/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Programmer: Jordan Henderson * 01/31/2017 * * This file contains tests for writing to and reading from * datasets in parallel with filters applied to the data. */ #include "t_filters_parallel.h" const char *FILENAME[] = {"t_filters_parallel", NULL}; char filenames[1][256]; static MPI_Comm comm = MPI_COMM_WORLD; static MPI_Info info = MPI_INFO_NULL; static int mpi_rank; static int mpi_size; int nerrors = 0; /* Arrays of filter ID values and filter names (should match each other) */ H5Z_filter_t filterIDs[] = { H5Z_FILTER_DEFLATE, H5Z_FILTER_SHUFFLE, H5Z_FILTER_FLETCHER32, H5Z_FILTER_SZIP, H5Z_FILTER_NBIT, H5Z_FILTER_SCALEOFFSET, }; const char *filterNames[] = {"Deflate", "Shuffle", "Fletcher32", "SZIP", "Nbit", "ScaleOffset"}; /* Function pointer typedef for test functions */ typedef void (*test_func)(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); /* Typedef for filter arguments for user-defined filters */ typedef struct filter_options_t { unsigned int flags; size_t cd_nelmts; const unsigned int cd_values[]; } filter_options_t; /* * Enum for verify_space_alloc_status which specifies * how many chunks have been written to in a dataset */ typedef enum num_chunks_written_t { DATASET_JUST_CREATED, NO_CHUNKS_WRITTEN, SOME_CHUNKS_WRITTEN, ALL_CHUNKS_WRITTEN } num_chunks_written_t; static herr_t set_dcpl_filter(hid_t dcpl_id, H5Z_filter_t filter_id, filter_options_t *filter_options); static herr_t verify_space_alloc_status(hid_t dset_id, hid_t dcpl_id, num_chunks_written_t chunks_written); #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES /* Tests for writing data in parallel */ static void test_write_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_no_overlap_partial(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_single_unlim_dim_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_single_unlim_dim_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_multi_unlim_dim_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_multi_unlim_dim_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_filtered_dataset_interleaved_write(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_transformed_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_3d_filtered_dataset_no_overlap_separate_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_3d_filtered_dataset_no_overlap_same_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_cmpd_filtered_dataset_no_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_cmpd_filtered_dataset_no_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_cmpd_filtered_dataset_type_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_write_cmpd_filtered_dataset_type_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); #endif /* Tests for reading data in parallel */ static void test_read_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_filtered_dataset_interleaved_read(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_transformed_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_3d_filtered_dataset_no_overlap_separate_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_3d_filtered_dataset_no_overlap_same_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_cmpd_filtered_dataset_no_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_cmpd_filtered_dataset_no_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_cmpd_filtered_dataset_type_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_read_cmpd_filtered_dataset_type_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); /* * Tests for attempting to round-trip the data going from * * written serially -> read in parallel * * and * * written in parallel -> read serially */ static void test_write_serial_read_parallel(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES static void test_write_parallel_read_serial(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); /* Other miscellaneous tests */ static void test_shrinking_growing_chunks(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_edge_chunks_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_edge_chunks_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_edge_chunks_partial_write(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_fill_values(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_fill_value_undefined(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); static void test_fill_time_never(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id); #endif static test_func tests[] = { #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES test_write_one_chunk_filtered_dataset, test_write_filtered_dataset_no_overlap, test_write_filtered_dataset_no_overlap_partial, test_write_filtered_dataset_overlap, test_write_filtered_dataset_single_unlim_dim_no_overlap, test_write_filtered_dataset_single_unlim_dim_overlap, test_write_filtered_dataset_multi_unlim_dim_no_overlap, test_write_filtered_dataset_multi_unlim_dim_overlap, test_write_filtered_dataset_single_no_selection, test_write_filtered_dataset_all_no_selection, test_write_filtered_dataset_point_selection, test_write_filtered_dataset_interleaved_write, test_write_transformed_filtered_dataset_no_overlap, test_write_3d_filtered_dataset_no_overlap_separate_pages, test_write_3d_filtered_dataset_no_overlap_same_pages, test_write_3d_filtered_dataset_overlap, test_write_cmpd_filtered_dataset_no_conversion_unshared, test_write_cmpd_filtered_dataset_no_conversion_shared, test_write_cmpd_filtered_dataset_type_conversion_unshared, test_write_cmpd_filtered_dataset_type_conversion_shared, #endif test_read_one_chunk_filtered_dataset, test_read_filtered_dataset_no_overlap, test_read_filtered_dataset_overlap, test_read_filtered_dataset_single_no_selection, test_read_filtered_dataset_all_no_selection, test_read_filtered_dataset_point_selection, test_read_filtered_dataset_interleaved_read, test_read_transformed_filtered_dataset_no_overlap, test_read_3d_filtered_dataset_no_overlap_separate_pages, test_read_3d_filtered_dataset_no_overlap_same_pages, test_read_3d_filtered_dataset_overlap, test_read_cmpd_filtered_dataset_no_conversion_unshared, test_read_cmpd_filtered_dataset_no_conversion_shared, test_read_cmpd_filtered_dataset_type_conversion_unshared, test_read_cmpd_filtered_dataset_type_conversion_shared, test_write_serial_read_parallel, #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES test_write_parallel_read_serial, test_shrinking_growing_chunks, test_edge_chunks_no_overlap, test_edge_chunks_overlap, test_edge_chunks_partial_write, test_fill_values, test_fill_value_undefined, test_fill_time_never, #endif }; /* * Function to call the appropriate HDF5 filter-setting function * depending on the given filter ID. Used to re-run the tests * with different filters to check that the data still comes back * correctly under a variety of circumstances, such as the * Fletcher32 checksum filter increasing the size of the chunk. */ static herr_t set_dcpl_filter(hid_t dcpl_id, H5Z_filter_t filter_id, filter_options_t *filter_options) { switch (filter_id) { case H5Z_FILTER_DEFLATE: return H5Pset_deflate(dcpl_id, DEFAULT_DEFLATE_LEVEL); case H5Z_FILTER_SHUFFLE: return H5Pset_shuffle(dcpl_id); case H5Z_FILTER_FLETCHER32: return H5Pset_fletcher32(dcpl_id); case H5Z_FILTER_SZIP: { unsigned pixels_per_block = H5_SZIP_MAX_PIXELS_PER_BLOCK; hsize_t chunk_dims[H5S_MAX_RANK] = {0}; size_t i, chunk_nelemts; VRFY(H5Pget_chunk(dcpl_id, H5S_MAX_RANK, chunk_dims) >= 0, "H5Pget_chunk succeeded"); for (i = 0, chunk_nelemts = 1; i < H5S_MAX_RANK; i++) if (chunk_dims[i] > 0) chunk_nelemts *= chunk_dims[i]; if (chunk_nelemts < H5_SZIP_MAX_PIXELS_PER_BLOCK) { /* * Can't set SZIP for chunk of 1 data element. * Pixels-per-block value must be both even * and non-zero. */ if (chunk_nelemts == 1) return SUCCEED; if ((chunk_nelemts % 2) == 0) pixels_per_block = (unsigned)chunk_nelemts; else pixels_per_block = (unsigned)(chunk_nelemts - 1); } else pixels_per_block = H5_SZIP_MAX_PIXELS_PER_BLOCK; return H5Pset_szip(dcpl_id, 0, pixels_per_block); } case H5Z_FILTER_NBIT: return H5Pset_nbit(dcpl_id); case H5Z_FILTER_SCALEOFFSET: return H5Pset_scaleoffset(dcpl_id, H5Z_SO_INT, 0); default: { if (!filter_options) return FAIL; return H5Pset_filter(dcpl_id, filter_id, filter_options->flags, filter_options->cd_nelmts, filter_options->cd_values); } } } /* * Function to verify the status of dataset storage space allocation * based on the dataset's allocation time setting and how many chunks * in the dataset have been written to. */ static herr_t verify_space_alloc_status(hid_t dset_id, hid_t dcpl_id, num_chunks_written_t chunks_written) { int nfilters; herr_t ret_value = SUCCEED; VRFY(((nfilters = H5Pget_nfilters(dcpl_id)) >= 0), "H5Pget_nfilters succeeded"); /* * Only verify space allocation status when there are filters * in the dataset's filter pipeline. When filters aren't in the * pipeline, the space allocation time and status can vary based * on whether the file was created in parallel or serial mode. */ if (nfilters > 0) { H5D_space_status_t space_status; H5D_alloc_time_t alloc_time; VRFY((H5Pget_alloc_time(dcpl_id, &alloc_time) >= 0), "H5Pget_alloc_time succeeded"); VRFY((H5Dget_space_status(dset_id, &space_status) >= 0), "H5Dget_space_status succeeded"); switch (alloc_time) { case H5D_ALLOC_TIME_EARLY: /* * Early space allocation should always result in the * full dataset storage space being allocated. */ VRFY(space_status == H5D_SPACE_STATUS_ALLOCATED, "verified space allocation status"); break; case H5D_ALLOC_TIME_LATE: /* * Late space allocation should always result in the * full dataset storage space being allocated when * the dataset gets written to. However, if the dataset * is extended the dataset's space allocation status * can become partly allocated until the dataset is * written to again. */ if (chunks_written == SOME_CHUNKS_WRITTEN || chunks_written == ALL_CHUNKS_WRITTEN) VRFY((space_status == H5D_SPACE_STATUS_ALLOCATED) || (space_status == H5D_SPACE_STATUS_PART_ALLOCATED), "verified space allocation status"); else if (chunks_written == NO_CHUNKS_WRITTEN) /* * A special case where we wrote to a dataset that * uses late space allocation, but the write was * either a no-op (no selection in the dataset * from any rank) or something caused the write to * fail late in the process of performing the actual * write. In either case, space should still have * been allocated. */ VRFY(space_status == H5D_SPACE_STATUS_ALLOCATED, "verified space allocation status"); else VRFY(space_status == H5D_SPACE_STATUS_NOT_ALLOCATED, "verified space allocation status"); break; case H5D_ALLOC_TIME_DEFAULT: case H5D_ALLOC_TIME_INCR: /* * Incremental space allocation should result in * the dataset's storage space being incrementally * allocated as chunks are written to. Once all chunks * have been written to, the space allocation should be * seen as fully allocated. */ if (chunks_written == SOME_CHUNKS_WRITTEN) VRFY((space_status == H5D_SPACE_STATUS_PART_ALLOCATED), "verified space allocation status"); else if (chunks_written == ALL_CHUNKS_WRITTEN) VRFY((space_status == H5D_SPACE_STATUS_ALLOCATED), "verified space allocation status"); else VRFY(space_status == H5D_SPACE_STATUS_NOT_ALLOCATED, "verified space allocation status"); break; default: if (MAINPROCESS) MESG("unknown space allocation time"); MPI_Abort(MPI_COMM_WORLD, 1); } } return ret_value; } #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES /* * Tests parallel write of filtered data in the special * case where a dataset is composed of a single chunk. * * Programmer: Jordan Henderson * 02/01/2017 */ static void test_write_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t chunk_dims[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t sel_dims[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t start[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t stride[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t count[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t block[WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to one-chunk filtered dataset"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_NROWS; dataset_dims[1] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_NCOLS; chunk_dims[0] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_NCOLS; filespace = H5Screate_simple(WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_ONE_CHUNK_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_ONE_CHUNK_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NROWS; stride[1] = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS; block[0] = sel_dims[0]; block[1] = sel_dims[1]; start[0] = ((hsize_t)mpi_rank * sel_dims[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NROWS * (hsize_t)WRITE_ONE_CHUNK_FILTERED_DATASET_NCOLS * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = ((C_DATATYPE)i % (WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NROWS / mpi_size * WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS)) + ((C_DATATYPE)i / (WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NROWS / mpi_size * WRITE_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS)); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_ONE_CHUNK_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where only * one process is writing to a particular chunk in the operation. * In this case, the write operation can be optimized because * chunks do not have to be redistributed to new owners. * * Programmer: Jordan Henderson * 02/01/2017 */ static void test_write_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_NCOLS; filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_NCOLS / (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_CH_NROWS * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where only * one process is writing to a particular chunk in the operation * and that process only writes to part of a chunk. */ static void test_write_filtered_dataset_no_overlap_partial(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing partial write to unshared filtered chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; sel_dims[1] = (hsize_t)(WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS / WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS); filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)(WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_NCOLS / WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS); stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS; block[1] = (hsize_t)1; start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < (size_t)mpi_size; i++) { size_t rank_n_elems = (size_t)(mpi_size * (WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NROWS * WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS)); size_t data_idx = i; for (size_t j = 0; j < rank_n_elems; j++) { if ((j % WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_CH_NCOLS) == 0) { correct_buf[(i * rank_n_elems) + j] = (C_DATATYPE)data_idx; data_idx++; } } } VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_PARTIAL_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * more than one process is writing to a particular chunk * in the operation. In this case, the chunks have to be * redistributed before the operation so that only one process * writes to a particular chunk. * * Programmer: Jordan Henderson * 02/01/2017 */ static void test_write_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; filespace = H5Screate_simple(WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_NROWS / (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NROWS; count[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_NCOLS / (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * a dataset has a single unlimited dimension and each * MPI rank writes to its own separate chunk. On each * iteration, the dataset is extended in its extensible * dimension by "MPI size" chunks per rank and the new * chunks are written to, read back and verified. */ static void test_write_filtered_dataset_single_unlim_dim_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t max_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks w/ single unlimited dimension"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS; max_dims[0] = dataset_dims[0]; max_dims[1] = H5S_UNLIMITED; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS; filespace = H5Screate_simple(WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); read_buf = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < (size_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NLOOPS; i++) { /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NCOLS / (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; stride[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_ONE_UNLIM_DIM_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * block[0] * count[0]); start[1] = i * count[1] * block[1]; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_ONE_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); HDmemset(read_buf, 255, data_size); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* Verify the correct data was written */ VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); if (i < (size_t)WRITE_UNSHARED_ONE_UNLIM_DIM_NLOOPS - 1) { /* Extend the dataset by count[1] chunks in the extensible dimension */ dataset_dims[1] += count[1] * block[1]; VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); } VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); } if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * a dataset has a single unlimited dimension and each * MPI rank writes to a portion of each chunk in the dataset. * On each iteration, the dataset is extended in its extensible * dimension by two chunks and the new chunks are written to * by all ranks, then read back and verified. */ static void test_write_filtered_dataset_single_unlim_dim_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t max_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t sel_dims[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t start[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t stride[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t count[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; hsize_t block[WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks w/ single unlimited dimension"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NROWS; dataset_dims[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NCOLS; max_dims[0] = dataset_dims[0]; max_dims[1] = H5S_UNLIMITED; chunk_dims[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; filespace = H5Screate_simple(WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_ONE_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SHARED_ONE_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); read_buf = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < (size_t)WRITE_SHARED_ONE_UNLIM_DIM_NLOOPS; i++) { /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NROWS / (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS; count[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_NCOLS / (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; stride[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS; stride[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; block[0] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)WRITE_SHARED_ONE_UNLIM_DIM_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = i * count[1] * block[1]; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); dset_id = H5Dopen2(group_id, WRITE_SHARED_ONE_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); HDmemset(read_buf, 255, data_size); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* Verify correct data was written */ VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); if (i < (size_t)WRITE_SHARED_ONE_UNLIM_DIM_NLOOPS - 1) { /* Extend the dataset by count[1] chunks in the extensible dimension */ dataset_dims[1] += count[1] * block[1]; VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); } VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); } if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * a dataset has two unlimited dimensions and each * MPI rank writes to its own separate chunks. On each * iteration, the dataset is extended in its first * extensible dimension by the size of one chunk per rank * and in its second extensible dimension by the size of * one chunk. Then, all chunks are written to, read back * and verified. */ static void test_write_filtered_dataset_multi_unlim_dim_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t max_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks w/ two unlimited dimensions"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NCOLS; max_dims[0] = H5S_UNLIMITED; max_dims[1] = H5S_UNLIMITED; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NCOLS; filespace = H5Screate_simple(WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); for (i = 0; i < (size_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NLOOPS; i++) { C_DATATYPE *tmp_realloc = NULL; size_t j; /* Set selected dimensions */ sel_dims[0] = (i + 1) * WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; sel_dims[1] = (i + 1) * WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); tmp_realloc = (C_DATATYPE *)HDrealloc(data, data_size); VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); data = tmp_realloc; tmp_realloc = (C_DATATYPE *)HDrealloc(read_buf, data_size); VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); read_buf = tmp_realloc; for (j = 0; j < data_size / sizeof(*data); j++) data[j] = (C_DATATYPE)GEN_DATA(j); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (i + 1); count[1] = (i + 1); stride[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_TWO_UNLIM_DIM_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * block[0] * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_TWO_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); HDmemset(read_buf, 255, data_size); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* Verify the correct data was written */ VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); if (i < (size_t)WRITE_UNSHARED_TWO_UNLIM_DIM_NLOOPS - 1) { /* * Extend the dataset by the size of one chunk per rank * in the first extensible dimension. Extend the dataset * by the size of chunk in the second extensible dimension. */ dataset_dims[0] += (hsize_t)mpi_size * block[0]; dataset_dims[1] += block[1]; VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); } VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); } if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * a dataset has two unlimited dimensions and each MPI * rank writes to a portion of each chunk in the dataset. * On each iteration, the dataset is extended in its extensible * dimensions by the size of a chunk and then all chunks are * written to by all ranks, then read back and verified. */ static void test_write_filtered_dataset_multi_unlim_dim_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t max_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t sel_dims[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t start[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t stride[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t count[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; hsize_t block[WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks w/ two unlimited dimensions"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_NROWS; dataset_dims[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_NCOLS; max_dims[0] = H5S_UNLIMITED; max_dims[1] = H5S_UNLIMITED; chunk_dims[0] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; filespace = H5Screate_simple(WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS, dataset_dims, max_dims); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_TWO_UNLIM_DIM_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SHARED_TWO_UNLIM_DIM_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); for (i = 0; i < (size_t)WRITE_SHARED_TWO_UNLIM_DIM_NLOOPS; i++) { C_DATATYPE *tmp_realloc = NULL; size_t j; /* Set selected dimensions */ sel_dims[0] = (i + 1); sel_dims[1] = (i + 1) * (size_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); tmp_realloc = (C_DATATYPE *)HDrealloc(data, data_size); VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); data = tmp_realloc; tmp_realloc = (C_DATATYPE *)HDrealloc(read_buf, data_size); VRFY((NULL != tmp_realloc), "HDrealloc succeeded"); read_buf = tmp_realloc; for (j = 0; j < data_size / sizeof(*data); j++) data[j] = (C_DATATYPE)GEN_DATA(j); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (i + 1); count[1] = (i + 1); stride[0] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; stride[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); dset_id = H5Dopen2(group_id, WRITE_SHARED_TWO_UNLIM_DIM_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); HDmemset(read_buf, 255, data_size); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* Verify correct data was written */ VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); if (i < (size_t)WRITE_SHARED_TWO_UNLIM_DIM_NLOOPS - 1) { /* Extend the dataset by the size of a chunk in each extensible dimension */ dataset_dims[0] += (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NROWS; dataset_dims[1] += (hsize_t)WRITE_SHARED_TWO_UNLIM_DIM_CH_NCOLS; VRFY(H5Dset_extent(dset_id, dataset_dims) >= 0, "H5Dset_extent succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); } VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); } if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * a single process in the write operation has no selection * in the dataset's dataspace. In this case, the process with * no selection still has to participate in the collective * space re-allocation for the filtered chunks and also must * participate in the re-insertion of the filtered chunks * into the chunk index. * * Programmer: Jordan Henderson * 02/01/2017 */ static void test_write_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; size_t segment_length; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to filtered chunks with a single process having no selection"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS; if (mpi_rank == WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) sel_dims[0] = sel_dims[1] = 0; filespace = H5Screate_simple(WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS / (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; block[1] = (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; start[0] = (hsize_t)mpi_rank * (hsize_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS * count[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); if (mpi_rank == WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) VRFY((H5Sselect_none(filespace) >= 0), "Select none succeeded"); else VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); if (mpi_rank != WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) { data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); } correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); /* Compute the correct offset into the buffer for the process having no selection and clear it */ segment_length = dataset_dims[0] * dataset_dims[1] / (hsize_t)mpi_size; HDmemset(correct_buf + ((size_t)WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC * segment_length), 0, segment_length * sizeof(*data)); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status - data should only have been written if MPI size > 1 */ verify_space_alloc_status(dset_id, plist_id, (mpi_size > 1 ? SOME_CHUNKS_WRITTEN : NO_CHUNKS_WRITTEN)); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case * where no process in the write operation has a * selection in the dataset's dataspace. This test is * to ensure that there are no assertion failures or * similar issues due to size 0 allocations and the * like. In this case, the file and dataset are created * but the dataset is populated with the default fill * value. * * Programmer: Jordan Henderson * 02/02/2017 */ static void test_write_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to filtered chunks with all processes having no selection"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; sel_dims[0] = sel_dims[1] = 0; filespace = H5Screate_simple(WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_none(filespace) >= 0), "Select none succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status - no ranks should have written any data */ verify_space_alloc_status(dset_id, plist_id, NO_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data by using * point selections instead of hyperslab selections. * * Programmer: Jordan Henderson * 02/02/2017 */ static void test_write_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *read_buf = NULL; hsize_t *coords = NULL; hsize_t dataset_dims[WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, j, data_size, correct_buf_size; size_t num_points; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to filtered chunks with point selection"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NCOLS; filespace = H5Screate_simple(WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Set up point selection */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); num_points = (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NROWS * (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NCOLS / (hsize_t)mpi_size; coords = (hsize_t *)HDcalloc(1, 2 * num_points * sizeof(*coords)); VRFY((NULL != coords), "Coords HDcalloc succeeded"); for (i = 0; i < num_points; i++) for (j = 0; j < WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS; j++) coords[(i * WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS) + j] = (j > 0) ? (i % (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NCOLS) : ((hsize_t)mpi_rank + ((hsize_t)mpi_size * (i / (hsize_t)WRITE_POINT_SELECTION_FILTERED_CHUNKS_NCOLS))); VRFY((H5Sselect_elements(filespace, H5S_SELECT_SET, (hsize_t)num_points, (const hsize_t *)coords) >= 0), "Point selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (coords) HDfree(coords); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * each process writes an equal amount of data to each chunk * in the dataset. Each chunk is distributed among the * processes in round-robin fashion by blocks of size 1 until * the whole chunk is selected, leading to an interleaved * write pattern. * * Programmer: Jordan Henderson * 02/02/2017 */ static void test_write_filtered_dataset_interleaved_write(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t chunk_dims[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t sel_dims[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t start[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t stride[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t count[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; hsize_t block[INTERLEAVED_WRITE_FILTERED_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing interleaved write to filtered chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NROWS; dataset_dims[1] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS; chunk_dims[0] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_CH_NROWS; chunk_dims[1] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_CH_NCOLS; sel_dims[0] = (hsize_t)(INTERLEAVED_WRITE_FILTERED_DATASET_NROWS / mpi_size); sel_dims[1] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS; filespace = H5Screate_simple(INTERLEAVED_WRITE_FILTERED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(INTERLEAVED_WRITE_FILTERED_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, INTERLEAVED_WRITE_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, INTERLEAVED_WRITE_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)(INTERLEAVED_WRITE_FILTERED_DATASET_NROWS / INTERLEAVED_WRITE_FILTERED_DATASET_CH_NROWS); count[1] = (hsize_t)(INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS / INTERLEAVED_WRITE_FILTERED_DATASET_CH_NCOLS); stride[0] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_CH_NROWS; stride[1] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) /* Add Column Index */ correct_buf[i] = (C_DATATYPE)((i % (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS) /* Add the Row Index */ + ((i % (hsize_t)(mpi_size * INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS)) / (hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS) /* Add the amount that gets added when a rank moves down to its next section vertically in the dataset */ + ((hsize_t)INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS * (i / (hsize_t)(mpi_size * INTERLEAVED_WRITE_FILTERED_DATASET_NCOLS)))); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, INTERLEAVED_WRITE_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of transformed and filtered data * in the case where only one process is writing to a * particular chunk in the operation. Normally, a data * transform function will cause the parallel library to * break to independent I/O and this isn't allowed when * there are filters in the pipeline. However, in this * case the parallel library recognizes that the used * data transform function "x" is the same as not applying * the transform function. Therefore it does not apply * the transform function resulting in not breaking to * independent I/O. * * Programmer: Jan-Willem Blokland * 08/20/2021 */ static void test_write_transformed_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared transformed and filtered chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS; filespace = H5Screate_simple(WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS / (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); /* Create property list for data transform */ plist_id = H5Pcopy(dxpl_id); VRFY((plist_id >= 0), "DXPL copy succeeded"); /* Set data transform expression */ VRFY((H5Pset_data_transform(plist_id, "x") >= 0), "Set data transform expression succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, data) >= 0), "Dataset write succeeded"); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); /* Verify space allocation status */ plist_id = H5Dget_create_plist(dset_id); VRFY((plist_id >= 0), "H5Dget_create_plist succeeded"); verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * the dataset has 3 dimensions and each process writes * to its own "page" in the 3rd dimension. * * Programmer: Jordan Henderson * 02/06/2017 */ static void test_write_3d_filtered_dataset_no_overlap_separate_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks on separate pages in 3D dataset"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS; dataset_dims[2] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DEPTH; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; chunk_dims[2] = 1; sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS; sel_dims[2] = 1; filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS / (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; count[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS / (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; count[2] = 1; stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; stride[2] = 1; block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; block[2] = 1; start[0] = 0; start[1] = 0; start[2] = (hsize_t)mpi_rank; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], count[2], stride[0], stride[1], stride[2], start[0], start[1], start[2], block[0], block[1], block[2]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sel_dims[2] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (hsize_t)mpi_size) + (i / (hsize_t)mpi_size)); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * the dataset has 3 dimensions and each process writes * to each "page" in the 3rd dimension. However, no chunk * on a given "page" is written to by more than one process. * * Programmer: Jordan Henderson * 02/06/2017 */ static void test_write_3d_filtered_dataset_no_overlap_same_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks on the same pages in 3D dataset"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS; dataset_dims[2] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DEPTH; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; chunk_dims[2] = 1; sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS; sel_dims[2] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DEPTH; filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS / (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; count[2] = (hsize_t)mpi_size; stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; stride[2] = 1; block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; block[2] = 1; start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS * count[0]); start[1] = 0; start[2] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], count[2], stride[0], stride[1], stride[2], start[0], start[1], start[2], block[0], block[1], block[2]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sel_dims[2] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] * dataset_dims[1])) + (i / (dataset_dims[0] * dataset_dims[1]))); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data in the case where * the dataset has 3 dimensions and each process writes * to each "page" in the 3rd dimension. Further, each chunk * in each "page" is written to equally by all processes. * * Programmer: Jordan Henderson * 02/06/2017 */ static void test_write_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t sel_dims[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t start[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t stride[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t count[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t block[WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks in 3D dataset"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_NROWS; dataset_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS; dataset_dims[2] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH; chunk_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; chunk_dims[2] = 1; sel_dims[0] = (hsize_t)(WRITE_SHARED_FILTERED_CHUNKS_3D_NROWS / mpi_size); sel_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS; sel_dims[2] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH; filespace = H5Screate_simple(WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)(WRITE_SHARED_FILTERED_CHUNKS_3D_NROWS / WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NROWS); count[1] = (hsize_t)(WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS / WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS); count[2] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH; stride[0] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NROWS; stride[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; stride[2] = 1; block[0] = 1; block[1] = (hsize_t)WRITE_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; block[2] = 1; start[0] = (hsize_t)mpi_rank; start[1] = 0; start[2] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], count[2], stride[0], stride[1], stride[2], start[0], start[1], start[2], block[0], block[1], block[2]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sel_dims[2] * sizeof(*data); correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) /* Add the Column Index */ correct_buf[i] = (C_DATATYPE)((i % (hsize_t)(WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH * WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS)) /* Add the Row Index */ + ((i % (hsize_t)(mpi_size * WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH * WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS)) / (hsize_t)(WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH * WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS)) /* Add the amount that gets added when a rank moves down to its next section vertically in the dataset */ + ((hsize_t)(WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH * WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS) * (i / (hsize_t)(mpi_size * WRITE_SHARED_FILTERED_CHUNKS_3D_DEPTH * WRITE_SHARED_FILTERED_CHUNKS_3D_NCOLS)))); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data to unshared * chunks using a compound datatype which doesn't * require a datatype conversion. * * Programmer: Jordan Henderson * 02/10/2017 */ static void test_write_cmpd_filtered_dataset_no_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t chunk_dims[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t sel_dims[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t start[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t stride[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; size_t i, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NROWS; dataset_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NCOLS; chunk_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; chunk_dims[1] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; sel_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_ENTRIES_PER_PROC; filespace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_ENTRIES_PER_PROC; stride[0] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; stride[1] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; block[0] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; block[1] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; start[0] = 0; start[1] = ((hsize_t)mpi_rank * WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); data = (COMPOUND_C_DATATYPE *)HDcalloc( 1, (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_ENTRIES_PER_PROC * sizeof(*data)); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(COMPOUND_C_DATATYPE); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); /* Fill data buffer */ for (i = 0; i < (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_ENTRIES_PER_PROC; i++) { data[i].field1 = (short)GEN_DATA(i); data[i].field2 = (int)GEN_DATA(i); data[i].field3 = (long)GEN_DATA(i); } for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) { correct_buf[i].field1 = (short)((i % dataset_dims[1]) + (i / dataset_dims[1])); correct_buf[i].field2 = (int)((i % dataset_dims[1]) + (i / dataset_dims[1])); correct_buf[i].field3 = (long)((i % dataset_dims[1]) + (i / dataset_dims[1])); } VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data to shared * chunks using a compound datatype which doesn't * require a datatype conversion. * * Programmer: Jordan Henderson * 02/10/2017 */ static void test_write_cmpd_filtered_dataset_no_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t chunk_dims[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t sel_dims[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t start[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t stride[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; size_t i, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NROWS; dataset_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NCOLS; chunk_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS; chunk_dims[1] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_ENTRIES_PER_PROC; filespace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_ENTRIES_PER_PROC; stride[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS; stride[1] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; block[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; block[1] = WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); data = (COMPOUND_C_DATATYPE *)HDcalloc( 1, (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_ENTRIES_PER_PROC * sizeof(*data)); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(COMPOUND_C_DATATYPE); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); /* Fill data buffer */ for (i = 0; i < (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_ENTRIES_PER_PROC; i++) { data[i].field1 = (short)GEN_DATA(i); data[i].field2 = (int)GEN_DATA(i); data[i].field3 = (long)GEN_DATA(i); } for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) { correct_buf[i].field1 = (short)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); correct_buf[i].field2 = (int)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); correct_buf[i].field3 = (long)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); } VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data to unshared * chunks using a compound datatype which requires a * datatype conversion. * * NOTE: This test currently should fail for mpi_size > 1 * because the datatype conversion causes the parallel * library to break to independent I/O and this isn't * allowed when there are filters in the pipeline, * unless there is only one MPI rank. * * Programmer: Jordan Henderson * 02/07/2017 */ static void test_write_cmpd_filtered_dataset_type_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t chunk_dims[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t sel_dims[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t start[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t stride[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; size_t i, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered chunks in Compound Datatype dataset with Datatype " "conversion"); /* Skip for MPI communicator size of 1 */ if (mpi_size == 1) { SKIPPED(); return; } /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NROWS; dataset_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NCOLS; chunk_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; chunk_dims[1] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; sel_dims[0] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_ENTRIES_PER_PROC; filespace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); /* Create the compound type for file. */ filetype = H5Tcreate(H5T_COMPOUND, 32); VRFY((filetype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(filetype, "ShortData", 0, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "IntData", 8, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "LongData", 16, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_ENTRIES_PER_PROC; stride[0] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; stride[1] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; block[0] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; block[1] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; start[0] = 0; start[1] = ((hsize_t)mpi_rank * WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); data = (COMPOUND_C_DATATYPE *)HDcalloc( 1, (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_ENTRIES_PER_PROC * sizeof(*data)); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(COMPOUND_C_DATATYPE); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); /* Fill data buffer */ for (i = 0; i < (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_ENTRIES_PER_PROC; i++) { data[i].field1 = (short)GEN_DATA(i); data[i].field2 = (int)GEN_DATA(i); data[i].field3 = (long)GEN_DATA(i); } /* Ensure that this test currently fails since type conversions break collective mode */ H5E_BEGIN_TRY { VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) < 0), "Dataset write succeeded"); } H5E_END_TRY; /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, NO_CHUNKS_WRITTEN); if (data) HDfree(data); /* Verify that no data was written */ VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(filetype) >= 0), "File datatype close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel write of filtered data to shared * chunks using a compound datatype which requires * a datatype conversion. * * NOTE: This test currently should fail for mpi_size > 1 * because the datatype conversion causes the parallel * library to break to independent I/O and this isn't * allowed when there are filters in the pipeline, * unless there is only one MPI rank. * * Programmer: Jordan Henderson * 02/10/2017 */ static void test_write_cmpd_filtered_dataset_type_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *data = NULL; COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t chunk_dims[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t sel_dims[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t start[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t stride[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t count[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t block[WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; size_t i, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs( "Testing write to shared filtered chunks in Compound Datatype dataset with Datatype conversion"); /* Skip for MPI communicator size of 1 */ if (mpi_size == 1) { SKIPPED(); return; } /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NROWS; dataset_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NCOLS; chunk_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS; chunk_dims[1] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_ENTRIES_PER_PROC; filespace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); /* Create the compound type for file. */ filetype = H5Tcreate(H5T_COMPOUND, 32); VRFY((filetype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(filetype, "ShortData", 0, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "IntData", 8, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "LongData", 16, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); dset_id = H5Dcreate2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_ENTRIES_PER_PROC; stride[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS; stride[1] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; block[0] = (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; block[1] = WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); data = (COMPOUND_C_DATATYPE *)HDcalloc( 1, (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_ENTRIES_PER_PROC * sizeof(*data)); VRFY((NULL != data), "HDcalloc succeeded"); correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(COMPOUND_C_DATATYPE); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); /* Fill data buffer */ for (i = 0; i < (hsize_t)WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_ENTRIES_PER_PROC; i++) { data[i].field1 = (short)GEN_DATA(i); data[i].field2 = (int)GEN_DATA(i); data[i].field3 = (long)GEN_DATA(i); } /* Ensure that this test currently fails since type conversions break collective mode */ H5E_BEGIN_TRY { VRFY((H5Dwrite(dset_id, memtype, memspace, filespace, dxpl_id, data) < 0), "Dataset write succeeded"); } H5E_END_TRY; /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, NO_CHUNKS_WRITTEN); if (data) HDfree(data); /* Verify that no data was written */ VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); dset_id = H5Dopen2(group_id, WRITE_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, memtype, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(filetype) >= 0), "File datatype close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } #endif /* * Tests parallel read of filtered data in the special * case where a dataset is composed of a single chunk. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * the singular chunk and contributes its piece to a * global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/14/2018 */ static void test_read_one_chunk_filtered_dataset(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t chunk_dims[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t sel_dims[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t start[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t stride[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t count[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t block[READ_ONE_CHUNK_FILTERED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from one-chunk filtered dataset"); dataset_dims[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NROWS; dataset_dims[1] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = ((C_DATATYPE)i % (READ_ONE_CHUNK_FILTERED_DATASET_CH_NROWS / mpi_size * READ_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS)) + ((C_DATATYPE)i / (READ_ONE_CHUNK_FILTERED_DATASET_CH_NROWS / mpi_size * READ_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS)); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_ONE_CHUNK_FILTERED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_CH_NROWS; chunk_dims[1] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_ONE_CHUNK_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_ONE_CHUNK_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_ONE_CHUNK_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_NCOLS; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_CH_NROWS; stride[1] = (hsize_t)READ_ONE_CHUNK_FILTERED_DATASET_CH_NCOLS; block[0] = sel_dims[0]; block[1] = sel_dims[1]; start[0] = ((hsize_t)mpi_rank * sel_dims[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)flat_dims[0]; displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0]); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where only * one process is reading from a particular chunk in the operation. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * the dataset and contributes its piece to a global buffer * that is checked for consistency. * * Programmer: Jordan Henderson * 05/15/2018 */ static void test_read_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks"); dataset_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NROWS * (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NCOLS * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_UNSHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NCOLS; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and reads * it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_NCOLS / (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS; block[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_CH_NROWS * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)flat_dims[0]; displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0]); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * more than one process is reading from a particular chunk * in the operation. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * each chunk of the dataset and contributes its pieces * to a global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/15/2018 */ static void test_read_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from shared filtered chunks"); dataset_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_SHARED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_SHARED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_SHARED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_NROWS / (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NROWS; count[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_NCOLS / (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* * Since these chunks are shared, run multiple rounds of MPI_Allgatherv * to collect all of the pieces into their appropriate locations. The * number of times MPI_Allgatherv is run should be equal to the number * of chunks in the first dimension of the dataset. */ { size_t loop_count = count[0]; size_t total_recvcounts = 0; recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) { recvcounts[i] = (int)dataset_dims[1]; total_recvcounts += (size_t)recvcounts[i]; } for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * dataset_dims[1]); for (; loop_count; loop_count--) { VRFY((MPI_SUCCESS == MPI_Allgatherv(&read_buf[(count[0] - loop_count) * dataset_dims[1]], recvcounts[mpi_rank], C_DATATYPE_MPI, &global_buf[(count[0] - loop_count) * total_recvcounts], recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); } } VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * a single process in the read operation has no selection * in the dataset's dataspace. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank (except for one) * reads a part of the dataset and contributes its piece * to a global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/15/2018 */ static void test_read_filtered_dataset_single_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; size_t segment_length; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from filtered chunks with a single process having no selection"); dataset_dims[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); /* Compute the correct offset into the buffer for the process having no selection and clear it */ segment_length = dataset_dims[0] * dataset_dims[1] / (hsize_t)mpi_size; HDmemset(correct_buf + ((size_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC * segment_length), 0, segment_length * sizeof(*correct_buf)); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS; if (mpi_rank == READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) sel_dims[0] = sel_dims[1] = 0; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS / (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; block[1] = (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; start[0] = (hsize_t)mpi_rank * (hsize_t)READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS * count[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } if (mpi_rank == READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) VRFY((H5Sselect_none(filespace) >= 0), "Select none succeeded"); else VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); if (mpi_rank == READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) { VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, NULL) >= 0), "Dataset read succeeded"); } else { VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); } global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)(READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS * READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS); recvcounts[READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC] = 0; displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * (size_t)(READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS * READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NCOLS)); if (mpi_rank == READ_SINGLE_NO_SELECTION_FILTERED_CHUNKS_NO_SELECT_PROC) VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, 0, C_DATATYPE_MPI, global_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); else VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * no process in the read operation has a selection in the * dataset's dataspace. This test is to ensure that there * are no assertion failures or similar issues due to size * 0 allocations and the like. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank will simply issue * a no-op read. * * Programmer: Jordan Henderson * 05/15/2018 */ static void test_read_filtered_dataset_all_no_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; size_t read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing read from filtered chunks with all processes having no selection"); dataset_dims[0] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_ALL_NO_SELECTION_FILTERED_CHUNKS_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = sel_dims[1] = 0; memspace = H5Screate_simple(READ_ALL_NO_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_none(filespace) >= 0), "Select none succeeded"); read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data by using point * selections instead of hyperslab selections. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank will read part * of the dataset using a point selection and will * contribute its piece to a global buffer that is * checked for consistency. * * Programmer: Jordan Henderson * 05/15/2018 */ static void test_read_filtered_dataset_point_selection(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *correct_buf = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t *coords = NULL; hsize_t dataset_dims[READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, j, read_buf_size, correct_buf_size; size_t num_points; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from filtered chunks with point selection"); dataset_dims[0] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NCOLS; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Set up point selection */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); num_points = (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NROWS * (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NCOLS / (hsize_t)mpi_size; coords = (hsize_t *)HDcalloc(1, 2 * num_points * sizeof(*coords)); VRFY((NULL != coords), "Coords HDcalloc succeeded"); for (i = 0; i < num_points; i++) for (j = 0; j < READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS; j++) coords[(i * READ_POINT_SELECTION_FILTERED_CHUNKS_DATASET_DIMS) + j] = (j > 0) ? (i % (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NCOLS) : ((hsize_t)mpi_rank + ((hsize_t)mpi_size * (i / (hsize_t)READ_POINT_SELECTION_FILTERED_CHUNKS_NCOLS))); VRFY((H5Sselect_elements(filespace, H5S_SELECT_SET, (hsize_t)num_points, (const hsize_t *)coords) >= 0), "Point selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* * Since these chunks are shared, run multiple rounds of MPI_Allgatherv * to collect all of the pieces into their appropriate locations. The * number of times MPI_Allgatherv is run should be equal to the number * of chunks in the first dimension of the dataset. */ { size_t original_loop_count = dataset_dims[0] / (hsize_t)mpi_size; size_t cur_loop_count = original_loop_count; size_t total_recvcounts = 0; recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) { recvcounts[i] = (int)dataset_dims[1]; total_recvcounts += (size_t)recvcounts[i]; } for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * dataset_dims[1]); for (; cur_loop_count; cur_loop_count--) { VRFY((MPI_SUCCESS == MPI_Allgatherv(&read_buf[(original_loop_count - cur_loop_count) * dataset_dims[1]], recvcounts[mpi_rank], C_DATATYPE_MPI, &global_buf[(original_loop_count - cur_loop_count) * total_recvcounts], recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); } } VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); HDfree(coords); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * each process reads an equal amount of data from each * chunk in the dataset. Each chunk is distributed among the * processes in round-robin fashion by blocks of size 1 until * the whole chunk is selected, leading to an interleaved * read pattern. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank will read part * of each chunk of the dataset and will contribute its * pieces to a global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/15/2018 */ static void test_read_filtered_dataset_interleaved_read(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t chunk_dims[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t sel_dims[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t start[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t stride[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t count[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t block[INTERLEAVED_READ_FILTERED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing interleaved read from filtered chunks"); dataset_dims[0] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NROWS; dataset_dims[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) /* Add Column Index */ correct_buf[i] = (C_DATATYPE)((i % (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NCOLS) /* Add the Row Index */ + ((i % (hsize_t)(mpi_size * INTERLEAVED_READ_FILTERED_DATASET_NCOLS)) / (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NCOLS) /* Add the amount that gets added when a rank moves down to its next section vertically in the dataset */ + ((hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NCOLS * (i / (hsize_t)(mpi_size * INTERLEAVED_READ_FILTERED_DATASET_NCOLS)))); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(INTERLEAVED_READ_FILTERED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NROWS; chunk_dims[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, INTERLEAVED_READ_FILTERED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, INTERLEAVED_READ_FILTERED_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, INTERLEAVED_READ_FILTERED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)(INTERLEAVED_READ_FILTERED_DATASET_NROWS / mpi_size); sel_dims[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_NCOLS; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = (hsize_t)(INTERLEAVED_READ_FILTERED_DATASET_NROWS / INTERLEAVED_READ_FILTERED_DATASET_CH_NROWS); count[1] = (hsize_t)(INTERLEAVED_READ_FILTERED_DATASET_NCOLS / INTERLEAVED_READ_FILTERED_DATASET_CH_NCOLS); stride[0] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NROWS; stride[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)INTERLEAVED_READ_FILTERED_DATASET_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* * Since these chunks are shared, run multiple rounds of MPI_Allgatherv * to collect all of the pieces into their appropriate locations. The * number of times MPI_Allgatherv is run should be equal to the number * of chunks in the first dimension of the dataset. */ { size_t loop_count = count[0]; size_t total_recvcounts = 0; recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) { recvcounts[i] = (int)dataset_dims[1]; total_recvcounts += (size_t)recvcounts[i]; } for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * dataset_dims[1]); for (; loop_count; loop_count--) { VRFY((MPI_SUCCESS == MPI_Allgatherv(&read_buf[(count[0] - loop_count) * dataset_dims[1]], recvcounts[mpi_rank], C_DATATYPE_MPI, &global_buf[(count[0] - loop_count) * total_recvcounts], recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); } } VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * the dataset has 3 dimensions and each process reads from * its own "page" in the 3rd dimension. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads its own "page" * of the dataset and contributes its piece to a global buffer * that is checked for consistency. * * Programmer: Jordan Henderson * 05/16/2018 */ static void test_read_3d_filtered_dataset_no_overlap_separate_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { MPI_Datatype vector_type; MPI_Datatype resized_vector_type; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t chunk_dims[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t sel_dims[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t start[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t stride[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t count[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t block[READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks on separate pages in 3D dataset"); dataset_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS; dataset_dims[2] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DEPTH; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (hsize_t)mpi_size) + (i / (hsize_t)mpi_size)); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; chunk_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; chunk_dims[2] = 1; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY( (H5Pset_chunk(plist_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS; sel_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS; sel_dims[2] = 1; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1] * sel_dims[2]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NROWS / (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; count[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_NCOLS / (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; count[2] = 1; stride[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; stride[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; stride[2] = 1; block[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NROWS; block[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SEP_PAGE_CH_NCOLS; block[2] = 1; start[0] = 0; start[1] = 0; start[2] = (hsize_t)mpi_rank; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* * Due to the nature of 3-dimensional reading, create an MPI vector type that allows each * rank to write to the nth position of the global data buffer, where n is the rank number. */ VRFY((MPI_SUCCESS == MPI_Type_vector((int)flat_dims[0], 1, mpi_size, C_DATATYPE_MPI, &vector_type)), "MPI_Type_vector succeeded"); VRFY((MPI_SUCCESS == MPI_Type_commit(&vector_type)), "MPI_Type_commit succeeded"); /* * Resize the type to allow interleaving, * so make it only one MPI_LONG wide */ VRFY((MPI_SUCCESS == MPI_Type_create_resized(vector_type, 0, sizeof(long), &resized_vector_type)), "MPI_Type_create_resized"); VRFY((MPI_SUCCESS == MPI_Type_commit(&resized_vector_type)), "MPI_Type_commit succeeded"); VRFY((MPI_SUCCESS == MPI_Allgather(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, 1, resized_vector_type, comm)), "MPI_Allgather succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); VRFY((MPI_SUCCESS == MPI_Type_free(&vector_type)), "MPI_Type_free succeeded"); VRFY((MPI_SUCCESS == MPI_Type_free(&resized_vector_type)), "MPI_Type_free succeeded"); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of transformed and filtered data in the * case where only one process is reading from a particular * chunk in the operation. Normally, a data transform function * will cause the parallel library to break to independent I/O * and this isn't allowed when there are filters in the pipeline. * However, in this case the parallel library recognizes that * the used data transform function "x" is the same as not * applying the transform function. Therefore it does not apply * the transform function resulting in not breaking to * independent I/O. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * the dataset and contributes its piece to a global buffer * that is checked for consistency. * * Programmer: Jan-Willem Blokland * 08/20/2021 */ static void test_read_transformed_filtered_dataset_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t start[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t stride[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t count[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t block[READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared transformed and filtered chunks"); dataset_dims[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NROWS * (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1])) + (i / (dataset_dims[0] / (hsize_t)mpi_size * dataset_dims[1]))); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY( (H5Pset_chunk(plist_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Create property list for collective dataset read */ plist_id = H5Pcreate(H5P_DATASET_XFER); VRFY((plist_id >= 0), "DXPL creation succeeded"); /* Set data transform expression */ VRFY((H5Pset_data_transform(plist_id, "x") >= 0), "Set data transform expression succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, plist_id, correct_buf) >= 0), "Dataset write succeeded"); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); /* Verify space allocation status */ plist_id = H5Dget_create_plist(dset_id); VRFY((plist_id >= 0), "H5Dget_create_plist succeeded"); verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and reads * it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_NCOLS / (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; stride[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; block[0] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS; block[1] = (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)READ_UNSHARED_TRANSFORMED_FILTERED_CHUNKS_CH_NROWS * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Create property list for data transform */ plist_id = H5Pcopy(dxpl_id); VRFY((plist_id >= 0), "DXPL copy succeeded"); /* Set data transform expression */ VRFY((H5Pset_data_transform(plist_id, "x") >= 0), "Set data transform expression succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, plist_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)flat_dims[0]; displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0]); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Pclose(plist_id) >= 0), "DXPL close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * the dataset has 3 dimensions and each process reads from * each "page" in the 3rd dimension. However, no chunk on a * given "page" is read from by more than one process. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * each "page" of the dataset and contributes its piece to a * global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/16/2018 */ static void test_read_3d_filtered_dataset_no_overlap_same_pages(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t chunk_dims[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t sel_dims[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t start[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t stride[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t count[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t block[READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks on the same pages in 3D dataset"); dataset_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NROWS; dataset_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS; dataset_dims[2] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DEPTH; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] * dataset_dims[1])) + (i / (dataset_dims[0] * dataset_dims[1]))); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; chunk_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; chunk_dims[2] = 1; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; sel_dims[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS; sel_dims[2] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_DEPTH; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1] * sel_dims[2]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_NCOLS / (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; count[2] = (hsize_t)mpi_size; stride[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; stride[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; stride[2] = 1; block[0] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS; block[1] = (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NCOLS; block[2] = 1; start[0] = ((hsize_t)mpi_rank * (hsize_t)READ_UNSHARED_FILTERED_CHUNKS_3D_SAME_PAGE_CH_NROWS * count[0]); start[1] = 0; start[2] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)flat_dims[0]; displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0]); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data in the case where * the dataset has 3 dimensions and each process reads from * each "page" in the 3rd dimension. Further, each chunk in * each "page" is read from equally by all processes. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads part of each * chunk of each "page" and contributes its pieces to a * global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/16/2018 */ static void test_read_3d_filtered_dataset_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { MPI_Datatype vector_type; MPI_Datatype resized_vector_type; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t chunk_dims[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t sel_dims[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t start[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t stride[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t count[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t block[READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing read from shared filtered chunks in 3D dataset"); dataset_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_NROWS; dataset_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_NCOLS; dataset_dims[2] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_DEPTH; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) /* Add the Column Index */ correct_buf[i] = (C_DATATYPE)((i % (hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_DEPTH * READ_SHARED_FILTERED_CHUNKS_3D_NCOLS)) /* Add the Row Index */ + ((i % (hsize_t)(mpi_size * READ_SHARED_FILTERED_CHUNKS_3D_DEPTH * READ_SHARED_FILTERED_CHUNKS_3D_NCOLS)) / (hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_DEPTH * READ_SHARED_FILTERED_CHUNKS_3D_NCOLS)) /* Add the amount that gets added when a rank moves down to its next section vertically in the dataset */ + ((hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_DEPTH * READ_SHARED_FILTERED_CHUNKS_3D_NCOLS) * (i / (hsize_t)(mpi_size * READ_SHARED_FILTERED_CHUNKS_3D_DEPTH * READ_SHARED_FILTERED_CHUNKS_3D_NCOLS)))); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_CH_NROWS; chunk_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; chunk_dims[2] = 1; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_SHARED_FILTERED_CHUNKS_3D_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_NROWS / mpi_size); sel_dims[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_NCOLS; sel_dims[2] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_DEPTH; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1] * sel_dims[2]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = (hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_NROWS / READ_SHARED_FILTERED_CHUNKS_3D_CH_NROWS); count[1] = (hsize_t)(READ_SHARED_FILTERED_CHUNKS_3D_NCOLS / READ_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS); count[2] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_DEPTH; stride[0] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_CH_NROWS; stride[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; stride[2] = 1; block[0] = 1; block[1] = (hsize_t)READ_SHARED_FILTERED_CHUNKS_3D_CH_NCOLS; block[2] = 1; start[0] = (hsize_t)mpi_rank; start[1] = 0; start[2] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); { size_t run_length = (size_t)(READ_SHARED_FILTERED_CHUNKS_3D_NCOLS * READ_SHARED_FILTERED_CHUNKS_3D_DEPTH); size_t num_blocks = (size_t)(READ_SHARED_FILTERED_CHUNKS_3D_NROWS / mpi_size); /* * Due to the nature of 3-dimensional reading, create an MPI vector type that allows each * rank to write to the nth position of the global data buffer, where n is the rank number. */ VRFY( (MPI_SUCCESS == MPI_Type_vector((int)num_blocks, (int)run_length, (int)(mpi_size * (int)run_length), C_DATATYPE_MPI, &vector_type)), "MPI_Type_vector succeeded"); VRFY((MPI_SUCCESS == MPI_Type_commit(&vector_type)), "MPI_Type_commit succeeded"); /* * Resize the type to allow interleaving, * so make it "run_length" MPI_LONGs wide */ VRFY((MPI_SUCCESS == MPI_Type_create_resized(vector_type, 0, (MPI_Aint)(run_length * sizeof(long)), &resized_vector_type)), "MPI_Type_create_resized"); VRFY((MPI_SUCCESS == MPI_Type_commit(&resized_vector_type)), "MPI_Type_commit succeeded"); } VRFY((MPI_SUCCESS == MPI_Allgather(read_buf, (int)flat_dims[0], C_DATATYPE_MPI, global_buf, 1, resized_vector_type, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); VRFY((MPI_SUCCESS == MPI_Type_free(&vector_type)), "MPI_Type_free succeeded"); VRFY((MPI_SUCCESS == MPI_Type_free(&resized_vector_type)), "MPI_Type_free succeeded"); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data to unshared * chunks using a compound datatype which doesn't * require a datatype conversion. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * the dataset and contributes its piece to a global * buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/17/2018 */ static void test_read_cmpd_filtered_dataset_no_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; COMPOUND_C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t chunk_dims[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t sel_dims[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t start[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t stride[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t count[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) { correct_buf[i].field1 = (short)((i % dataset_dims[1]) + (i / dataset_dims[1])); correct_buf[i].field2 = (int)((i % dataset_dims[1]) + (i / dataset_dims[1])); correct_buf[i].field3 = (long)((i % dataset_dims[1]) + (i / dataset_dims[1])); } /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; chunk_dims[1] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; sel_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_ENTRIES_PER_PROC; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_ENTRIES_PER_PROC; stride[0] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; stride[1] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; block[0] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NROWS; block[1] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS; start[0] = 0; start[1] = ((hsize_t)mpi_rank * READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_UNSHARED_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)(flat_dims[0] * sizeof(*read_buf)); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0] * sizeof(*read_buf)); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)(flat_dims[0] * sizeof(COMPOUND_C_DATATYPE)), MPI_BYTE, global_buf, recvcounts, displs, MPI_BYTE, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data from shared * chunks using a compound datatype which doesn't * require a datatype conversion. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * each chunk of the dataset and contributes its piece * to a global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/17/2018 */ static void test_read_cmpd_filtered_dataset_no_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; COMPOUND_C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t chunk_dims[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t sel_dims[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t start[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t stride[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t count[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from shared filtered chunks in Compound Datatype dataset without Datatype " "conversion"); /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) { correct_buf[i].field1 = (short)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); correct_buf[i].field2 = (int)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); correct_buf[i].field3 = (long)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); } /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS; chunk_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, memtype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_ENTRIES_PER_PROC; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_ENTRIES_PER_PROC; stride[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS; stride[1] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; block[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; block[1] = READ_COMPOUND_FILTERED_CHUNKS_NO_CONVERSION_SHARED_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)(flat_dims[0] * sizeof(*read_buf)); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0] * sizeof(*read_buf)); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)(flat_dims[0] * sizeof(COMPOUND_C_DATATYPE)), MPI_BYTE, global_buf, recvcounts, displs, MPI_BYTE, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data from unshared * chunks using a compound datatype which requires a * datatype conversion. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * the dataset and contributes its piece to a global * buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/17/2018 */ static void test_read_cmpd_filtered_dataset_type_conversion_unshared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; COMPOUND_C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t chunk_dims[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t sel_dims[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t start[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t stride[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t count[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing read from unshared filtered chunks in Compound Datatype dataset with Datatype " "conversion"); /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) { correct_buf[i].field1 = (short)((i % dataset_dims[1]) + (i / dataset_dims[1])); correct_buf[i].field2 = (int)((i % dataset_dims[1]) + (i / dataset_dims[1])); correct_buf[i].field3 = (long)((i % dataset_dims[1]) + (i / dataset_dims[1])); } /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); /* Create the compound type for file. */ filetype = H5Tcreate(H5T_COMPOUND, 32); VRFY((filetype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(filetype, "ShortData", 0, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "IntData", 8, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "LongData", 16, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; chunk_dims[1] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; sel_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_ENTRIES_PER_PROC; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_ENTRIES_PER_PROC; stride[0] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; stride[1] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; block[0] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NROWS; block[1] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS; start[0] = 0; start[1] = ((hsize_t)mpi_rank * READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_UNSHARED_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)(flat_dims[0] * sizeof(*read_buf)); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0] * sizeof(*read_buf)); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)(flat_dims[0] * sizeof(COMPOUND_C_DATATYPE)), MPI_BYTE, global_buf, recvcounts, displs, MPI_BYTE, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(filetype) >= 0), "File datatype close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests parallel read of filtered data from shared * chunks using a compound datatype which requires * a datatype conversion. * * The MAINPROCESS rank will first write out all of the * data to the dataset. Then, each rank reads a part of * each chunk of the dataset and contributes its pieces * to a global buffer that is checked for consistency. * * Programmer: Jordan Henderson * 05/17/2018 */ static void test_read_cmpd_filtered_dataset_type_conversion_shared(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { COMPOUND_C_DATATYPE *read_buf = NULL; COMPOUND_C_DATATYPE *correct_buf = NULL; COMPOUND_C_DATATYPE *global_buf = NULL; hsize_t dataset_dims[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t chunk_dims[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t sel_dims[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t start[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t stride[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t count[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t block[READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS]; hsize_t flat_dims[1]; size_t i, read_buf_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t filetype = H5I_INVALID_HID, memtype = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs( "Testing read from shared filtered chunks in Compound Datatype dataset with Datatype conversion"); /* SZIP and ScaleOffset filters don't support compound types */ if (filter_id == H5Z_FILTER_SZIP || filter_id == H5Z_FILTER_SCALEOFFSET) { if (MAINPROCESS) SKIPPED(); return; } dataset_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NROWS; dataset_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_NCOLS; /* Setup the buffer for writing and for comparison */ correct_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*correct_buf); correct_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) { correct_buf[i].field1 = (short)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); correct_buf[i].field2 = (int)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); correct_buf[i].field3 = (long)((dataset_dims[1] * (i / ((hsize_t)mpi_size * dataset_dims[1]))) + (i % dataset_dims[1]) + (((i % ((hsize_t)mpi_size * dataset_dims[1])) / dataset_dims[1]) % dataset_dims[1])); } /* Create the compound type for memory. */ memtype = H5Tcreate(H5T_COMPOUND, sizeof(COMPOUND_C_DATATYPE)); VRFY((memtype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(memtype, "ShortData", HOFFSET(COMPOUND_C_DATATYPE, field1), H5T_NATIVE_SHORT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "IntData", HOFFSET(COMPOUND_C_DATATYPE, field2), H5T_NATIVE_INT) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(memtype, "LongData", HOFFSET(COMPOUND_C_DATATYPE, field3), H5T_NATIVE_LONG) >= 0), "Datatype insertion succeeded"); /* Create the compound type for file. */ filetype = H5Tcreate(H5T_COMPOUND, 32); VRFY((filetype >= 0), "Datatype creation succeeded"); VRFY((H5Tinsert(filetype, "ShortData", 0, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "IntData", 8, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); VRFY((H5Tinsert(filetype, "LongData", 16, H5T_STD_I64BE) >= 0), "Datatype insertion succeeded"); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ filespace = H5Screate_simple(READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ chunk_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS; chunk_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, filetype, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dwrite(dset_id, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, correct_buf) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } file_id = H5Fopen(filenames[0], H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); sel_dims[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; sel_dims[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_ENTRIES_PER_PROC; /* Setup one-dimensional memory dataspace for reading the dataset data into a contiguous buffer */ flat_dims[0] = sel_dims[0] * sel_dims[1]; memspace = H5Screate_simple(1, flat_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); /* * Each process defines the dataset selection in the file and * reads it to the selection in memory */ count[0] = 1; count[1] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_ENTRIES_PER_PROC; stride[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS; stride[1] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; block[0] = (hsize_t)READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NROWS / (hsize_t)mpi_size; block[1] = READ_COMPOUND_FILTERED_CHUNKS_TYPE_CONVERSION_SHARED_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is reading with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); read_buf_size = flat_dims[0] * sizeof(*read_buf); read_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); VRFY((H5Dread(dset_id, memtype, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); global_buf = (COMPOUND_C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != global_buf), "HDcalloc succeeded"); /* Collect each piece of data from all ranks into a global buffer on all ranks */ recvcounts = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) recvcounts[i] = (int)(flat_dims[0] * sizeof(*read_buf)); displs = (int *)HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) displs[i] = (int)(i * flat_dims[0] * sizeof(*read_buf)); VRFY((MPI_SUCCESS == MPI_Allgatherv(read_buf, (int)(flat_dims[0] * sizeof(COMPOUND_C_DATATYPE)), MPI_BYTE, global_buf, recvcounts, displs, MPI_BYTE, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(global_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (global_buf) HDfree(global_buf); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Tclose(memtype) >= 0), "Memory datatype close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests write of filtered data to a dataset * by a single process. After the write has * succeeded, the dataset is closed and then * re-opened in parallel and read by all * processes to ensure data correctness. * * Programmer: Jordan Henderson * 08/03/2017 */ static void test_write_serial_read_parallel(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write file serially; read file in parallel"); dataset_dims[0] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_NROWS; dataset_dims[1] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_NCOLS; dataset_dims[2] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_DEPTH; /* Write the file on the MAINPROCESS rank */ if (MAINPROCESS) { /* Set up file access property list */ plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ chunk_dims[0] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SERIAL_READ_PARALLEL_CH_NCOLS; chunk_dims[2] = 1; filespace = H5Screate_simple(WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SERIAL_READ_PARALLEL_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SERIAL_READ_PARALLEL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); data_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); } correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (long)i; /* All ranks open the file and verify their "portion" of the dataset is correct */ file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, WRITE_SERIAL_READ_PARALLEL_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); if (correct_buf) HDfree(correct_buf); if (read_buf) HDfree(read_buf); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES /* * Tests parallel write of filtered data * to a dataset. After the write has * succeeded, the dataset is closed and * then re-opened and read by a single * process to ensure data correctness. * * Programmer: Jordan Henderson * 08/03/2017 */ static void test_write_parallel_read_serial(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; hsize_t dataset_dims[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t chunk_dims[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t sel_dims[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t count[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t stride[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t block[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; hsize_t offset[WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS]; size_t i, data_size, correct_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write file in parallel; read serially"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_NROWS; dataset_dims[1] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_NCOLS; dataset_dims[2] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_DEPTH; chunk_dims[0] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NCOLS; chunk_dims[2] = 1; sel_dims[0] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_NCOLS; sel_dims[2] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_DEPTH; filespace = H5Screate_simple(WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_PARALLEL_READ_SERIAL_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_PARALLEL_READ_SERIAL_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_NCOLS / (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NCOLS; count[2] = (hsize_t)mpi_size; stride[0] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NROWS; stride[1] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NCOLS; stride[2] = 1; block[0] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NROWS; block[1] = (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NCOLS; block[2] = 1; offset[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_PARALLEL_READ_SERIAL_CH_NROWS * count[0]); offset[1] = 0; offset[2] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], offset[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], count[2], stride[0], stride[1], stride[2], offset[0], offset[1], offset[2], block[0], block[1], block[2]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sel_dims[2] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (data) HDfree(data); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); if (MAINPROCESS) { plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_libver_bounds(plist_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, plist_id); VRFY((file_id >= 0), "Test file open succeeded"); VRFY((H5Pclose(plist_id) >= 0), "FAPL close succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); dset_id = H5Dopen2(group_id, WRITE_PARALLEL_READ_SERIAL_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); correct_buf_size = dataset_dims[0] * dataset_dims[1] * dataset_dims[2] * sizeof(*correct_buf); correct_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); read_buf = (C_DATATYPE *)HDcalloc(1, correct_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < correct_buf_size / sizeof(*correct_buf); i++) correct_buf[i] = (C_DATATYPE)((i % (dataset_dims[0] * dataset_dims[1])) + (i / (dataset_dims[0] * dataset_dims[1]))); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, H5P_DEFAULT, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, correct_buf_size)), "Data verification succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); HDfree(correct_buf); HDfree(read_buf); } return; } /* * Tests that causing chunks to continually grow and shrink * by writing random data followed by zeroed-out data (and * thus controlling the compression ratio) does not cause * problems. * * Programmer: Jordan Henderson * 06/04/2018 */ static void test_shrinking_growing_chunks(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { double *data = NULL; double *read_buf = NULL; hsize_t dataset_dims[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t start[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t stride[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t count[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; hsize_t block[SHRINKING_GROWING_CHUNKS_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID, memspace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing continually shrinking/growing chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)SHRINKING_GROWING_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)SHRINKING_GROWING_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)SHRINKING_GROWING_CHUNKS_NCOLS; filespace = H5Screate_simple(SHRINKING_GROWING_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); memspace = H5Screate_simple(SHRINKING_GROWING_CHUNKS_DATASET_DIMS, sel_dims, NULL); VRFY((memspace >= 0), "Memory dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, SHRINKING_GROWING_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, SHRINKING_GROWING_CHUNKS_DATASET_NAME, H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* * Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = (hsize_t)SHRINKING_GROWING_CHUNKS_NCOLS / (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NCOLS; stride[0] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NROWS; stride[1] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NCOLS; block[0] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NROWS; block[1] = (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)SHRINKING_GROWING_CHUNKS_CH_NROWS * count[0]); start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((dset_id >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); data_size = sel_dims[0] * sel_dims[1] * sizeof(double); data = (double *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); read_buf = (double *)HDcalloc(1, data_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < SHRINKING_GROWING_CHUNKS_NLOOPS; i++) { /* Continually write random float data, followed by zeroed-out data */ if (i % 2) HDmemset(data, 0, data_size); else { size_t j; for (j = 0; j < data_size / sizeof(*data); j++) { data[j] = (rand() / (double)(RAND_MAX / (double)1.0L)); } } VRFY((H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); if (i % 2) { HDmemset(read_buf, 255, data_size); } else { HDmemset(read_buf, 0, data_size); } VRFY((H5Dread(dset_id, H5T_NATIVE_DOUBLE, memspace, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, data, data_size)), "data verification succeeded"); } if (read_buf) HDfree(read_buf); if (data) HDfree(data); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Sclose(memspace) >= 0), "Memory dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests that filtered and unfiltered partial edge chunks can be * written to and read from correctly in parallel when only one MPI * rank writes to a particular partial edge chunk in the dataset. * * The dataset contains partial edge chunks in the second dimension. * Each MPI rank selects a hyperslab in the shape of a single chunk * that is offset to cover the whole edge chunk and part of the * full chunk next to the edge chunk. */ static void test_edge_chunks_no_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t start[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t stride[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t count[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to unshared filtered edge chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; sel_dims[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; filespace = H5Screate_simple(WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); start[1] = (hsize_t)(WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); read_buf = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, (mpi_size > 1) ? SOME_CHUNKS_WRITTEN : ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Repeat the previous, but set option to not filter partial edge chunks */ if (MAINPROCESS) HDputs("Testing write to unshared unfiltered edge chunks"); H5Pset_chunk_opts(plist_id, H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS); dset_id = H5Dcreate2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; block[0] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; block[1] = (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; start[0] = ((hsize_t)mpi_rank * (hsize_t)WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); start[1] = (hsize_t)(WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, (mpi_size > 1) ? SOME_CHUNKS_WRITTEN : ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ dset_id = H5Dopen2(group_id, WRITE_UNSHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); HDmemset(read_buf, 255, data_size); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests that filtered and unfiltered partial edge chunks can be * written to and read from correctly in parallel when every MPI * rank writes to every partial edge chunk in the dataset. * * The dataset contains partial edge chunks in the second dimension. * Each MPI rank selects a hyperslab in the shape of one row of each * chunk that is offset in the second dimension to cover the whole * edge chunk and part of the full chunk next to the edge chunk. */ static void test_edge_chunks_overlap(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t chunk_dims[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t sel_dims[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t start[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t stride[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t count[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; hsize_t block[WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS]; size_t i, data_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing write to shared filtered edge chunks"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS; dataset_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS; chunk_dims[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; chunk_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; filespace = H5Screate_simple(WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS / WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); count[1] = 1; stride[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; block[0] = (hsize_t)1; block[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); read_buf = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Repeat the previous, but set option to not filter partial edge chunks */ if (MAINPROCESS) HDputs("Testing write to shared unfiltered edge chunks"); H5Pset_chunk_opts(plist_id, H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS); dset_id = H5Dcreate2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NROWS / WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS); count[1] = 1; stride[0] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NROWS; stride[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; block[0] = (hsize_t)1; block[1] = (hsize_t)WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS; start[0] = (hsize_t)mpi_rank; start[1] = (hsize_t)(WRITE_SHARED_FILTERED_EDGE_CHUNKS_NCOLS - WRITE_SHARED_FILTERED_EDGE_CHUNKS_CH_NCOLS); if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify the correct data was written */ dset_id = H5Dopen2(group_id, WRITE_SHARED_FILTERED_EDGE_CHUNKS_DATASET_NAME2, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); HDmemset(read_buf, 255, data_size); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); VRFY((0 == HDmemcmp(read_buf, data, data_size)), "Data verification succeeded"); if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests that filtered and unfiltered partial edge chunks can be * written to and read from correctly in parallel when only one * MPI rank writes to a particular edge chunk in the dataset and * only performs a partial write to the edge chunk. * * The dataset contains partial edge chunks in the second dimension. * Each MPI rank selects a hyperslab in the shape of part of a single * edge chunk and writes to just a portion of the edge chunk. */ static void test_edge_chunks_partial_write(const char H5_ATTR_PARALLEL_UNUSED *parent_group, H5Z_filter_t H5_ATTR_PARALLEL_UNUSED filter_id, hid_t H5_ATTR_PARALLEL_UNUSED fapl_id, hid_t H5_ATTR_PARALLEL_UNUSED dcpl_id, hid_t H5_ATTR_PARALLEL_UNUSED dxpl_id) { /* TODO */ } /* * Tests that the parallel compression feature correctly handles * writing fill values to a dataset and reading fill values from * unallocated parts of a dataset. */ static void test_fill_values(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *correct_buf = NULL; C_DATATYPE fill_value; hsize_t dataset_dims[FILL_VALUES_TEST_DATASET_DIMS]; hsize_t chunk_dims[FILL_VALUES_TEST_DATASET_DIMS]; hsize_t sel_dims[FILL_VALUES_TEST_DATASET_DIMS]; hsize_t start[FILL_VALUES_TEST_DATASET_DIMS]; hsize_t stride[FILL_VALUES_TEST_DATASET_DIMS]; hsize_t count[FILL_VALUES_TEST_DATASET_DIMS]; hsize_t block[FILL_VALUES_TEST_DATASET_DIMS]; size_t i, data_size, read_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing fill values"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)FILL_VALUES_TEST_NROWS; dataset_dims[1] = (hsize_t)FILL_VALUES_TEST_NCOLS; chunk_dims[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; chunk_dims[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; filespace = H5Screate_simple(FILL_VALUES_TEST_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, FILL_VALUES_TEST_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Set a fill value */ fill_value = FILL_VALUES_TEST_FILL_VAL; VRFY((H5Pset_fill_value(plist_id, HDF5_DATATYPE_NAME, &fill_value) >= 0), "Fill Value set"); dset_id = H5Dcreate2(group_id, FILL_VALUES_TEST_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Allocate buffer for reading entire dataset */ read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); read_buf = HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); correct_buf = HDcalloc(1, read_buf_size); VRFY((NULL != correct_buf), "HDcalloc succeeded"); /* Read entire dataset and verify that the fill value is returned */ VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) correct_buf[i] = FILL_VALUES_TEST_FILL_VAL; VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); /* * Write to part of the first chunk in the dataset with * all ranks, then read the whole dataset and ensure that * the fill value is returned for the unwritten part of * the chunk, as well as for the rest of the dataset that * hasn't been written to yet. */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)(FILL_VALUES_TEST_CH_NCOLS - 1); start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* * Each MPI rank communicates their written piece of data * into each other rank's correctness-checking buffer */ recvcounts = HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); displs = HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) { recvcounts[i] = (int)(count[1] * block[1]); displs[i] = (int)(i * dataset_dims[1]); } VRFY((MPI_SUCCESS == MPI_Allgatherv(data, recvcounts[mpi_rank], C_DATATYPE_MPI, correct_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); /* * Write to whole dataset and ensure fill value isn't returned * after reading whole dataset back */ /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)FILL_VALUES_TEST_NROWS / (hsize_t)FILL_VALUES_TEST_CH_NROWS; count[1] = (hsize_t)FILL_VALUES_TEST_NCOLS / (hsize_t)FILL_VALUES_TEST_CH_NCOLS; stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; block[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) VRFY((read_buf[i] != FILL_VALUES_TEST_FILL_VAL), "Data verification succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /******************************************************************** * Set the fill time to H5D_FILL_TIME_ALLOC and repeat the previous * ********************************************************************/ VRFY((H5Pset_fill_time(plist_id, H5D_FILL_TIME_ALLOC) >= 0), "H5Pset_fill_time succeeded"); dset_id = H5Dcreate2(group_id, FILL_VALUES_TEST_DATASET_NAME2, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Read entire dataset and verify that the fill value is returned */ VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) correct_buf[i] = FILL_VALUES_TEST_FILL_VAL; VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); /* * Write to part of the first chunk in the dataset with * all ranks, then read the whole dataset and ensure that * the fill value is returned for the unwritten part of * the chunk, as well as for the rest of the dataset that * hasn't been written to yet. */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)(FILL_VALUES_TEST_CH_NCOLS - 1); start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME2, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < (size_t)mpi_size; i++) { recvcounts[i] = (int)(count[1] * block[1]); displs[i] = (int)(i * dataset_dims[1]); } /* * Each MPI rank communicates their written piece of data * into each other rank's correctness-checking buffer */ VRFY((MPI_SUCCESS == MPI_Allgatherv(data, recvcounts[mpi_rank], C_DATATYPE_MPI, correct_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); VRFY((0 == HDmemcmp(read_buf, correct_buf, read_buf_size)), "Data verification succeeded"); /* * Write to whole dataset and ensure fill value isn't returned * after reading whole dataset back */ /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)FILL_VALUES_TEST_NROWS / (hsize_t)FILL_VALUES_TEST_CH_NROWS; count[1] = (hsize_t)FILL_VALUES_TEST_NCOLS / (hsize_t)FILL_VALUES_TEST_CH_NCOLS; stride[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; block[0] = (hsize_t)FILL_VALUES_TEST_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)FILL_VALUES_TEST_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_VALUES_TEST_DATASET_NAME2, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) VRFY((read_buf[i] != FILL_VALUES_TEST_FILL_VAL), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (data) HDfree(data); if (read_buf) HDfree(read_buf); if (correct_buf) HDfree(correct_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests that the parallel compression feature can handle * an undefined fill value. Nothing is verified in this * test since the fill value isn't defined. */ static void test_fill_value_undefined(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { H5D_alloc_time_t alloc_time; C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; hsize_t dataset_dims[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; hsize_t chunk_dims[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; hsize_t sel_dims[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; hsize_t start[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; hsize_t stride[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; hsize_t count[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; hsize_t block[FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS]; size_t i, data_size, read_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; if (MAINPROCESS) HDputs("Testing undefined fill value"); VRFY((H5Pget_alloc_time(dcpl_id, &alloc_time) >= 0), "H5Pget_alloc_time succeeded"); file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NROWS; dataset_dims[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NCOLS; chunk_dims[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; chunk_dims[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; filespace = H5Screate_simple(FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, FILL_VALUE_UNDEFINED_TEST_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Set an undefined fill value */ VRFY((H5Pset_fill_value(plist_id, HDF5_DATATYPE_NAME, NULL) >= 0), "Fill Value set"); dset_id = H5Dcreate2(group_id, FILL_VALUE_UNDEFINED_TEST_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Allocate buffer for reading entire dataset */ read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); read_buf = HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); /* * Read entire dataset - nothing to verify since there's no fill value. * If not using early space allocation, the read should fail since storage * isn't allocated yet and no fill value is defined. */ if (alloc_time == H5D_ALLOC_TIME_EARLY) { VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); } else { H5E_BEGIN_TRY { VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) < 0), "Dataset read succeeded"); } H5E_END_TRY; } /* * Write to part of the first chunk in the dataset with * all ranks, then read the whole dataset. Don't verify * anything since there's no fill value defined. */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)(FILL_VALUE_UNDEFINED_TEST_CH_NCOLS - 1); start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); dset_id = H5Dopen2(group_id, FILL_VALUE_UNDEFINED_TEST_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* * Write to whole dataset and ensure data is correct * after reading whole dataset back */ /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NROWS / (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; count[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_NCOLS / (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; stride[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; block[0] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)FILL_VALUE_UNDEFINED_TEST_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_VALUE_UNDEFINED_TEST_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); if (data) HDfree(data); if (read_buf) HDfree(read_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } /* * Tests that the parallel compression feature correctly handles * avoiding writing fill values to a dataset when the fill time * is set as H5D_FILL_TIME_NEVER. */ static void test_fill_time_never(const char *parent_group, H5Z_filter_t filter_id, hid_t fapl_id, hid_t dcpl_id, hid_t dxpl_id) { C_DATATYPE *data = NULL; C_DATATYPE *read_buf = NULL; C_DATATYPE *fill_buf = NULL; C_DATATYPE fill_value; hsize_t dataset_dims[FILL_TIME_NEVER_TEST_DATASET_DIMS]; hsize_t chunk_dims[FILL_TIME_NEVER_TEST_DATASET_DIMS]; hsize_t sel_dims[FILL_TIME_NEVER_TEST_DATASET_DIMS]; hsize_t start[FILL_TIME_NEVER_TEST_DATASET_DIMS]; hsize_t stride[FILL_TIME_NEVER_TEST_DATASET_DIMS]; hsize_t count[FILL_TIME_NEVER_TEST_DATASET_DIMS]; hsize_t block[FILL_TIME_NEVER_TEST_DATASET_DIMS]; size_t i, data_size, read_buf_size; hid_t file_id = H5I_INVALID_HID, dset_id = H5I_INVALID_HID, plist_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t filespace = H5I_INVALID_HID; int *recvcounts = NULL; int *displs = NULL; if (MAINPROCESS) HDputs("Testing fill time H5D_FILL_TIME_NEVER"); /* * Only run this test when incremental file space allocation is * used, as HDF5's chunk allocation code always writes fill values * when filters are in the pipeline, but parallel compression does * incremental file space allocation differently. */ { H5D_alloc_time_t alloc_time; VRFY((H5Pget_alloc_time(dcpl_id, &alloc_time) >= 0), "H5Pget_alloc_time succeeded"); if (alloc_time != H5D_ALLOC_TIME_INCR) { if (MAINPROCESS) SKIPPED(); return; } } file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "Test file open succeeded"); group_id = H5Gopen2(file_id, parent_group, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gopen2 succeeded"); /* Create the dataspace for the dataset */ dataset_dims[0] = (hsize_t)FILL_TIME_NEVER_TEST_NROWS; dataset_dims[1] = (hsize_t)FILL_TIME_NEVER_TEST_NCOLS; chunk_dims[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; chunk_dims[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; sel_dims[0] = (hsize_t)DIM0_SCALE_FACTOR; sel_dims[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS * (hsize_t)DIM1_SCALE_FACTOR; filespace = H5Screate_simple(FILL_TIME_NEVER_TEST_DATASET_DIMS, dataset_dims, NULL); VRFY((filespace >= 0), "File dataspace creation succeeded"); /* Create chunked dataset */ plist_id = H5Pcopy(dcpl_id); VRFY((plist_id >= 0), "DCPL copy succeeded"); VRFY((H5Pset_chunk(plist_id, FILL_TIME_NEVER_TEST_DATASET_DIMS, chunk_dims) >= 0), "Chunk size set"); /* Add test filter to the pipeline */ VRFY((set_dcpl_filter(plist_id, filter_id, NULL) >= 0), "Filter set"); /* Set a fill value */ fill_value = FILL_VALUES_TEST_FILL_VAL; VRFY((H5Pset_fill_value(plist_id, HDF5_DATATYPE_NAME, &fill_value) >= 0), "Fill Value set"); /* Set fill time of 'never' */ VRFY((H5Pset_fill_time(plist_id, H5D_FILL_TIME_NEVER) >= 0), "H5Pset_fill_time succeeded"); dset_id = H5Dcreate2(group_id, FILL_TIME_NEVER_TEST_DATASET_NAME, HDF5_DATATYPE_NAME, filespace, H5P_DEFAULT, plist_id, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset creation succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, DATASET_JUST_CREATED); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); /* Allocate buffer for reading entire dataset */ read_buf_size = dataset_dims[0] * dataset_dims[1] * sizeof(*read_buf); read_buf = HDcalloc(1, read_buf_size); VRFY((NULL != read_buf), "HDcalloc succeeded"); fill_buf = HDcalloc(1, read_buf_size); VRFY((NULL != fill_buf), "HDcalloc succeeded"); /* Read entire dataset and verify that the fill value isn't returned */ VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) fill_buf[i] = FILL_TIME_NEVER_TEST_FILL_VAL; /* * It should be very unlikely for the dataset's random * values to all be the fill value, so this should be * a safe comparison in theory. */ VRFY((0 != HDmemcmp(read_buf, fill_buf, read_buf_size)), "Data verification succeeded"); /* * Write to part of the first chunk in the dataset with * all ranks, then read the whole dataset and ensure that * the fill value isn't returned for the unwritten part of * the chunk, as well as for the rest of the dataset that * hasn't been written to yet. */ count[0] = 1; count[1] = 1; stride[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; block[0] = 1; block[1] = (hsize_t)(FILL_TIME_NEVER_TEST_CH_NCOLS - 1); start[0] = (hsize_t)mpi_rank; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } /* Select hyperslab in the file */ filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "File dataspace retrieval succeeded"); VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); /* Fill data buffer */ data_size = sel_dims[0] * sel_dims[1] * sizeof(*data); data = (C_DATATYPE *)HDcalloc(1, data_size); VRFY((NULL != data), "HDcalloc succeeded"); for (i = 0; i < data_size / sizeof(*data); i++) data[i] = (C_DATATYPE)GEN_DATA(i); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, SOME_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_TIME_NEVER_TEST_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); /* * Each MPI rank communicates their written piece of data * into each other rank's correctness-checking buffer */ recvcounts = HDcalloc(1, (size_t)mpi_size * sizeof(*recvcounts)); VRFY((NULL != recvcounts), "HDcalloc succeeded"); displs = HDcalloc(1, (size_t)mpi_size * sizeof(*displs)); VRFY((NULL != displs), "HDcalloc succeeded"); for (i = 0; i < (size_t)mpi_size; i++) { recvcounts[i] = (int)(count[1] * block[1]); displs[i] = (int)(i * dataset_dims[1]); } VRFY((MPI_SUCCESS == MPI_Allgatherv(data, recvcounts[mpi_rank], C_DATATYPE_MPI, fill_buf, recvcounts, displs, C_DATATYPE_MPI, comm)), "MPI_Allgatherv succeeded"); /* * It should be very unlikely for the dataset's random * values to all be the fill value, so this should be * a safe comparison in theory. */ VRFY((0 != HDmemcmp(read_buf, fill_buf, read_buf_size)), "Data verification succeeded"); /* * Write to whole dataset and ensure fill value isn't returned * after reading whole dataset back */ /* Each process defines the dataset selection in memory and writes * it to the hyperslab in the file */ count[0] = (hsize_t)FILL_TIME_NEVER_TEST_NROWS / (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; count[1] = (hsize_t)FILL_TIME_NEVER_TEST_NCOLS / (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; stride[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS; stride[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; block[0] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NROWS / (hsize_t)mpi_size; block[1] = (hsize_t)FILL_TIME_NEVER_TEST_CH_NCOLS; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) { HDprintf("Process %d is writing with count[ %" PRIuHSIZE ", %" PRIuHSIZE " ], stride[ %" PRIuHSIZE ", %" PRIuHSIZE " ], start[ %" PRIuHSIZE ", %" PRIuHSIZE " ], block size[ %" PRIuHSIZE ", %" PRIuHSIZE " ]\n", mpi_rank, count[0], count[1], stride[0], stride[1], start[0], start[1], block[0], block[1]); HDfflush(stdout); } VRFY((H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride, count, block) >= 0), "Hyperslab selection succeeded"); VRFY((H5Dwrite(dset_id, HDF5_DATATYPE_NAME, H5S_BLOCK, filespace, dxpl_id, data) >= 0), "Dataset write succeeded"); /* Verify space allocation status */ verify_space_alloc_status(dset_id, plist_id, ALL_CHUNKS_WRITTEN); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); /* Verify correct data was written */ dset_id = H5Dopen2(group_id, FILL_TIME_NEVER_TEST_DATASET_NAME, H5P_DEFAULT); VRFY((dset_id >= 0), "Dataset open succeeded"); VRFY((H5Dread(dset_id, HDF5_DATATYPE_NAME, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "Dataset read succeeded"); for (i = 0; i < read_buf_size / sizeof(*read_buf); i++) VRFY((read_buf[i] != FILL_TIME_NEVER_TEST_FILL_VAL), "Data verification succeeded"); if (displs) HDfree(displs); if (recvcounts) HDfree(recvcounts); if (data) HDfree(data); if (read_buf) HDfree(read_buf); if (fill_buf) HDfree(fill_buf); VRFY((H5Pclose(plist_id) >= 0), "DCPL close succeeded"); VRFY((H5Dclose(dset_id) >= 0), "Dataset close succeeded"); VRFY((H5Sclose(filespace) >= 0), "File dataspace close succeeded"); VRFY((H5Gclose(group_id) >= 0), "Group close succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); return; } #endif int main(int argc, char **argv) { size_t cur_filter_idx = 0; size_t num_filters = 0; hid_t file_id = H5I_INVALID_HID; hid_t fcpl_id = H5I_INVALID_HID; hid_t group_id = H5I_INVALID_HID; hid_t fapl_id = H5I_INVALID_HID; hid_t dxpl_id = H5I_INVALID_HID; hid_t dcpl_id = H5I_INVALID_HID; int mpi_code; /* Initialize MPI */ MPI_Init(&argc, &argv); MPI_Comm_size(comm, &mpi_size); MPI_Comm_rank(comm, &mpi_rank); if (mpi_size <= 0) { if (MAINPROCESS) { HDprintf("The Parallel Filters tests require at least 1 rank.\n"); HDprintf("Quitting...\n"); } MPI_Abort(MPI_COMM_WORLD, 1); } if (H5dont_atexit() < 0) { if (MAINPROCESS) { HDprintf("Failed to turn off atexit processing. Continue.\n"); } } H5open(); if (MAINPROCESS) { HDprintf("==========================\n"); HDprintf(" Parallel Filters tests\n"); HDprintf("==========================\n\n"); } if (VERBOSE_MED) h5_show_hostname(); TestAlarmOn(); num_filters = ARRAY_SIZE(filterIDs); /* Set up file access property list with parallel I/O access, * collective metadata reads/writes and the latest library * version bounds */ fapl_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((fapl_id >= 0), "FAPL creation succeeded"); VRFY((H5Pset_fapl_mpio(fapl_id, comm, info) >= 0), "Set FAPL MPIO succeeded"); VRFY((H5Pset_all_coll_metadata_ops(fapl_id, TRUE) >= 0), "H5Pset_all_coll_metadata_ops succeeded"); VRFY((H5Pset_coll_metadata_write(fapl_id, TRUE) >= 0), "H5Pset_coll_metadata_write succeeded"); VRFY((H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) >= 0), "Set libver bounds succeeded"); /* * Set up Paged and Persistent Free Space Management */ fcpl_id = H5Pcreate(H5P_FILE_CREATE); VRFY((fcpl_id >= 0), "FCPL creation succeeded"); VRFY((H5Pset_file_space_strategy(fcpl_id, H5F_FSPACE_STRATEGY_PAGE, TRUE, 1) >= 0), "H5Pset_file_space_strategy succeeded"); VRFY((h5_fixname(FILENAME[0], fapl_id, filenames[0], sizeof(filenames[0])) != NULL), "Test file name created"); file_id = H5Fcreate(filenames[0], H5F_ACC_TRUNC, fcpl_id, fapl_id); VRFY((file_id >= 0), "Test file creation succeeded"); VRFY((H5Fclose(file_id) >= 0), "File close succeeded"); file_id = H5I_INVALID_HID; /* Create property list for collective dataset write */ dxpl_id = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl_id >= 0), "DXPL creation succeeded"); VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded"); /* Create DCPL for dataset creation */ dcpl_id = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl_id >= 0), "DCPL creation succeeded"); /* Run tests with all available filters */ for (cur_filter_idx = 0; cur_filter_idx < num_filters; cur_filter_idx++) { H5FD_mpio_chunk_opt_t chunk_opt; H5Z_filter_t cur_filter = filterIDs[cur_filter_idx]; /* Run tests with both linked-chunk and multi-chunk I/O */ for (chunk_opt = H5FD_MPIO_CHUNK_ONE_IO; chunk_opt <= H5FD_MPIO_CHUNK_MULTI_IO; chunk_opt++) { H5D_alloc_time_t space_alloc_time; /* Run tests with all available space allocation times */ for (space_alloc_time = H5D_ALLOC_TIME_EARLY; space_alloc_time <= H5D_ALLOC_TIME_INCR; space_alloc_time++) { const char *alloc_time; unsigned filter_config; htri_t filter_avail; size_t i; char group_name[512]; switch (space_alloc_time) { case H5D_ALLOC_TIME_EARLY: alloc_time = "Early"; break; case H5D_ALLOC_TIME_LATE: alloc_time = "Late"; break; case H5D_ALLOC_TIME_INCR: alloc_time = "Incremental"; break; default: alloc_time = "Unknown"; } if (MAINPROCESS) HDprintf("== Running tests with filter '%s' using '%s' and '%s' allocation time ==\n\n", filterNames[cur_filter_idx], H5FD_MPIO_CHUNK_ONE_IO == chunk_opt ? "Linked-Chunk I/O" : "Multi-Chunk I/O", alloc_time); /* Make sure current filter is available before testing with it */ filter_avail = H5Zfilter_avail(cur_filter); VRFY((filter_avail >= 0), "H5Zfilter_avail succeeded"); if (!filter_avail) { if (MAINPROCESS) HDprintf(" ** SKIPPED tests with filter '%s' - filter unavailable **\n\n", filterNames[cur_filter_idx]); continue; } /* Get the current filter's info */ VRFY((H5Zget_filter_info(cur_filter, &filter_config) >= 0), "H5Zget_filter_info succeeded"); /* Determine if filter is encode-enabled */ if (0 == (filter_config & H5Z_FILTER_CONFIG_ENCODE_ENABLED)) { if (MAINPROCESS) HDprintf(" ** SKIPPED tests with filter '%s' - filter not encode-enabled **\n\n", filterNames[cur_filter_idx]); continue; } /* Set space allocation time */ VRFY((H5Pset_alloc_time(dcpl_id, space_alloc_time) >= 0), "H5Pset_alloc_time succeeded"); /* Set chunk I/O optimization method */ VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, chunk_opt) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded"); /* Create a group to hold all the datasets for this combination * of filter and chunk optimization mode. Then, close the file * again since some tests may need to open the file in a special * way, like on rank 0 only */ file_id = H5Fopen(filenames[0], H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "H5Fopen succeeded"); HDsnprintf(group_name, sizeof(group_name), "%s_%s_%s", filterNames[cur_filter_idx], H5FD_MPIO_CHUNK_ONE_IO == chunk_opt ? "linked-chunk-io" : "multi-chunk-io", alloc_time); group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((group_id >= 0), "H5Gcreate2 succeeded"); VRFY((H5Gclose(group_id) >= 0), "H5Gclose failed"); group_id = H5I_INVALID_HID; VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); file_id = H5I_INVALID_HID; for (i = 0; i < ARRAY_SIZE(tests); i++) { test_func func = tests[i]; if (MPI_SUCCESS == (mpi_code = MPI_Barrier(comm))) { func(group_name, cur_filter, fapl_id, dcpl_id, dxpl_id); } else { if (MAINPROCESS) MESG("MPI_Barrier failed"); nerrors++; } } if (MAINPROCESS) HDputs(""); } } } VRFY((H5Pclose(dcpl_id) >= 0), "DCPL close succeeded"); dcpl_id = H5I_INVALID_HID; VRFY((H5Pclose(dxpl_id) >= 0), "DXPL close succeeded"); dxpl_id = H5I_INVALID_HID; if (nerrors) goto exit; if (MAINPROCESS) HDputs("All Parallel Filters tests passed\n"); exit: if (nerrors) if (MAINPROCESS) HDprintf("*** %d TEST ERROR%s OCCURRED ***\n", nerrors, nerrors > 1 ? "S" : ""); TestAlarmOff(); h5_clean_files(FILENAME, fapl_id); fapl_id = H5I_INVALID_HID; if (dcpl_id >= 0) VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded"); if (dxpl_id >= 0) VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded"); if (fapl_id >= 0) VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded"); if (fcpl_id >= 0) VRFY((H5Pclose(fcpl_id) >= 0), "H5Pclose succeeded"); if (group_id >= 0) VRFY((H5Gclose(group_id) >= 0), "H5Gclose succeeded"); if (file_id >= 0) VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); H5close(); MPI_Finalize(); exit((nerrors ? EXIT_FAILURE : EXIT_SUCCESS)); }