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* decl_hdf5 MPIO Collective or Independent, fix #419 * fix compilation error + add compatibilty test with independent I/O * fix419:resolve Datatype_template_sptr error + Add change in local CHANGELOG.md * fix419: add mpio in full configuration example of the doc * fix419: fix name of parameter * fixing review * replace MPIIO by MPI-I/O + add argument to main + fix some typo * fix review * Update plugins/decl_hdf5/dataset_op.cxx Co-authored-by: Benoit Martin <[email protected]> * Update plugins/decl_hdf5/dataset_op.cxx Co-authored-by: Benoit Martin <[email protected]> * Update plugins/decl_hdf5/dataset_op.cxx Co-authored-by: Benoit Martin <[email protected]> * fix bug --------- Co-authored-by: Karol Sierocinski <[email protected]> Co-authored-by: yushan wang <[email protected]> Co-authored-by: Benoit Martin <[email protected]> Co-authored-by: Yacine Ould Rouis - CNRS <[email protected]> Co-authored-by: Julien Bigot <[email protected]>
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@@ -11,6 +11,12 @@ Julien Bigot - CEA ([email protected]) | |
| * Run tests that depend on the filesystem in their own temporary directory | ||
| * Buildsystem | ||
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| Jacques Morice - CEA ([email protected]) | ||
| * contribution to feature improvement, validation | ||
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| Yacine Ould Rouis - CNRS ([email protected]) | ||
| * contribution to feature design, validation | ||
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| Thomas Padioleau - CEA ([email protected]) | ||
| * Fixed a bug with parallel file deletion | ||
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144 changes: 144 additions & 0 deletions
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plugins/decl_hdf5/tests/compatibility_tests/HDF5_C/mpi_independent_read_test.c
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| /******************************************************************************* | ||
| * 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. | ||
| ******************************************************************************/ | ||
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| #include <mpi.h> | ||
| #include <assert.h> | ||
| #include <hdf5.h> | ||
| #include <unistd.h> | ||
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| #define FILE "mpi_independent_test.h5" | ||
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| /** | ||
| * Test : Read a file using hdf5 parallel version with the option independent parallel pointer. | ||
| */ | ||
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| 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; | ||
| } | ||
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| 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; | ||
| } | ||
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| int dset_data[5][5]; | ||
| for (int i = 0; i < 5; i++) { | ||
| for (int j = 0; j < 5; j++) { | ||
| dset_data[i][j] = 0; | ||
| } | ||
| } | ||
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| hsize_t coords[2] = {5, 10}; | ||
| hid_t dataspace_id = H5Screate_simple(2, coords, NULL); | ||
| if (dataspace_id < 0) { | ||
| return 1; | ||
| } | ||
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| hid_t dataset_id = H5Dopen2(file_id, "array_data", H5P_DEFAULT); | ||
| if (dataset_id < 0) { | ||
| return 1; | ||
| } | ||
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| 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}; | ||
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| 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; | ||
| } | ||
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| hid_t dxpl_id = H5Pcreate(H5P_DATASET_XFER); | ||
| H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_INDEPENDENT); | ||
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| status = H5Dread(dataset_id, H5T_NATIVE_INT, memory_dataspace_id, dataspace_id, dxpl_id, dset_data); | ||
| if (status < 0) { | ||
| return 1; | ||
| } | ||
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| 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; | ||
| } | ||
| } | ||
| } | ||
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| 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; | ||
| } | ||
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| H5close(); | ||
| if (status < 0) { | ||
| return 1; | ||
| } | ||
| MPI_Finalize(); | ||
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| printf("[Rank: %d] HDF5 mpi_read_test finalized\n", mpi_rank); | ||
| return 0; | ||
| } |
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