/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "testphdf5.h" #include "H5Dprivate.h" #include "H5private.h" #define DIM 2 #define SIZE 32 #define NDATASET 4 #define GROUP_DEPTH 128 enum obj_type { is_group, is_dset }; static int get_size(void); static void write_dataset(hid_t, hid_t, hid_t); static int read_dataset(hid_t, hid_t, hid_t); static void create_group_recursive(hid_t, hid_t, hid_t, int); static void recursive_read_group(hid_t, hid_t, hid_t, int); static void group_dataset_read(hid_t fid, int mpi_rank, int m); static void write_attribute(hid_t, int, int); static int read_attribute(hid_t, int, int); static int check_value(DATATYPE *, DATATYPE *, int); static void get_slab(hsize_t[], hsize_t[], hsize_t[], hsize_t[], int); /* * The size value computed by this function is used extensively in * configuring tests for the current number of processes. * * This function was created as part of an effort to allow the * test functions in this file to run on an arbitrary number of * processors. * JRM - 8/11/04 */ static int get_size(void) { int mpi_rank; int mpi_size; int size = SIZE; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* needed for VRFY */ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); if (mpi_size > size) { if ((mpi_size % 2) == 0) { size = mpi_size; } else { size = mpi_size + 1; } } VRFY((mpi_size <= size), "mpi_size <= size"); VRFY(((size % 2) == 0), "size isn't even"); return (size); } /* get_size() */ /* * Example of using PHDF5 to create a zero sized dataset. * */ void zero_dim_dset(void) { int mpi_size, mpi_rank; const char *filename; hid_t fid, plist, dcpl, dsid, sid; hsize_t dim, chunk_dim; herr_t ret; int data[1]; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file or dataset aren't supported with this connector\n"); fflush(stdout); } return; } filename = GetTestParameters(); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); VRFY((plist >= 0), "create_faccess_plist succeeded"); fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist); VRFY((fid >= 0), "H5Fcreate succeeded"); ret = H5Pclose(plist); VRFY((ret >= 0), "H5Pclose succeeded"); dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "failed H5Pcreate"); /* Set 1 chunk size */ chunk_dim = 1; ret = H5Pset_chunk(dcpl, 1, &chunk_dim); VRFY((ret >= 0), "failed H5Pset_chunk"); /* Create 1D dataspace with 0 dim size */ dim = 0; sid = H5Screate_simple(1, &dim, NULL); VRFY((sid >= 0), "failed H5Screate_simple"); /* Create chunked dataset */ dsid = H5Dcreate2(fid, "dset", H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dsid >= 0), "failed H5Dcreate2"); /* write 0 elements from dataset */ ret = H5Dwrite(dsid, H5T_NATIVE_INT, sid, sid, H5P_DEFAULT, data); VRFY((ret >= 0), "failed H5Dwrite"); /* Read 0 elements from dataset */ ret = H5Dread(dsid, H5T_NATIVE_INT, sid, sid, H5P_DEFAULT, data); VRFY((ret >= 0), "failed H5Dread"); H5Pclose(dcpl); H5Dclose(dsid); H5Sclose(sid); H5Fclose(fid); } /* * Example of using PHDF5 to create ndatasets datasets. Each process write * a slab of array to the file. */ void multiple_dset_write(void) { int i, j, n, mpi_size, mpi_rank, size; hid_t iof, plist, dataset, memspace, filespace; hid_t dcpl; /* Dataset creation property list */ hsize_t chunk_origin[DIM]; hsize_t chunk_dims[DIM], file_dims[DIM]; hsize_t count[DIM] = {1, 1}; double *outme = NULL; double fill = 1.0; /* Fill value */ char dname[100]; herr_t ret; const H5Ptest_param_t *pt; char *filename; int ndatasets; pt = GetTestParameters(); filename = pt->name; ndatasets = pt->count; size = get_size(); H5_CHECK_OVERFLOW(size, int, size_t); MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file or dataset aren't supported with this connector\n"); fflush(stdout); } return; } outme = malloc((size_t)size * (size_t)size * sizeof(double)); VRFY((outme != NULL), "malloc succeeded for outme"); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); VRFY((plist >= 0), "create_faccess_plist succeeded"); iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist); VRFY((iof >= 0), "H5Fcreate succeeded"); ret = H5Pclose(plist); VRFY((ret >= 0), "H5Pclose succeeded"); /* decide the hyperslab according to process number. */ get_slab(chunk_origin, chunk_dims, count, file_dims, size); memspace = H5Screate_simple(DIM, chunk_dims, NULL); filespace = H5Screate_simple(DIM, file_dims, NULL); ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); VRFY((ret >= 0), "mdata hyperslab selection"); /* Create a dataset creation property list */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "dataset creation property list succeeded"); ret = H5Pset_fill_value(dcpl, H5T_NATIVE_DOUBLE, &fill); VRFY((ret >= 0), "set fill-value succeeded"); for (n = 0; n < ndatasets; n++) { snprintf(dname, sizeof(dname), "dataset %d", n); dataset = H5Dcreate2(iof, dname, H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset > 0), dname); /* calculate data to write */ for (i = 0; i < size; i++) for (j = 0; j < size; j++) outme[(i * size) + j] = n * 1000 + mpi_rank; H5Dwrite(dataset, H5T_NATIVE_DOUBLE, memspace, filespace, H5P_DEFAULT, outme); H5Dclose(dataset); #ifdef BARRIER_CHECKS if (!((n + 1) % 10)) { printf("created %d datasets\n", n + 1); MPI_Barrier(MPI_COMM_WORLD); } #endif /* BARRIER_CHECKS */ } H5Sclose(filespace); H5Sclose(memspace); H5Pclose(dcpl); H5Fclose(iof); free(outme); } /* Example of using PHDF5 to create, write, and read compact dataset. */ void compact_dataset(void) { int i, j, mpi_size, mpi_rank, size, err_num = 0; hid_t iof, plist, dcpl, dxpl, dataset, filespace; hsize_t file_dims[DIM]; double *outme; double *inme; char dname[] = "dataset"; herr_t ret; const char *filename; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY bool prop_value; #endif size = get_size(); for (i = 0; i < DIM; i++) file_dims[i] = (hsize_t)size; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file or dataset aren't supported with this connector\n"); fflush(stdout); } return; } outme = malloc((size_t)((size_t)size * (size_t)size * sizeof(double))); VRFY((outme != NULL), "malloc succeeded for outme"); inme = malloc((size_t)size * (size_t)size * sizeof(double)); VRFY((outme != NULL), "malloc succeeded for inme"); filename = GetTestParameters(); VRFY((mpi_size <= size), "mpi_size <= size"); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist); /* Define data space */ filespace = H5Screate_simple(DIM, file_dims, NULL); /* Create a compact dataset */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "dataset creation property list succeeded"); ret = H5Pset_layout(dcpl, H5D_COMPACT); VRFY((dcpl >= 0), "set property list for compact dataset"); ret = H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY); VRFY((ret >= 0), "set space allocation time for compact dataset"); dataset = H5Dcreate2(iof, dname, H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2 succeeded"); /* set up the collective transfer properties list */ dxpl = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl >= 0), ""); ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* Recalculate data to write. Each process writes the same data. */ for (i = 0; i < size; i++) for (j = 0; j < size; j++) outme[(i * size) + j] = (i + j) * 1000; ret = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, outme); VRFY((ret >= 0), "H5Dwrite succeeded"); H5Pclose(dcpl); H5Pclose(plist); H5Dclose(dataset); H5Sclose(filespace); H5Fclose(iof); /* Open the file and dataset, read and compare the data. */ plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); iof = H5Fopen(filename, H5F_ACC_RDONLY, plist); VRFY((iof >= 0), "H5Fopen succeeded"); /* set up the collective transfer properties list */ dxpl = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl >= 0), ""); ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } dataset = H5Dopen2(iof, dname, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dopen2 succeeded"); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY prop_value = H5D_XFER_COLL_RANK0_BCAST_DEF; ret = H5Pinsert2(dxpl, H5D_XFER_COLL_RANK0_BCAST_NAME, H5D_XFER_COLL_RANK0_BCAST_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((ret >= 0), "H5Pinsert2() succeeded"); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ ret = H5Dread(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, inme); VRFY((ret >= 0), "H5Dread succeeded"); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY prop_value = false; ret = H5Pget(dxpl, H5D_XFER_COLL_RANK0_BCAST_NAME, &prop_value); VRFY((ret >= 0), "H5Pget succeeded"); VRFY((prop_value == false && dxfer_coll_type == DXFER_COLLECTIVE_IO), "rank 0 Bcast optimization was performed for a compact dataset"); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /* Verify data value */ for (i = 0; i < size; i++) for (j = 0; j < size; j++) if (!H5_DBL_ABS_EQUAL(inme[(i * size) + j], outme[(i * size) + j])) if (err_num++ < MAX_ERR_REPORT || VERBOSE_MED) printf("Dataset Verify failed at [%d][%d]: expect %f, got %f\n", i, j, outme[(i * size) + j], inme[(i * size) + j]); H5Pclose(plist); H5Pclose(dxpl); H5Dclose(dataset); H5Fclose(iof); free(inme); free(outme); } /* * Example of using PHDF5 to create, write, and read dataset and attribute * of Null dataspace. */ void null_dataset(void) { int mpi_size, mpi_rank; hid_t iof, plist, dxpl, dataset, attr, sid; unsigned uval = 2; /* Buffer for writing to dataset */ int val = 1; /* Buffer for writing to attribute */ hssize_t nelem; char dname[] = "dataset"; char attr_name[] = "attribute"; herr_t ret; const char *filename; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_ATTR_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file, dataset, or attribute aren't supported with this " "connector\n"); fflush(stdout); } return; } filename = GetTestParameters(); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist); /* Define data space */ sid = H5Screate(H5S_NULL); /* Check that the null dataspace actually has 0 elements */ nelem = H5Sget_simple_extent_npoints(sid); VRFY((nelem == 0), "H5Sget_simple_extent_npoints"); /* Create a compact dataset */ dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2 succeeded"); /* set up the collective transfer properties list */ dxpl = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl >= 0), ""); ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* Write "nothing" to the dataset(with type conversion) */ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl, &uval); VRFY((ret >= 0), "H5Dwrite succeeded"); /* Create an attribute for the group */ attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT); VRFY((attr >= 0), "H5Acreate2"); /* Write "nothing" to the attribute(with type conversion) */ ret = H5Awrite(attr, H5T_NATIVE_INT, &val); VRFY((ret >= 0), "H5Awrite"); H5Aclose(attr); H5Dclose(dataset); H5Pclose(plist); H5Sclose(sid); H5Fclose(iof); /* Open the file and dataset, read and compare the data. */ plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); iof = H5Fopen(filename, H5F_ACC_RDONLY, plist); VRFY((iof >= 0), "H5Fopen succeeded"); /* set up the collective transfer properties list */ dxpl = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl >= 0), ""); ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } dataset = H5Dopen2(iof, dname, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dopen2 succeeded"); /* Try reading from the dataset(make certain our buffer is unmodified) */ ret = H5Dread(dataset, H5T_NATIVE_UINT, H5S_ALL, H5S_ALL, dxpl, &uval); VRFY((ret >= 0), "H5Dread"); VRFY((uval == 2), "H5Dread"); /* Open the attribute for the dataset */ attr = H5Aopen(dataset, attr_name, H5P_DEFAULT); VRFY((attr >= 0), "H5Aopen"); /* Try reading from the attribute(make certain our buffer is unmodified) */ ret = H5Aread(attr, H5T_NATIVE_INT, &val); VRFY((ret >= 0), "H5Aread"); VRFY((val == 1), "H5Aread"); H5Pclose(plist); H5Pclose(dxpl); H5Aclose(attr); H5Dclose(dataset); H5Fclose(iof); } /* Example of using PHDF5 to create "large" datasets. (>2GB, >4GB, >8GB) * Actual data is _not_ written to these datasets. Dataspaces are exact * sizes(2GB, 4GB, etc.), but the metadata for the file pushes the file over * the boundary of interest. */ void big_dataset(void) { int mpi_size, mpi_rank; /* MPI info */ hid_t iof, /* File ID */ fapl, /* File access property list ID */ dataset, /* Dataset ID */ filespace; /* Dataset's dataspace ID */ hsize_t file_dims[4]; /* Dimensions of dataspace */ char dname[] = "dataset"; /* Name of dataset */ MPI_Offset file_size; /* Size of file on disk */ bool vol_is_native; herr_t ret; /* Generic return value */ const char *filename; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file or dataset aren't supported with this connector\n"); fflush(stdout); } return; } /* Verify MPI_Offset can handle larger than 2GB sizes */ VRFY((sizeof(MPI_Offset) > 4), "sizeof(MPI_Offset)>4"); filename = GetTestParameters(); fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); VRFY((fapl >= 0), "create_faccess_plist succeeded"); /* * Create >2GB HDF5 file */ iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((iof >= 0), "H5Fcreate succeeded"); /* Check if native VOL is being used */ VRFY((h5_using_native_vol(H5P_DEFAULT, iof, &vol_is_native) >= 0), "h5_using_native_vol"); /* Define dataspace for 2GB dataspace */ file_dims[0] = 2; file_dims[1] = 1024; file_dims[2] = 1024; file_dims[3] = 1024; filespace = H5Screate_simple(4, file_dims, NULL); VRFY((filespace >= 0), "H5Screate_simple succeeded"); dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2 succeeded"); /* Close all file objects */ ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(filespace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Fclose(iof); VRFY((ret >= 0), "H5Fclose succeeded"); if (vol_is_native) { /* Check that file of the correct size was created */ file_size = h5_get_file_size(filename, fapl); VRFY((file_size == 2147485696ULL), "File is correct size(~2GB)"); } /* * Create >4GB HDF5 file */ iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((iof >= 0), "H5Fcreate succeeded"); /* Define dataspace for 4GB dataspace */ file_dims[0] = 4; file_dims[1] = 1024; file_dims[2] = 1024; file_dims[3] = 1024; filespace = H5Screate_simple(4, file_dims, NULL); VRFY((filespace >= 0), "H5Screate_simple succeeded"); dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2 succeeded"); /* Close all file objects */ ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(filespace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Fclose(iof); VRFY((ret >= 0), "H5Fclose succeeded"); if (vol_is_native) { /* Check that file of the correct size was created */ file_size = h5_get_file_size(filename, fapl); VRFY((file_size == 4294969344ULL), "File is correct size(~4GB)"); } /* * Create >8GB HDF5 file */ iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((iof >= 0), "H5Fcreate succeeded"); /* Define dataspace for 8GB dataspace */ file_dims[0] = 8; file_dims[1] = 1024; file_dims[2] = 1024; file_dims[3] = 1024; filespace = H5Screate_simple(4, file_dims, NULL); VRFY((filespace >= 0), "H5Screate_simple succeeded"); dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2 succeeded"); /* Close all file objects */ ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(filespace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Fclose(iof); VRFY((ret >= 0), "H5Fclose succeeded"); if (vol_is_native) { /* Check that file of the correct size was created */ file_size = h5_get_file_size(filename, fapl); VRFY((file_size == 8589936640ULL), "File is correct size(~8GB)"); } /* Close fapl */ ret = H5Pclose(fapl); VRFY((ret >= 0), "H5Pclose succeeded"); } /* Example of using PHDF5 to read a partial written dataset. The dataset does * not have actual data written to the entire raw data area and relies on the * default fill value of zeros to work correctly. */ void dataset_fillvalue(void) { int mpi_size, mpi_rank; /* MPI info */ int err_num; /* Number of errors */ hid_t iof, /* File ID */ fapl, /* File access property list ID */ dxpl, /* Data transfer property list ID */ dataset, /* Dataset ID */ memspace, /* Memory dataspace ID */ filespace; /* Dataset's dataspace ID */ char dname[] = "dataset"; /* Name of dataset */ hsize_t dset_dims[4] = {0, 6, 7, 8}; hsize_t req_start[4] = {0, 0, 0, 0}; hsize_t req_count[4] = {1, 6, 7, 8}; hsize_t dset_size; /* Dataset size */ int *rdata, *wdata; /* Buffers for data to read and write */ int *twdata, *trdata; /* Temporary pointer into buffer */ int acc, i, ii, j, k, l; /* Local index variables */ herr_t ret; /* Generic return value */ const char *filename; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY bool prop_value; #endif MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file or dataset aren't supported with this connector\n"); fflush(stdout); } return; } filename = GetTestParameters(); /* Set the dataset dimension to be one row more than number of processes */ /* and calculate the actual dataset size. */ dset_dims[0] = (hsize_t)(mpi_size + 1); dset_size = dset_dims[0] * dset_dims[1] * dset_dims[2] * dset_dims[3]; /* Allocate space for the buffers */ rdata = malloc((size_t)(dset_size * sizeof(int))); VRFY((rdata != NULL), "calloc succeeded for read buffer"); wdata = malloc((size_t)(dset_size * sizeof(int))); VRFY((wdata != NULL), "malloc succeeded for write buffer"); fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); VRFY((fapl >= 0), "create_faccess_plist succeeded"); /* * Create HDF5 file */ iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((iof >= 0), "H5Fcreate succeeded"); filespace = H5Screate_simple(4, dset_dims, NULL); VRFY((filespace >= 0), "File H5Screate_simple succeeded"); dataset = H5Dcreate2(iof, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreate2 succeeded"); memspace = H5Screate_simple(4, dset_dims, NULL); VRFY((memspace >= 0), "Memory H5Screate_simple succeeded"); /* * Read dataset before any data is written. */ /* Create DXPL for I/O */ dxpl = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl >= 0), "H5Pcreate succeeded"); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY prop_value = H5D_XFER_COLL_RANK0_BCAST_DEF; ret = H5Pinsert2(dxpl, H5D_XFER_COLL_RANK0_BCAST_NAME, H5D_XFER_COLL_RANK0_BCAST_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((ret >= 0), "testing property list inserted succeeded"); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ for (ii = 0; ii < 2; ii++) { if (ii == 0) ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_INDEPENDENT); else ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* set entire read buffer with the constant 2 */ memset(rdata, 2, (size_t)(dset_size * sizeof(int))); /* Read the entire dataset back */ ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl, rdata); VRFY((ret >= 0), "H5Dread succeeded"); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY prop_value = false; ret = H5Pget(dxpl, H5D_XFER_COLL_RANK0_BCAST_NAME, &prop_value); VRFY((ret >= 0), "testing property list get succeeded"); if (ii == 0) VRFY((prop_value == false), "correctly handled rank 0 Bcast"); else VRFY((prop_value == true), "correctly handled rank 0 Bcast"); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /* Verify all data read are the fill value 0 */ trdata = rdata; err_num = 0; for (i = 0; i < (int)dset_dims[0]; i++) for (j = 0; j < (int)dset_dims[1]; j++) for (k = 0; k < (int)dset_dims[2]; k++) for (l = 0; l < (int)dset_dims[3]; l++, trdata++) if (*trdata != 0) if (err_num++ < MAX_ERR_REPORT || VERBOSE_MED) printf( "Rank %d: Dataset Verify failed at [%d][%d][%d][%d]: expect 0, got %d\n", mpi_rank, i, j, k, l, *trdata); if (err_num > MAX_ERR_REPORT && !VERBOSE_MED) printf("Rank %d: [more errors ...]\n", mpi_rank); if (err_num) { printf("Rank %d: %d errors found in check_value\n", mpi_rank, err_num); nerrors++; } } /* Barrier to ensure all processes have completed the above test. */ MPI_Barrier(MPI_COMM_WORLD); /* * Each process writes 1 row of data. Thus last row is not written. */ /* Create hyperslabs in memory and file dataspaces */ req_start[0] = (hsize_t)mpi_rank; ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, req_start, NULL, req_count, NULL); VRFY((ret >= 0), "H5Sselect_hyperslab succeeded on memory dataspace"); ret = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, req_start, NULL, req_count, NULL); VRFY((ret >= 0), "H5Sselect_hyperslab succeeded on memory dataspace"); ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret >= 0), "set independent IO collectively succeeded"); } /* Fill write buffer with some values */ twdata = wdata; for (i = 0, acc = 0; i < (int)dset_dims[0]; i++) for (j = 0; j < (int)dset_dims[1]; j++) for (k = 0; k < (int)dset_dims[2]; k++) for (l = 0; l < (int)dset_dims[3]; l++) *twdata++ = acc++; /* Collectively write a hyperslab of data to the dataset */ ret = H5Dwrite(dataset, H5T_NATIVE_INT, memspace, filespace, dxpl, wdata); VRFY((ret >= 0), "H5Dwrite succeeded"); /* Barrier here, to allow processes to sync */ MPI_Barrier(MPI_COMM_WORLD); /* * Read dataset after partial write. */ #ifdef H5_HAVE_INSTRUMENTED_LIBRARY prop_value = H5D_XFER_COLL_RANK0_BCAST_DEF; ret = H5Pset(dxpl, H5D_XFER_COLL_RANK0_BCAST_NAME, &prop_value); VRFY((ret >= 0), " H5Pset succeeded"); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ for (ii = 0; ii < 2; ii++) { if (ii == 0) ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_INDEPENDENT); else ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* set entire read buffer with the constant 2 */ memset(rdata, 2, (size_t)(dset_size * sizeof(int))); /* Read the entire dataset back */ ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl, rdata); VRFY((ret >= 0), "H5Dread succeeded"); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY prop_value = false; ret = H5Pget(dxpl, H5D_XFER_COLL_RANK0_BCAST_NAME, &prop_value); VRFY((ret >= 0), "testing property list get succeeded"); if (ii == 0) VRFY((prop_value == false), "correctly handled rank 0 Bcast"); else VRFY((prop_value == true), "correctly handled rank 0 Bcast"); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /* Verify correct data read */ twdata = wdata; trdata = rdata; err_num = 0; for (i = 0; i < (int)dset_dims[0]; i++) for (j = 0; j < (int)dset_dims[1]; j++) for (k = 0; k < (int)dset_dims[2]; k++) for (l = 0; l < (int)dset_dims[3]; l++, twdata++, trdata++) if (i < mpi_size) { if (*twdata != *trdata) if (err_num++ < MAX_ERR_REPORT || VERBOSE_MED) printf("Dataset Verify failed at [%d][%d][%d][%d]: expect %d, got %d\n", i, j, k, l, *twdata, *trdata); } /* end if */ else { if (*trdata != 0) if (err_num++ < MAX_ERR_REPORT || VERBOSE_MED) printf("Dataset Verify failed at [%d][%d][%d][%d]: expect 0, got %d\n", i, j, k, l, *trdata); } /* end else */ if (err_num > MAX_ERR_REPORT && !VERBOSE_MED) printf("[more errors ...]\n"); if (err_num) { printf("%d errors found in check_value\n", err_num); nerrors++; } } /* Close all file objects */ ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Sclose(filespace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Fclose(iof); VRFY((ret >= 0), "H5Fclose succeeded"); /* Close memory dataspace */ ret = H5Sclose(memspace); VRFY((ret >= 0), "H5Sclose succeeded"); /* Close dxpl */ ret = H5Pclose(dxpl); VRFY((ret >= 0), "H5Pclose succeeded"); /* Close fapl */ ret = H5Pclose(fapl); VRFY((ret >= 0), "H5Pclose succeeded"); /* free the buffers */ free(rdata); free(wdata); } /* combined cngrpw and ingrpr tests because ingrpr reads file created by cngrpw. */ void collective_group_write_independent_group_read(void) { collective_group_write(); independent_group_read(); } /* Write multiple groups with a chunked dataset in each group collectively. * These groups and datasets are for testing independent read later. */ void collective_group_write(void) { int mpi_rank, mpi_size, size; int i, j, m; char gname[64], dname[32]; hid_t fid, gid, did, plist, dcpl, memspace, filespace; DATATYPE *outme = NULL; hsize_t chunk_origin[DIM]; hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM]; hsize_t chunk_size[2]; /* Chunk dimensions - computed shortly */ herr_t ret1, ret2; const H5Ptest_param_t *pt; char *filename; int ngroups; pt = GetTestParameters(); filename = pt->name; ngroups = pt->count; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_GROUP_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf( " API functions for basic file, group, or dataset aren't supported with this connector\n"); fflush(stdout); } return; } size = get_size(); chunk_size[0] = (hsize_t)(size / 2); chunk_size[1] = (hsize_t)(size / 2); outme = malloc((size_t)size * (size_t)size * sizeof(DATATYPE)); VRFY((outme != NULL), "malloc succeeded for outme"); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist); VRFY((fid >= 0), "H5Fcreate"); H5Pclose(plist); /* decide the hyperslab according to process number. */ get_slab(chunk_origin, chunk_dims, count, file_dims, size); /* select hyperslab in memory and file spaces. These two operations are * identical since the datasets are the same. */ memspace = H5Screate_simple(DIM, file_dims, NULL); ret1 = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); filespace = H5Screate_simple(DIM, file_dims, NULL); ret2 = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); VRFY((memspace >= 0), "memspace"); VRFY((filespace >= 0), "filespace"); VRFY((ret1 == 0), "mgroup memspace selection"); VRFY((ret2 == 0), "mgroup filespace selection"); dcpl = H5Pcreate(H5P_DATASET_CREATE); ret1 = H5Pset_chunk(dcpl, 2, chunk_size); VRFY((dcpl >= 0), "dataset creation property"); VRFY((ret1 == 0), "set chunk for dataset creation property"); /* creates ngroups groups under the root group, writes chunked * datasets in parallel. */ for (m = 0; m < ngroups; m++) { snprintf(gname, sizeof(gname), "group%d", m); gid = H5Gcreate2(fid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((gid > 0), gname); snprintf(dname, sizeof(dname), "dataset%d", m); did = H5Dcreate2(gid, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((did > 0), dname); for (i = 0; i < size; i++) for (j = 0; j < size; j++) outme[(i * size) + j] = (i + j) * 1000 + mpi_rank; ret1 = H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, outme); VRFY((ret1 == 0), "H5Dwrite"); ret1 = H5Dclose(did); VRFY((ret1 == 0), "H5Dclose"); ret1 = H5Gclose(gid); VRFY((ret1 == 0), "H5Gclose"); #ifdef BARRIER_CHECKS if (!((m + 1) % 10)) { printf("created %d groups\n", m + 1); MPI_Barrier(MPI_COMM_WORLD); } #endif /* BARRIER_CHECKS */ } H5Pclose(dcpl); H5Sclose(filespace); H5Sclose(memspace); ret1 = H5Fclose(fid); VRFY((ret1 == 0), "H5Fclose"); free(outme); } /* Let two sets of processes open and read different groups and chunked * datasets independently. */ void independent_group_read(void) { int mpi_rank, m; hid_t plist, fid; const H5Ptest_param_t *pt; char *filename; int ngroups; herr_t ret; pt = GetTestParameters(); filename = pt->name; ngroups = pt->count; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_GROUP_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf( " API functions for basic file, group, or dataset aren't supported with this connector\n"); fflush(stdout); } return; } plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); H5Pset_all_coll_metadata_ops(plist, false); fid = H5Fopen(filename, H5F_ACC_RDONLY, plist); VRFY((fid > 0), "H5Fopen"); H5Pclose(plist); /* open groups and read datasets. Odd number processes read even number * groups from the end; even number processes read odd number groups * from the beginning. */ if (mpi_rank % 2 == 0) { for (m = ngroups - 1; m == 0; m -= 2) group_dataset_read(fid, mpi_rank, m); } else { for (m = 0; m < ngroups; m += 2) group_dataset_read(fid, mpi_rank, m); } ret = H5Fclose(fid); VRFY((ret == 0), "H5Fclose"); } /* Open and read datasets and compare data */ static void group_dataset_read(hid_t fid, int mpi_rank, int m) { int ret, i, j, size; char gname[64], dname[32]; hid_t gid, did; DATATYPE *outdata = NULL; DATATYPE *indata = NULL; size = get_size(); indata = (DATATYPE *)malloc((size_t)size * (size_t)size * sizeof(DATATYPE)); VRFY((indata != NULL), "malloc succeeded for indata"); outdata = (DATATYPE *)malloc((size_t)size * (size_t)size * sizeof(DATATYPE)); VRFY((outdata != NULL), "malloc succeeded for outdata"); /* open every group under root group. */ snprintf(gname, sizeof(gname), "group%d", m); gid = H5Gopen2(fid, gname, H5P_DEFAULT); VRFY((gid > 0), gname); /* check the data. */ snprintf(dname, sizeof(dname), "dataset%d", m); did = H5Dopen2(gid, dname, H5P_DEFAULT); VRFY((did > 0), dname); H5Dread(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, indata); /* this is the original value */ for (i = 0; i < size; i++) for (j = 0; j < size; j++) outdata[(i * size) + j] = (i + j) * 1000 + mpi_rank; /* compare the original value(outdata) to the value in file(indata).*/ ret = check_value(indata, outdata, size); VRFY((ret == 0), "check the data"); ret = H5Dclose(did); VRFY((ret == 0), "H5Dclose"); ret = H5Gclose(gid); VRFY((ret == 0), "H5Gclose"); free(indata); free(outdata); } /* * Example of using PHDF5 to create multiple groups. Under the root group, * it creates ngroups groups. Under the first group just created, it creates * recursive subgroups of depth GROUP_DEPTH. In each created group, it * generates NDATASETS datasets. Each process write a hyperslab of an array * into the file. The structure is like * * root group * | * ---------------------------- ... ... ------------------------ * | | | ... ... | | * group0*+' group1*+' group2*+' ... ... group ngroups*+' * | * 1st_child_group*' * | * 2nd_child_group*' * | * : * : * | * GROUP_DEPTHth_child_group*' * * * means the group has dataset(s). * + means the group has attribute(s). * ' means the datasets in the groups have attribute(s). * */ void multiple_group_write(void) { int mpi_rank, mpi_size, size; int m; char gname[64]; hid_t fid, gid, plist, memspace, filespace; hsize_t chunk_origin[DIM]; hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM]; herr_t ret; const H5Ptest_param_t *pt; char *filename; int ngroups; pt = GetTestParameters(); filename = pt->name; ngroups = pt->count; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_GROUP_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_ATTR_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file, group, dataset, or attribute aren't supported with " "this connector\n"); fflush(stdout); } return; } size = get_size(); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist); H5Pclose(plist); /* decide the hyperslab according to process number. */ get_slab(chunk_origin, chunk_dims, count, file_dims, size); /* select hyperslab in memory and file spaces. These two operations are * identical since the datasets are the same. */ memspace = H5Screate_simple(DIM, file_dims, NULL); VRFY((memspace >= 0), "memspace"); ret = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); VRFY((ret >= 0), "mgroup memspace selection"); filespace = H5Screate_simple(DIM, file_dims, NULL); VRFY((filespace >= 0), "filespace"); ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); VRFY((ret >= 0), "mgroup filespace selection"); /* creates ngroups groups under the root group, writes datasets in * parallel. */ for (m = 0; m < ngroups; m++) { snprintf(gname, sizeof(gname), "group%d", m); gid = H5Gcreate2(fid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((gid > 0), gname); /* create attribute for these groups. */ write_attribute(gid, is_group, m); if (m != 0) write_dataset(memspace, filespace, gid); H5Gclose(gid); #ifdef BARRIER_CHECKS if (!((m + 1) % 10)) { printf("created %d groups\n", m + 1); MPI_Barrier(MPI_COMM_WORLD); } #endif /* BARRIER_CHECKS */ } /* recursively creates subgroups under the first group. */ gid = H5Gopen2(fid, "group0", H5P_DEFAULT); create_group_recursive(memspace, filespace, gid, 0); ret = H5Gclose(gid); VRFY((ret >= 0), "H5Gclose"); ret = H5Sclose(filespace); VRFY((ret >= 0), "H5Sclose"); ret = H5Sclose(memspace); VRFY((ret >= 0), "H5Sclose"); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose"); } /* * In a group, creates NDATASETS datasets. Each process writes a hyperslab * of a data array to the file. */ static void write_dataset(hid_t memspace, hid_t filespace, hid_t gid) { int i, j, n, size; int mpi_rank, mpi_size; char dname[32]; DATATYPE *outme = NULL; hid_t did; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); size = get_size(); outme = malloc((size_t)size * (size_t)size * sizeof(double)); VRFY((outme != NULL), "malloc succeeded for outme"); for (n = 0; n < NDATASET; n++) { snprintf(dname, sizeof(dname), "dataset%d", n); did = H5Dcreate2(gid, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((did > 0), dname); for (i = 0; i < size; i++) for (j = 0; j < size; j++) outme[(i * size) + j] = n * 1000 + mpi_rank; H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, outme); /* create attribute for these datasets.*/ write_attribute(did, is_dset, n); H5Dclose(did); } free(outme); } /* * Creates subgroups of depth GROUP_DEPTH recursively. Also writes datasets * in parallel in each group. */ static void create_group_recursive(hid_t memspace, hid_t filespace, hid_t gid, int counter) { hid_t child_gid; int mpi_rank; char gname[64]; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); #ifdef BARRIER_CHECKS if (!((counter + 1) % 10)) { printf("created %dth child groups\n", counter + 1); MPI_Barrier(MPI_COMM_WORLD); } #endif /* BARRIER_CHECKS */ snprintf(gname, sizeof(gname), "%dth_child_group", counter + 1); child_gid = H5Gcreate2(gid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((child_gid > 0), gname); /* write datasets in parallel. */ write_dataset(memspace, filespace, gid); if (counter < GROUP_DEPTH) create_group_recursive(memspace, filespace, child_gid, counter + 1); H5Gclose(child_gid); } /* * This function is to verify the data from multiple group testing. It opens * every dataset in every group and check their correctness. */ void multiple_group_read(void) { int mpi_rank, mpi_size, error_num, size; int m; char gname[64]; hid_t plist, fid, gid, memspace, filespace; hsize_t chunk_origin[DIM]; hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM]; const H5Ptest_param_t *pt; char *filename; int ngroups; pt = GetTestParameters(); filename = pt->name; ngroups = pt->count; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_GROUP_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_ATTR_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file, group, dataset, or attribute aren't supported with " "this connector\n"); fflush(stdout); } return; } size = get_size(); plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); fid = H5Fopen(filename, H5F_ACC_RDONLY, plist); H5Pclose(plist); /* decide hyperslab for each process */ get_slab(chunk_origin, chunk_dims, count, file_dims, size); /* select hyperslab for memory and file space */ memspace = H5Screate_simple(DIM, file_dims, NULL); H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); filespace = H5Screate_simple(DIM, file_dims, NULL); H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims); /* open every group under root group. */ for (m = 0; m < ngroups; m++) { snprintf(gname, sizeof(gname), "group%d", m); gid = H5Gopen2(fid, gname, H5P_DEFAULT); VRFY((gid > 0), gname); /* check the data. */ if (m != 0) if ((error_num = read_dataset(memspace, filespace, gid)) > 0) nerrors += error_num; /* check attribute.*/ error_num = 0; if ((error_num = read_attribute(gid, is_group, m)) > 0) nerrors += error_num; H5Gclose(gid); #ifdef BARRIER_CHECKS if (!((m + 1) % 10)) MPI_Barrier(MPI_COMM_WORLD); #endif /* BARRIER_CHECKS */ } /* open all the groups in vertical direction. */ gid = H5Gopen2(fid, "group0", H5P_DEFAULT); VRFY((gid > 0), "group0"); recursive_read_group(memspace, filespace, gid, 0); H5Gclose(gid); H5Sclose(filespace); H5Sclose(memspace); H5Fclose(fid); } /* * This function opens all the datasets in a certain, checks the data using * dataset_vrfy function. */ static int read_dataset(hid_t memspace, hid_t filespace, hid_t gid) { int i, j, n, mpi_rank, mpi_size, size, attr_errors = 0, vrfy_errors = 0; char dname[32]; DATATYPE *outdata = NULL, *indata = NULL; hid_t did; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); size = get_size(); indata = (DATATYPE *)malloc((size_t)size * (size_t)size * sizeof(DATATYPE)); VRFY((indata != NULL), "malloc succeeded for indata"); outdata = (DATATYPE *)malloc((size_t)size * (size_t)size * sizeof(DATATYPE)); VRFY((outdata != NULL), "malloc succeeded for outdata"); for (n = 0; n < NDATASET; n++) { snprintf(dname, sizeof(dname), "dataset%d", n); did = H5Dopen2(gid, dname, H5P_DEFAULT); VRFY((did > 0), dname); H5Dread(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, indata); /* this is the original value */ for (i = 0; i < size; i++) for (j = 0; j < size; j++) { *outdata = n * 1000 + mpi_rank; outdata++; } outdata -= size * size; /* compare the original value(outdata) to the value in file(indata).*/ vrfy_errors = check_value(indata, outdata, size); /* check attribute.*/ if ((attr_errors = read_attribute(did, is_dset, n)) > 0) vrfy_errors += attr_errors; H5Dclose(did); } free(indata); free(outdata); return vrfy_errors; } /* * This recursive function opens all the groups in vertical direction and * checks the data. */ static void recursive_read_group(hid_t memspace, hid_t filespace, hid_t gid, int counter) { hid_t child_gid; int mpi_rank, err_num = 0; char gname[64]; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); #ifdef BARRIER_CHECKS if ((counter + 1) % 10) MPI_Barrier(MPI_COMM_WORLD); #endif /* BARRIER_CHECKS */ if ((err_num = read_dataset(memspace, filespace, gid))) nerrors += err_num; if (counter < GROUP_DEPTH) { snprintf(gname, sizeof(gname), "%dth_child_group", counter + 1); child_gid = H5Gopen2(gid, gname, H5P_DEFAULT); VRFY((child_gid > 0), gname); recursive_read_group(memspace, filespace, child_gid, counter + 1); H5Gclose(child_gid); } } /* Create and write attribute for a group or a dataset. For groups, attribute * is a scalar datum; for dataset, it is a one-dimensional array. */ static void write_attribute(hid_t obj_id, int this_type, int num) { hid_t sid, aid; hsize_t dspace_dims[1] = {8}; int i, mpi_rank, attr_data[8], dspace_rank = 1; char attr_name[32]; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); if (this_type == is_group) { snprintf(attr_name, sizeof(attr_name), "Group Attribute %d", num); sid = H5Screate(H5S_SCALAR); aid = H5Acreate2(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT); H5Awrite(aid, H5T_NATIVE_INT, &num); H5Aclose(aid); H5Sclose(sid); } /* end if */ else if (this_type == is_dset) { snprintf(attr_name, sizeof(attr_name), "Dataset Attribute %d", num); for (i = 0; i < 8; i++) attr_data[i] = i; sid = H5Screate_simple(dspace_rank, dspace_dims, NULL); aid = H5Acreate2(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT); H5Awrite(aid, H5T_NATIVE_INT, attr_data); H5Aclose(aid); H5Sclose(sid); } /* end else-if */ } /* Read and verify attribute for group or dataset. */ static int read_attribute(hid_t obj_id, int this_type, int num) { hid_t aid; hsize_t group_block[2] = {1, 1}, dset_block[2] = {1, 8}; int i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0; char attr_name[32]; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); if (this_type == is_group) { snprintf(attr_name, sizeof(attr_name), "Group Attribute %d", num); aid = H5Aopen(obj_id, attr_name, H5P_DEFAULT); H5Aread(aid, H5T_NATIVE_INT, &in_num); vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block, &in_num, &num); H5Aclose(aid); } else if (this_type == is_dset) { snprintf(attr_name, sizeof(attr_name), "Dataset Attribute %d", num); for (i = 0; i < 8; i++) out_data[i] = i; aid = H5Aopen(obj_id, attr_name, H5P_DEFAULT); H5Aread(aid, H5T_NATIVE_INT, in_data); vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data, out_data); H5Aclose(aid); } return vrfy_errors; } /* This functions compares the original data with the read-in data for its * hyperslab part only by process ID. */ static int check_value(DATATYPE *indata, DATATYPE *outdata, int size) { int mpi_rank, mpi_size, err_num = 0; hsize_t i, j; hsize_t chunk_origin[DIM]; hsize_t chunk_dims[DIM], count[DIM]; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); get_slab(chunk_origin, chunk_dims, count, NULL, size); indata += chunk_origin[0] * (hsize_t)size; outdata += chunk_origin[0] * (hsize_t)size; for (i = chunk_origin[0]; i < (chunk_origin[0] + chunk_dims[0]); i++) for (j = chunk_origin[1]; j < (chunk_origin[1] + chunk_dims[1]); j++) { if (*indata != *outdata) if (err_num++ < MAX_ERR_REPORT || VERBOSE_MED) printf("Dataset Verify failed at [%lu][%lu](row %lu, col%lu): expect %d, got %d\n", (unsigned long)i, (unsigned long)j, (unsigned long)i, (unsigned long)j, *outdata, *indata); } if (err_num > MAX_ERR_REPORT && !VERBOSE_MED) printf("[more errors ...]\n"); if (err_num) printf("%d errors found in check_value\n", err_num); return err_num; } /* Decide the portion of data chunk in dataset by process ID. */ static void get_slab(hsize_t chunk_origin[], hsize_t chunk_dims[], hsize_t count[], hsize_t file_dims[], int size) { int mpi_rank, mpi_size; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); if (chunk_origin != NULL) { chunk_origin[0] = (hsize_t)mpi_rank * (hsize_t)(size / mpi_size); chunk_origin[1] = 0; } if (chunk_dims != NULL) { chunk_dims[0] = (hsize_t)(size / mpi_size); chunk_dims[1] = (hsize_t)size; } if (file_dims != NULL) file_dims[0] = file_dims[1] = (hsize_t)size; if (count != NULL) count[0] = count[1] = 1; } /* * This function is based on bug demonstration code provided by Thomas * Guignon(thomas.guignon@ifp.fr), and is intended to verify the * correctness of my fix for that bug. * * In essence, the bug appeared when at least one process attempted to * write a point selection -- for which collective I/O is not supported, * and at least one other attempted to write some other type of selection * for which collective I/O is supported. * * Since the processes did not compare notes before performing the I/O, * some would attempt collective I/O while others performed independent * I/O. A hang resulted. * * This function reproduces this situation. At present the test hangs * on failure. * JRM - 9/13/04 */ #define N 4 void io_mode_confusion(void) { /* * HDF5 APIs definitions */ const int rank = 1; const char *dataset_name = "IntArray"; hid_t file_id, dset_id; /* file and dataset identifiers */ hid_t filespace, memspace; /* file and memory dataspace */ /* identifiers */ hsize_t dimsf[1]; /* dataset dimensions */ int data[N] = {1}; /* pointer to data buffer to write */ hsize_t coord[N] = {0L, 1L, 2L, 3L}; hid_t plist_id; /* property list identifier */ herr_t status; /* * MPI variables */ int mpi_size, mpi_rank; /* * test bed related variables */ const char *fcn_name = "io_mode_confusion"; const bool verbose = false; const H5Ptest_param_t *pt; char *filename; pt = GetTestParameters(); filename = pt->name; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_MORE)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file, dataset, or dataset more aren't supported with this " "connector\n"); fflush(stdout); } return; } /* * Set up file access property list with parallel I/O access */ if (verbose) fprintf(stdout, "%0d:%s: Setting up property list.\n", mpi_rank, fcn_name); plist_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((plist_id != -1), "H5Pcreate() failed"); status = H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL); VRFY((status >= 0), "H5Pset_fapl_mpio() failed"); /* * Create a new file collectively and release property list identifier. */ if (verbose) fprintf(stdout, "%0d:%s: Creating new file.\n", mpi_rank, fcn_name); file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id); VRFY((file_id >= 0), "H5Fcreate() failed"); status = H5Pclose(plist_id); VRFY((status >= 0), "H5Pclose() failed"); /* * Create the dataspace for the dataset. */ if (verbose) fprintf(stdout, "%0d:%s: Creating the dataspace for the dataset.\n", mpi_rank, fcn_name); dimsf[0] = N; filespace = H5Screate_simple(rank, dimsf, NULL); VRFY((filespace >= 0), "H5Screate_simple() failed."); /* * Create the dataset with default properties and close filespace. */ if (verbose) fprintf(stdout, "%0d:%s: Creating the dataset, and closing filespace.\n", mpi_rank, fcn_name); dset_id = H5Dcreate2(file_id, dataset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dset_id >= 0), "H5Dcreate2() failed"); status = H5Sclose(filespace); VRFY((status >= 0), "H5Sclose() failed"); if (verbose) fprintf(stdout, "%0d:%s: Calling H5Screate_simple().\n", mpi_rank, fcn_name); memspace = H5Screate_simple(rank, dimsf, NULL); VRFY((memspace >= 0), "H5Screate_simple() failed."); if (mpi_rank == 0) { if (verbose) fprintf(stdout, "%0d:%s: Calling H5Sselect_all(memspace).\n", mpi_rank, fcn_name); status = H5Sselect_all(memspace); VRFY((status >= 0), "H5Sselect_all() failed"); } else { if (verbose) fprintf(stdout, "%0d:%s: Calling H5Sselect_none(memspace).\n", mpi_rank, fcn_name); status = H5Sselect_none(memspace); VRFY((status >= 0), "H5Sselect_none() failed"); } if (verbose) fprintf(stdout, "%0d:%s: Calling MPI_Barrier().\n", mpi_rank, fcn_name); MPI_Barrier(MPI_COMM_WORLD); if (verbose) fprintf(stdout, "%0d:%s: Calling H5Dget_space().\n", mpi_rank, fcn_name); filespace = H5Dget_space(dset_id); VRFY((filespace >= 0), "H5Dget_space() failed"); /* select all */ if (mpi_rank == 0) { if (verbose) fprintf(stdout, "%0d:%s: Calling H5Sselect_elements() -- set up hang?\n", mpi_rank, fcn_name); status = H5Sselect_elements(filespace, H5S_SELECT_SET, N, (const hsize_t *)&coord); VRFY((status >= 0), "H5Sselect_elements() failed"); } else { /* select nothing */ if (verbose) fprintf(stdout, "%0d:%s: Calling H5Sselect_none().\n", mpi_rank, fcn_name); status = H5Sselect_none(filespace); VRFY((status >= 0), "H5Sselect_none() failed"); } if (verbose) fprintf(stdout, "%0d:%s: Calling MPI_Barrier().\n", mpi_rank, fcn_name); MPI_Barrier(MPI_COMM_WORLD); if (verbose) fprintf(stdout, "%0d:%s: Calling H5Pcreate().\n", mpi_rank, fcn_name); plist_id = H5Pcreate(H5P_DATASET_XFER); VRFY((plist_id != -1), "H5Pcreate() failed"); if (verbose) fprintf(stdout, "%0d:%s: Calling H5Pset_dxpl_mpio().\n", mpi_rank, fcn_name); status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE); VRFY((status >= 0), "H5Pset_dxpl_mpio() failed"); if (dxfer_coll_type == DXFER_INDEPENDENT_IO) { status = H5Pset_dxpl_mpio_collective_opt(plist_id, H5FD_MPIO_INDIVIDUAL_IO); VRFY((status >= 0), "set independent IO collectively succeeded"); } if (verbose) fprintf(stdout, "%0d:%s: Calling H5Dwrite() -- hang here?.\n", mpi_rank, fcn_name); status = H5Dwrite(dset_id, H5T_NATIVE_INT, memspace, filespace, plist_id, data); if (verbose) fprintf(stdout, "%0d:%s: Returned from H5Dwrite(), status=%d.\n", mpi_rank, fcn_name, status); VRFY((status >= 0), "H5Dwrite() failed"); /* * Close/release resources. */ if (verbose) fprintf(stdout, "%0d:%s: Cleaning up from test.\n", mpi_rank, fcn_name); status = H5Dclose(dset_id); VRFY((status >= 0), "H5Dclose() failed"); status = H5Sclose(filespace); VRFY((status >= 0), "H5Dclose() failed"); status = H5Sclose(memspace); VRFY((status >= 0), "H5Sclose() failed"); status = H5Pclose(plist_id); VRFY((status >= 0), "H5Pclose() failed"); status = H5Fclose(file_id); VRFY((status >= 0), "H5Fclose() failed"); if (verbose) fprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name); return; } /* io_mode_confusion() */ #undef N /* * At present, the object header code maintains an image of its on disk * representation, which is updates as necessary instead of generating on * request. * * Prior to the fix that this test in designed to verify, the image of the * on disk representation was only updated on flush -- not when the object * header was marked clean. * * This worked perfectly well as long as all writes of a given object * header were written from a single process. However, with the implementation * of round robin metadata data writes in parallel HDF5, this is no longer * the case -- it is possible for a given object header to be flushed from * several different processes, with the object header simply being marked * clean in all other processes on each flush. This resulted in NULL or * out of data object header information being written to disk. * * To repair this, I modified the object header code to update its * on disk image both on flush on when marked clean. * * This test is directed at verifying that the fix performs as expected. * * The test functions by creating a HDF5 file with several small datasets, * and then flushing the file. This should result of at least one of * the associated object headers being flushed by a process other than * process 0. * * Then for each data set, add an attribute and flush the file again. * * Close the file and re-open it. * * Open the each of the data sets in turn. If all opens are successful, * the test passes. Otherwise the test fails. * * Note that this test will probably become irrelevant shortly, when we * land the journaling modifications on the trunk -- at which point all * cache clients will have to construct on disk images on demand. * * JRM -- 10/13/10 */ #define NUM_DATA_SETS 4 #define LOCAL_DATA_SIZE 4 #define LARGE_ATTR_SIZE 256 /* Since all even and odd processes are split into writer and reader comm * respectively, process 0 and 1 in COMM_WORLD become the root process of * the writer and reader comm respectively. */ #define Writer_Root 0 #define Reader_Root 1 #define Reader_wait(mpi_err, xsteps) mpi_err = MPI_Bcast(&xsteps, 1, MPI_INT, Writer_Root, MPI_COMM_WORLD) #define Reader_result(mpi_err, xsteps_done) \ mpi_err = MPI_Bcast(&xsteps_done, 1, MPI_INT, Reader_Root, MPI_COMM_WORLD) #define Reader_check(mpi_err, xsteps, xsteps_done) \ { \ Reader_wait(mpi_err, xsteps); \ Reader_result(mpi_err, xsteps_done); \ } /* object names used by both rr_obj_hdr_flush_confusion and * rr_obj_hdr_flush_confusion_reader. */ const char *dataset_name[NUM_DATA_SETS] = {"dataset_0", "dataset_1", "dataset_2", "dataset_3"}; const char *att_name[NUM_DATA_SETS] = {"attribute_0", "attribute_1", "attribute_2", "attribute_3"}; const char *lg_att_name[NUM_DATA_SETS] = {"large_attribute_0", "large_attribute_1", "large_attribute_2", "large_attribute_3"}; void rr_obj_hdr_flush_confusion(void) { /* MPI variables */ /* private communicator size and rank */ int mpi_size; int mpi_rank; int mrc; /* mpi error code */ int is_reader; /* 1 for reader process; 0 for writer process. */ MPI_Comm comm; /* test bed related variables */ const char *fcn_name = "rr_obj_hdr_flush_confusion"; const bool verbose = false; /* Create two new private communicators from MPI_COMM_WORLD. * Even and odd ranked processes go to comm_writers and comm_readers * respectively. */ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_FLUSH_REFRESH) || !(vol_cap_flags_g & H5VL_CAP_FLAG_ATTR_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_ATTR_MORE)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file, dataset, attribute, dataset more, attribute more, or " "file flush aren't supported with this connector\n"); fflush(stdout); } return; } assert(mpi_size > 2); is_reader = mpi_rank % 2; mrc = MPI_Comm_split(MPI_COMM_WORLD, is_reader, mpi_rank, &comm); VRFY((mrc == MPI_SUCCESS), "MPI_Comm_split"); /* The reader processes branches off to do reading * while the writer processes continues to do writing * Whenever writers finish one writing step, including a H5Fflush, * they inform the readers, via MPI_COMM_WORLD, to verify. * They will wait for the result from the readers before doing the next * step. When all steps are done, they inform readers to end. */ if (is_reader) rr_obj_hdr_flush_confusion_reader(comm); else rr_obj_hdr_flush_confusion_writer(comm); MPI_Comm_free(&comm); if (verbose) fprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name); return; } /* rr_obj_hdr_flush_confusion() */ void rr_obj_hdr_flush_confusion_writer(MPI_Comm comm) { int i; int j; hid_t file_id = H5I_INVALID_HID; hid_t fapl_id = H5I_INVALID_HID; hid_t dxpl_id = H5I_INVALID_HID; hid_t att_id[NUM_DATA_SETS]; hid_t att_space[NUM_DATA_SETS]; hid_t lg_att_id[NUM_DATA_SETS]; hid_t lg_att_space[NUM_DATA_SETS]; hid_t disk_space[NUM_DATA_SETS]; hid_t mem_space[NUM_DATA_SETS]; hid_t dataset[NUM_DATA_SETS]; hsize_t att_size[1]; hsize_t lg_att_size[1]; hsize_t disk_count[1]; hsize_t disk_size[1]; hsize_t disk_start[1]; hsize_t mem_count[1]; hsize_t mem_size[1]; hsize_t mem_start[1]; herr_t err; double data[LOCAL_DATA_SIZE]; double att[LOCAL_DATA_SIZE]; double lg_att[LARGE_ATTR_SIZE]; /* MPI variables */ /* world communication size and rank */ int mpi_world_size; int mpi_world_rank; /* private communicator size and rank */ int mpi_size; int mpi_rank; int mrc; /* mpi error code */ /* steps to verify and have been verified */ int steps = 0; int steps_done = 0; /* test bed related variables */ const char *fcn_name = "rr_obj_hdr_flush_confusion_writer"; const bool verbose = false; const H5Ptest_param_t *pt; char *filename; /* * setup test bed related variables: */ pt = (const H5Ptest_param_t *)GetTestParameters(); filename = pt->name; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_world_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_world_size); MPI_Comm_rank(comm, &mpi_rank); MPI_Comm_size(comm, &mpi_size); /* * Set up file access property list with parallel I/O access */ if (verbose) fprintf(stdout, "%0d:%s: Setting up property list.\n", mpi_rank, fcn_name); fapl_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((fapl_id != -1), "H5Pcreate(H5P_FILE_ACCESS) failed"); err = H5Pset_fapl_mpio(fapl_id, comm, MPI_INFO_NULL); VRFY((err >= 0), "H5Pset_fapl_mpio() failed"); /* * Create a new file collectively and release property list identifier. */ if (verbose) fprintf(stdout, "%0d:%s: Creating new file \"%s\".\n", mpi_rank, fcn_name, filename); file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); VRFY((file_id >= 0), "H5Fcreate() failed"); err = H5Pclose(fapl_id); VRFY((err >= 0), "H5Pclose(fapl_id) failed"); /* * Step 1: create the data sets and write data. */ if (verbose) fprintf(stdout, "%0d:%s: Creating the datasets.\n", mpi_rank, fcn_name); disk_size[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_size); mem_size[0] = (hsize_t)(LOCAL_DATA_SIZE); for (i = 0; i < NUM_DATA_SETS; i++) { disk_space[i] = H5Screate_simple(1, disk_size, NULL); VRFY((disk_space[i] >= 0), "H5Screate_simple(1) failed.\n"); dataset[i] = H5Dcreate2(file_id, dataset_name[i], H5T_NATIVE_DOUBLE, disk_space[i], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset[i] >= 0), "H5Dcreate(1) failed.\n"); } /* * setup data transfer property list */ if (verbose) fprintf(stdout, "%0d:%s: Setting up dxpl.\n", mpi_rank, fcn_name); dxpl_id = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl_id != -1), "H5Pcreate(H5P_DATASET_XFER) failed.\n"); err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); VRFY((err >= 0), "H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) failed.\n"); /* * write data to the data sets */ if (verbose) fprintf(stdout, "%0d:%s: Writing datasets.\n", mpi_rank, fcn_name); disk_count[0] = (hsize_t)(LOCAL_DATA_SIZE); disk_start[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_rank); mem_count[0] = (hsize_t)(LOCAL_DATA_SIZE); mem_start[0] = (hsize_t)(0); for (j = 0; j < LOCAL_DATA_SIZE; j++) { data[j] = (double)(mpi_rank + 1); } for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Sselect_hyperslab(disk_space[i], H5S_SELECT_SET, disk_start, NULL, disk_count, NULL); VRFY((err >= 0), "H5Sselect_hyperslab(1) failed.\n"); mem_space[i] = H5Screate_simple(1, mem_size, NULL); VRFY((mem_space[i] >= 0), "H5Screate_simple(2) failed.\n"); err = H5Sselect_hyperslab(mem_space[i], H5S_SELECT_SET, mem_start, NULL, mem_count, NULL); VRFY((err >= 0), "H5Sselect_hyperslab(2) failed.\n"); err = H5Dwrite(dataset[i], H5T_NATIVE_DOUBLE, mem_space[i], disk_space[i], dxpl_id, data); VRFY((err >= 0), "H5Dwrite(1) failed.\n"); for (j = 0; j < LOCAL_DATA_SIZE; j++) data[j] *= 10.0; } /* * close the data spaces */ if (verbose) fprintf(stdout, "%0d:%s: closing dataspaces.\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Sclose(disk_space[i]); VRFY((err >= 0), "H5Sclose(disk_space[i]) failed.\n"); err = H5Sclose(mem_space[i]); VRFY((err >= 0), "H5Sclose(mem_space[i]) failed.\n"); } /* End of Step 1: create the data sets and write data. */ /* * flush the metadata cache */ if (verbose) fprintf(stdout, "%0d:%s: flushing metadata cache.\n", mpi_rank, fcn_name); err = H5Fflush(file_id, H5F_SCOPE_GLOBAL); VRFY((err >= 0), "H5Fflush(1) failed.\n"); /* Tell the reader to check the file up to steps. */ steps++; Reader_check(mrc, steps, steps_done); VRFY((MPI_SUCCESS == mrc), "Reader_check failed"); /* * Step 2: write attributes to each dataset */ if (verbose) fprintf(stdout, "%0d:%s: writing attributes.\n", mpi_rank, fcn_name); att_size[0] = (hsize_t)(LOCAL_DATA_SIZE); for (j = 0; j < LOCAL_DATA_SIZE; j++) { att[j] = (double)(j + 1); } for (i = 0; i < NUM_DATA_SETS; i++) { att_space[i] = H5Screate_simple(1, att_size, NULL); VRFY((att_space[i] >= 0), "H5Screate_simple(3) failed.\n"); att_id[i] = H5Acreate2(dataset[i], att_name[i], H5T_NATIVE_DOUBLE, att_space[i], H5P_DEFAULT, H5P_DEFAULT); VRFY((att_id[i] >= 0), "H5Acreate(1) failed.\n"); err = H5Awrite(att_id[i], H5T_NATIVE_DOUBLE, att); VRFY((err >= 0), "H5Awrite(1) failed.\n"); for (j = 0; j < LOCAL_DATA_SIZE; j++) { att[j] /= 10.0; } } /* * close attribute IDs and spaces */ if (verbose) fprintf(stdout, "%0d:%s: closing attr ids and spaces .\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Sclose(att_space[i]); VRFY((err >= 0), "H5Sclose(att_space[i]) failed.\n"); err = H5Aclose(att_id[i]); VRFY((err >= 0), "H5Aclose(att_id[i]) failed.\n"); } /* End of Step 2: write attributes to each dataset */ /* * flush the metadata cache again */ if (verbose) fprintf(stdout, "%0d:%s: flushing metadata cache.\n", mpi_rank, fcn_name); err = H5Fflush(file_id, H5F_SCOPE_GLOBAL); VRFY((err >= 0), "H5Fflush(2) failed.\n"); /* Tell the reader to check the file up to steps. */ steps++; Reader_check(mrc, steps, steps_done); VRFY((MPI_SUCCESS == mrc), "Reader_check failed"); /* * Step 3: write large attributes to each dataset */ if (verbose) fprintf(stdout, "%0d:%s: writing large attributes.\n", mpi_rank, fcn_name); lg_att_size[0] = (hsize_t)(LARGE_ATTR_SIZE); for (j = 0; j < LARGE_ATTR_SIZE; j++) { lg_att[j] = (double)(j + 1); } for (i = 0; i < NUM_DATA_SETS; i++) { lg_att_space[i] = H5Screate_simple(1, lg_att_size, NULL); VRFY((lg_att_space[i] >= 0), "H5Screate_simple(4) failed.\n"); lg_att_id[i] = H5Acreate2(dataset[i], lg_att_name[i], H5T_NATIVE_DOUBLE, lg_att_space[i], H5P_DEFAULT, H5P_DEFAULT); VRFY((lg_att_id[i] >= 0), "H5Acreate(2) failed.\n"); err = H5Awrite(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att); VRFY((err >= 0), "H5Awrite(2) failed.\n"); for (j = 0; j < LARGE_ATTR_SIZE; j++) { lg_att[j] /= 10.0; } } /* Step 3: write large attributes to each dataset */ /* * flush the metadata cache yet again to clean the object headers. * * This is an attempt to create a situation where we have dirty * object header continuation chunks, but clean object headers * to verify a speculative bug fix -- it doesn't seem to work, * but I will leave the code in anyway, as the object header * code is going to change a lot in the near future. */ if (verbose) fprintf(stdout, "%0d:%s: flushing metadata cache.\n", mpi_rank, fcn_name); err = H5Fflush(file_id, H5F_SCOPE_GLOBAL); VRFY((err >= 0), "H5Fflush(3) failed.\n"); /* Tell the reader to check the file up to steps. */ steps++; Reader_check(mrc, steps, steps_done); VRFY((MPI_SUCCESS == mrc), "Reader_check failed"); /* * Step 4: write different large attributes to each dataset */ if (verbose) fprintf(stdout, "%0d:%s: writing different large attributes.\n", mpi_rank, fcn_name); for (j = 0; j < LARGE_ATTR_SIZE; j++) { lg_att[j] = (double)(j + 2); } for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Awrite(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att); VRFY((err >= 0), "H5Awrite(2) failed.\n"); for (j = 0; j < LARGE_ATTR_SIZE; j++) { lg_att[j] /= 10.0; } } /* End of Step 4: write different large attributes to each dataset */ /* * flush the metadata cache again */ if (verbose) fprintf(stdout, "%0d:%s: flushing metadata cache.\n", mpi_rank, fcn_name); err = H5Fflush(file_id, H5F_SCOPE_GLOBAL); VRFY((err >= 0), "H5Fflush(3) failed.\n"); /* Tell the reader to check the file up to steps. */ steps++; Reader_check(mrc, steps, steps_done); VRFY((MPI_SUCCESS == mrc), "Reader_check failed"); /* Step 5: Close all objects and the file */ /* * close large attribute IDs and spaces */ if (verbose) fprintf(stdout, "%0d:%s: closing large attr ids and spaces .\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Sclose(lg_att_space[i]); VRFY((err >= 0), "H5Sclose(lg_att_space[i]) failed.\n"); err = H5Aclose(lg_att_id[i]); VRFY((err >= 0), "H5Aclose(lg_att_id[i]) failed.\n"); } /* * close the data sets */ if (verbose) fprintf(stdout, "%0d:%s: closing datasets .\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Dclose(dataset[i]); VRFY((err >= 0), "H5Dclose(dataset[i])1 failed.\n"); } /* * close the data transfer property list. */ if (verbose) fprintf(stdout, "%0d:%s: closing dxpl .\n", mpi_rank, fcn_name); err = H5Pclose(dxpl_id); VRFY((err >= 0), "H5Pclose(dxpl_id) failed.\n"); /* * Close file. */ if (verbose) fprintf(stdout, "%0d:%s: closing file.\n", mpi_rank, fcn_name); err = H5Fclose(file_id); VRFY((err >= 0), "H5Fclose(1) failed"); /* End of Step 5: Close all objects and the file */ /* Tell the reader to check the file up to steps. */ steps++; Reader_check(mrc, steps, steps_done); VRFY((MPI_SUCCESS == mrc), "Reader_check failed"); /* All done. Inform reader to end. */ steps = 0; Reader_check(mrc, steps, steps_done); VRFY((MPI_SUCCESS == mrc), "Reader_check failed"); if (verbose) fprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name); return; } /* rr_obj_hdr_flush_confusion_writer() */ void rr_obj_hdr_flush_confusion_reader(MPI_Comm comm) { int i; int j; hid_t file_id = H5I_INVALID_HID; hid_t fapl_id = H5I_INVALID_HID; hid_t dxpl_id = H5I_INVALID_HID; hid_t lg_att_id[NUM_DATA_SETS]; hid_t lg_att_type[NUM_DATA_SETS]; hid_t disk_space[NUM_DATA_SETS]; hid_t mem_space[NUM_DATA_SETS]; hid_t dataset[NUM_DATA_SETS]; hsize_t disk_count[1]; hsize_t disk_start[1]; hsize_t mem_count[1]; hsize_t mem_size[1]; hsize_t mem_start[1]; herr_t err; htri_t tri_err; double data[LOCAL_DATA_SIZE]; double data_read[LOCAL_DATA_SIZE]; double att[LOCAL_DATA_SIZE]; double att_read[LOCAL_DATA_SIZE]; double lg_att[LARGE_ATTR_SIZE]; double lg_att_read[LARGE_ATTR_SIZE]; /* MPI variables */ /* world communication size and rank */ int mpi_world_size; int mpi_world_rank; /* private communicator size and rank */ int mpi_size; int mpi_rank; int mrc; /* mpi error code */ int steps = -1; /* How far (steps) to verify the file */ int steps_done = -1; /* How far (steps) have been verified */ /* test bed related variables */ const char *fcn_name = "rr_obj_hdr_flush_confusion_reader"; const bool verbose = false; const H5Ptest_param_t *pt; char *filename; /* * setup test bed related variables: */ pt = (const H5Ptest_param_t *)GetTestParameters(); filename = pt->name; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_world_rank); MPI_Comm_size(MPI_COMM_WORLD, &mpi_world_size); MPI_Comm_rank(comm, &mpi_rank); MPI_Comm_size(comm, &mpi_size); /* Repeatedly re-open the file and verify its contents until it is */ /* told to end (when steps=0). */ while (steps_done != 0) { Reader_wait(mrc, steps); VRFY((mrc >= 0), "Reader_wait failed"); steps_done = 0; if (steps > 0) { /* * Set up file access property list with parallel I/O access */ if (verbose) fprintf(stdout, "%0d:%s: Setting up property list.\n", mpi_rank, fcn_name); fapl_id = H5Pcreate(H5P_FILE_ACCESS); VRFY((fapl_id != -1), "H5Pcreate(H5P_FILE_ACCESS) failed"); err = H5Pset_fapl_mpio(fapl_id, comm, MPI_INFO_NULL); VRFY((err >= 0), "H5Pset_fapl_mpio() failed"); /* * Create a new file collectively and release property list identifier. */ if (verbose) fprintf(stdout, "%0d:%s: Re-open file \"%s\".\n", mpi_rank, fcn_name, filename); file_id = H5Fopen(filename, H5F_ACC_RDONLY, fapl_id); VRFY((file_id >= 0), "H5Fopen() failed"); err = H5Pclose(fapl_id); VRFY((err >= 0), "H5Pclose(fapl_id) failed"); #if 1 if (steps >= 1) { /*=====================================================* * Step 1: open the data sets and read data. *=====================================================*/ if (verbose) fprintf(stdout, "%0d:%s: opening the datasets.\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { dataset[i] = -1; } for (i = 0; i < NUM_DATA_SETS; i++) { dataset[i] = H5Dopen2(file_id, dataset_name[i], H5P_DEFAULT); VRFY((dataset[i] >= 0), "H5Dopen(1) failed.\n"); disk_space[i] = H5Dget_space(dataset[i]); VRFY((disk_space[i] >= 0), "H5Dget_space failed.\n"); } /* * setup data transfer property list */ if (verbose) fprintf(stdout, "%0d:%s: Setting up dxpl.\n", mpi_rank, fcn_name); dxpl_id = H5Pcreate(H5P_DATASET_XFER); VRFY((dxpl_id != -1), "H5Pcreate(H5P_DATASET_XFER) failed.\n"); err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); VRFY((err >= 0), "H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) failed.\n"); /* * read data from the data sets */ if (verbose) fprintf(stdout, "%0d:%s: Reading datasets.\n", mpi_rank, fcn_name); disk_count[0] = (hsize_t)(LOCAL_DATA_SIZE); disk_start[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_rank); mem_size[0] = (hsize_t)(LOCAL_DATA_SIZE); mem_count[0] = (hsize_t)(LOCAL_DATA_SIZE); mem_start[0] = (hsize_t)(0); /* set up expected data for verification */ for (j = 0; j < LOCAL_DATA_SIZE; j++) { data[j] = (double)(mpi_rank + 1); } for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Sselect_hyperslab(disk_space[i], H5S_SELECT_SET, disk_start, NULL, disk_count, NULL); VRFY((err >= 0), "H5Sselect_hyperslab(1) failed.\n"); mem_space[i] = H5Screate_simple(1, mem_size, NULL); VRFY((mem_space[i] >= 0), "H5Screate_simple(2) failed.\n"); err = H5Sselect_hyperslab(mem_space[i], H5S_SELECT_SET, mem_start, NULL, mem_count, NULL); VRFY((err >= 0), "H5Sselect_hyperslab(2) failed.\n"); err = H5Dread(dataset[i], H5T_NATIVE_DOUBLE, mem_space[i], disk_space[i], dxpl_id, data_read); VRFY((err >= 0), "H5Dread(1) failed.\n"); /* compare read data with expected data */ for (j = 0; j < LOCAL_DATA_SIZE; j++) if (!H5_DBL_ABS_EQUAL(data_read[j], data[j])) { fprintf(stdout, "%0d:%s: Reading datasets value failed in " "Dataset %d, at position %d: expect %f, got %f.\n", mpi_rank, fcn_name, i, j, data[j], data_read[j]); nerrors++; } for (j = 0; j < LOCAL_DATA_SIZE; j++) data[j] *= 10.0; } /* * close the data spaces */ if (verbose) fprintf(stdout, "%0d:%s: closing dataspaces.\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { err = H5Sclose(disk_space[i]); VRFY((err >= 0), "H5Sclose(disk_space[i]) failed.\n"); err = H5Sclose(mem_space[i]); VRFY((err >= 0), "H5Sclose(mem_space[i]) failed.\n"); } steps_done++; } /* End of Step 1: open the data sets and read data. */ #endif #if 1 /*=====================================================* * Step 2: reading attributes from each dataset *=====================================================*/ if (steps >= 2) { if (verbose) fprintf(stdout, "%0d:%s: reading attributes.\n", mpi_rank, fcn_name); for (j = 0; j < LOCAL_DATA_SIZE; j++) { att[j] = (double)(j + 1); } for (i = 0; i < NUM_DATA_SETS; i++) { hid_t att_id, att_type; att_id = H5Aopen(dataset[i], att_name[i], H5P_DEFAULT); VRFY((att_id >= 0), "H5Aopen failed.\n"); att_type = H5Aget_type(att_id); VRFY((att_type >= 0), "H5Aget_type failed.\n"); tri_err = H5Tequal(att_type, H5T_NATIVE_DOUBLE); VRFY((tri_err >= 0), "H5Tequal failed.\n"); if (tri_err == 0) { fprintf(stdout, "%0d:%s: Mismatched Attribute type of Dataset %d.\n", mpi_rank, fcn_name, i); nerrors++; } else { /* should verify attribute size before H5Aread */ err = H5Aread(att_id, H5T_NATIVE_DOUBLE, att_read); VRFY((err >= 0), "H5Aread failed.\n"); /* compare read attribute data with expected data */ for (j = 0; j < LOCAL_DATA_SIZE; j++) if (!H5_DBL_ABS_EQUAL(att_read[j], att[j])) { fprintf(stdout, "%0d:%s: Mismatched attribute data read in Dataset %d, at position " "%d: expect %f, got %f.\n", mpi_rank, fcn_name, i, j, att[j], att_read[j]); nerrors++; } for (j = 0; j < LOCAL_DATA_SIZE; j++) { att[j] /= 10.0; } } err = H5Aclose(att_id); VRFY((err >= 0), "H5Aclose failed.\n"); } steps_done++; } /* End of Step 2: reading attributes from each dataset */ #endif #if 1 /*=====================================================* * Step 3 or 4: read large attributes from each dataset. * Step 4 has different attribute value from step 3. *=====================================================*/ if (steps >= 3) { if (verbose) fprintf(stdout, "%0d:%s: reading large attributes.\n", mpi_rank, fcn_name); for (j = 0; j < LARGE_ATTR_SIZE; j++) { lg_att[j] = (steps == 3) ? (double)(j + 1) : (double)(j + 2); } for (i = 0; i < NUM_DATA_SETS; i++) { lg_att_id[i] = H5Aopen(dataset[i], lg_att_name[i], H5P_DEFAULT); VRFY((lg_att_id[i] >= 0), "H5Aopen(2) failed.\n"); lg_att_type[i] = H5Aget_type(lg_att_id[i]); VRFY((err >= 0), "H5Aget_type failed.\n"); tri_err = H5Tequal(lg_att_type[i], H5T_NATIVE_DOUBLE); VRFY((tri_err >= 0), "H5Tequal failed.\n"); if (tri_err == 0) { fprintf(stdout, "%0d:%s: Mismatched Large attribute type of Dataset %d.\n", mpi_rank, fcn_name, i); nerrors++; } else { /* should verify large attribute size before H5Aread */ err = H5Aread(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att_read); VRFY((err >= 0), "H5Aread failed.\n"); /* compare read attribute data with expected data */ for (j = 0; j < LARGE_ATTR_SIZE; j++) if (!H5_DBL_ABS_EQUAL(lg_att_read[j], lg_att[j])) { fprintf(stdout, "%0d:%s: Mismatched large attribute data read in Dataset %d, at " "position %d: expect %f, got %f.\n", mpi_rank, fcn_name, i, j, lg_att[j], lg_att_read[j]); nerrors++; } for (j = 0; j < LARGE_ATTR_SIZE; j++) { lg_att[j] /= 10.0; } } err = H5Tclose(lg_att_type[i]); VRFY((err >= 0), "H5Tclose failed.\n"); err = H5Aclose(lg_att_id[i]); VRFY((err >= 0), "H5Aclose failed.\n"); } /* Both step 3 and 4 use this same read checking code. */ steps_done = (steps == 3) ? 3 : 4; } /* End of Step 3 or 4: read large attributes from each dataset */ #endif /*=====================================================* * Step 5: read all objects from the file *=====================================================*/ if (steps >= 5) { /* nothing extra to verify. The file is closed normally. */ /* Just increment steps_done */ steps_done++; } /* * Close the data sets */ if (verbose) fprintf(stdout, "%0d:%s: closing datasets again.\n", mpi_rank, fcn_name); for (i = 0; i < NUM_DATA_SETS; i++) { if (dataset[i] >= 0) { err = H5Dclose(dataset[i]); VRFY((err >= 0), "H5Dclose(dataset[i])1 failed.\n"); } } /* * close the data transfer property list. */ if (verbose) fprintf(stdout, "%0d:%s: closing dxpl .\n", mpi_rank, fcn_name); err = H5Pclose(dxpl_id); VRFY((err >= 0), "H5Pclose(dxpl_id) failed.\n"); /* * Close the file */ if (verbose) fprintf(stdout, "%0d:%s: closing file again.\n", mpi_rank, fcn_name); err = H5Fclose(file_id); VRFY((err >= 0), "H5Fclose(1) failed"); } /* else if (steps_done==0) */ Reader_result(mrc, steps_done); } /* end while(1) */ if (verbose) fprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name); return; } /* rr_obj_hdr_flush_confusion_reader() */ #undef NUM_DATA_SETS #undef LOCAL_DATA_SIZE #undef LARGE_ATTR_SIZE #undef Reader_check #undef Reader_wait #undef Reader_result #undef Writer_Root #undef Reader_Root /* * Test creating a chunked dataset in parallel in a file with an alignment set * and an alignment threshold large enough to avoid aligning the chunks but * small enough that the raw data aggregator will be aligned if it is treated as * an object that must be aligned by the library */ #define CHUNK_SIZE 72 #define NCHUNKS 32 #define AGGR_SIZE 2048 #define EXTRA_ALIGN 100 void chunk_align_bug_1(void) { int mpi_rank; hid_t file_id, dset_id, fapl_id, dcpl_id, space_id; hsize_t dims = CHUNK_SIZE * NCHUNKS, cdims = CHUNK_SIZE; h5_stat_size_t file_size; hsize_t align = 1; bool vol_is_native; herr_t ret; const char *filename; MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* Make sure the connector supports the API functions being tested */ if (!(vol_cap_flags_g & H5VL_CAP_FLAG_FILE_BASIC) || !(vol_cap_flags_g & H5VL_CAP_FLAG_DATASET_BASIC)) { if (MAINPROCESS) { puts("SKIPPED"); printf(" API functions for basic file or dataset aren't supported with this connector\n"); fflush(stdout); } return; } filename = (const char *)GetTestParameters(); /* Create file without alignment */ fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type); VRFY((fapl_id >= 0), "create_faccess_plist succeeded"); file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); VRFY((file_id >= 0), "H5Fcreate succeeded"); /* Check if native VOL is being used */ VRFY((h5_using_native_vol(H5P_DEFAULT, file_id, &vol_is_native) >= 0), "h5_using_native_vol"); /* Close file */ ret = H5Fclose(file_id); VRFY((ret >= 0), "H5Fclose succeeded"); if (vol_is_native) { /* Get file size */ file_size = h5_get_file_size(filename, fapl_id); VRFY((file_size >= 0), "h5_get_file_size succeeded"); /* Calculate alignment value, set to allow a chunk to squeak in between the * original EOF and the aligned location of the aggregator. Add some space * for the dataset metadata */ align = (hsize_t)file_size + CHUNK_SIZE + EXTRA_ALIGN; } /* Set aggregator size and alignment, disable metadata aggregator */ assert(AGGR_SIZE > CHUNK_SIZE); ret = H5Pset_small_data_block_size(fapl_id, AGGR_SIZE); VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded"); ret = H5Pset_meta_block_size(fapl_id, 0); VRFY((ret >= 0), "H5Pset_meta_block_size succeeded"); ret = H5Pset_alignment(fapl_id, CHUNK_SIZE + 1, align); VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded"); /* Reopen file with new settings */ file_id = H5Fopen(filename, H5F_ACC_RDWR, fapl_id); VRFY((file_id >= 0), "H5Fopen succeeded"); /* Create dataset */ space_id = H5Screate_simple(1, &dims, NULL); VRFY((space_id >= 0), "H5Screate_simple succeeded"); dcpl_id = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl_id >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dcpl_id, 1, &cdims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); dset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_CHAR, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT); VRFY((dset_id >= 0), "H5Dcreate2 succeeded"); /* Close ids */ ret = H5Dclose(dset_id); VRFY((dset_id >= 0), "H5Dclose succeeded"); ret = H5Sclose(space_id); VRFY((space_id >= 0), "H5Sclose succeeded"); ret = H5Pclose(dcpl_id); VRFY((dcpl_id >= 0), "H5Pclose succeeded"); ret = H5Pclose(fapl_id); VRFY((fapl_id >= 0), "H5Pclose succeeded"); /* Close file */ ret = H5Fclose(file_id); VRFY((ret >= 0), "H5Fclose succeeded"); return; } /* end chunk_align_bug_1() */ /*============================================================================= * End of t_mdset.c *===========================================================================*/