulk_element_ids 1e-7 1e-13
+ square_5x5_tris_32_left_boundary.xdmf square_5x5_tris_32_square_5x5_tris_32_left_boundary.xdmf bulk_node_ids bulk_node_ids 1e-7 1e-13
)
diff --git a/ProcessLib/Output/CreateOutput.cpp b/ProcessLib/Output/CreateOutput.cpp
index c93ad98f6baa5a096f8bb92fa6d80d1d427c2436..18df762c16118713cf469bd452ecd619ef3dd4d5 100644
--- a/ProcessLib/Output/CreateOutput.cpp
+++ b/ProcessLib/Output/CreateOutput.cpp
@@ -28,7 +28,8 @@ std::unique_ptr<Output> createOutput(
std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes)
{
DBUG("Parse output configuration:");
- OutputType const output_type = [](auto output_type) {
+ OutputType const output_type = [](auto output_type)
+ {
try
{
const std::map<std::string, OutputType> outputType_to_enum = {
@@ -60,6 +61,23 @@ std::unique_ptr<Output> createOutput(
//! \ogs_file_param{prj__time_loop__output__compress_output}
config.getConfigParameter("compress_output", true);
+ auto const hdf =
+ //! \ogs_file_param{prj__time_loop__output__hdf}
+ config.getConfigSubtreeOptional("hdf");
+
+ auto number_of_files = [&hdf]() -> unsigned int
+ {
+ if (hdf)
+ {
+ //! \ogs_file_param{prj__time_loop__output__hdf__number_of_files}
+ return hdf->getConfigParameter<unsigned int>("number_of_files");
+ }
+ else
+ {
+ return 1;
+ }
+ }();
+
auto const data_mode =
//! \ogs_file_param{prj__time_loop__output__data_mode}
config.getConfigParameter<std::string>("data_mode", "Appended");
@@ -156,9 +174,10 @@ std::unique_ptr<Output> createOutput(
return std::make_unique<Output>(
output_directory, output_type, prefix, suffix, compress_output,
- data_mode, output_iteration_results, std::move(repeats_each_steps),
- std::move(fixed_output_times), std::move(output_data_specification),
- std::move(mesh_names_for_output), meshes);
+ number_of_files, data_mode, output_iteration_results,
+ std::move(repeats_each_steps), std::move(fixed_output_times),
+ std::move(output_data_specification), std::move(mesh_names_for_output),
+ meshes);
}
} // namespace ProcessLib
diff --git a/ProcessLib/Output/Output.cpp b/ProcessLib/Output/Output.cpp
index c9376decfe85ea6dda33c9462b003300376653d6..6a6f80c6f6f548dbcf8211789d69e5cdb90d6cd1 100644
--- a/ProcessLib/Output/Output.cpp
+++ b/ProcessLib/Output/Output.cpp
@@ -95,7 +95,8 @@ bool Output::shallDoOutput(int timestep, double const t)
Output::Output(std::string directory, OutputType file_type,
std::string file_prefix, std::string file_suffix,
- bool const compress_output, std::string const& data_mode,
+ bool const compress_output, unsigned int const num_of_files,
+ std::string const& data_mode,
bool const output_nonlinear_iteration_results,
std::vector<PairRepeatEachSteps> repeats_each_steps,
std::vector<double>&& fixed_output_times,
@@ -107,6 +108,7 @@ Output::Output(std::string directory, OutputType file_type,
_output_file_prefix(std::move(file_prefix)),
_output_file_suffix(std::move(file_suffix)),
_output_file_compression(compress_output),
+ _num_of_files(num_of_files),
_output_file_data_mode(convertVtkDataMode(data_mode)),
_output_nonlinear_iteration_results(output_nonlinear_iteration_results),
_repeats_each_steps(std::move(repeats_each_steps)),
@@ -180,14 +182,16 @@ struct Output::OutputFile
std::string const& mesh_name, int const timestep, double const t,
int const iteration, int const data_mode_,
bool const compression_,
- std::set<std::string> const& outputnames)
+ std::set<std::string> const& outputnames,
+ unsigned int const num_of_files)
: name(constructFilename(type, prefix, suffix, mesh_name, timestep, t,
iteration)),
path(BaseLib::joinPaths(directory, name)),
type(type),
data_mode(data_mode_),
compression(compression_),
- outputnames(outputnames)
+ outputnames(outputnames),
+ num_of_files(num_of_files)
{
}
@@ -199,12 +203,10 @@ struct Output::OutputFile
/// documentation
/// http://www.vtk.org/doc/nightly/html/classvtkXMLWriter.html
int const data_mode;
-
//! Enables or disables zlib-compression of the output files.
bool const compression;
-
std::set<std::string> outputnames;
-
+ unsigned int num_of_files;
static std::string constructFilename(OutputType const type,
std::string prefix, std::string suffix,
std::string mesh_name,
@@ -248,7 +250,7 @@ void Output::outputMeshXdmf(
_mesh_xdmf_hdf_writer = std::make_unique<MeshLib::IO::XdmfHdfWriter>(
std::move(meshes), path, timestep, t,
_output_data_specification.output_variables,
- output_file.compression);
+ output_file.compression, output_file.num_of_files);
}
else
{
@@ -321,7 +323,7 @@ void Output::doOutputAlways(Process const& process,
_output_directory, _output_file_type, _output_file_prefix,
_output_file_suffix, mesh.get().getName(), timestep, t,
iteration, _output_file_data_mode, _output_file_compression,
- _output_data_specification.output_variables);
+ _output_data_specification.output_variables, 1);
pvd_file =
findPVDFile(process, process_id, mesh.get().getName());
@@ -331,11 +333,11 @@ void Output::doOutputAlways(Process const& process,
else if (_output_file_type == ProcessLib::OutputType::xdmf)
{
std::string name = meshes[0].get().getName();
- OutputFile const file(_output_directory, _output_file_type,
- _output_file_prefix, "", name, timestep, t,
- iteration, _output_file_data_mode,
- _output_file_compression,
- _output_data_specification.output_variables);
+ OutputFile const file(
+ _output_directory, _output_file_type, _output_file_prefix, "",
+ name, timestep, t, iteration, _output_file_data_mode,
+ _output_file_compression,
+ _output_data_specification.output_variables, _num_of_files);
outputMeshXdmf(std::move(file), std::move(meshes), timestep, t);
}
diff --git a/ProcessLib/Output/Output.h b/ProcessLib/Output/Output.h
index 6e530c7f220dbe3e33034f5f747ea905bbb24eb6..075f9f98241eb3470a7252ef8147c0f805e80ae3 100644
--- a/ProcessLib/Output/Output.h
+++ b/ProcessLib/Output/Output.h
@@ -40,7 +40,7 @@ public:
public:
Output(std::string directory, OutputType const type, std::string prefix,
std::string suffix, bool const compress_output,
- std::string const& data_mode,
+ unsigned int num_of_files, std::string const& data_mode,
bool const output_nonlinear_iteration_results,
std::vector<PairRepeatEachSteps> repeats_each_steps,
std::vector<double>&& fixed_output_times,
@@ -108,6 +108,8 @@ private:
//! Enables or disables zlib-compression of the output files.
bool const _output_file_compression;
+ //! Specifies the number of hdf5 output files.
+ unsigned int const _num_of_files;
//! Chooses vtk's data mode for output following the enumeration given in
/// the vtkXMLWriter: {Ascii, Binary, Appended}. See vtkXMLWriter
diff --git a/ProcessLib/SteadyStateDiffusion/Tests.cmake b/ProcessLib/SteadyStateDiffusion/Tests.cmake
index 688763e93af237bb9a713c0c1f4e1da8d851e9ee..8ca8c99f3c7a5f4bd818bbf76190fbf32d19b99f 100644
--- a/ProcessLib/SteadyStateDiffusion/Tests.cmake
+++ b/ProcessLib/SteadyStateDiffusion/Tests.cmake
@@ -425,8 +425,36 @@ AddTest(
TESTER xdmfdiff
REQUIREMENTS OGS_USE_MPI
DIFF_DATA
- cube_1e3_np3.xdmf cube_1x1x1_hex_1e3.xdmf pressure pressure 1e-3 1e-3
- cube_1e3_np3.xdmf cube_1x1x1_hex_1e3.xdmf v v 1e-3 1e-3
+ cube_1e3_np3.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf pressure pressure 1e-3 1e-3
+ cube_1e3_np3.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf v v 1e-3 1e-3
+)
+
+AddTest(
+ NAME ParallelFEM_GroundWaterFlow3D_NeumannBC_XDMF_np3_2files
+ PATH EllipticPETSc
+ EXECUTABLE ogs
+ EXECUTABLE_ARGS cube_1e3_XDMF_np3_2files.prj
+ WRAPPER mpirun
+ WRAPPER_ARGS -np 3
+ TESTER xdmfdiff
+ REQUIREMENTS OGS_USE_MPI
+ DIFF_DATA
+ cube_1e3_np3_2files_0.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf pressure pressure 1e-3 1e-3
+ cube_1e3_np3_2files_0.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf v v 1e-3 1e-3
+)
+
+AddTest(
+ NAME ParallelFEM_GroundWaterFlow3D_NeumannBC_XDMF_np3_3files
+ PATH EllipticPETSc
+ EXECUTABLE ogs
+ EXECUTABLE_ARGS cube_1e3_XDMF_np3_3files.prj
+ WRAPPER mpirun
+ WRAPPER_ARGS -np 3
+ TESTER xdmfdiff
+ REQUIREMENTS OGS_USE_MPI
+ DIFF_DATA
+ cube_1e3_np3_3files_0.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf pressure pressure 1e-3 1e-3
+ cube_1e3_np3_3files_0.xdmf cube_1e3_np3_cube_1x1x1_hex_1e3.xdmf v v 1e-3 1e-3
)
AddTest(
@@ -439,8 +467,8 @@ AddTest(
TESTER xdmfdiff
REQUIREMENTS OGS_USE_MPI
DIFF_DATA
- cube_1e3_np2.xdmf cube_1x1x1_hex_1e3.xdmf pressure pressure 1e-3 1e-3
- cube_1e3_np2.xdmf cube_1x1x1_hex_1e3.xdmf v v 1e-3 1e-3
+ cube_1e3_np2.xdmf cube_1e3_np2_cube_1x1x1_hex_1e3.xdmf pressure pressure 1e-3 1e-3
+ cube_1e3_np2.xdmf cube_1e3_np2_cube_1x1x1_hex_1e3.xdmf v v 1e-3 1e-3
)
AddTest(
diff --git a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj
index 74c0442b221169a2add593fbc652967a4940882d..3fb3aef3a66e5fd5b1cdf8cd8e95de8d567f7714 100644
--- a/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj
+++ b/Tests/Data/EllipticPETSc/cube_1e3_XDMF_np3.prj
@@ -65,6 +65,9 @@
<variable> v </variable>
</variables>
<suffix>_ts_{:timestep}_t_{:time}</suffix>
+ <hdf>
+ <num_of_files>1</num_of_files>
+ </hdf>
</output>
</time_loop>
<parameters>