/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Parallel tests for datasets */ /* * Example of using the parallel HDF5 library to access datasets. * * This program contains three major parts. Part 1 tests fixed dimension * datasets, for both independent and collective transfer modes. * Part 2 tests extendible datasets, for independent transfer mode * only. * Part 3 tests extendible datasets, for collective transfer mode * only. */ #include "testphdf5.h" /* * The following are various utility routines used by the tests. */ /* * Setup the dimensions of the hyperslab. * Two modes--by rows or by columns. * Assume dimension rank is 2. * BYROW divide into slabs of rows * BYCOL divide into blocks of columns * ZROW same as BYROW except process 0 gets 0 rows * ZCOL same as BYCOL except process 0 gets 0 columns */ static void slab_set(int mpi_rank, int mpi_size, hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], int mode) { switch (mode){ case BYROW: /* Each process takes a slabs of rows. */ block[0] = dim0/mpi_size; block[1] = dim1; stride[0] = block[0]; stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = mpi_rank*block[0]; start[1] = 0; if(VERBOSE_MED) printf("slab_set BYROW\n"); break; case BYCOL: /* Each process takes a block of columns. */ block[0] = dim0; block[1] = dim1/mpi_size; stride[0] = block[0]; stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = 0; start[1] = mpi_rank*block[1]; if(VERBOSE_MED) printf("slab_set BYCOL\n"); break; case ZROW: /* Similar to BYROW except process 0 gets 0 row */ block[0] = (mpi_rank ? dim0/mpi_size : 0); block[1] = dim1; stride[0] = (mpi_rank ? block[0] : 1); /* avoid setting stride to 0 */ stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = (mpi_rank? mpi_rank*block[0] : 0); start[1] = 0; if(VERBOSE_MED) printf("slab_set ZROW\n"); break; case ZCOL: /* Similar to BYCOL except process 0 gets 0 column */ block[0] = dim0; block[1] = (mpi_rank ? dim1/mpi_size : 0); stride[0] = block[0]; stride[1] = (mpi_rank ? block[1] : 1); /* avoid setting stride to 0 */ count[0] = 1; count[1] = 1; start[0] = 0; start[1] = (mpi_rank? mpi_rank*block[1] : 0); if(VERBOSE_MED) printf("slab_set ZCOL\n"); break; default: /* Unknown mode. Set it to cover the whole dataset. */ printf("unknown slab_set mode (%d)\n", mode); block[0] = dim0; block[1] = dim1; stride[0] = block[0]; stride[1] = block[1]; count[0] = 1; count[1] = 1; start[0] = 0; start[1] = 0; if(VERBOSE_MED) printf("slab_set wholeset\n"); break; } if(VERBOSE_MED){ printf("start[]=(%lu,%lu), count[]=(%lu,%lu), stride[]=(%lu,%lu), block[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1], (unsigned long)(block[0]*block[1]*count[0]*count[1])); } } /* * Fill the dataset with trivial data for testing. * Assume dimension rank is 2 and data is stored contiguous. */ static void dataset_fill(hsize_t start[], hsize_t block[], DATATYPE * dataset) { DATATYPE *dataptr = dataset; hsize_t i, j; /* put some trivial data in the data_array */ for (i=0; i < block[0]; i++){ for (j=0; j < block[1]; j++){ *dataptr = (DATATYPE)((i+start[0])*100 + (j+start[1]+1)); dataptr++; } } } /* * Print the content of the dataset. */ static void dataset_print(hsize_t start[], hsize_t block[], DATATYPE * dataset) { DATATYPE *dataptr = dataset; hsize_t i, j; /* print the column heading */ printf("%-8s", "Cols:"); for (j=0; j < block[1]; j++){ printf("%3lu ", (unsigned long)(start[1]+j)); } printf("\n"); /* print the slab data */ for (i=0; i < block[0]; i++){ printf("Row %2lu: ", (unsigned long)(i+start[0])); for (j=0; j < block[1]; j++){ printf("%03d ", *dataptr++); } printf("\n"); } } /* * Print the content of the dataset. */ int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original) { hsize_t i, j; int vrfyerrs; /* print it if VERBOSE_MED */ if(VERBOSE_MED) { printf("dataset_vrfy dumping:::\n"); printf("start(%lu, %lu), count(%lu, %lu), stride(%lu, %lu), block(%lu, %lu)\n", (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1]); printf("original values:\n"); dataset_print(start, block, original); printf("compared values:\n"); dataset_print(start, block, dataset); } vrfyerrs = 0; for (i=0; i < block[0]; i++){ for (j=0; j < block[1]; j++){ if(*dataset != *original){ if(vrfyerrs++ < MAX_ERR_REPORT || VERBOSE_MED){ 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+start[0]), (unsigned long)(j+start[1]), *(original), *(dataset)); } dataset++; original++; } } } if(vrfyerrs > MAX_ERR_REPORT && !VERBOSE_MED) printf("[more errors ...]\n"); if(vrfyerrs) printf("%d errors found in dataset_vrfy\n", vrfyerrs); return(vrfyerrs); } /* * Part 1.a--Independent read/write for fixed dimension datasets. */ /* * Example of using the parallel HDF5 library to create two datasets * in one HDF5 files with parallel MPIO access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. */ void dataset_writeInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE *data_array1 = NULL; /* data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); /* ---------------------------------------- * CREATE AN HDF5 FILE WITH PARALLEL ACCESS * ---------------------------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* --------------------------------------------- * Define the dimensions of the overall datasets * and the slabs local to the MPI process. * ------------------------------------------- */ /* setup dimensionality object */ dims[0] = dim0; dims[1] = dim1; sid = H5Screate_simple (RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create a dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* * To test the independent orders of writes between processes, all * even number processes write to dataset1 first, then dataset2. * All odd number processes write to dataset2 first, then dataset1. */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* write data independently */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); /* setup dimensions again to write with zero rows for process 0 */ if(VERBOSE_MED) printf("writeInd by some with zero row\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if(MAINPROCESS){ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("writeInd by some with zero row"); if((mpi_rank/2)*2 != mpi_rank){ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded"); } #ifdef BARRIER_CHECKS MPI_Barrier(MPI_COMM_WORLD); #endif /* BARRIER_CHECKS */ /* release dataspace ID */ H5Sclose(file_dataspace); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* release all IDs created */ H5Sclose(sid); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); } /* Example of using the parallel HDF5 library to read a dataset */ void dataset_readInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ DATATYPE *data_array1 = NULL; /* data buffer */ DATATYPE *data_origin1 = NULL; /* expected data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Independent read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl); VRFY((fid >= 0), ""); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), ""); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset2 >= 0), ""); /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); /* read data independently */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if(ret) nerrors++; /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if(ret) nerrors++; /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), ""); ret = H5Dclose(dataset2); VRFY((ret >= 0), ""); /* release all IDs created */ H5Sclose(file_dataspace); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); if(data_origin1) free(data_origin1); } /* * Part 1.b--Collective read/write for fixed dimension datasets. */ /* * Example of using the parallel HDF5 library to create two datasets * in one HDF5 file with collective parallel access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and * each process controls a hyperslab within.] */ void dataset_writeAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2, dataset3, dataset4; /* Dataset ID */ hid_t datatype; /* Datatype ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE *data_array1 = NULL; /* data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Collective write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------- * Define the dimensions of the overall datasets * and create the dataset * ------------------------- */ /* setup 2-D dimensionality object */ dims[0] = dim0; dims[1] = dim1; sid = H5Screate_simple (RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create a dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another dataset collectively */ datatype = H5Tcopy(H5T_NATIVE_INT); ret = H5Tset_order(datatype, H5T_ORDER_LE); VRFY((ret >= 0), "H5Tset_order succeeded"); dataset2 = H5Dcreate2(fid, DATASETNAME2, datatype, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 2 succeeded"); /* create a third dataset collectively */ dataset3 = H5Dcreate2(fid, DATASETNAME3, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset3 >= 0), "H5Dcreate2 succeeded"); /* release 2-D space ID created */ H5Sclose(sid); /* setup scalar dimensionality object */ sid = H5Screate(H5S_SCALAR); VRFY((sid >= 0), "H5Screate succeeded"); /* create a fourth dataset collectively */ dataset4 = H5Dcreate2(fid, DATASETNAME4, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset4 >= 0), "H5Dcreate2 succeeded"); /* release scalar space ID created */ H5Sclose(sid); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of rows. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* write data collectively */ MESG("writeAll by Row"); ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); /* setup dimensions again to writeAll with zero rows for process 0 */ if(VERBOSE_MED) printf("writeAll by some with zero row\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if(MAINPROCESS){ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("writeAll by some with zero row"); ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded"); /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset2: each process takes a block of columns. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); /* setup dimensions again to writeAll with zero columns for process 0 */ if(VERBOSE_MED) printf("writeAll by some with zero col\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if(MAINPROCESS){ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("writeAll by some with zero col"); ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset1 by ZCOL succeeded"); /* release all temporary handles. */ /* Could have used them for dataset3 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset3: each process takes a block of rows, except process zero uses "none" selection. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset3); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); if(MAINPROCESS) { ret = H5Sselect_none(file_dataspace); VRFY((ret >= 0), "H5Sselect_none file_dataspace succeeded"); } /* end if */ else { ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sselect_hyperslab succeeded"); } /* end else */ /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); if(MAINPROCESS) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sselect_none mem_dataspace succeeded"); } /* end if */ /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* end if */ /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* write data collectively */ MESG("writeAll with none"); ret = H5Dwrite(dataset3, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset3 succeeded"); /* write data collectively (with datatype conversion) */ MESG("writeAll with none"); ret = H5Dwrite(dataset3, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset3 succeeded"); /* release all temporary handles. */ /* Could have used them for dataset4 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset4: each process writes no data, except process zero uses "all" selection. */ /* Additionally, these are in a scalar dataspace */ /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset4); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); if(MAINPROCESS) { ret = H5Sselect_none(file_dataspace); VRFY((ret >= 0), "H5Sselect_all file_dataspace succeeded"); } /* end if */ else { ret = H5Sselect_all(file_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* end else */ /* create a memory dataspace independently */ mem_dataspace = H5Screate(H5S_SCALAR); VRFY((mem_dataspace >= 0), ""); if(MAINPROCESS) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sselect_all mem_dataspace succeeded"); } /* end if */ else { ret = H5Sselect_all(mem_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* end else */ /* fill the local slab with some trivial data */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* end if */ /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* write data collectively */ MESG("writeAll with scalar dataspace"); ret = H5Dwrite(dataset4, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset4 succeeded"); /* write data collectively (with datatype conversion) */ MESG("writeAll with scalar dataspace"); ret = H5Dwrite(dataset4, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite dataset4 succeeded"); /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* * All writes completed. Close datasets collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); ret = H5Dclose(dataset3); VRFY((ret >= 0), "H5Dclose3 succeeded"); ret = H5Dclose(dataset4); VRFY((ret >= 0), "H5Dclose3 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); } /* * Example of using the parallel HDF5 library to read two datasets * in one HDF5 file with collective parallel access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and * each process controls a hyperslab within.] */ void dataset_readAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ DATATYPE *data_array1 = NULL; /* data buffer */ DATATYPE *data_origin1 = NULL; /* expected data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Collective read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl); VRFY((fid >= 0), "H5Fopen succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------- * Open the datasets in it * ------------------------- */ /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dopen2 succeeded"); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME2, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dopen2 2 succeeded"); /* * Set up dimensions of the slab this process accesses. */ /* Dataset1: each process takes a block of columns. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_origin1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset1 succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if(ret) nerrors++; /* setup dimensions again to readAll with zero columns for process 0 */ if(VERBOSE_MED) printf("readAll by some with zero col\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if(MAINPROCESS){ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("readAll by some with zero col"); ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset1 by ZCOL succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if(ret) nerrors++; /* release all temporary handles. */ /* Could have used them for dataset2 but it is cleaner */ /* to create them again.*/ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* Dataset2: each process takes a block of rows. */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_origin1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), ""); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pcreate xfer succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset2 succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if(ret) nerrors++; /* setup dimensions again to readAll with zero rows for process 0 */ if(VERBOSE_MED) printf("readAll by some with zero row\n"); slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* need to make mem_dataspace to match for process 0 */ if(MAINPROCESS){ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded"); } MESG("readAll by some with zero row"); ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread dataset1 by ZROW succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); if(ret) nerrors++; /* release all temporary handles. */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* * All reads completed. Close datasets collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); if(data_origin1) free(data_origin1); } /* * Part 2--Independent read/write for extendible datasets. */ /* * Example of using the parallel HDF5 library to create two extendible * datasets in one HDF5 file with independent parallel MPIO access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. */ void extend_writeInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ hsize_t max_dims[RANK] = {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */ DATATYPE *data_array1 = NULL; /* data buffer */ hsize_t chunk_dims[RANK]; /* chunk sizes */ hid_t dataset_pl; /* dataset create prop. list */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK]; /* for hyperslab setting */ hsize_t stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Extend independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* setup chunk-size. Make sure sizes are > 0 */ chunk_dims[0] = chunkdim0; chunk_dims[1] = chunkdim1; /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* Reduce the number of metadata cache slots, so that there are cache * collisions during the raw data I/O on the chunked dataset. This stresses * the metadata cache and tests for cache bugs. -QAK */ { int mdc_nelmts; size_t rdcc_nelmts; size_t rdcc_nbytes; double rdcc_w0; ret = H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0); VRFY((ret >= 0), "H5Pget_cache succeeded"); mdc_nelmts=4; ret = H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0); VRFY((ret >= 0), "H5Pset_cache succeeded"); } /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ if(VERBOSE_MED) printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); dataset_pl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ /* start out with no rows, extend it later. */ dims[0] = dims[1] = 0; sid = H5Screate_simple (RANK, dims, max_dims); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another extendible dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* release resource */ H5Sclose(sid); H5Pclose(dataset_pl); /* ------------------------- * Test writing to dataset1 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Extend its current dim sizes before writing */ dims[0] = dim0; dims[1] = dim1; ret = H5Dset_extent(dataset1, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); /* ------------------------- * Test writing to dataset2 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Try write to dataset2 beyond its current dim sizes. Should fail. */ /* Temporary turn off auto error reporting */ H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently. Should fail. */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret < 0), "H5Dwrite failed as expected"); /* restore auto error reporting */ H5Eset_auto2(H5E_DEFAULT, old_func, old_client_data); H5Sclose(file_dataspace); /* Extend dataset2 and try again. Should succeed. */ dims[0] = dim0; dims[1] = dim1; ret = H5Dset_extent(dataset2, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); } /* * Example of using the parallel HDF5 library to create an extendable dataset * and perform I/O on it in a way that verifies that the chunk cache is * bypassed for parallel I/O. */ void extend_writeInd2(void) { const char *filename; hid_t fid; /* HDF5 file ID */ hid_t fapl; /* File access templates */ hid_t fs; /* File dataspace ID */ hid_t ms; /* Memory dataspace ID */ hid_t dataset; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ hsize_t orig_size=10; /* Original dataset dim size */ hsize_t new_size=20; /* Extended dataset dim size */ hsize_t one=1; hsize_t max_size = H5S_UNLIMITED; /* dataset maximum dim size */ hsize_t chunk_size = 16384; /* chunk size */ hid_t dcpl; /* dataset create prop. list */ int written[10], /* Data to write */ retrieved[10]; /* Data read in */ int mpi_size, mpi_rank; /* MPI settings */ int i; /* Local index variable */ herr_t ret; /* Generic return value */ filename = GetTestParameters(); if(VERBOSE_MED) printf("Extend independent write test #2 on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs); VRFY((fapl >= 0), "create_faccess_plist succeeded"); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(fapl); VRFY((ret >= 0), "H5Pclose succeeded"); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dcpl, 1, &chunk_size); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ fs = H5Screate_simple (1, &orig_size, &max_size); VRFY((fs >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, fs, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dcreat2e succeeded"); /* release resource */ ret = H5Pclose(dcpl); VRFY((ret >= 0), "H5Pclose succeeded"); /* ------------------------- * Test writing to dataset * -------------------------*/ /* create a memory dataspace independently */ ms = H5Screate_simple(1, &orig_size, &max_size); VRFY((ms >= 0), "H5Screate_simple succeeded"); /* put some trivial data in the data_array */ for(i = 0; i < (int)orig_size; i++) written[i] = i; MESG("data array initialized"); if(VERBOSE_MED) { MESG("writing at offset zero: "); for(i = 0; i < (int)orig_size; i++) printf("%s%d", i?", ":"", written[i]); printf("\n"); } ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written); VRFY((ret >= 0), "H5Dwrite succeeded"); /* ------------------------- * Read initial data from dataset. * -------------------------*/ ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved); VRFY((ret >= 0), "H5Dread succeeded"); for (i=0; i<(int)orig_size; i++) if(written[i]!=retrieved[i]) { printf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__, i,written[i], i,retrieved[i]); nerrors++; } if(VERBOSE_MED){ MESG("read at offset zero: "); for (i=0; i<(int)orig_size; i++) printf("%s%d", i?", ":"", retrieved[i]); printf("\n"); } /* ------------------------- * Extend the dataset & retrieve new dataspace * -------------------------*/ ret = H5Dset_extent(dataset, &new_size); VRFY((ret >= 0), "H5Dset_extent succeeded"); ret = H5Sclose(fs); VRFY((ret >= 0), "H5Sclose succeeded"); fs = H5Dget_space(dataset); VRFY((fs >= 0), "H5Dget_space succeeded"); /* ------------------------- * Write to the second half of the dataset * -------------------------*/ for (i=0; i<(int)orig_size; i++) written[i] = orig_size + i; MESG("data array re-initialized"); if(VERBOSE_MED) { MESG("writing at offset 10: "); for (i=0; i<(int)orig_size; i++) printf("%s%d", i?", ":"", written[i]); printf("\n"); } ret = H5Sselect_hyperslab(fs, H5S_SELECT_SET, &orig_size, NULL, &one, &orig_size); VRFY((ret >= 0), "H5Sselect_hyperslab succeeded"); ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written); VRFY((ret >= 0), "H5Dwrite succeeded"); /* ------------------------- * Read the new data * -------------------------*/ ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved); VRFY((ret >= 0), "H5Dread succeeded"); for (i=0; i<(int)orig_size; i++) if(written[i]!=retrieved[i]) { printf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__, i,written[i], i,retrieved[i]); nerrors++; } if(VERBOSE_MED){ MESG("read at offset 10: "); for (i=0; i<(int)orig_size; i++) printf("%s%d", i?", ":"", retrieved[i]); printf("\n"); } /* Close dataset collectively */ ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); /* Close the file collectively */ ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } /* Example of using the parallel HDF5 library to read an extendible dataset */ void extend_readInd(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE *data_array1 = NULL; /* data buffer */ DATATYPE *data_array2 = NULL; /* data buffer */ DATATYPE *data_origin1 = NULL; /* expected data buffer */ const char *filename; hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Extend independent read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); data_array2 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array2 != NULL), "data_array2 malloc succeeded"); data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl); VRFY((fid >= 0), ""); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), ""); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset2 >= 0), ""); /* Try extend dataset1 which is open RDONLY. Should fail. */ /* first turn off auto error reporting */ H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sget_simple_extent_dims(file_dataspace, dims, NULL); VRFY((ret > 0), "H5Sget_simple_extent_dims succeeded"); dims[0]++; ret = H5Dset_extent(dataset1, dims); VRFY((ret < 0), "H5Dset_extent failed as expected"); /* restore auto error reporting */ H5Eset_auto2(H5E_DEFAULT, old_func, old_client_data); H5Sclose(file_dataspace); /* Read dataset1 using BYROW pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* read data independently */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset1 read verified correct"); if(ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); /* Read dataset2 using BYCOL pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset2); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset2 read verified correct"); if(ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), ""); ret = H5Dclose(dataset2); VRFY((ret >= 0), ""); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); if(data_array2) free(data_array2); if(data_origin1) free(data_origin1); } /* * Part 3--Collective read/write for extendible datasets. */ /* * Example of using the parallel HDF5 library to create two extendible * datasets in one HDF5 file with collective parallel MPIO access support. * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. * Each process controls only a slab of size dim0 x dim1 within each * dataset. */ void extend_writeAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ hsize_t max_dims[RANK] = {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */ DATATYPE *data_array1 = NULL; /* data buffer */ hsize_t chunk_dims[RANK]; /* chunk sizes */ hid_t dataset_pl; /* dataset create prop. list */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK]; /* for hyperslab setting */ hsize_t stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Extend independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* setup chunk-size. Make sure sizes are > 0 */ chunk_dims[0] = chunkdim0; chunk_dims[1] = chunkdim1; /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* Reduce the number of metadata cache slots, so that there are cache * collisions during the raw data I/O on the chunked dataset. This stresses * the metadata cache and tests for cache bugs. -QAK */ { int mdc_nelmts; size_t rdcc_nelmts; size_t rdcc_nbytes; double rdcc_w0; ret = H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0); VRFY((ret >= 0), "H5Pget_cache succeeded"); mdc_nelmts=4; ret = H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0); VRFY((ret >= 0), "H5Pset_cache succeeded"); } /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ if(VERBOSE_MED) printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); dataset_pl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ /* start out with no rows, extend it later. */ dims[0] = dims[1] = 0; sid = H5Screate_simple (RANK, dims, max_dims); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another extendible dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* release resource */ H5Sclose(sid); H5Pclose(dataset_pl); /* ------------------------- * Test writing to dataset1 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED) { MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Extend its current dim sizes before writing */ dims[0] = dim0; dims[1] = dim1; ret = H5Dset_extent(dataset1, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* write data collectively */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ H5Sclose(file_dataspace); H5Sclose(mem_dataspace); H5Pclose(xfer_plist); /* ------------------------- * Test writing to dataset2 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* put some trivial data in the data_array */ dataset_fill(start, block, data_array1); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* Try write to dataset2 beyond its current dim sizes. Should fail. */ /* Temporary turn off auto error reporting */ H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently. Should fail. */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret < 0), "H5Dwrite failed as expected"); /* restore auto error reporting */ H5Eset_auto2(H5E_DEFAULT, old_func, old_client_data); H5Sclose(file_dataspace); /* Extend dataset2 and try again. Should succeed. */ dims[0] = dim0; dims[1] = dim1; ret = H5Dset_extent(dataset2, dims); VRFY((ret >= 0), "H5Dset_extent succeeded"); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset2); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* write data independently */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dwrite succeeded"); /* release resource */ ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Pclose(xfer_plist); VRFY((ret >= 0), "H5Pclose succeeded"); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); } /* Example of using the parallel HDF5 library to read an extendible dataset */ void extend_readAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE *data_array1 = NULL; /* data buffer */ DATATYPE *data_array2 = NULL; /* data buffer */ DATATYPE *data_origin1 = NULL; /* expected data buffer */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Extend independent read test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* allocate memory for data buffer */ data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); data_array2 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_array2 != NULL), "data_array2 malloc succeeded"); data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl); VRFY((fid >= 0), ""); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* open the dataset1 collectively */ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset1 >= 0), ""); /* open another dataset collectively */ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT); VRFY((dataset2 >= 0), ""); /* Try extend dataset1 which is open RDONLY. Should fail. */ /* first turn off auto error reporting */ H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sget_simple_extent_dims(file_dataspace, dims, NULL); VRFY((ret > 0), "H5Sget_simple_extent_dims succeeded"); dims[0]++; ret = H5Dset_extent(dataset1, dims); VRFY((ret < 0), "H5Dset_extent failed as expected"); /* restore auto error reporting */ H5Eset_auto2(H5E_DEFAULT, old_func, old_client_data); H5Sclose(file_dataspace); /* Read dataset1 using BYROW pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset1 read verified correct"); if(ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); H5Pclose(xfer_plist); /* Read dataset2 using BYCOL pattern */ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset2); VRFY((file_dataspace >= 0), ""); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), ""); /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* fill dataset with test data */ dataset_fill(start, block, data_origin1); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(start, block, data_array1); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* read data collectively */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((ret >= 0), "H5Dread succeeded"); /* verify the read data with original expected data */ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); VRFY((ret == 0), "dataset2 read verified correct"); if(ret) nerrors++; H5Sclose(mem_dataspace); H5Sclose(file_dataspace); H5Pclose(xfer_plist); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), ""); ret = H5Dclose(dataset2); VRFY((ret >= 0), ""); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_array1) free(data_array1); if(data_array2) free(data_array2); if(data_origin1) free(data_origin1); } /* * Example of using the parallel HDF5 library to read a compressed * dataset in an HDF5 file with collective parallel access support. */ #ifdef H5_HAVE_FILTER_DEFLATE void compress_readAll(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t dcpl; /* Dataset creation property list */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t dataspace; /* Dataspace ID */ hid_t dataset; /* Dataset ID */ int rank=1; /* Dataspace rank */ hsize_t dim=dim0; /* Dataspace dimensions */ unsigned u; /* Local index variable */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ DATATYPE *data_read = NULL; /* data buffer */ DATATYPE *data_orig = NULL; /* expected data buffer */ const char *filename; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; int mpi_size, mpi_rank; herr_t ret; /* Generic return value */ filename = GetTestParameters(); if(VERBOSE_MED) printf("Collective chunked dataset read test on file %s\n", filename); /* Retrieve MPI parameters */ MPI_Comm_size(comm,&mpi_size); MPI_Comm_rank(comm,&mpi_rank); /* Allocate data buffer */ data_orig = (DATATYPE *)HDmalloc((size_t)dim*sizeof(DATATYPE)); VRFY((data_orig != NULL), "data_origin1 malloc succeeded"); data_read = (DATATYPE *)HDmalloc((size_t)dim*sizeof(DATATYPE)); VRFY((data_read != NULL), "data_array1 malloc succeeded"); /* Initialize data buffers */ for(u=0; u 0), "H5Fcreate succeeded"); /* Create property list for chunking and compression */ dcpl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dcpl > 0), "H5Pcreate succeeded"); ret = H5Pset_layout(dcpl, H5D_CHUNKED); VRFY((ret >= 0), "H5Pset_layout succeeded"); /* Use eight chunks */ chunk_dim = dim / 8; ret = H5Pset_chunk(dcpl, rank, &chunk_dim); VRFY((ret >= 0), "H5Pset_chunk succeeded"); ret = H5Pset_deflate(dcpl, 9); VRFY((ret >= 0), "H5Pset_deflate succeeded"); /* Create dataspace */ dataspace = H5Screate_simple(rank, &dim, NULL); VRFY((dataspace > 0), "H5Screate_simple succeeded"); /* Create dataset */ dataset = H5Dcreate2(fid, "compressed_data", H5T_NATIVE_INT, dataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT); VRFY((dataset > 0), "H5Dcreate2 succeeded"); /* Write compressed data */ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_orig); VRFY((ret >= 0), "H5Dwrite succeeded"); /* Close objects */ ret = H5Pclose(dcpl); VRFY((ret >= 0), "H5Pclose succeeded"); ret = H5Sclose(dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); } /* Wait for file to be created */ MPI_Barrier(comm); /* ------------------- * OPEN AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* open the file collectively */ fid=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl); VRFY((fid > 0), "H5Fopen succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), "H5Pclose succeeded"); /* Open dataset with compressed chunks */ dataset = H5Dopen2(fid, "compressed_data", H5P_DEFAULT); VRFY((dataset > 0), "H5Dopen2 succeeded"); /* Try reading & writing data */ if(dataset>0) { /* Create dataset transfer property list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); VRFY((xfer_plist > 0), "H5Pcreate succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); VRFY((ret>= 0),"set independent IO collectively succeeded"); } /* Try reading the data */ ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* Verify data read */ for(u=0; u= 0), "H5Pclose succeeded"); ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose succeeded"); } /* end if */ ret = H5Fclose(fid); VRFY((ret >= 0), "H5Fclose succeeded"); /* release data buffers */ if(data_read) HDfree(data_read); if(data_orig) HDfree(data_orig); } #endif /* H5_HAVE_FILTER_DEFLATE */ /* * Part 4--Non-selection for chunked dataset */ /* * Example of using the parallel HDF5 library to create chunked * dataset in one HDF5 file with collective and independent parallel * MPIO access support. The Datasets are of sizes dim0 x dim1. * Each process controls only a slab of size dim0 x dim1 within the * dataset with the exception that one processor selects no element. */ void none_selection_chunk(void) { hid_t fid; /* HDF5 file ID */ hid_t acc_tpl; /* File access templates */ hid_t xfer_plist; /* Dataset transfer properties list */ hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ hid_t dataset1, dataset2; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ const char *filename; hsize_t dims[RANK]; /* dataset dim sizes */ DATATYPE *data_origin = NULL; /* data buffer */ DATATYPE *data_array = NULL; /* data buffer */ hsize_t chunk_dims[RANK]; /* chunk sizes */ hid_t dataset_pl; /* dataset create prop. list */ hsize_t start[RANK]; /* for hyperslab setting */ hsize_t count[RANK]; /* for hyperslab setting */ hsize_t stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ hsize_t mstart[RANK]; /* for data buffer in memory */ herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; filename = GetTestParameters(); if(VERBOSE_MED) printf("Extend independent write test on file %s\n", filename); /* set up MPI parameters */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); /* setup chunk-size. Make sure sizes are > 0 */ chunk_dims[0] = chunkdim0; chunk_dims[1] = chunkdim1; /* ------------------- * START AN HDF5 FILE * -------------------*/ /* setup file access template */ acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); VRFY((acc_tpl >= 0), ""); /* create the file collectively */ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); /* -------------------------------------------------------------- * Define the dimensions of the overall datasets and create them. * ------------------------------------------------------------- */ /* set up dataset storage chunk sizes and creation property list */ if(VERBOSE_MED) printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); dataset_pl = H5Pcreate(H5P_DATASET_CREATE); VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); VRFY((ret >= 0), "H5Pset_chunk succeeded"); /* setup dimensionality object */ dims[0] = dim0; dims[1] = dim1; sid = H5Screate_simple(RANK, dims, NULL); VRFY((sid >= 0), "H5Screate_simple succeeded"); /* create an extendible dataset collectively */ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); /* create another extendible dataset collectively */ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); /* release resource */ H5Sclose(sid); H5Pclose(dataset_pl); /* ------------------------- * Test collective writing to dataset1 * -------------------------*/ /* set up dimensions of the slab this process accesses */ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); /* allocate memory for data buffer. Only allocate enough buffer for * each processor's data. */ if(mpi_rank) { data_origin = (DATATYPE *)malloc(block[0]*block[1]*sizeof(DATATYPE)); VRFY((data_origin != NULL), "data_origin malloc succeeded"); data_array = (DATATYPE *)malloc(block[0]*block[1]*sizeof(DATATYPE)); VRFY((data_array != NULL), "data_array malloc succeeded"); /* put some trivial data in the data_array */ mstart[0] = mstart[1] = 0; dataset_fill(mstart, block, data_origin); MESG("data_array initialized"); if(VERBOSE_MED){ MESG("data_array created"); dataset_print(mstart, block, data_origin); } } /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, block, NULL); VRFY((mem_dataspace >= 0), ""); /* Process 0 has no selection */ if(!mpi_rank) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset1); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); /* Process 0 has no selection */ if(!mpi_rank) { ret = H5Sselect_none(file_dataspace); VRFY((ret >= 0), "H5Sselect_none succeeded"); } /* set up the collective transfer properties list */ xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* write data collectively */ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_origin); VRFY((ret >= 0), "H5Dwrite succeeded"); /* read data independently */ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ if(mpi_rank) { ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin); if(ret) nerrors++; } /* ------------------------- * Test independent writing to dataset2 * -------------------------*/ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT); VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); /* write data collectively */ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_origin); VRFY((ret >= 0), "H5Dwrite succeeded"); /* read data independently */ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array); VRFY((ret >= 0), ""); /* verify the read data with original expected data */ if(mpi_rank) { ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin); if(ret) nerrors++; } /* release resource */ ret = H5Sclose(file_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Sclose(mem_dataspace); VRFY((ret >= 0), "H5Sclose succeeded"); ret = H5Pclose(xfer_plist); VRFY((ret >= 0), "H5Pclose succeeded"); /* close dataset collectively */ ret = H5Dclose(dataset1); VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); /* close the file collectively */ H5Fclose(fid); /* release data buffers */ if(data_origin) free(data_origin); if(data_array) free(data_array); }