decl_hdf5 MPI-I/O Collective or Independent, fix #419

example/decl_hdf5.yml

@@ -28,6 +28,7 @@ pdi:
       write:
         main_field: # the name of the data to write
           dataset: data
+          mpio: COLLECTIVE # or INDEPENDENT
           when: '$iter<10'   # do only write the first 10 iterations (0...9)
           memory_selection:  # exclude ghosts from the data in memory
             size:  ['$dsize[0]-2', '$dsize[1]-2']

plugins/decl_hdf5/AUTHORS

@@ -11,6 +11,12 @@ Julien Bigot - CEA ([email protected])
 * Run tests that depend on the filesystem in their own temporary directory
 * Buildsystem
 
+Yacine Ould Rouis - CNRS ([email protected])
+* contribution to feature design, validation
+
+Jacques Morice - CEA ([email protected])
+* contribution to feature improvement, validation
+
 Thomas Padioleau - CEA ([email protected])
 * Fixed a bug with parallel file deletion
 

plugins/decl_hdf5/CHANGELOG.md

@@ -7,6 +7,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 ## [Unreleased]
 
 ### Added
+* Possibility to choose parallel MPI-I/O mode: either COLLECTIVE or INDEPENDENT
+  [#419](https://gitlab.maisondelasimulation.fr/pdidev/pdi/-/issues/419)
 
 ### Changed
 

plugins/decl_hdf5/README.md

@@ -145,6 +145,8 @@ The possible values for the keys are as follow:
   See
   https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFletcher32
   for more information.
+* `mpio` : a string expression to define the type of MPI-I/O parallel pointer 
+for the operation among two choices : `COLLECTIVE` (default) and `INDEPENDENT`.
 
 ### SELECTION_DESC
 
@@ -219,6 +221,7 @@ plugins:
         - dataset: data/array      # a dataset name (default: the data name)
           when: "$iter>0&$iter<11" # an additional condition when to actually trigger the actions (default: always true)
           communicator: $MPI_COMM_SELF   # the MPI communicator used for HDF5 parallel synchronized write (default: that of the file)
+          mpio: INDEPENDENT              # the type of MPI-I/O parallel pointer (default: COLLECTIVE)
           memory_selection:
             size:  [$width-2, $height-2] # number of elements to transfer in each dimension (default: size of the full data)
             start: [1, 1]                # coordinate of the start point in memory relative to the shared data (default: 0 in each dimensions)

plugins/decl_hdf5/dataset_op.cxx

@@ -1,6 +1,6 @@
 /*******************************************************************************
  * Copyright (C) 2015-2024 Commissariat a l'energie atomique et aux energies alternatives (CEA)
- * Copyright (C) 2021 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
+ * Copyright (C) 2021-2022 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -164,6 +164,14 @@ Dataset_op::Dataset_op(Direction dir, string name, Expression default_when, PC_t
 				m_fletcher = value;
 			} else if (key == "attributes") {
 				// pass
+			} else if (key == "mpio") {
+				if (to_string(value) == "INDEPENDENT") {
+					m_mpio = H5FD_MPIO_INDEPENDENT;
+				} else if (to_string(value) == "COLLECTIVE") {
+					m_mpio = H5FD_MPIO_COLLECTIVE;
+				} else {
+					throw Config_error{key_tree, "Not valid mpio value: `{}'. Expecting INDEPENDENT or COLLECTIVE.", to_string(value)};
+				}
 			} else if (key == "collision_policy") {
 				m_collision_policy = to_collision_policy(to_string(value));
 			} else {
@@ -203,8 +211,12 @@ void Dataset_op::fletcher(Context& ctx, Expression value)
 	}
 }
 
-void Dataset_op::execute(Context& ctx, hid_t h5_file, hid_t xfer_lst, const unordered_map<string, Datatype_template_sptr>& dsets)
+void Dataset_op::execute(Context& ctx, hid_t h5_file, bool use_mpio, const unordered_map<string, Datatype_template_sptr>& dsets)
 {
+	Raii_hid xfer_lst = make_raii_hid(H5Pcreate(H5P_DATASET_XFER), H5Pclose);
+	if (use_mpio) {
+		if (0 > H5Pset_dxpl_mpio(xfer_lst, m_mpio)) handle_hdf5_err();
+	}
 	if (m_direction == READ)
 		do_read(ctx, h5_file, xfer_lst);
 	else
@@ -328,7 +340,7 @@ hid_t Dataset_op::dataset_creation_plist(Context& ctx, const Datatype* dataset_t
 	return dset_plist;
 }
 
-void Dataset_op::do_write(Context& ctx, hid_t h5_file, hid_t write_lst, const unordered_map<string, PDI::Datatype_template_sptr>& dsets)
+void Dataset_op::do_write(Context& ctx, hid_t h5_file, hid_t write_lst, const unordered_map<string, Datatype_template_sptr>& dsets)
 {
 	string dataset_name = m_dataset.to_string(ctx);
 	ctx.logger().trace("Preparing for writing `{}' dataset", dataset_name);

plugins/decl_hdf5/dataset_op.h

@@ -1,6 +1,6 @@
 /*******************************************************************************
  * Copyright (C) 2015-2024 Commissariat a l'energie atomique et aux energies alternatives (CEA)
- * Copyright (C) 2021 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
+ * Copyright (C) 2021-2022 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -67,6 +67,9 @@ class Dataset_op
 	/// direction of the transfer (read or write)
 	Direction m_direction;
 
+	/// the type of MPI-I/O parallel pointer (default = COLLECTIVE)
+	H5FD_mpio_xfer_t m_mpio = H5FD_MPIO_COLLECTIVE;
+
 	/// the name of the dataset where to transfer
 	PDI::Expression m_dataset;
 
@@ -182,11 +185,10 @@ class Dataset_op
 	 *
 	 * \param ctx the context in which to operate
 	 * \param h5_file the already opened HDF5 file id
-	 * \param xfer_lst the already created transfer property list including any
-	 *                 parallel HDF5 required property.
+	 * \param use_mpio whether the hdf5 read/write is parallel
 	 * \param dsets the type of the explicitly typed datasets
 	 */
-	void execute(PDI::Context& ctx, hid_t h5_file, hid_t xfer_lst, const std::unordered_map<std::string, PDI::Datatype_template_sptr>& dsets);
+	void execute(PDI::Context& ctx, hid_t h5_file, bool use_mpio, const std::unordered_map<std::string, PDI::Datatype_template_sptr>& dsets);
 
 private:
 	void do_read(PDI::Context& ctx, hid_t h5_file, hid_t read_lst);

plugins/decl_hdf5/file_op.cxx

@@ -1,6 +1,6 @@
 /*******************************************************************************
  * Copyright (C) 2015-2024 Commissariat a l'energie atomique et aux energies alternatives (CEA)
- * Copyright (C) 2021 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
+ * Copyright (C) 2021-2022 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
  * All rights reserved.
  *
  * Redistribution and use in source and binary forms, with or without
@@ -280,15 +280,15 @@ void File_op::execute(Context& ctx)
 	std::string filename = m_file.to_string(ctx);
 
 	Raii_hid file_lst = make_raii_hid(H5Pcreate(H5P_FILE_ACCESS), H5Pclose);
-	Raii_hid xfer_lst = make_raii_hid(H5Pcreate(H5P_DATASET_XFER), H5Pclose);
+	bool use_mpio = false;
 #ifdef H5_HAVE_PARALLEL
 	MPI_Comm comm = MPI_COMM_SELF;
 	if (communicator()) {
 		comm = *(static_cast<const MPI_Comm*>(Ref_r{communicator().to_ref(ctx)}.get()));
 	}
 	if (comm != MPI_COMM_SELF) {
 		if (0 > H5Pset_fapl_mpio(file_lst, comm, MPI_INFO_NULL)) handle_hdf5_err();
-		if (0 > H5Pset_dxpl_mpio(xfer_lst, H5FD_MPIO_COLLECTIVE)) handle_hdf5_err();
+		use_mpio = true;
 		ctx.logger().debug("Opening `{}' file in parallel mode", filename);
 	}
 #endif
@@ -337,10 +337,10 @@ void File_op::execute(Context& ctx)
 	Raii_hid h5_file = make_raii_hid(h5_file_raw, H5Fclose, ("Cannot open `" + filename + "' file").c_str());
 
 	for (auto&& one_dset_op: dset_writes) {
-		one_dset_op.execute(ctx, h5_file, xfer_lst, m_datasets);
+		one_dset_op.execute(ctx, h5_file, use_mpio, m_datasets);
 	}
 	for (auto&& one_dset_op: dset_reads) {
-		one_dset_op.execute(ctx, h5_file, xfer_lst, m_datasets);
+		one_dset_op.execute(ctx, h5_file, use_mpio, m_datasets);
 	}
 	for (auto&& one_attr_op: attr_writes) {
 		one_attr_op.execute(ctx, h5_file);

plugins/decl_hdf5/tests/CMakeLists.txt

@@ -1,7 +1,7 @@
 #=============================================================================
 # Copyright (C) 2015-2024 Commissariat a l'energie atomique et aux energies alternatives (CEA)
 # Copyright (C) 2021 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
-#
+# Copyright (C) 2022 Centre National de Recherche Scientifique (CNRS)
 # All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
@@ -95,7 +95,7 @@ if("${BUILD_HDF5_PARALLEL}")
 	set_property(TEST decl_hdf5_mpi_04_C PROPERTY PROCESSORS 4)
 endif()
 
-# bcommunicator as a reference
+# communicator as a reference
 if("${BUILD_HDF5_PARALLEL}")
 	add_executable(decl_hdf5_mpi_05_C decl_hdf5_mpi_test_05.c)
 	target_link_libraries(decl_hdf5_mpi_05_C PDI::PDI_C MPI::MPI_C)
@@ -113,6 +113,15 @@ if("${BUILD_HDF5_PARALLEL}")
 	set_property(TEST decl_hdf5_mpi_06_C PROPERTY PROCESSORS 4)
 endif()
 
+# mpio dataset attribute
+if("${BUILD_HDF5_PARALLEL}")
+	add_executable(decl_hdf5_mpi_07_C decl_hdf5_mpi_test_07.c)
+	target_link_libraries(decl_hdf5_mpi_07_C PDI::PDI_C MPI::MPI_C)
+	add_test(NAME decl_hdf5_mpi_07_C COMMAND "${RUNTEST_DIR}" "${MPIEXEC}" "${MPIEXEC_NUMPROC_FLAG}" 4 ${MPIEXEC_PREFLAGS} "$<TARGET_FILE:decl_hdf5_mpi_07_C>" ${MPIEXEC_POSTFLAGS})
+	set_property(TEST decl_hdf5_mpi_07_C PROPERTY TIMEOUT 15)
+	set_property(TEST decl_hdf5_mpi_07_C PROPERTY PROCESSORS 4)
+endif()
+
 add_executable(decl_hdf5_IO_options_C decl_hdf5_test_IO_options.c)
 target_link_libraries(decl_hdf5_IO_options_C PDI::PDI_C  ${HDF5_DEPS})
 add_test(NAME decl_hdf5_IO_options_C COMMAND "${RUNTEST_DIR}" "$<TARGET_FILE:decl_hdf5_IO_options_C>")

plugins/decl_hdf5/tests/compatibility_tests/CMakeLists.txt

@@ -29,7 +29,7 @@ set(RUNTEST_DIR "${CMAKE_CURRENT_LIST_DIR}/../../cmake/runtest-dir")
 
 set(ALL_TEST_NAMES array dataset group struct variables)
 if("${BUILD_HDF5_PARALLEL}")
-    list(APPEND ALL_TEST_NAMES mpi)
+    list(APPEND ALL_TEST_NAMES mpi mpi_independent)
 endif()
 
 foreach(test_name ${ALL_TEST_NAMES})
@@ -39,7 +39,7 @@ foreach(test_name ${ALL_TEST_NAMES})
 
         add_executable("PDI_C_${test_name}_${io_operation}_test" "PDI_C/${test_name}_${io_operation}_test.c")
         target_link_libraries("PDI_C_${test_name}_${io_operation}_test" PDI::PDI_C)
-        if ("${test_name}" STREQUAL "mpi")
+        if ( ("${test_name}" STREQUAL "mpi") OR ("${test_name}" STREQUAL "mpi_independent") )
             target_link_libraries("HDF5_C_${test_name}_${io_operation}_test" MPI::MPI_C)
             target_link_libraries("PDI_C_${test_name}_${io_operation}_test"  MPI::MPI_C)
         endif()
@@ -49,7 +49,7 @@ foreach(test_name ${ALL_TEST_NAMES})
         foreach(read_prefix HDF5_C_ PDI_C_)
             set(write_test_name "${write_prefix}${test_name}_write_test")
             set(read_test_name "${read_prefix}${test_name}_read_test")
-            if ("${test_name}" STREQUAL "mpi")
+            if ( ("${test_name}" STREQUAL "mpi") OR ("${test_name}" STREQUAL "mpi_independent") )
                 set(MPI_CASE_CMD "${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} 2 ${MPIEXEC_PREFLAGS}")
                 set(MPI_POST_CMD " ${MPIEXEC_POSTFLAGS}")
             else()

plugins/decl_hdf5/tests/compatibility_tests/HDF5_C/mpi_independent_read_test.c

@@ -0,0 +1,144 @@
+/*******************************************************************************
+ * Copyright (C) 2020 Institute of Bioorganic Chemistry Polish Academy of Science (PSNC)
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * * Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ * * Redistributions in binary form must reproduce the above copyright
+ *   notice, this list of conditions and the following disclaimer in the
+ *   documentation and/or other materials provided with the distribution.
+ * * Neither the name of CEA nor the names of its contributors may be used to
+ *   endorse or promote products derived from this software without specific
+ *   prior written permission.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ ******************************************************************************/
+
+#include <mpi.h>
+#include <assert.h>
+#include <hdf5.h>
+#include <unistd.h>
+
+#define FILE "mpi_independent_test.h5"
+
+/*
+Test : Read a file using hdf5 parallel version with the option independent parallel pointer.
+*/
+
+int main(int argc, char* argv[])
+{
+	printf("HDF5 mpi_independent_read_test started\n");
+	MPI_Init(&argc, &argv);
+	int mpi_rank;
+	MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+	herr_t status = H5open();
+	if (status < 0) {
+		return 1;
+	}
+
+	hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS);
+	H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL);
+	hid_t file_id = H5Fopen(FILE, H5F_ACC_RDONLY, fapl_id);
+	if (file_id < 0) {
+		return 1;
+	}
+
+	int dset_data[5][5];
+	for (int i = 0; i < 5; i++) {
+		for (int j = 0; j < 5; j++) {
+			dset_data[i][j] = 0;
+		}
+	}
+
+	hsize_t coords[2] = {5, 10};
+	hid_t dataspace_id = H5Screate_simple(2, coords, NULL);
+	if (dataspace_id < 0) {
+		return 1;
+	}
+
+	hid_t dataset_id = H5Dopen2(file_id, "array_data", H5P_DEFAULT);
+	if (dataset_id < 0) {
+		return 1;
+	}
+
+	hsize_t count[2] = {5, 5};
+	hsize_t stride[2] = {1, 1};
+	hsize_t dataset_offset[2] = {0, 5 * mpi_rank};
+	hsize_t memory_offset[2] = {0, 0};
+	hsize_t block[2] = {1, 1};
+
+	status = H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, dataset_offset, stride, count, block);
+	if (status < 0) {
+		return 1;
+	}
+	hid_t memory_dataspace_id = H5Screate_simple(2, count, NULL);
+	if (memory_dataspace_id < 0) {
+		return 1;
+	}
+	status = H5Sselect_hyperslab(memory_dataspace_id, H5S_SELECT_SET, memory_offset, stride, count, block);
+	if (status < 0) {
+		return 1;
+	}
+
+	hid_t dxpl_id = H5Pcreate(H5P_DATASET_XFER);
+	H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_INDEPENDENT);
+
+	status = H5Dread(dataset_id, H5T_NATIVE_INT, memory_dataspace_id, dataspace_id, dxpl_id, dset_data);
+	if (status < 0) {
+		return 1;
+	}
+
+	for (int i = 0; i < 5; i++) {
+		for (int j = 0; j < 5; j++) {
+			if (dset_data[i][j] != i * 10 + j + (5 * mpi_rank)) {
+				fprintf(stderr, "[%d][%d] %d != %d\n ", i, j, dset_data[i][j], i * 10 + j + (5 * mpi_rank));
+				return 1;
+			}
+		}
+	}
+
+	status = H5Dclose(dataset_id);
+	if (status < 0) {
+		return 1;
+	}
+	status = H5Pclose(dxpl_id);
+	if (status != 0) {
+		return status;
+	}
+	status = H5Sclose(memory_dataspace_id);
+	if (status < 0) {
+		return 1;
+	}
+	status = H5Sclose(dataspace_id);
+	if (status < 0) {
+		return 1;
+	}
+	status = H5Fclose(file_id);
+	if (file_id < 0) {
+		return 1;
+	}
+	if (status != 0) {
+		return status;
+	}
+	status = H5Pclose(fapl_id);
+	if (status != 0) {
+		return status;
+	}
+
+	H5close();
+	if (status < 0) {
+		return 1;
+	}
+	MPI_Finalize();
+
+	printf("[Rank: %d] HDF5 mpi_read_test finalized\n", mpi_rank);
+	return 0;
+}