/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * 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. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Parallel tests for datasets */ /* * Example of using the parallel HDF5 library to access datasets. * * This program contains three major parts. Part 1 tests fixed dimension * datasets, for both independent and collective transfer modes. * Part 2 tests extendible datasets, for independent transfer mode * only. * Part 3 tests extendible datasets, for collective transfer mode * only. */ #include "testphdf5.h" /* * The following are various utility routines used by the tests. */ /* * Setup the dimensions of the hyperslab. * Two modes--by rows or by columns. * Assume dimension rank is 2. * BYROW divide into slabs of rows * BYCOL divide into blocks of columns * ZROW same as BYROW except process 0 gets 0 rows * ZCOL same as BYCOL except process 0 gets 0 columns */ static void slab_set(int mpi_rank, int mpi_size, hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], int mode) { switch (mode) { case BYROW: /* Each process takes a slabs of rows. */ block[0] = (hsize_t)(dim0 / mpi_size); block[1] = (hsize_t)dim1; stride[0] = block[0]; stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = (hsize_t)mpi_rank * block[0]; start[1] = 0; if (VERBOSE_MED) HDprintf("slab_set BYROW\n"); break; case BYCOL: /* Each process takes a block of columns. */ block[0] = (hsize_t)dim0; block[1] = (hsize_t)(dim1 / mpi_size); stride[0] = block[0]; stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = 0; start[1] = (hsize_t)mpi_rank * block[1]; if (VERBOSE_MED) HDprintf("slab_set BYCOL\n"); break; case ZROW: /* Similar to BYROW except process 0 gets 0 row */ block[0] = (hsize_t)(mpi_rank ? dim0 / mpi_size : 0); block[1] = (hsize_t)dim1; stride[0] = (mpi_rank ? block[0] : 1); /* avoid setting stride to 0 */ stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = (mpi_rank ? (hsize_t)mpi_rank * block[0] : 0); start[1] = 0; if (VERBOSE_MED) HDprintf("slab_set ZROW\n"); break; case ZCOL: /* Similar to BYCOL except process 0 gets 0 column */ block[0] = (hsize_t)dim0; block[1] = (hsize_t)(mpi_rank ? dim1 / mpi_size : 0); stride[0] = block[0]; stride[1] = (hsize_t)(mpi_rank ? block[1] : 1); /* avoid setting stride to 0 */ count[0] = 1; count[1] = 1; start[0] = 0; start[1] = (mpi_rank ? (hsize_t)mpi_rank * block[1] : 0); if (VERBOSE_MED) HDprintf("slab_set ZCOL\n"); break; default: /* Unknown mode. Set it to cover the whole dataset. */ HDprintf("unknown slab_set mode (%d)\n", mode); block[0] = (hsize_t)dim0; block[1] = (hsize_t)dim1; stride[0] = block[0]; stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = 0; start[1] = 0; if (VERBOSE_MED) HDprintf("slab_set wholeset\n"); break; } if (VERBOSE_MED) { HDprintf("start[]=(%lu,%lu), count[]=(%lu,%lu), stride[]=(%lu,%lu), block[]=(%lu,%lu), total " "datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1], (unsigned long)(block[0] * block[1] * count[0] * count[1])); } } /* * Setup the coordinates for point selection. */ void point_set(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], size_t num_points, hsize_t coords[], int order) { hsize_t i, j, k = 0, m, n, s1, s2; HDcompile_assert(RANK == 2); if (OUT_OF_ORDER == order) k = (num_points * RANK) - 1; else if (IN_ORDER == order) k = 0; s1 = start[0]; s2 = start[1]; for (i = 0; i < count[0]; i++) for (j = 0; j < count[1]; j++) for (m = 0; m < block[0]; m++) for (n = 0; n < block[1]; n++) if (OUT_OF_ORDER == order) { coords[k--] = s2 + (stride[1] * j) + n; coords[k--] = s1 + (stride[0] * i) + m; } else if (IN_ORDER == order) { coords[k++] = s1 + stride[0] * i + m; coords[k++] = s2 + stride[1] * j + n; } if (VERBOSE_MED) { HDprintf("start[]=(%lu, %lu), count[]=(%lu, %lu), stride[]=(%lu, %lu), block[]=(%lu, %lu), total " "datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1], (unsigned long)(block[0] * block[1] * count[0] * count[1])); k = 0; for (i = 0; i < num_points; i++) { HDprintf("(%d, %d)\n", (int)coords[k], (int)coords[k + 1]); k += 2; } } } /* * Fill the dataset with trivial data for testing. * Assume dimension rank is 2 and data is stored contiguous. */ static void dataset_fill(hsize_t start[], hsize_t block[], DATATYPE *dataset) { DATATYPE *dataptr = dataset; hsize_t i, j; /* put some trivial data in the data_array */ for (i = 0; i < block[0]; i++) { for (j = 0; j < block[1]; j++) { *dataptr = (DATATYPE)((i + start[0]) * 100 + (j + start[1] + 1)); dataptr++; } } } /* * Print the content of the dataset. */ static void dataset_print(hsize_t start[], hsize_t block[], DATATYPE *dataset) { DATATYPE *dataptr = dataset; hsize_t i, j; /* print the column heading */ HDprintf("%-8s", "Cols:"); for (j = 0; j < block[1]; j++) { HDprintf("%3lu ", (unsigned long)(start[1] + j)); } HDprintf("\n"); /* print the slab data */ for (i = 0; i < block[0]; i++) { HDprintf("Row %2lu: ", (unsigned long)(i + start[0])); for (j = 0; j < block[1]; j++) { HDprintf("%03d ", *dataptr++); } HDprintf("\n"); } } /* * Print the content of the dataset. */ int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original) { hsize_t i, j; int vrfyerrs; /* print it if VERBOSE_MED */ if (VERBOSE_MED) { HDprintf("dataset_vrfy dumping:::\n"); HDprintf("start(%lu, %lu), count(%lu, %lu), stride(%lu, %lu), block(%lu, %lu)\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1]); HDprintf("original values:\n"); dataset_print(start, block, original); HDprintf("compared values:\n"); dataset_print(start, block, dataset); } vrfyerrs = 0; for (i = 0; i < block[0]; i++) { for (j = 0; j < block[1]; j++) { if (*dataset != *original) { if (vrfyerrs++ < MAX_ERR_REPORT || VERBOSE_MED) { HDprintf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n", (unsigned long)i, (unsigned long)j, (unsigned long)(i + start[0]), (unsigned long)(j + start[1]), *(original), *(dataset)); } dataset++; original++; } } } if (vrfyerrs > MAX_ERR_REPORT && !VERBOSE_MED) HDprintf("[more errors ...]\n"); if (vrfyerrs) HDprintf("%d errors found in dataset_vrfy\n", vrfyerrs); return (vrfyerrs); } /* * Part 1.a--Independent read/write for fixed dimension datasets. */ /* * Example of using the parallel HDF5 library to create two datasets * in one HDF5 files with parallel MPIO access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. */ void dataset_writeInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE * data_array1 = NULL; /* data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); /* ---------------------------------------- * CREATE AN HDF5 FILE WITH PARALLEL ACCESS * ---------------------------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* --------------------------------------------- * Define the dimensions of the overall datasets * and the slabs local to the MPI process. * ------------------------------------------- */ /* setup dimensionality object */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create a dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* * To test the independent orders of writes between processes, all * even number processes write to dataset1 first, then dataset2. * All odd number processes write to dataset2 first, then dataset1. */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* write data independently */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); /* setup dimensions again to write with zero rows for process 0 */ if (VERBOSE_MED) HDprintf("writeInd by some with zero row\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if (MAINPROCESS) { ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("writeInd by some with zero row"); if ((mpi_rank / 2) * 2 != mpi_rank) { ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded"); } #ifdef BARRIER_CHECKS MPI_Barrier(MPI_COMM_WORLD); #endif /* BARRIER_CHECKS */ /* release dataspace ID */ H5Sclose(file_dataspace); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* release all IDs created */ H5Sclose(sid); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_array1) HDfree(data_array1); } /* Example of using the parallel HDF5 library to read a dataset */ void dataset_readInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ DATATYPE * data_array1 = NULL; /* data buffer */ DATATYPE * data_origin1 = NULL; /* expected data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Independent read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded"); /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl); VRFY((fid >= 0), ""); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), ""); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset2 >= 0), ""); /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); /* read data independently */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), ""); ret = H5Dclose(dataset2); VRFY((ret >= 0), ""); /* release all IDs created */ H5Sclose(file_dataspace); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_array1) HDfree(data_array1); if (data_origin1) HDfree(data_origin1); } /* * Part 1.b--Collective read/write for fixed dimension datasets. */ /* * Example of using the parallel HDF5 library to create two datasets * in one HDF5 file with collective parallel access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and * each process controls a hyperslab within.] */ void dataset_writeAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2, dataset3, dataset4; /* Dataset ID */ hid_t dataset5, dataset6, dataset7; /* Dataset ID */ hid_t datatype; /* Datatype ID */ hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE * data_array1 = NULL; /* data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ size_t num_points; /* for point selection */ hsize_t *coords = NULL; /* for point selection */ hsize_t current_dims; /* for point selection */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Collective write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* set up the coords array selection */ num_points = (size_t)dim1; coords = (hsize_t *)HDmalloc((size_t)dim1 * (size_t)RANK * sizeof(hsize_t)); VRFY((coords != NULL), "coords malloc succeeded"); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------- * Define the dimensions of the overall datasets * and create the dataset * ------------------------- */ /* setup 2-D dimensionality object */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create a dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another dataset collectively */ datatype = H5Tcopy(H5T_NATIVE_INT); ret = H5Tset_order(datatype, H5T_ORDER_LE); VRFY((ret >= 0), "H5Tset_order succeeded"); dataset2 = H5Dcreate2(fid, DATASETNAME2, datatype, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 2 succeeded"); /* create a third dataset collectively */ dataset3 = H5Dcreate2(fid, DATASETNAME3, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset3 >= 0), "H5Dcreate2 succeeded"); dataset5 = H5Dcreate2(fid, DATASETNAME7, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset5 >= 0), "H5Dcreate2 succeeded"); dataset6 = H5Dcreate2(fid, DATASETNAME8, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset6 >= 0), "H5Dcreate2 succeeded"); dataset7 = H5Dcreate2(fid, DATASETNAME9, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset7 >= 0), "H5Dcreate2 succeeded"); /* release 2-D space ID created */ H5Sclose(sid); /* setup scalar dimensionality object */ sid = H5Screate(H5S_SCALAR); VRFY((sid >= 0), "H5Screate succeeded"); /* create a fourth dataset collectively */ dataset4 = H5Dcreate2(fid, DATASETNAME4, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset4 >= 0), "H5Dcreate2 succeeded"); /* release scalar space ID created */ H5Sclose(sid); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of rows. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ MESG("writeAll by Row"); ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); /* setup dimensions again to writeAll with zero rows for process 0 */ if (VERBOSE_MED) HDprintf("writeAll by some with zero row\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if (MAINPROCESS) { ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("writeAll by some with zero row"); ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded"); /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset2: each process takes a block of columns. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); /* setup dimensions again to writeAll with zero columns for process 0 */ if (VERBOSE_MED) HDprintf("writeAll by some with zero col\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if (MAINPROCESS) { ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("writeAll by some with zero col"); ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 by ZCOL succeeded"); /* release all temporary handles. */ /* Could have used them for dataset3 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset3: each process takes a block of rows, except process zero uses "none" selection. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset3); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); if (MAINPROCESS) { ret = H5Sselect_none(file_dataspace); VRFY((ret >= 0), "H5Sselect_none file_dataspace succeeded"); } /* end if */ else { ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sselect_hyperslab succeeded"); } /* end else */ /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); if (MAINPROCESS) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sselect_none mem_dataspace succeeded"); } /* end if */ /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* end if */ /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ MESG("writeAll with none"); ret = H5Dwrite(dataset3, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset3 succeeded"); /* write data collectively (with datatype conversion) */ MESG("writeAll with none"); ret = H5Dwrite(dataset3, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset3 succeeded"); /* release all temporary handles. */ /* Could have used them for dataset4 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset4: each process writes no data, except process zero uses "all" selection. */ /* Additionally, these are in a scalar dataspace */ /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset4); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); if (MAINPROCESS) { ret = H5Sselect_none(file_dataspace); VRFY((ret >= 0), "H5Sselect_all file_dataspace succeeded"); } /* end if */ else { ret = H5Sselect_all(file_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* end else */ /* create a memory dataspace independently */ mem_dataspace = H5Screate(H5S_SCALAR); VRFY((mem_dataspace >= 0), ""); if (MAINPROCESS) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sselect_all mem_dataspace succeeded"); } /* end if */ else { ret = H5Sselect_all(mem_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* end else */ /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* end if */ /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ MESG("writeAll with scalar dataspace"); ret = H5Dwrite(dataset4, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset4 succeeded"); /* write data collectively (with datatype conversion) */ MESG("writeAll with scalar dataspace"); ret = H5Dwrite(dataset4, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset4 succeeded"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); if (data_array1) free(data_array1); data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); block[0] = 1; block[1] = (hsize_t)dim1; stride[0] = 1; stride[1] = (hsize_t)dim1; count[0] = 1; count[1] = 1; start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank); start[1] = 0; dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* Dataset5: point selection in File - Hyperslab selection in Memory*/ /* create a file dataspace independently */ point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER); file_dataspace = H5Dget_space(dataset5); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); start[0] = 0; start[1] = 0; mem_dataspace = H5Dget_space(dataset5); VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ ret = H5Dwrite(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset5 succeeded"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset6: point selection in File - Point selection in Memory*/ /* create a file dataspace independently */ start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank); start[1] = 0; point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER); file_dataspace = H5Dget_space(dataset6); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); start[0] = 0; start[1] = 0; point_set(start, count, stride, block, num_points, coords, IN_ORDER); mem_dataspace = H5Dget_space(dataset6); VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ ret = H5Dwrite(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset6 succeeded"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset7: point selection in File - All selection in Memory*/ /* create a file dataspace independently */ start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank); start[1] = 0; point_set(start, count, stride, block, num_points, coords, IN_ORDER); file_dataspace = H5Dget_space(dataset7); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); current_dims = num_points; mem_dataspace = H5Screate_simple(1, ¤t_dims, NULL); VRFY((mem_dataspace >= 0), "mem_dataspace create succeeded"); ret = H5Sselect_all(mem_dataspace); VRFY((ret >= 0), "H5Sselect_all succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ ret = H5Dwrite(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset7 succeeded"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* * All writes completed. Close datasets collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); ret = H5Dclose(dataset3); VRFY((ret >= 0), "H5Dclose3 succeeded"); ret = H5Dclose(dataset4); VRFY((ret >= 0), "H5Dclose4 succeeded"); ret = H5Dclose(dataset5); VRFY((ret >= 0), "H5Dclose5 succeeded"); ret = H5Dclose(dataset6); VRFY((ret >= 0), "H5Dclose6 succeeded"); ret = H5Dclose(dataset7); VRFY((ret >= 0), "H5Dclose7 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (coords) HDfree(coords); if (data_array1) HDfree(data_array1); } /* * Example of using the parallel HDF5 library to read two datasets * in one HDF5 file with collective parallel access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and * each process controls a hyperslab within.] */ void dataset_readAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2, dataset5, dataset6, dataset7; /* Dataset ID */ DATATYPE * data_array1 = NULL; /* data buffer */ DATATYPE * data_origin1 = NULL; /* expected data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ size_t num_points; /* for point selection */ hsize_t *coords = NULL; /* for point selection */ int i, j, k; herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Collective read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* set up the coords array selection */ num_points = (size_t)dim1; coords = (hsize_t *)HDmalloc((size_t)dim0 * (size_t)dim1 * RANK * sizeof(hsize_t)); VRFY((coords != NULL), "coords malloc succeeded"); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded"); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl); VRFY((fid >= 0), "H5Fopen succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------- * Open the datasets in it * ------------------------- */ /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dopen2 succeeded"); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME2, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dopen2 2 succeeded"); /* open another dataset collectively */ dataset5 = H5Dopen2(fid, DATASETNAME7, H5P_DEFAULT); VRFY((dataset5 >= 0), "H5Dopen2 5 succeeded"); dataset6 = H5Dopen2(fid, DATASETNAME8, H5P_DEFAULT); VRFY((dataset6 >= 0), "H5Dopen2 6 succeeded"); dataset7 = H5Dopen2(fid, DATASETNAME9, H5P_DEFAULT); VRFY((dataset7 >= 0), "H5Dopen2 7 succeeded"); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of columns. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_origin1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset1 succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* setup dimensions again to readAll with zero columns for process 0 */ if (VERBOSE_MED) HDprintf("readAll by some with zero col\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if (MAINPROCESS) { ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("readAll by some with zero col"); ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset1 by ZCOL succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset2: each process takes a block of rows. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_origin1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset2 succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* setup dimensions again to readAll with zero rows for process 0 */ if (VERBOSE_MED) HDprintf("readAll by some with zero row\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if (MAINPROCESS) { ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("readAll by some with zero row"); ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset1 by ZROW succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); if (data_array1) free(data_array1); if (data_origin1) free(data_origin1); data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); block[0] = 1; block[1] = (hsize_t)dim1; stride[0] = 1; stride[1] = (hsize_t)dim1; count[0] = 1; count[1] = 1; start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank); start[1] = 0; dataset_fill(start, block, data_origin1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_origin1); } /* Dataset5: point selection in memory - Hyperslab selection in file*/ /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset5); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); start[0] = 0; start[1] = 0; point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER); mem_dataspace = H5Dget_space(dataset5); VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset5 succeeded"); ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); if (data_array1) free(data_array1); data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); /* Dataset6: point selection in File - Point selection in Memory*/ /* create a file dataspace independently */ start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank); start[1] = 0; point_set(start, count, stride, block, num_points, coords, IN_ORDER); file_dataspace = H5Dget_space(dataset6); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); start[0] = 0; start[1] = 0; point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER); mem_dataspace = H5Dget_space(dataset6); VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset6 succeeded"); ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if (ret) nerrors++; /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); if (data_array1) free(data_array1); data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); /* Dataset7: point selection in memory - All selection in file*/ /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset7); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_all(file_dataspace); VRFY((ret >= 0), "H5Sselect_all succeeded"); num_points = (size_t)(dim0 * dim1); k = 0; for (i = 0; i < dim0; i++) { for (j = 0; j < dim1; j++) { coords[k++] = (hsize_t)i; coords[k++] = (hsize_t)j; } } mem_dataspace = H5Dget_space(dataset7); VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); VRFY((ret >= 0), "H5Sselect_elements succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset7 succeeded"); start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank); start[1] = 0; ret = dataset_vrfy(start, count, stride, block, data_array1 + (dim0 / mpi_size * dim1 * mpi_rank), data_origin1); if (ret) nerrors++; /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* * All reads completed. Close datasets collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); ret = H5Dclose(dataset5); VRFY((ret >= 0), "H5Dclose5 succeeded"); ret = H5Dclose(dataset6); VRFY((ret >= 0), "H5Dclose6 succeeded"); ret = H5Dclose(dataset7); VRFY((ret >= 0), "H5Dclose7 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (coords) HDfree(coords); if (data_array1) HDfree(data_array1); if (data_origin1) HDfree(data_origin1); } /* * Part 2--Independent read/write for extendible datasets. */ /* * Example of using the parallel HDF5 library to create two extendible * datasets in one HDF5 file with independent parallel MPIO access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. */ void extend_writeInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ hsize_t max_dims[RANK] = {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */ DATATYPE * data_array1 = NULL; /* data buffer */ hsize_t chunk_dims[RANK]; /* chunk sizes */ hid_t dataset_pl; /* dataset create prop. list */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK]; /* for hyperslab setting */ hsize_t stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Extend independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* setup chunk-size. Make sure sizes are > 0 */ chunk_dims[0] = (hsize_t)chunkdim0; chunk_dims[1] = (hsize_t)chunkdim1; /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* Reduce the number of metadata cache slots, so that there are cache * collisions during the raw data I/O on the chunked dataset. This stresses * the metadata cache and tests for cache bugs. -QAK */ { int mdc_nelmts; size_t rdcc_nelmts; size_t rdcc_nbytes; double rdcc_w0; ret = H5Pget_cache(acc_tpl, &mdc_nelmts, &rdcc_nelmts, &rdcc_nbytes, &rdcc_w0); VRFY((ret >= 0), "H5Pget_cache succeeded"); mdc_nelmts = 4; ret = H5Pset_cache(acc_tpl, mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0); VRFY((ret >= 0), "H5Pset_cache succeeded"); } /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ if (VERBOSE_MED) HDprintf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); dataset_pl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ /* start out with no rows, extend it later. */ dims[0] = dims[1] = 0; sid = H5Screate_simple(RANK, dims, max_dims); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another extendible dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* release resource */ H5Sclose(sid); H5Pclose(dataset_pl); /* ------------------------- * Test writing to dataset1 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Extend its current dim sizes before writing */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; ret = H5Dset_extent(dataset1, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); /* ------------------------- * Test writing to dataset2 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Try write to dataset2 beyond its current dim sizes. Should fail. */ /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently. Should fail. */ H5E_BEGIN_TRY { ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); } H5E_END_TRY VRFY((ret < 0), "H5Dwrite failed as expected"); H5Sclose(file_dataspace); /* Extend dataset2 and try again. Should succeed. */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; ret = H5Dset_extent(dataset2, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_array1) HDfree(data_array1); } /* * Example of using the parallel HDF5 library to create an extendable dataset * and perform I/O on it in a way that verifies that the chunk cache is * bypassed for parallel I/O. */ void extend_writeInd2(void) { const char *filename; hid_t fid; /* HDF5 file ID */ hid_t fapl; /* File access templates */ hid_t fs; /* File dataspace ID */ hid_t ms; /* Memory dataspace ID */ hid_t dataset; /* Dataset ID */ hsize_t orig_size = 10; /* Original dataset dim size */ hsize_t new_size = 20; /* Extended dataset dim size */ hsize_t one = 1; hsize_t max_size = H5S_UNLIMITED; /* dataset maximum dim size */ hsize_t chunk_size = 16384; /* chunk size */ hid_t dcpl; /* dataset create prop. list */ int written[10], /* Data to write */ retrieved[10]; /* Data read in */ int mpi_size, mpi_rank; /* MPI settings */ int i; /* Local index variable */ herr_t ret; /* Generic return value */ filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Extend independent write test #2 on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); VRFY((fapl >= 0), "create_faccess_plist succeeded"); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(fapl); VRFY((ret >= 0), "H5Pclose succeeded"); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dcpl, 1, &chunk_size); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ fs = H5Screate_simple(1, &orig_size, &max_size); VRFY((fs >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, fs, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreat2e succeeded"); /* release resource */ ret = H5Pclose(dcpl); VRFY((ret >= 0), "H5Pclose succeeded"); /* ------------------------- * Test writing to dataset * -------------------------*/ /* create a memory dataspace independently */ ms = H5Screate_simple(1, &orig_size, &max_size); VRFY((ms >= 0), "H5Screate_simple succeeded"); /* put some trivial data in the data_array */ for (i = 0; i < (int)orig_size; i++) written[i] = i; MESG("data array initialized"); if (VERBOSE_MED) { MESG("writing at offset zero: "); for (i = 0; i < (int)orig_size; i++) HDprintf("%s%d", i ? ", " : "", written[i]); HDprintf("\n"); } ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written); VRFY((ret >= 0), "H5Dwrite succeeded"); /* ------------------------- * Read initial data from dataset. * -------------------------*/ ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved); VRFY((ret >= 0), "H5Dread succeeded"); for (i = 0; i < (int)orig_size; i++) if (written[i] != retrieved[i]) { HDprintf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n", __LINE__, i, written[i], i, retrieved[i]); nerrors++; } if (VERBOSE_MED) { MESG("read at offset zero: "); for (i = 0; i < (int)orig_size; i++) HDprintf("%s%d", i ? ", " : "", retrieved[i]); HDprintf("\n"); } /* ------------------------- * Extend the dataset & retrieve new dataspace * -------------------------*/ ret = H5Dset_extent(dataset, &new_size); VRFY((ret >= 0), "H5Dset_extent succeeded"); ret = H5Sclose(fs); VRFY((ret >= 0), "H5Sclose succeeded"); fs = H5Dget_space(dataset); VRFY((fs >= 0), "H5Dget_space succeeded"); /* ------------------------- * Write to the second half of the dataset * -------------------------*/ H5_CHECK_OVERFLOW(orig_size, hsize_t, int); for (i = 0; i < (int)orig_size; i++) written[i] = (int)orig_size + i; MESG("data array re-initialized"); if (VERBOSE_MED) { MESG("writing at offset 10: "); for (i = 0; i < (int)orig_size; i++) HDprintf("%s%d", i ? ", " : "", written[i]); HDprintf("\n"); } ret = H5Sselect_hyperslab(fs, H5S_SELECT_SET, &orig_size, NULL, &one, &orig_size); VRFY((ret >= 0), "H5Sselect_hyperslab succeeded"); ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written); VRFY((ret >= 0), "H5Dwrite succeeded"); /* ------------------------- * Read the new data * -------------------------*/ ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved); VRFY((ret >= 0), "H5Dread succeeded"); for (i = 0; i < (int)orig_size; i++) if (written[i] != retrieved[i]) { HDprintf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n", __LINE__, i, written[i], i, retrieved[i]); nerrors++; } if (VERBOSE_MED) { MESG("read at offset 10: "); for (i = 0; i < (int)orig_size; i++) HDprintf("%s%d", i ? ", " : "", retrieved[i]); HDprintf("\n"); } /* Close dataset collectively */ ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); /* Close the file collectively */ ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } /* Example of using the parallel HDF5 library to read an extendible dataset */ void extend_readInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE * data_array1 = NULL; /* data buffer */ DATATYPE * data_array2 = NULL; /* data buffer */ DATATYPE * data_origin1 = NULL; /* expected data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Extend independent read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); data_array2 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded"); data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded"); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl); VRFY((fid >= 0), ""); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), ""); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset2 >= 0), ""); /* Try extend dataset1 which is open RDONLY. Should fail. */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sget_simple_extent_dims(file_dataspace, dims, NULL); VRFY((ret > 0), "H5Sget_simple_extent_dims succeeded"); dims[0]++; H5E_BEGIN_TRY { ret = H5Dset_extent(dataset1, dims); } H5E_END_TRY VRFY((ret < 0), "H5Dset_extent failed as expected"); H5Sclose(file_dataspace); /* Read dataset1 using BYROW pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* read data independently */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset1 read verified correct"); if (ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); /* Read dataset2 using BYCOL pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset2 read verified correct"); if (ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), ""); ret = H5Dclose(dataset2); VRFY((ret >= 0), ""); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_array1) HDfree(data_array1); if (data_array2) HDfree(data_array2); if (data_origin1) HDfree(data_origin1); } /* * Part 3--Collective read/write for extendible datasets. */ /* * Example of using the parallel HDF5 library to create two extendible * datasets in one HDF5 file with collective parallel MPIO access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. */ void extend_writeAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ hsize_t max_dims[RANK] = {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */ DATATYPE * data_array1 = NULL; /* data buffer */ hsize_t chunk_dims[RANK]; /* chunk sizes */ hid_t dataset_pl; /* dataset create prop. list */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK]; /* for hyperslab setting */ hsize_t stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Extend independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* setup chunk-size. Make sure sizes are > 0 */ chunk_dims[0] = (hsize_t)chunkdim0; chunk_dims[1] = (hsize_t)chunkdim1; /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* Reduce the number of metadata cache slots, so that there are cache * collisions during the raw data I/O on the chunked dataset. This stresses * the metadata cache and tests for cache bugs. -QAK */ { int mdc_nelmts; size_t rdcc_nelmts; size_t rdcc_nbytes; double rdcc_w0; ret = H5Pget_cache(acc_tpl, &mdc_nelmts, &rdcc_nelmts, &rdcc_nbytes, &rdcc_w0); VRFY((ret >= 0), "H5Pget_cache succeeded"); mdc_nelmts = 4; ret = H5Pset_cache(acc_tpl, mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0); VRFY((ret >= 0), "H5Pset_cache succeeded"); } /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ if (VERBOSE_MED) HDprintf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); dataset_pl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ /* start out with no rows, extend it later. */ dims[0] = dims[1] = 0; sid = H5Screate_simple(RANK, dims, max_dims); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another extendible dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* release resource */ H5Sclose(sid); H5Pclose(dataset_pl); /* ------------------------- * Test writing to dataset1 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Extend its current dim sizes before writing */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; ret = H5Dset_extent(dataset1, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* write data collectively */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* ------------------------- * Test writing to dataset2 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* Try write to dataset2 beyond its current dim sizes. Should fail. */ /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently. Should fail. */ H5E_BEGIN_TRY { ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); } H5E_END_TRY VRFY((ret < 0), "H5Dwrite failed as expected"); H5Sclose(file_dataspace); /* Extend dataset2 and try again. Should succeed. */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; ret = H5Dset_extent(dataset2, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Pclose(xfer_plist); VRFY((ret >= 0), "H5Pclose succeeded"); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_array1) HDfree(data_array1); } /* Example of using the parallel HDF5 library to read an extendible dataset */ void extend_readAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE * data_array1 = NULL; /* data buffer */ DATATYPE * data_array2 = NULL; /* data buffer */ DATATYPE * data_origin1 = NULL; /* expected data buffer */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Extend independent read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded"); data_array2 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded"); data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded"); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl); VRFY((fid >= 0), ""); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), ""); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset2 >= 0), ""); /* Try extend dataset1 which is open RDONLY. Should fail. */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sget_simple_extent_dims(file_dataspace, dims, NULL); VRFY((ret > 0), "H5Sget_simple_extent_dims succeeded"); dims[0]++; H5E_BEGIN_TRY { ret = H5Dset_extent(dataset1, dims); } H5E_END_TRY VRFY((ret < 0), "H5Dset_extent failed as expected"); H5Sclose(file_dataspace); /* Read dataset1 using BYROW pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset1 read verified correct"); if (ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); H5Pclose(xfer_plist); /* Read dataset2 using BYCOL pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset2 read verified correct"); if (ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); H5Pclose(xfer_plist); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), ""); ret = H5Dclose(dataset2); VRFY((ret >= 0), ""); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_array1) HDfree(data_array1); if (data_array2) HDfree(data_array2); if (data_origin1) HDfree(data_origin1); } /* * Example of using the parallel HDF5 library to read a compressed * dataset in an HDF5 file with collective parallel access support. */ #ifdef H5_HAVE_FILTER_DEFLATE void compress_readAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t dcpl; /* Dataset creation property list */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t dataspace; /* Dataspace ID */ hid_t dataset; /* Dataset ID */ int rank = 1; /* Dataspace rank */ hsize_t dim = (hsize_t)dim0; /* Dataspace dimensions */ unsigned u; /* Local index variable */ unsigned chunk_opts; /* Chunk options */ unsigned disable_partial_chunk_filters; /* Whether filters are disabled on partial chunks */ DATATYPE * data_read = NULL; /* data buffer */ DATATYPE * data_orig = NULL; /* expected data buffer */ const char *filename; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; int mpi_size, mpi_rank; herr_t ret; /* Generic return value */ filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Collective chunked dataset read test on file %s\n", filename); /* Retrieve MPI parameters */ MPI_Comm_size(comm, &mpi_size); MPI_Comm_rank(comm, &mpi_rank); /* Allocate data buffer */ data_orig = (DATATYPE *)HDmalloc((size_t)dim * sizeof(DATATYPE)); VRFY((data_orig != NULL), "data_origin1 HDmalloc succeeded"); data_read = (DATATYPE *)HDmalloc((size_t)dim * sizeof(DATATYPE)); VRFY((data_read != NULL), "data_array1 HDmalloc succeeded"); /* Initialize data buffers */ for (u = 0; u < dim; u++) data_orig[u] = (DATATYPE)u; /* Run test both with and without filters disabled on partial chunks */ for (disable_partial_chunk_filters = 0; disable_partial_chunk_filters <= 1; disable_partial_chunk_filters++) { /* Process zero creates the file with a compressed, chunked dataset */ if (mpi_rank == 0) { hsize_t chunk_dim; /* Chunk dimensions */ /* Create the file */ fid = H5Fcreate(h5_rmprefix(filename), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); VRFY((fid > 0), "H5Fcreate succeeded"); /* Create property list for chunking and compression */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl > 0), "H5Pcreate succeeded"); ret = H5Pset_layout(dcpl, H5D_CHUNKED); VRFY((ret >= 0), "H5Pset_layout succeeded"); /* Use eight chunks */ chunk_dim = dim / 8; ret = H5Pset_chunk(dcpl, rank, &chunk_dim); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* Set chunk options appropriately */ if (disable_partial_chunk_filters) { ret = H5Pget_chunk_opts(dcpl, &chunk_opts); VRFY((ret >= 0), "H5Pget_chunk_opts succeeded"); chunk_opts |= H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS; ret = H5Pset_chunk_opts(dcpl, chunk_opts); VRFY((ret >= 0), "H5Pset_chunk_opts succeeded"); } /* end if */ ret = H5Pset_deflate(dcpl, 9); VRFY((ret >= 0), "H5Pset_deflate succeeded"); /* Create dataspace */ dataspace = H5Screate_simple(rank, &dim, NULL); VRFY((dataspace > 0), "H5Screate_simple succeeded"); /* Create dataset */ dataset = H5Dcreate2(fid, "compressed_data", H5T_NATIVE_INT, dataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset > 0), "H5Dcreate2 succeeded"); /* Write compressed data */ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_orig); VRFY((ret >= 0), "H5Dwrite succeeded"); /* Close objects */ ret = H5Pclose(dcpl); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Sclose(dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } /* Wait for file to be created */ MPI_Barrier(comm); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl); VRFY((fid > 0), "H5Fopen succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), "H5Pclose succeeded"); /* Open dataset with compressed chunks */ dataset = H5Dopen2(fid, "compressed_data", H5P_DEFAULT); VRFY((dataset > 0), "H5Dopen2 succeeded"); /* Try reading & writing data */ if (dataset > 0) { /* Create dataset transfer property list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist > 0), "H5Pcreate succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* Try reading the data */ ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read); VRFY((ret >= 0), "H5Dread succeeded"); /* Verify data read */ for (u = 0; u < dim; u++) if (data_orig[u] != data_read[u]) { HDprintf("Line #%d: written!=retrieved: data_orig[%u]=%d, data_read[%u]=%d\n", __LINE__, (unsigned)u, data_orig[u], (unsigned)u, data_read[u]); nerrors++; } #ifdef H5_HAVE_PARALLEL_FILTERED_WRITES ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read); VRFY((ret >= 0), "H5Dwrite succeeded"); #endif ret = H5Pclose(xfer_plist); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); } /* end if */ /* Close file */ ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } /* end for */ /* release data buffers */ if (data_read) HDfree(data_read); if (data_orig) HDfree(data_orig); } #endif /* H5_HAVE_FILTER_DEFLATE */ /* * Part 4--Non-selection for chunked dataset */ /* * Example of using the parallel HDF5 library to create chunked * dataset in one HDF5 file with collective and independent parallel * MPIO access support. The Datasets are of sizes dim0 x dim1. * Each process controls only a slab of size dim0 x dim1 within the * dataset with the exception that one processor selects no element. */ void none_selection_chunk(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE * data_origin = NULL; /* data buffer */ DATATYPE * data_array = NULL; /* data buffer */ hsize_t chunk_dims[RANK]; /* chunk sizes */ hid_t dataset_pl; /* dataset create prop. list */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK]; /* for hyperslab setting */ hsize_t stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ hsize_t mstart[RANK]; /* for data buffer in memory */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if (VERBOSE_MED) HDprintf("Extend independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* setup chunk-size. Make sure sizes are > 0 */ chunk_dims[0] = (hsize_t)chunkdim0; chunk_dims[1] = (hsize_t)chunkdim1; /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ if (VERBOSE_MED) HDprintf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); dataset_pl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another extendible dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* release resource */ H5Sclose(sid); H5Pclose(dataset_pl); /* ------------------------- * Test collective writing to dataset1 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* allocate memory for data buffer. Only allocate enough buffer for * each processor's data. */ if (mpi_rank) { data_origin = (DATATYPE *)HDmalloc(block[0] * block[1] * sizeof(DATATYPE)); VRFY((data_origin != NULL), "data_origin HDmalloc succeeded"); data_array = (DATATYPE *)HDmalloc(block[0] * block[1] * sizeof(DATATYPE)); VRFY((data_array != NULL), "data_array HDmalloc succeeded"); /* put some trivial data in the data_array */ mstart[0] = mstart[1] = 0; dataset_fill(mstart, block, data_origin); MESG("data_array initialized"); if (VERBOSE_MED) { MESG("data_array created"); dataset_print(mstart, block, data_origin); } } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple(RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Process 0 has no selection */ if (!mpi_rank) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* create a file dataspace independently */ file_dataspace = H5Dget_space(dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* Process 0 has no selection */ if (!mpi_rank) { ret = H5Sselect_none(file_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* write data collectively */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_origin); VRFY((ret >= 0), "H5Dwrite succeeded"); /* read data independently */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ if (mpi_rank) { ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin); if (ret) nerrors++; } /* ------------------------- * Test independent writing to dataset2 * -------------------------*/ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* write data collectively */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_origin); VRFY((ret >= 0), "H5Dwrite succeeded"); /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ if (mpi_rank) { ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin); if (ret) nerrors++; } /* release resource */ ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Pclose(xfer_plist); VRFY((ret >= 0), "H5Pclose succeeded"); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if (data_origin) HDfree(data_origin); if (data_array) HDfree(data_array); } /* Function: test_actual_io_mode * * Purpose: tests one specific case of collective I/O and checks that the * actual_chunk_opt_mode property and the actual_io_mode * properties in the DXPL have the correct values. * * Input: selection_mode: changes the way processes select data from the space, as well * as some dxpl flags to get collective I/O to break in different ways. * * The relevant I/O function and expected response for each mode: * TEST_ACTUAL_IO_MULTI_CHUNK_IND: * H5D_mpi_chunk_collective_io, each process reports independent I/O * * TEST_ACTUAL_IO_MULTI_CHUNK_COL: * H5D_mpi_chunk_collective_io, each process reports collective I/O * * TEST_ACTUAL_IO_MULTI_CHUNK_MIX: * H5D_mpi_chunk_collective_io, each process reports mixed I/O * * TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE: * H5D_mpi_chunk_collective_io, processes disagree. The root reports * collective, the rest report independent I/O * * TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND: * Same test TEST_ACTUAL_IO_MULTI_CHUNK_IND. * Set directly go to multi-chunk-io without num threshold calc. * TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL: * Same test TEST_ACTUAL_IO_MULTI_CHUNK_COL. * Set directly go to multi-chunk-io without num threshold calc. * * TEST_ACTUAL_IO_LINK_CHUNK: * H5D_link_chunk_collective_io, processes report linked chunk I/O * * TEST_ACTUAL_IO_CONTIGUOUS: * H5D__contig_collective_write or H5D__contig_collective_read * each process reports contiguous collective I/O * * TEST_ACTUAL_IO_NO_COLLECTIVE: * Simple independent I/O. This tests that the defaults are properly set. * * TEST_ACTUAL_IO_RESET: * Performs collective and then independent I/O with hthe same dxpl to * make sure the peroperty is correctly reset to the default on each use. * Specifically, this test runs TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE * (The most complex case that works on all builds) and then performs * an independent read and write with the same dxpls. * * Note: DIRECT_MULTI_CHUNK_MIX and DIRECT_MULTI_CHUNK_MIX_DISAGREE * is not needed as they are covered by DIRECT_CHUNK_MIX and * MULTI_CHUNK_MIX_DISAGREE cases. _DIRECT_ cases are only for testing * path way to multi-chunk-io by H5FD_MPIO_CHUNK_MULTI_IO instead of num-threshold. * * Modification: * - Refctore to remove multi-chunk-without-opimization test and update for * testing direct to multi-chunk-io * Programmer: Jonathan Kim * Date: 2012-10-10 * * * Programmer: Jacob Gruber * Date: 2011-04-06 */ static void test_actual_io_mode(int selection_mode) { H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_write = H5D_MPIO_NO_CHUNK_OPTIMIZATION; H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_read = H5D_MPIO_NO_CHUNK_OPTIMIZATION; H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION; H5D_mpio_actual_io_mode_t actual_io_mode_write = H5D_MPIO_NO_COLLECTIVE; H5D_mpio_actual_io_mode_t actual_io_mode_read = H5D_MPIO_NO_COLLECTIVE; H5D_mpio_actual_io_mode_t actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE; const char * filename; const char * test_name; hbool_t direct_multi_chunk_io; hbool_t multi_chunk_io; hbool_t is_chunked; hbool_t is_collective; int mpi_size = -1; int mpi_rank = -1; int length; int * buffer; int i; MPI_Comm mpi_comm = MPI_COMM_NULL; MPI_Info mpi_info = MPI_INFO_NULL; hid_t fid = -1; hid_t sid = -1; hid_t dataset = -1; hid_t data_type = H5T_NATIVE_INT; hid_t fapl = -1; hid_t mem_space = -1; hid_t file_space = -1; hid_t dcpl = -1; hid_t dxpl_write = -1; hid_t dxpl_read = -1; hsize_t dims[RANK]; hsize_t chunk_dims[RANK]; hsize_t start[RANK]; hsize_t stride[RANK]; hsize_t count[RANK]; hsize_t block[RANK]; char message[256]; herr_t ret; /* Set up some flags to make some future if statements slightly more readable */ direct_multi_chunk_io = (selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND || selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL); /* Note: RESET performs the same tests as MULTI_CHUNK_MIX_DISAGREE and then * tests independent I/O */ multi_chunk_io = (selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_IND || selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_COL || selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX || selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE || selection_mode == TEST_ACTUAL_IO_RESET); is_chunked = (selection_mode != TEST_ACTUAL_IO_CONTIGUOUS && selection_mode != TEST_ACTUAL_IO_NO_COLLECTIVE); is_collective = selection_mode != TEST_ACTUAL_IO_NO_COLLECTIVE; /* Set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Barrier(MPI_COMM_WORLD); HDassert(mpi_size >= 1); mpi_comm = MPI_COMM_WORLD; mpi_info = MPI_INFO_NULL; filename = (const char *)GetTestParameters(); HDassert(filename != NULL); /* Setup the file access template */ fapl = create_faccess_plist(mpi_comm, mpi_info, facc_type); VRFY((fapl >= 0), "create_faccess_plist() succeeded"); /* Create the file */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Create the basic Space */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* Create the dataset creation plist */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "dataset creation plist created successfully"); /* If we are not testing contiguous datasets */ if (is_chunked) { /* Set up chunk information. */ chunk_dims[0] = dims[0] / (hsize_t)mpi_size; chunk_dims[1] = dims[1]; ret = H5Pset_chunk(dcpl, 2, chunk_dims); VRFY((ret >= 0), "chunk creation property list succeeded"); } /* Create the dataset */ dataset = H5Dcreate2(fid, "actual_io", data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded"); /* Create the file dataspace */ file_space = H5Dget_space(dataset); VRFY((file_space >= 0), "H5Dget_space succeeded"); /* Choose a selection method based on the type of I/O we want to occur, * and also set up some selection-dependeent test info. */ switch (selection_mode) { /* Independent I/O with optimization */ case TEST_ACTUAL_IO_MULTI_CHUNK_IND: case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND: /* Since the dataset is chunked by row and each process selects a row, * each process writes to a different chunk. This forces all I/O to be * independent. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); test_name = "Multi Chunk - Independent"; actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK; actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT; break; /* Collective I/O with optimization */ case TEST_ACTUAL_IO_MULTI_CHUNK_COL: case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL: /* The dataset is chunked by rows, so each process takes a column which * spans all chunks. Since the processes write non-overlapping regular * selections to each chunk, the operation is purely collective. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); test_name = "Multi Chunk - Collective"; actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK; if (mpi_size > 1) actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE; else actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT; break; /* Mixed I/O with optimization */ case TEST_ACTUAL_IO_MULTI_CHUNK_MIX: /* A chunk will be assigned collective I/O only if it is selected by each * process. To get mixed I/O, have the root select all chunks and each * subsequent process select the first and nth chunk. The first chunk, * accessed by all, will be assigned collective I/O while each other chunk * will be accessed only by the root and the nth procecess and will be * assigned independent I/O. Each process will access one chunk collectively * and at least one chunk independently, reporting mixed I/O. */ if (mpi_rank == 0) { /* Select the first column */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); } else { /* Select the first and the nth chunk in the nth column */ block[0] = (hsize_t)(dim0 / mpi_size); block[1] = (hsize_t)(dim1 / mpi_size); count[0] = 2; count[1] = 1; stride[0] = (hsize_t)mpi_rank * block[0]; stride[1] = 1; start[0] = 0; start[1] = (hsize_t)mpi_rank * block[1]; } test_name = "Multi Chunk - Mixed"; actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK; actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED; break; /* RESET tests that the properties are properly reset to defaults each time I/O is * performed. To achieve this, we have RESET perform collective I/O (which would change * the values from the defaults) followed by independent I/O (which should report the * default values). RESET doesn't need to have a unique selection, so we reuse * MULTI_CHUMK_MIX_DISAGREE, which was chosen because it is a complex case that works * on all builds. The independent section of RESET can be found at the end of this function. */ case TEST_ACTUAL_IO_RESET: /* Mixed I/O with optimization and internal disagreement */ case TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE: /* A chunk will be assigned collective I/O only if it is selected by each * process. To get mixed I/O with disagreement, assign process n to the * first chunk and the nth chunk. The first chunk, selected by all, is * assgigned collective I/O, while each other process gets independent I/O. * Since the root process with only access the first chunk, it will report * collective I/O. The subsequent processes will access the first chunk * collectively, and their other chunk independently, reporting mixed I/O. */ if (mpi_rank == 0) { /* Select the first chunk in the first column */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); block[0] = block[0] / (hsize_t)mpi_size; } else { /* Select the first and the nth chunk in the nth column */ block[0] = (hsize_t)(dim0 / mpi_size); block[1] = (hsize_t)(dim1 / mpi_size); count[0] = 2; count[1] = 1; stride[0] = (hsize_t)mpi_rank * block[0]; stride[1] = 1; start[0] = 0; start[1] = (hsize_t)mpi_rank * block[1]; } /* If the testname was not already set by the RESET case */ if (selection_mode == TEST_ACTUAL_IO_RESET) test_name = "RESET"; else test_name = "Multi Chunk - Mixed (Disagreement)"; actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK; if (mpi_size > 1) { if (mpi_rank == 0) actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE; else actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED; } else actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT; break; /* Linked Chunk I/O */ case TEST_ACTUAL_IO_LINK_CHUNK: /* Nothing special; link chunk I/O is forced in the dxpl settings. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); test_name = "Link Chunk"; actual_chunk_opt_mode_expected = H5D_MPIO_LINK_CHUNK; actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE; break; /* Contiguous Dataset */ case TEST_ACTUAL_IO_CONTIGUOUS: /* A non overlapping, regular selection in a contiguous dataset leads to * collective I/O */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); test_name = "Contiguous"; actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION; actual_io_mode_expected = H5D_MPIO_CONTIGUOUS_COLLECTIVE; break; case TEST_ACTUAL_IO_NO_COLLECTIVE: slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); test_name = "Independent"; actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION; actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE; break; default: test_name = "Undefined Selection Mode"; actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION; actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE; break; } ret = H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* Create a memory dataspace mirroring the dataset and select the same hyperslab * as in the file space. */ mem_space = H5Screate_simple(RANK, dims, NULL); VRFY((mem_space >= 0), "mem_space created"); ret = H5Sselect_hyperslab(mem_space, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* Get the number of elements in the selection */ length = dim0 * dim1; /* Allocate and initialize the buffer */ buffer = (int *)HDmalloc(sizeof(int) * (size_t)length); VRFY((buffer != NULL), "HDmalloc of buffer succeeded"); for (i = 0; i < length; i++) buffer[i] = i; /* Set up the dxpl for the write */ dxpl_write = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl_write >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded"); /* Set collective I/O properties in the dxpl. */ if (is_collective) { /* Request collective I/O */ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* Set the threshold number of processes per chunk to twice mpi_size. * This will prevent the threshold from ever being met, thus forcing * multi chunk io instead of link chunk io. * This is via default. */ if (multi_chunk_io) { /* force multi-chunk-io by threshold */ ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl_write, (unsigned)mpi_size * 2); VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_num succeeded"); /* set this to manipulate testing scenario about allocating processes * to chunks */ ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl_write, (unsigned)99); VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_ratio succeeded"); } /* Set directly go to multi-chunk-io without threshold calc. */ if (direct_multi_chunk_io) { /* set for multi chunk io by property*/ ret = H5Pset_dxpl_mpio_chunk_opt(dxpl_write, H5FD_MPIO_CHUNK_MULTI_IO); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); } } /* Make a copy of the dxpl to test the read operation */ dxpl_read = H5Pcopy(dxpl_write); VRFY((dxpl_read >= 0), "H5Pcopy succeeded"); /* Write */ ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl_write, buffer); if (ret < 0) H5Eprint2(H5E_DEFAULT, stdout); VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); /* Retrieve Actual io values */ ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write); VRFY((ret >= 0), "retrieving actual io mode succeeded"); ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write); VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded"); /* Read */ ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl_read, buffer); if (ret < 0) H5Eprint2(H5E_DEFAULT, stdout); VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded"); /* Retrieve Actual io values */ ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read); VRFY((ret >= 0), "retrieving actual io mode succeeded"); ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read); VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded"); /* Check write vs read */ VRFY((actual_io_mode_read == actual_io_mode_write), "reading and writing are the same for actual_io_mode"); VRFY((actual_chunk_opt_mode_read == actual_chunk_opt_mode_write), "reading and writing are the same for actual_chunk_opt_mode"); /* Test values */ if (actual_chunk_opt_mode_expected != (H5D_mpio_actual_chunk_opt_mode_t)-1 && actual_io_mode_expected != (H5D_mpio_actual_io_mode_t)-1) { HDsprintf(message, "Actual Chunk Opt Mode has the correct value for %s.\n", test_name); VRFY((actual_chunk_opt_mode_write == actual_chunk_opt_mode_expected), message); HDsprintf(message, "Actual IO Mode has the correct value for %s.\n", test_name); VRFY((actual_io_mode_write == actual_io_mode_expected), message); } else { HDfprintf(stderr, "%s %d -> (%d,%d)\n", test_name, mpi_rank, actual_chunk_opt_mode_write, actual_io_mode_write); } /* To test that the property is successfully reset to the default, we perform some * independent I/O after the collective I/O */ if (selection_mode == TEST_ACTUAL_IO_RESET) { if (mpi_rank == 0) { /* Switch to independent io */ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_INDEPENDENT); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); ret = H5Pset_dxpl_mpio(dxpl_read, H5FD_MPIO_INDEPENDENT); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* Write */ ret = H5Dwrite(dataset, data_type, H5S_ALL, H5S_ALL, dxpl_write, buffer); VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); /* Check Properties */ ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write); VRFY((ret >= 0), "retrieving actual io mode succeeded"); ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write); VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded"); VRFY(actual_chunk_opt_mode_write == H5D_MPIO_NO_CHUNK_OPTIMIZATION, "actual_chunk_opt_mode has correct value for reset write (independent)"); VRFY(actual_io_mode_write == H5D_MPIO_NO_COLLECTIVE, "actual_io_mode has correct value for reset write (independent)"); /* Read */ ret = H5Dread(dataset, data_type, H5S_ALL, H5S_ALL, dxpl_read, buffer); VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); /* Check Properties */ ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read); VRFY((ret >= 0), "retrieving actual io mode succeeded"); ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read); VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded"); VRFY(actual_chunk_opt_mode_read == H5D_MPIO_NO_CHUNK_OPTIMIZATION, "actual_chunk_opt_mode has correct value for reset read (independent)"); VRFY(actual_io_mode_read == H5D_MPIO_NO_COLLECTIVE, "actual_io_mode has correct value for reset read (independent)"); } } /* Release some resources */ ret = H5Sclose(sid); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Pclose(fapl); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Pclose(dcpl); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Pclose(dxpl_write); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Pclose(dxpl_read); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(mem_space); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(file_space); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); HDfree(buffer); return; } /* Function: actual_io_mode_tests * * Purpose: Tests all possible cases of the actual_io_mode property. * * Programmer: Jacob Gruber * Date: 2011-04-06 */ void actual_io_mode_tests(void) { int mpi_size = -1; MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); test_actual_io_mode(TEST_ACTUAL_IO_NO_COLLECTIVE); /* * Test multi-chunk-io via proc_num threshold */ test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_IND); test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_COL); /* The Multi Chunk Mixed test requires at least three processes. */ if (mpi_size > 2) test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX); else HDfprintf(stdout, "Multi Chunk Mixed test requires 3 processes minimum\n"); test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE); /* * Test multi-chunk-io via setting direct property */ test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND); test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL); test_actual_io_mode(TEST_ACTUAL_IO_LINK_CHUNK); test_actual_io_mode(TEST_ACTUAL_IO_CONTIGUOUS); test_actual_io_mode(TEST_ACTUAL_IO_RESET); return; } /* * Function: test_no_collective_cause_mode * * Purpose: * tests cases for broken collective I/O and checks that the * H5Pget_mpio_no_collective_cause properties in the DXPL have the correct values. * * Input: * selection_mode: various mode to cause broken collective I/O * Note: Originally, each TEST case is supposed to be used alone. * After some discussion, this is updated to take multiple TEST cases * with '|'. However there is no error check for any of combined * test cases, so a tester is responsible to understand and feed * proper combination of TESTs if needed. * * * TEST_COLLECTIVE: * Test for regular collective I/O without cause of breaking. * Just to test normal behavior. * * TEST_SET_INDEPENDENT: * Test for Independent I/O as the cause of breaking collective I/O. * * TEST_DATATYPE_CONVERSION: * Test for Data Type Conversion as the cause of breaking collective I/O. * * TEST_DATA_TRANSFORMS: * Test for Data Transform feature as the cause of breaking collective I/O. * * TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES: * Test for NULL dataspace as the cause of breaking collective I/O. * * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT: * Test for Compact layout as the cause of breaking collective I/O. * * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL: * Test for Externl-File storage as the cause of breaking collective I/O. * * Programmer: Jonathan Kim * Date: Aug, 2012 */ #ifdef LATER #define DSET_NOCOLCAUSE "nocolcause" #endif #define FILE_EXTERNAL "nocolcause_extern.data" static void test_no_collective_cause_mode(int selection_mode) { uint32_t no_collective_cause_local_write = 0; uint32_t no_collective_cause_local_read = 0; uint32_t no_collective_cause_local_expected = 0; uint32_t no_collective_cause_global_write = 0; uint32_t no_collective_cause_global_read = 0; uint32_t no_collective_cause_global_expected = 0; const char *filename; const char *test_name; hbool_t is_chunked = 1; hbool_t is_independent = 0; int mpi_size = -1; int mpi_rank = -1; int length; int * buffer; int i; MPI_Comm mpi_comm; MPI_Info mpi_info; hid_t fid = -1; hid_t sid = -1; hid_t dataset = -1; hid_t data_type = H5T_NATIVE_INT; hid_t fapl = -1; hid_t dcpl = -1; hid_t dxpl_write = -1; hid_t dxpl_read = -1; hsize_t dims[RANK]; hid_t mem_space = -1; hid_t file_space = -1; hsize_t chunk_dims[RANK]; herr_t ret; /* set to global value as default */ int l_facc_type = facc_type; char message[256]; /* Set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Barrier(MPI_COMM_WORLD); HDassert(mpi_size >= 1); mpi_comm = MPI_COMM_WORLD; mpi_info = MPI_INFO_NULL; /* Create the dataset creation plist */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "dataset creation plist created successfully"); if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT) { ret = H5Pset_layout(dcpl, H5D_COMPACT); VRFY((ret >= 0), "set COMPACT layout succeeded"); is_chunked = 0; } if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) { ret = H5Pset_external(dcpl, FILE_EXTERNAL, (off_t)0, H5F_UNLIMITED); VRFY((ret >= 0), "set EXTERNAL file layout succeeded"); is_chunked = 0; } if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) { sid = H5Screate(H5S_NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); is_chunked = 0; } else { /* Create the basic Space */ /* if this is a compact dataset, create a small dataspace that does not exceed 64K */ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT) { dims[0] = ROW_FACTOR * 6; dims[1] = COL_FACTOR * 6; } else { dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; } sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); } filename = (const char *)GetTestParameters(); HDassert(filename != NULL); /* Setup the file access template */ fapl = create_faccess_plist(mpi_comm, mpi_info, l_facc_type); VRFY((fapl >= 0), "create_faccess_plist() succeeded"); /* Create the file */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* If we are not testing contiguous datasets */ if (is_chunked) { /* Set up chunk information. */ chunk_dims[0] = dims[0] / (hsize_t)mpi_size; chunk_dims[1] = dims[1]; ret = H5Pset_chunk(dcpl, 2, chunk_dims); VRFY((ret >= 0), "chunk creation property list succeeded"); } /* Create the dataset */ dataset = H5Dcreate2(fid, "nocolcause", data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded"); /* * Set expected causes and some tweaks based on the type of test */ if (selection_mode & TEST_DATATYPE_CONVERSION) { test_name = "Broken Collective I/O - Datatype Conversion"; no_collective_cause_local_expected |= H5D_MPIO_DATATYPE_CONVERSION; no_collective_cause_global_expected |= H5D_MPIO_DATATYPE_CONVERSION; /* set different sign to trigger type conversion */ data_type = H5T_NATIVE_UINT; } if (selection_mode & TEST_DATA_TRANSFORMS) { test_name = "Broken Collective I/O - DATA Transforms"; no_collective_cause_local_expected |= H5D_MPIO_DATA_TRANSFORMS; no_collective_cause_global_expected |= H5D_MPIO_DATA_TRANSFORMS; } if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) { test_name = "Broken Collective I/O - No Simple or Scalar DataSpace"; no_collective_cause_local_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES; no_collective_cause_global_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES; } if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT || selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) { test_name = "Broken Collective I/O - No CONTI or CHUNKED Dataset"; no_collective_cause_local_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; no_collective_cause_global_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; } if (selection_mode & TEST_COLLECTIVE) { test_name = "Broken Collective I/O - Not Broken"; no_collective_cause_local_expected = H5D_MPIO_COLLECTIVE; no_collective_cause_global_expected = H5D_MPIO_COLLECTIVE; } if (selection_mode & TEST_SET_INDEPENDENT) { test_name = "Broken Collective I/O - Independent"; no_collective_cause_local_expected = H5D_MPIO_SET_INDEPENDENT; no_collective_cause_global_expected = H5D_MPIO_SET_INDEPENDENT; /* switch to independent io */ is_independent = 1; } /* use all spaces for certain tests */ if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES || selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) { file_space = H5S_ALL; mem_space = H5S_ALL; } else { /* Get the file dataspace */ file_space = H5Dget_space(dataset); VRFY((file_space >= 0), "H5Dget_space succeeded"); /* Create the memory dataspace */ mem_space = H5Screate_simple(RANK, dims, NULL); VRFY((mem_space >= 0), "mem_space created"); } /* Get the number of elements in the selection */ H5_CHECKED_ASSIGN(length, int, dims[0] * dims[1], uint64_t); /* Allocate and initialize the buffer */ buffer = (int *)HDmalloc(sizeof(int) * (size_t)length); VRFY((buffer != NULL), "HDmalloc of buffer succeeded"); for (i = 0; i < length; i++) buffer[i] = i; /* Set up the dxpl for the write */ dxpl_write = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl_write >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded"); if (is_independent) { /* Set Independent I/O */ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_INDEPENDENT); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); } else { /* Set Collective I/O */ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); } if (selection_mode & TEST_DATA_TRANSFORMS) { ret = H5Pset_data_transform(dxpl_write, "x+1"); VRFY((ret >= 0), "H5Pset_data_transform succeeded"); } /*--------------------- * Test Write access *---------------------*/ /* Write */ ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl_write, buffer); if (ret < 0) H5Eprint2(H5E_DEFAULT, stdout); VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); /* Get the cause of broken collective I/O */ ret = H5Pget_mpio_no_collective_cause(dxpl_write, &no_collective_cause_local_write, &no_collective_cause_global_write); VRFY((ret >= 0), "retrieving no collective cause succeeded"); /*--------------------- * Test Read access *---------------------*/ /* Make a copy of the dxpl to test the read operation */ dxpl_read = H5Pcopy(dxpl_write); VRFY((dxpl_read >= 0), "H5Pcopy succeeded"); /* Read */ ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl_read, buffer); if (ret < 0) H5Eprint2(H5E_DEFAULT, stdout); VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded"); /* Get the cause of broken collective I/O */ ret = H5Pget_mpio_no_collective_cause(dxpl_read, &no_collective_cause_local_read, &no_collective_cause_global_read); VRFY((ret >= 0), "retrieving no collective cause succeeded"); /* Check write vs read */ VRFY((no_collective_cause_local_read == no_collective_cause_local_write), "reading and writing are the same for local cause of Broken Collective I/O"); VRFY((no_collective_cause_global_read == no_collective_cause_global_write), "reading and writing are the same for global cause of Broken Collective I/O"); /* Test values */ HDmemset(message, 0, sizeof(message)); HDsnprintf(message, sizeof(message), "Local cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_local_write == no_collective_cause_local_expected), message); HDmemset(message, 0, sizeof(message)); HDsnprintf(message, sizeof(message), "Global cause of Broken Collective I/O has the correct value for %s.\n", test_name); VRFY((no_collective_cause_global_write == no_collective_cause_global_expected), message); /* Release some resources */ if (sid) H5Sclose(sid); if (fapl) H5Pclose(fapl); if (dcpl) H5Pclose(dcpl); if (dxpl_write) H5Pclose(dxpl_write); if (dxpl_read) H5Pclose(dxpl_read); if (dataset) H5Dclose(dataset); if (mem_space) H5Sclose(mem_space); if (file_space) H5Sclose(file_space); if (fid) H5Fclose(fid); HDfree(buffer); /* clean up external file */ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) HDremove(FILE_EXTERNAL); return; } /* Function: no_collective_cause_tests * * Purpose: Tests cases for broken collective IO. * * Programmer: Jonathan Kim * Date: Aug, 2012 */ void no_collective_cause_tests(void) { /* * Test individual cause */ test_no_collective_cause_mode(TEST_COLLECTIVE); test_no_collective_cause_mode(TEST_SET_INDEPENDENT); test_no_collective_cause_mode(TEST_DATATYPE_CONVERSION); test_no_collective_cause_mode(TEST_DATA_TRANSFORMS); test_no_collective_cause_mode(TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL); /* * Test combined causes */ test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL | TEST_DATATYPE_CONVERSION); test_no_collective_cause_mode(TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS); test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL | TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS); return; } /* * Test consistency semantics of atomic mode */ /* * Example of using the parallel HDF5 library to create a dataset, * where process 0 writes and the other processes read at the same * time. If atomic mode is set correctly, the other processes should * read the old values in the dataset or the new ones. */ void dataset_atomicity(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t sid; /* Dataspace ID */ hid_t dataset1; /* Dataset IDs */ hsize_t dims[RANK]; /* dataset dim sizes */ int * write_buf = NULL; /* data buffer */ int * read_buf = NULL; /* data buffer */ int buf_size; hid_t dataset2; hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* Memory dataspace ID */ hsize_t start[RANK]; hsize_t stride[RANK]; hsize_t count[RANK]; hsize_t block[RANK]; const char *filename; herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; int i, j, k; hbool_t atomicity = FALSE; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; dim0 = 64; dim1 = 32; filename = GetTestParameters(); if (facc_type != FACC_MPIO) { HDprintf("Atomicity tests will not work without the MPIO VFD\n"); return; } if (VERBOSE_MED) HDprintf("atomic writes to file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); buf_size = dim0 * dim1; /* allocate memory for data buffer */ write_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int)); VRFY((write_buf != NULL), "write_buf HDcalloc succeeded"); /* allocate memory for data buffer */ read_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int)); VRFY((read_buf != NULL), "read_buf HDcalloc succeeded"); /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), "H5Pclose succeeded"); /* setup dimensionality object */ dims[0] = (hsize_t)dim0; dims[1] = (hsize_t)dim1; sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create datasets */ dataset1 = H5Dcreate2(fid, DATASETNAME5, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); dataset2 = H5Dcreate2(fid, DATASETNAME6, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* initialize datasets to 0s */ if (0 == mpi_rank) { ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); ret = H5Dwrite(dataset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf); VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); } ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(sid); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); MPI_Barrier(comm); /* make sure setting atomicity fails on a serial file ID */ /* file locking allows only one file open (serial) for writing */ if (MAINPROCESS) { fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT); VRFY((fid >= 0), "H5Fopen succeeded"); /* should fail */ H5E_BEGIN_TRY { ret = H5Fset_mpi_atomicity(fid, TRUE); } H5E_END_TRY VRFY((ret == FAIL), "H5Fset_mpi_atomicity failed"); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } MPI_Barrier(comm); /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl); VRFY((fid >= 0), "H5Fopen succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Fset_mpi_atomicity(fid, TRUE); VRFY((ret >= 0), "H5Fset_mpi_atomicity succeeded"); /* open dataset1 (contiguous case) */ dataset1 = H5Dopen2(fid, DATASETNAME5, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dopen2 succeeded"); if (0 == mpi_rank) { for (i = 0; i < buf_size; i++) { write_buf[i] = 5; } } else { for (i = 0; i < buf_size; i++) { read_buf[i] = 8; } } /* check that the atomicity flag is set */ ret = H5Fget_mpi_atomicity(fid, &atomicity); VRFY((ret >= 0), "atomcity get failed"); VRFY((atomicity == TRUE), "atomcity set failed"); MPI_Barrier(comm); /* Process 0 writes contiguously to the entire dataset */ if (0 == mpi_rank) { ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); } /* The other processes read the entire dataset */ else { ret = H5Dread(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, read_buf); VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); } if (VERBOSE_MED) { i = 0; j = 0; k = 0; for (i = 0; i < dim0; i++) { HDprintf("\n"); for (j = 0; j < dim1; j++) HDprintf("%d ", read_buf[k++]); } } /* The processes that read the dataset must either read all values as 0 (read happened before process 0 wrote to dataset 1), or 5 (read happened after process 0 wrote to dataset 1) */ if (0 != mpi_rank) { int compare = read_buf[0]; VRFY((compare == 0 || compare == 5), "Atomicity Test Failed Process %d: Value read should be 0 or 5\n"); for (i = 1; i < buf_size; i++) { if (read_buf[i] != compare) { HDprintf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, i, read_buf[i], compare); nerrors++; } } } ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5D close succeeded"); /* release data buffers */ if (write_buf) HDfree(write_buf); if (read_buf) HDfree(read_buf); /* open dataset2 (non-contiguous case) */ dataset2 = H5Dopen2(fid, DATASETNAME6, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dopen2 succeeded"); /* allocate memory for data buffer */ write_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int)); VRFY((write_buf != NULL), "write_buf HDcalloc succeeded"); /* allocate memory for data buffer */ read_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int)); VRFY((read_buf != NULL), "read_buf HDcalloc succeeded"); for (i = 0; i < buf_size; i++) { write_buf[i] = 5; } for (i = 0; i < buf_size; i++) { read_buf[i] = 8; } atomicity = FALSE; /* check that the atomicity flag is set */ ret = H5Fget_mpi_atomicity(fid, &atomicity); VRFY((ret >= 0), "atomcity get failed"); VRFY((atomicity == TRUE), "atomcity set failed"); block[0] = (hsize_t)(dim0 / mpi_size - 1); block[1] = (hsize_t)(dim1 / mpi_size - 1); stride[0] = block[0] + 1; stride[1] = block[1] + 1; count[0] = (hsize_t)mpi_size; count[1] = (hsize_t)mpi_size; start[0] = 0; start[1] = 0; /* create a file dataspace */ file_dataspace = H5Dget_space(dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace */ mem_dataspace = H5Screate_simple(RANK, dims, NULL); VRFY((mem_dataspace >= 0), ""); ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); MPI_Barrier(comm); /* Process 0 writes to the dataset */ if (0 == mpi_rank) { ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, write_buf); VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); } /* All processes wait for the write to finish. This works because atomicity is set to true */ MPI_Barrier(comm); /* The other processes read the entire dataset */ if (0 != mpi_rank) { ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, read_buf); VRFY((ret >= 0), "H5Dread dataset2 succeeded"); } if (VERBOSE_MED) { if (mpi_rank == 1) { i = 0; j = 0; k = 0; for (i = 0; i < dim0; i++) { HDprintf("\n"); for (j = 0; j < dim1; j++) HDprintf("%d ", read_buf[k++]); } HDprintf("\n"); } } /* The processes that read the dataset must either read all values as 5 (read happened after process 0 wrote to dataset 1) */ if (0 != mpi_rank) { int compare; i = 0; j = 0; k = 0; compare = 5; H5_CHECK_OVERFLOW(block[0], hsize_t, int); H5_CHECK_OVERFLOW(block[1], hsize_t, int); for (i = 0; i < dim0; i++) { if (i >= mpi_rank * ((int)block[0] + 1)) { break; } if ((i + 1) % ((int)block[0] + 1) == 0) { k += dim1; continue; } for (j = 0; j < dim1; j++) { if (j >= mpi_rank * ((int)block[1] + 1)) { k += dim1 - mpi_rank * ((int)block[1] + 1); break; } if ((j + 1) % ((int)block[1] + 1) == 0) { k++; continue; } else if (compare != read_buf[k]) { HDprintf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, k, read_buf[k], compare); nerrors++; } k++; } } } ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); /* release data buffers */ if (write_buf) HDfree(write_buf); if (read_buf) HDfree(read_buf); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } /* Function: dense_attr_test * * Purpose: Test cases for writing dense attributes in parallel * * Programmer: Quincey Koziol * Date: April, 2013 */ void test_dense_attr(void) { int mpi_size, mpi_rank; hid_t fpid, fid; hid_t gid, gpid; hid_t atFileSpace, atid; hsize_t atDims[1] = {10000}; herr_t status; const char *filename; /* get filename */ filename = (const char *)GetTestParameters(); HDassert(filename != NULL); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); fpid = H5Pcreate(H5P_FILE_ACCESS); VRFY((fpid > 0), "H5Pcreate succeeded"); status = H5Pset_libver_bounds(fpid, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST); VRFY((status >= 0), "H5Pset_libver_bounds succeeded"); status = H5Pset_fapl_mpio(fpid, MPI_COMM_WORLD, MPI_INFO_NULL); VRFY((status >= 0), "H5Pset_fapl_mpio succeeded"); fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fpid); VRFY((fid > 0), "H5Fcreate succeeded"); status = H5Pclose(fpid); VRFY((status >= 0), "H5Pclose succeeded"); gpid = H5Pcreate(H5P_GROUP_CREATE); VRFY((gpid > 0), "H5Pcreate succeeded"); status = H5Pset_attr_phase_change(gpid, 0, 0); VRFY((status >= 0), "H5Pset_attr_phase_change succeeded"); gid = H5Gcreate2(fid, "foo", H5P_DEFAULT, gpid, H5P_DEFAULT); VRFY((gid > 0), "H5Gcreate2 succeeded"); status = H5Pclose(gpid); VRFY((status >= 0), "H5Pclose succeeded"); atFileSpace = H5Screate_simple(1, atDims, NULL); VRFY((atFileSpace > 0), "H5Screate_simple succeeded"); atid = H5Acreate2(gid, "bar", H5T_STD_U64LE, atFileSpace, H5P_DEFAULT, H5P_DEFAULT); VRFY((atid > 0), "H5Acreate succeeded"); status = H5Sclose(atFileSpace); VRFY((status >= 0), "H5Sclose succeeded"); status = H5Aclose(atid); VRFY((status >= 0), "H5Aclose succeeded"); status = H5Gclose(gid); VRFY((status >= 0), "H5Gclose succeeded"); status = H5Fclose(fid); VRFY((status >= 0), "H5Fclose succeeded"); return; }