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Diffstat (limited to 'testpar/t_ph5_vds.c')
| -rw-r--r-- | testpar/t_ph5_vds.c | 504 |
1 files changed, 504 insertions, 0 deletions
diff --git a/testpar/t_ph5_vds.c b/testpar/t_ph5_vds.c new file mode 100644 index 0000000..a56164c --- /dev/null +++ b/testpar/t_ph5_vds.c @@ -0,0 +1,504 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/************************************************************ + + This example illustrates the concept of virtual dataset. + The program creates three 1-dim source datasets and writes + data to them. Then it creates a 2-dim virtual dataset and + maps the first three rows of the virtual dataset to the data + in the source datasets. Elements of a row are mapped to all + elements of the corresponding source dataset. + The fourth row is not mapped and will be filled with the fill + values when virtual dataset is read back. + + The program closes all datasets, and then reopens the virtual + dataset, and finds and prints its creation properties. + Then it reads the values. + + This file is intended for use with HDF5 Library version 1.10 + + ************************************************************ + RAW - This example was modified for testing parallel VDS + functionality. + ************************************************************/ +/* EIP Add link to the picture */ +#include "h5test.h" +#include "testpar.h" + +#include <stdio.h> +#include <stdlib.h> + +#define FILE "vds.h5" +#define DATASET "VDS" +#define VDSDIM1 100 +#define VDSDIM0 4 +#define DIM0 100 +#define RANK1 1 +#define RANK2 2 + +#define NFILENAME 4 +const char *FILENAMES[NFILENAME + 1] = { "a.h5", + "b.h5", + "c.h5", + "vds.h5", + NULL }; + +const char *SRC_DATASET[] = { + "A", + "B", + "C" +}; + + +int +main (int argc, char **argv) +{ + hid_t + memspace = -1, + dataspace = -1, + filespace = -1, + src_space = -1, + src_dset = -1, + vds_file = -1, + file_id = -1, + fapl_id = -1, + dxpl_id = -1, + vspace = -1, + vdsset = -1, + dcpl = -1; + herr_t status; + hsize_t vdsdims[2] = {VDSDIM0, VDSDIM1}, /* Virtual datasets dimension */ + dims[1] = {DIM0}, /* Source datasets dimensions */ + start[2], /* Hyperslab parameters */ + count[2], + block[2]; + hsize_t start_out[2], + stride_out[2], + count_out[2], + block_out[2]; + int wdata[DIM0], /* Write buffer for source dataset */ + rdata[VDSDIM0][VDSDIM1], /* Read buffer for virtual dataset */ + i, j, k, l; + int fill_value = -1; /* Fill value for VDS */ + H5D_layout_t layout; /* Storage layout */ + size_t num_map; /* Number of mappings */ + ssize_t len; /* Length of the string; also a return value */ + char *filename; + char *dsetname; + hsize_t nblocks; + hsize_t elements; + hsize_t offset; + hsize_t *buf; /* Buffer to hold hyperslab coordinates */ + + int group_status = 0, nerrs = 0; + int mpi_rank; + int mpi_size; + int workgroup; + MPI_Comm group_comm = MPI_COMM_NULL; + + if ( (MPI_Init(&argc, &argv)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: Unable to initialize MPI\n"); + HDexit(EXIT_FAILURE); + } + + if ( (MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: MPI_Comm_rank returned an error\n"); + HDexit(EXIT_FAILURE); + } + + if ( (MPI_Comm_size(MPI_COMM_WORLD, &mpi_size)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: MPI_Comm_size returned an error\n"); + HDexit(EXIT_FAILURE); + } + + workgroup = (mpi_rank < VDSDIM0 ? 0 : 1); + if ( (MPI_Comm_split(MPI_COMM_WORLD, + workgroup, + 0, + &group_comm)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: MPI_Comm_split returned an error\n"); + HDexit(EXIT_FAILURE); + } + + H5open(); + + if ( mpi_rank == 0 ) { + HDfprintf(stdout, "========================================\n"); + HDfprintf(stdout, "Parallel VDS functionality tests\n"); + HDfprintf(stdout, " mpi_size = %d\n", mpi_size); + HDfprintf(stdout, "========================================\n"); + } + + /* + * Create source files and datasets. + * we'll assign one MPI rank per file... + */ + for (i=0; i < 3; i++) { + + if (mpi_rank == i) { + /* + * Initialize data for i-th source dataset. + */ + for (j = 0; j < DIM0; j++) wdata[j] = i+1; + + /* + * Create the source files and datasets. Write data to each dataset and + * close all resources. + */ + + if ((file_id = H5Fcreate (FILENAMES[i], H5F_ACC_TRUNC, + H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR; + if ((src_space = H5Screate_simple (RANK1, dims, NULL)) < 0) TEST_ERROR; + if ((src_dset = H5Dcreate2 (file_id, SRC_DATASET[i], H5T_NATIVE_INT, + src_space, H5P_DEFAULT, H5P_DEFAULT, + H5P_DEFAULT)) < 0) TEST_ERROR; + if ((status = H5Dwrite (src_dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, + H5P_DEFAULT, wdata)) < 0) TEST_ERROR; + + if ((status = H5Dclose (src_dset)) < 0) TEST_ERROR; + if ((status = H5Sclose (src_space)) < 0) TEST_ERROR; + if ((status = H5Fclose (file_id)) < 0) TEST_ERROR; + } + } + + src_dset = -1; + src_space = -1; + file_id = -1; + + /* We allow at most VDSDIM0 mpi ranks to participate + * in the actual VDS testing, i.e. in the best case we + * do 1 mpi rank per data slice. We accomplished this + * by creating an MPI 'group_comm' communicator which + * contains at most VDSDIM0 ranks. All other processes + * skip the testing part but need participate in the + * MPI_Allgather to exchange global status. + */ + if ( mpi_rank < VDSDIM0) { + + if ( (fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0 ) TEST_ERROR; + if ( (H5Pset_fapl_mpio(fapl_id, group_comm, + MPI_INFO_NULL)) < 0) TEST_ERROR; + + /* Create file in which virtual dataset will be stored. */ + if ( (vds_file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, + fapl_id)) < 0 ) TEST_ERROR; + + if ( (dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0 ) TEST_ERROR; + if ( (H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE)) < 0 ) TEST_ERROR; + + /* Create VDS dataspace. */ + if ( (dataspace = H5Screate_simple (RANK2, vdsdims, NULL)) < 0 ) TEST_ERROR; + + /* Set VDS creation property. */ + if ( (dcpl = H5Pcreate (H5P_DATASET_CREATE)) < 0 ) TEST_ERROR; + + if ( (H5Pset_fill_value (dcpl, H5T_NATIVE_INT, &fill_value)) < 0 ) TEST_ERROR; + + /* Initialize hyperslab values. */ + start[0] = 0; + start[1] = 0; + count[0] = 1; + count[1] = 1; + block[0] = 1; + block[1] = VDSDIM1; + + /* + * Build the mappings. + * Selections in the source datasets are H5S_ALL. + * In the virtual dataset we select the first, the second and the third rows + * and map each row to the data in the corresponding source dataset. + */ + if ((src_space = H5Screate_simple (RANK1, dims, NULL)) < 0 ) TEST_ERROR; + + for (i=0; i < 3; i++) { + start[0] = (hsize_t)i; + /* Select i-th row in the virtual dataset; + * selection in the source datasets is the same. + */ + if ((status = H5Sselect_hyperslab (dataspace, H5S_SELECT_SET, + start, NULL, count, block)) < 0) TEST_ERROR; + if ((status = H5Pset_virtual (dcpl, dataspace, FILENAMES[i], + SRC_DATASET[i], src_space)) < 0) TEST_ERROR; + } + + /* Create a virtual dataset. */ + if ((vdsset = H5Dcreate2 (vds_file, DATASET, H5T_NATIVE_INT, + dataspace, H5P_DEFAULT, + dcpl, H5P_DEFAULT)) < 0) TEST_ERROR; + /* Now close up the file and close the various + * other HDF5 descriptors */ + if ((status = H5Dclose (vdsset)) < 0) TEST_ERROR; + vdsset = -1; + if ((status = H5Sclose (dataspace)) < 0) TEST_ERROR; + dataspace = -1; + if ((status = H5Sclose (src_space)) < 0) TEST_ERROR; + src_space = -1; + if ((status = H5Fclose (vds_file)) < 0) TEST_ERROR; + vds_file = -1; + + /* + * Now we begin the read section of this example. + */ + + if ( (fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0 ) { + HDfprintf(stderr, "H5Pcreate - returned an error\n"); + HDexit(EXIT_FAILURE); + } + if ( (status = H5Pset_fapl_mpio(fapl_id, group_comm, + MPI_INFO_NULL)) < 0 ) { + HDfprintf(stderr, "H5Pset_fapl_mpio - returned an error\n"); + HDexit(EXIT_FAILURE); + } + /* + * Open the file and virtual dataset. + */ + if ((vds_file = H5Fopen (FILE, H5F_ACC_RDONLY, fapl_id)) + < 0) { + HDfprintf(stderr, "H5Fopen - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + if ((vdsset = H5Dopen2 (vds_file, DATASET, H5P_DEFAULT)) + < 0) { + HDfprintf(stderr, "H5Fopen2 - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + /* + * Get creation property list and mapping properties. + */ + if ((dcpl = H5Dget_create_plist (vdsset)) < 0) { + HDfprintf(stderr, "H5Dget_create_plist - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + /* + * Get storage layout. + */ + if ((layout = H5Pget_layout (dcpl)) < 0) { + HDfprintf(stderr, "H5Pget_layout - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + if (mpi_rank == 0) { + if (layout == H5D_VIRTUAL ) + HDfprintf(stdout, " Dataset has a virtual layout\n"); + else + HDfprintf(stdout, " Wrong layout found \n"); + + /* + * Find the number of mappings. + */ + if ((status = H5Pget_virtual_count (dcpl, &num_map)) + < 0) { + HDfprintf(stderr, "H5Pget_layout - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + HDfprintf(stdout, " Number of mappings is %lu\n", + (unsigned long)num_map); + + /* + * Get mapping parameters for each mapping. + */ + nerrs = 0; + for (i = 0; i < (int)num_map; i++) { + HDfprintf(stdout, " Mapping %d \n", i); + HDfprintf(stdout, " Selection in the virtual dataset "); + /* Get selection in the virtual dataset */ + if ((vspace = H5Pget_virtual_vspace (dcpl, (size_t)i)) + < 0) { + HDfprintf(stderr, "H5Pget_virtual_vspace - returned an error\n"); + HDexit(EXIT_FAILURE); + } + /* Make sure that this is a hyperslab selection + * and then print information. + */ + if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) { + if ((nblocks = H5Sget_select_hyper_nblocks (vspace)) < 0) { + HDfprintf(stderr, "H5Pget_virtual_vspace - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + if ((buf = (hsize_t *)HDmalloc(sizeof(hsize_t)*2*RANK2*nblocks)) + == NULL) { + HDfprintf(stderr, "HDmalloc - returned a NULL\n"); + HDexit(EXIT_FAILURE); + } + + if ((H5Sget_select_hyper_blocklist (vspace, (hsize_t)0, + nblocks, buf)) < 0) { + HDfprintf(stderr, "H5Sget_select_hyper_blocklist - returned an error\n"); + HDexit(EXIT_FAILURE); + } + for (l=0; l<nblocks; l++) { + HDfprintf(stdout, "("); + for (k=0; k<RANK2-1; k++) + HDfprintf(stdout ,"%d,", (int)buf[k]); + HDfprintf(stdout, "%d ) - (", (int)buf[k]); + for (k=0; k<RANK2-1; k++) + HDfprintf(stdout, "%d,", (int)buf[RANK2+k]); + HDfprintf(stdout, "%d)\n", (int)buf[RANK2+k]); + } + + /* We also can use new APIs to get the 'start', + * 'stride', 'count' and 'block' values */ + if (H5Sis_regular_hyperslab(vspace)) { + if ((H5Sget_regular_hyperslab (vspace, start_out, + stride_out, count_out, + block_out)) < 0) { + HDfprintf(stderr, + "H5Sget_regular_hyperslab - returned an error\n"); + HDexit(EXIT_FAILURE); + } + printf(" start = [%llu, %llu] \n", + (unsigned long long)start_out[0], + (unsigned long long)start_out[1]); + printf(" stride = [%llu, %llu] \n", + (unsigned long long)stride_out[0], + (unsigned long long)stride_out[1]); + printf(" count = [%llu, %llu] \n", + (unsigned long long)count_out[0], + (unsigned long long)count_out[1]); + printf(" block = [%llu, %llu] \n", + (unsigned long long)block_out[0], + (unsigned long long)block_out[1]); + } + } + /* Get source file name. */ + if ((len = H5Pget_virtual_filename (dcpl, (size_t)i, NULL, 0)) < 0) { + HDfprintf(stderr, "H5Pget_virtual_filename - returned an error\n"); + HDexit(EXIT_FAILURE); + } + if ((filename = (char *)HDmalloc((size_t)len*sizeof(char)+1)) == NULL) { + HDfprintf(stderr, "HDmalloc - returned NULL\n"); + HDexit(EXIT_FAILURE); + } + + if ((H5Pget_virtual_filename (dcpl, (size_t)i, filename, len+1)) < 0) { + HDfprintf(stderr, "H5Pget_virtual_filename - returned an error\n"); + HDexit(EXIT_FAILURE); + } + HDfprintf(stdout, " Source filename %s\n", filename); + + /* Get source dataset name. */ + if ((len = H5Pget_virtual_dsetname (dcpl, (size_t)i, NULL, 0)) < 0) { + HDfprintf(stderr, "H5Pget_virtual_dsetname - returned an error\n"); + HDexit(EXIT_FAILURE); + } + if ((dsetname = (char *)HDmalloc((size_t)len*sizeof(char)+1)) == NULL) { + HDfprintf(stderr, "HDmalloc - returned NULL\n"); + HDexit(EXIT_FAILURE); + } + if ((H5Pget_virtual_dsetname (dcpl, (size_t)i, dsetname, len+1)) < 0) { + HDfprintf(stderr, "H5Pget_virtual_dsetname - returned an error\n"); + HDexit(EXIT_FAILURE); + } + HDfprintf(stdout," Source dataset name %s\n", dsetname); + + /* Get selection in the source dataset. */ + HDprintf(" Selection in the source dataset "); + if ((src_space = H5Pget_virtual_srcspace (dcpl, (size_t)i)) < 0) { + HDfprintf(stderr, "H5Pget_virtual_filename - returned an error\n"); + HDexit(EXIT_FAILURE); + } + + /* Make sure it is ALL selection and then print the coordinates. */ + if(H5Sget_select_type(src_space) == H5S_SEL_ALL) { + HDfprintf(stdout, "(0) - (%d) \n", DIM0-1); + } + } + } + + HDmemset(rdata,0,sizeof(rdata)); + elements = DIM0; + dims[0] = elements; + if ( (memspace = H5Screate_simple(1, dims, NULL)) < 0 ) { + HDfprintf(stderr, "H5Screate_simple - returned an error\n"); + HDexit(EXIT_FAILURE); + } + if ( (filespace = H5Dget_space(vdsset)) < 0 ) { + HDfprintf(stderr, "H5Dget_space - returned an error\n"); + HDexit(EXIT_FAILURE); + } + offset = (hsize_t)mpi_rank * elements; + if ( (H5Sselect_hyperslab(filespace, H5S_SELECT_SET, + &offset, NULL, &elements, NULL)) < 0 ) { + HDfprintf(stderr, "H5Sselect_hyperslab - returned an error\n"); + HDexit(EXIT_FAILURE); + } + if ((status = H5Dread (vdsset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, + rdata[0])) < 0) { + HDfprintf(stderr, "H5Dread - returned an error\n"); + HDexit(EXIT_FAILURE); + } + if (mpi_rank == 0) { + for(i=0; i<VDSDIM0; i++) { + HDfprintf (stdout, " VDS Data: [%d][0-99]\n [", i); + for (j=0; j<VDSDIM1; j++) { + if ((j < 6) || (j > VDSDIM1 -3)) + HDfprintf (stdout," %3d", rdata[i][j]); + else if (j == 6) + HDfprintf (stdout, " ... "); + } + HDfprintf (stdout, "]\n"); + } + } + } + + if (mpi_size > 1) { + if ((MPI_Allreduce(&nerrs, &group_status, 1, + MPI_INT, MPI_SUM, MPI_COMM_WORLD)) + != MPI_SUCCESS) + group_status = 1; + } + if (mpi_rank == 0) { + if (group_status > 0) + HDfprintf(stderr, "There were internal errors encountered during this test\n"); + else + HDfprintf(stdout, "No Errors!\n"); + + /* remove the files that a no longer needed */ + for(i=0; i < NFILENAME; i++) { + HDremove(FILENAMES[i]); + } + } + +error: + /* + * Close and release resources. + */ + if (group_comm != MPI_COMM_NULL) { + MPI_Comm_free(&group_comm); + } + + if (dcpl != -1) H5Pclose (dcpl); + if (vdsset != -1) H5Dclose (vdsset); + if (dataspace != -1) H5Sclose (dataspace); + if (fapl_id != -1) H5Pclose (fapl_id); + if (vds_file != -1) H5Fclose (vds_file); + + /* close HDF5 library */ + if (H5close() != SUCCEED) { + HDfprintf(stdout, "H5close() failed. (Ignoring)\n"); + } + + /* MPI_Finalize must be called AFTER H5close which may use MPI calls */ + + MPI_Finalize(); + + /* cannot just return (nerrs) because exit code is limited to 1byte */ + return((nerrs > 0) ? EXIT_FAILURE : EXIT_SUCCESS ); +} + |