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1103 lines
36 KiB
C
1103 lines
36 KiB
C
/* $Id$ */
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/*
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* Parallel tests for datasets
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*/
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/*
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* Example of using the parallel HDF5 library to access datasets.
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*
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* This program contains two major parts. Part 1 tests fixed dimension
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* datasets, for both independent and collective transfer modes.
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* Part 2 tests extendable datasets, for independent transfer mode
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* only. Collective mode for extendable datasets are not supported yet.
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*/
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#include <testphdf5.h>
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/*
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* The following are various utility routines used by the tests.
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*/
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/*
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* Setup the dimensions of the hyperslab.
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* Two modes--by rows or by columns.
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* Assume dimension rank is 2.
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*/
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void
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slab_set(int mpi_rank, int mpi_size, hssize_t start[], hsize_t count[],
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hsize_t stride[], int mode)
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{
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switch (mode){
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case BYROW:
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/* Each process takes a slabs of rows. */
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stride[0] = 1;
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stride[1] = 1;
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count[0] = DIM1/mpi_size;
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count[1] = DIM2;
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start[0] = mpi_rank*count[0];
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start[1] = 0;
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if (verbose) printf("slab_set BYROW\n");
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break;
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case BYCOL:
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/* Each process takes a block of columns. */
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stride[0] = 1;
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stride[1] = 1;
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count[0] = DIM1;
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count[1] = DIM2/mpi_size;
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start[0] = 0;
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start[1] = mpi_rank*count[1];
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#ifdef DISABLED
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/* change the above macro to #ifndef if you want to test */
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/* zero elements access. */
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printf("set to size 0\n");
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if (!(mpi_rank % 3))
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count[1]=0;
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#endif
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if (verbose) printf("slab_set BYCOL\n");
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break;
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default:
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/* Unknown mode. Set it to cover the whole dataset. */
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printf("unknown slab_set mode (%d)\n", mode);
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stride[0] = 1;
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stride[1] = 1;
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count[0] = DIM1;
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count[1] = DIM2;
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start[0] = 0;
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start[1] = 0;
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if (verbose) printf("slab_set wholeset\n");
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break;
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}
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if (verbose){
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printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\n",
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start[0], start[1], count[0], count[1], count[0]*count[1]);
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}
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}
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/*
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* Fill the dataset with trivial data for testing.
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* Assume dimension rank is 2 and data is stored contiguous.
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*/
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void
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dataset_fill(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
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{
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DATATYPE *dataptr = dataset;
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int i, j;
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/* put some trivial data in the data_array */
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for (i=0; i < count[0]; i++){
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for (j=0; j < count[1]; j++){
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*dataptr = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1);
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dataptr++;
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}
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}
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}
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/*
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* Print the content of the dataset.
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*/
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void dataset_print(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
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{
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DATATYPE *dataptr = dataset;
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int i, j;
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/* print the column heading */
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printf("%-8s", "Cols:");
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for (j=0; j < count[1]; j++){
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printf("%3d ", start[1]+j);
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}
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printf("\n");
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/* print the slab data */
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for (i=0; i < count[0]; i++){
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printf("Row %2d: ", (int)(i*stride[0]+start[0]));
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for (j=0; j < count[1]; j++){
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printf("%03d ", *dataptr++);
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}
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printf("\n");
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}
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}
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/*
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* Print the content of the dataset.
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*/
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int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original)
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{
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#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */
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DATATYPE *dataptr = dataset;
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DATATYPE *originptr = original;
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int i, j, vrfyerrs;
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/* print it if verbose */
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if (verbose)
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dataset_print(start, count, stride, dataset);
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vrfyerrs = 0;
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for (i=0; i < count[0]; i++){
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for (j=0; j < count[1]; j++){
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if (*dataset != *original){
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if (vrfyerrs++ < MAX_ERR_REPORT || verbose){
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printf("Dataset Verify failed at [%d][%d](row %d, col %d): expect %d, got %d\n",
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i, j,
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(int)(i*stride[0]+start[0]), (int)(j*stride[1]+start[1]),
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*(original), *(dataset));
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}
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dataset++;
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original++;
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}
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}
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}
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if (vrfyerrs > MAX_ERR_REPORT && !verbose)
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printf("[more errors ...]\n");
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if (vrfyerrs)
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printf("%d errors found in dataset_vrfy\n", vrfyerrs);
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return(vrfyerrs);
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}
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/*
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* Part 1.a--Independent read/write for fixed dimension datasets.
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*/
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/*
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* Example of using the parallel HDF5 library to create two datasets
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* in one HDF5 files with parallel MPIO access support.
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* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
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* Each process controls only a slab of size DIM1 x DIM2 within each
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* dataset.
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*/
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void
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dataset_writeInd(char *filename)
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{
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hid_t fid; /* HDF5 file ID */
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hid_t acc_tpl; /* File access templates */
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hid_t sid; /* Dataspace ID */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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hsize_t dims[RANK] = {DIM1,DIM2}; /* dataset dim sizes */
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hsize_t dimslocal1[RANK] = {DIM1,DIM2}; /* local dataset dim sizes */
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DATATYPE data_array1[DIM1][DIM2]; /* data buffer */
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hssize_t start[RANK]; /* for hyperslab setting */
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hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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int i, j;
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int mpi_size, mpi_rank;
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char *fname;
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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if (verbose)
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printf("Independent write test on file %s\n", filename);
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/* set up MPI parameters */
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MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
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MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
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/* -------------------
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* START AN HDF5 FILE
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* -------------------*/
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/* setup file access template with parallel IO access. */
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acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
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VRFY((acc_tpl != FAIL), "H5Pcreate access succeeded");
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/* set Parallel access with communicator */
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ret = H5Pset_mpi(acc_tpl, comm, info);
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VRFY((ret != FAIL), "H5Pset_mpi succeeded");
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/* create the file collectively */
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fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
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VRFY((fid != FAIL), "H5Fcreate succeeded");
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/* Release file-access template */
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ret=H5Pclose(acc_tpl);
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VRFY((ret != FAIL), "");
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/* --------------------------
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* Define the dimensions of the overall datasets
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* and the slabs local to the MPI process.
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* ------------------------- */
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/* setup dimensionality object */
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sid = H5Screate_simple (RANK, dims, NULL);
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VRFY((sid != FAIL), "H5Screate_simple succeeded");
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/* create a dataset collectively */
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dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid,
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H5P_DEFAULT);
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VRFY((dataset1 != FAIL), "H5Dcreate succeeded");
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/* create another dataset collectively */
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dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid,
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H5P_DEFAULT);
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VRFY((dataset2 != FAIL), "H5Dcreate succeeded");
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/* set up dimensions of the slab this process accesses */
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slab_set(mpi_rank, mpi_size, start, count, stride, BYROW);
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/* put some trivial data in the data_array */
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dataset_fill(start, count, stride, &data_array1[0][0]);
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MESG("data_array initialized");
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
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VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (RANK, count, NULL);
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VRFY((mem_dataspace != FAIL), "");
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/* write data independently */
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ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret != FAIL), "H5Dwrite succeeded");
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/* write data independently */
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ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret != FAIL), "H5Dwrite succeeded");
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/* release dataspace ID */
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H5Sclose(file_dataspace);
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/* close dataset collectively */
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ret=H5Dclose(dataset1);
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VRFY((ret != FAIL), "H5Dclose1 succeeded");
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ret=H5Dclose(dataset2);
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VRFY((ret != FAIL), "H5Dclose2 succeeded");
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/* release all IDs created */
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H5Sclose(sid);
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/* close the file collectively */
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H5Fclose(fid);
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}
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/* Example of using the parallel HDF5 library to read a dataset */
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void
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dataset_readInd(char *filename)
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{
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hid_t fid; /* HDF5 file ID */
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hid_t acc_tpl; /* File access templates */
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hid_t sid; /* Dataspace ID */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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hsize_t dims[] = {DIM1,DIM2}; /* dataset dim sizes */
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DATATYPE data_array1[DIM1][DIM2]; /* data buffer */
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DATATYPE data_origin1[DIM1][DIM2]; /* expected data buffer */
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hssize_t start[RANK]; /* for hyperslab setting */
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hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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int i, j;
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int mpi_size, mpi_rank;
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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if (verbose)
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printf("Independent read test on file %s\n", filename);
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/* set up MPI parameters */
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MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
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MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
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/* setup file access template */
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acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
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VRFY((acc_tpl != FAIL), "");
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/* set Parallel access with communicator */
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ret = H5Pset_mpi(acc_tpl, comm, info);
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VRFY((ret != FAIL), "");
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/* open the file collectively */
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fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
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VRFY((fid != FAIL), "");
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/* Release file-access template */
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ret=H5Pclose(acc_tpl);
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VRFY((ret != FAIL), "");
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/* open the dataset1 collectively */
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dataset1 = H5Dopen(fid, DATASETNAME1);
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VRFY((dataset1 != FAIL), "");
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/* open another dataset collectively */
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dataset2 = H5Dopen(fid, DATASETNAME1);
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VRFY((dataset2 != FAIL), "");
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/* set up dimensions of the slab this process accesses */
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slab_set(mpi_rank, mpi_size, start, count, stride, BYROW);
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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VRFY((file_dataspace != FAIL), "");
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
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VRFY((ret != FAIL), "");
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (RANK, count, NULL);
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VRFY((mem_dataspace != FAIL), "");
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/* fill dataset with test data */
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dataset_fill(start, count, stride, &data_origin1[0][0]);
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/* read data independently */
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ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret != FAIL), "");
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/* verify the read data with original expected data */
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ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
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if (ret) nerrors++;
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/* read data independently */
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ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret != FAIL), "");
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/* verify the read data with original expected data */
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ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
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if (ret) nerrors++;
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/* close dataset collectively */
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ret=H5Dclose(dataset1);
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VRFY((ret != FAIL), "");
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ret=H5Dclose(dataset2);
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VRFY((ret != FAIL), "");
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/* release all IDs created */
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H5Sclose(file_dataspace);
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/* close the file collectively */
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H5Fclose(fid);
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}
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/*
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* Part 1.b--Collective read/write for fixed dimension datasets.
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*/
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/*
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* Example of using the parallel HDF5 library to create two datasets
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* in one HDF5 file with collective parallel access support.
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* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
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* Each process controls only a slab of size DIM1 x DIM2 within each
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* dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and
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* each process controls a hyperslab within.]
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*/
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void
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dataset_writeAll(char *filename)
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{
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hid_t fid; /* HDF5 file ID */
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hid_t acc_tpl; /* File access templates */
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hid_t xfer_plist; /* Dataset transfer properties list */
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hid_t sid; /* Dataspace ID */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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hid_t datatype; /* Datatype ID */
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hsize_t dims[RANK] = {DIM1,DIM2}; /* dataset dim sizes */
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DATATYPE data_array1[DIM1][DIM2]; /* data buffer */
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hssize_t start[RANK]; /* for hyperslab setting */
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hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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int mpi_size, mpi_rank;
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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if (verbose)
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printf("Collective write test on file %s\n", filename);
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/* set up MPI parameters */
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MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
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MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
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/* -------------------
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* START AN HDF5 FILE
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* -------------------*/
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/* setup file access template with parallel IO access. */
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acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
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VRFY((acc_tpl != FAIL), "H5Pcreate access succeeded");
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/* set Parallel access with communicator */
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ret = H5Pset_mpi(acc_tpl, comm, info);
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VRFY((ret != FAIL), "H5Pset_mpi succeeded");
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/* create the file collectively */
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fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
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VRFY((fid != FAIL), "H5Fcreate succeeded");
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/* Release file-access template */
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ret=H5Pclose(acc_tpl);
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VRFY((ret != FAIL), "");
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/* --------------------------
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* Define the dimensions of the overall datasets
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* and create the dataset
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* ------------------------- */
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/* setup dimensionality object */
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sid = H5Screate_simple (RANK, dims, NULL);
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VRFY((sid != FAIL), "H5Screate_simple succeeded");
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/* create a dataset collectively */
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dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT);
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VRFY((dataset1 != FAIL), "H5Dcreate succeeded");
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/* create another dataset collectively */
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datatype = H5Tcopy(H5T_NATIVE_INT);
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ret = H5Tset_order(datatype, H5T_ORDER_LE);
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VRFY((ret != FAIL), "H5Tset_order succeeded");
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dataset2 = H5Dcreate(fid, DATASETNAME2, datatype, sid, H5P_DEFAULT);
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VRFY((dataset2 != FAIL), "H5Dcreate 2 succeeded");
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/*
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* Set up dimensions of the slab this process accesses.
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*/
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/* Dataset1: each process takes a block of rows. */
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slab_set(mpi_rank, mpi_size, start, count, stride, BYROW);
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
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VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* fill the local slab with some trivial data */
|
|
dataset_fill(start, count, stride, &data_array1[0][0]);
|
|
MESG("data_array initialized");
|
|
if (verbose){
|
|
MESG("data_array created");
|
|
dataset_print(start, count, stride, &data_array1[0][0]);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist != FAIL), "");
|
|
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
|
|
VRFY((ret != FAIL), "H5Pcreate xfer succeeded");
|
|
|
|
/* write data collectively */
|
|
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret != FAIL), "H5Dwrite dataset1 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, BYCOL);
|
|
|
|
/* put some trivial data in the data_array */
|
|
dataset_fill(start, count, stride, &data_array1[0][0]);
|
|
MESG("data_array initialized");
|
|
if (verbose){
|
|
MESG("data_array created");
|
|
dataset_print(start, count, stride, &data_array1[0][0]);
|
|
}
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* fill the local slab with some trivial data */
|
|
dataset_fill(start, count, stride, &data_array1[0][0]);
|
|
MESG("data_array initialized");
|
|
if (verbose){
|
|
MESG("data_array created");
|
|
dataset_print(start, count, stride, &data_array1[0][0]);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist != FAIL), "");
|
|
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
|
|
VRFY((ret != FAIL), "H5Pcreate xfer succeeded");
|
|
|
|
/* write data independently */
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret != FAIL), "H5Dwrite dataset2 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 != FAIL), "H5Dclose1 succeeded");
|
|
ret=H5Dclose(dataset2);
|
|
VRFY((ret != FAIL), "H5Dclose2 succeeded");
|
|
|
|
/* release all IDs created */
|
|
H5Sclose(sid);
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
}
|
|
|
|
/*
|
|
* 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 DIM1) x DIM2.
|
|
* Each process controls only a slab of size DIM1 x DIM2 within each
|
|
* dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and
|
|
* each process controls a hyperslab within.]
|
|
*/
|
|
|
|
void
|
|
dataset_readAll(char *filename)
|
|
{
|
|
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 */
|
|
hsize_t dims[] = {DIM1,DIM2}; /* dataset dim sizes */
|
|
DATATYPE data_array1[DIM1][DIM2]; /* data buffer */
|
|
DATATYPE data_origin1[DIM1][DIM2]; /* expected data buffer */
|
|
|
|
hssize_t start[RANK]; /* for hyperslab setting */
|
|
hsize_t count[RANK], stride[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;
|
|
|
|
if (verbose)
|
|
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);
|
|
|
|
/* -------------------
|
|
* OPEN AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template with parallel IO access. */
|
|
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
|
|
VRFY((acc_tpl != FAIL), "H5Pcreate access succeeded");
|
|
/* set Parallel access with communicator */
|
|
ret = H5Pset_mpi(acc_tpl, comm, info);
|
|
VRFY((ret != FAIL), "H5Pset_mpi succeeded");
|
|
|
|
/* open the file collectively */
|
|
fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
|
|
VRFY((fid != FAIL), "H5Fopen succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret=H5Pclose(acc_tpl);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
|
|
/* --------------------------
|
|
* Open the datasets in it
|
|
* ------------------------- */
|
|
/* open the dataset1 collectively */
|
|
dataset1 = H5Dopen(fid, DATASETNAME1);
|
|
VRFY((dataset1 != FAIL), "H5Dopen succeeded");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen(fid, DATASETNAME2);
|
|
VRFY((dataset2 != FAIL), "H5Dopen 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, BYCOL);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* fill dataset with test data */
|
|
dataset_fill(start, count, stride, &data_origin1[0][0]);
|
|
MESG("data_array initialized");
|
|
if (verbose){
|
|
MESG("data_array created");
|
|
dataset_print(start, count, stride, &data_origin1[0][0]);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist != FAIL), "");
|
|
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
|
|
VRFY((ret != FAIL), "H5Pcreate xfer succeeded");
|
|
|
|
/* read data collectively */
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret != FAIL), "H5Dread succeeded");
|
|
|
|
/* verify the read data with original expected data */
|
|
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
|
|
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, BYROW);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* fill dataset with test data */
|
|
dataset_fill(start, count, stride, &data_origin1[0][0]);
|
|
MESG("data_array initialized");
|
|
if (verbose){
|
|
MESG("data_array created");
|
|
dataset_print(start, count, stride, &data_origin1[0][0]);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist != FAIL), "");
|
|
ret=H5Pset_xfer(xfer_plist, H5D_XFER_COLLECTIVE);
|
|
VRFY((ret != FAIL), "H5Pcreate xfer succeeded");
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret != FAIL), "H5Dread succeeded");
|
|
|
|
/* verify the read data with original expected data */
|
|
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
|
|
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 != FAIL), "H5Dclose1 succeeded");
|
|
ret=H5Dclose(dataset2);
|
|
VRFY((ret != FAIL), "H5Dclose2 succeeded");
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
}
|
|
|
|
|
|
/*
|
|
* Part 2--Independent read/write for extendable datasets.
|
|
*/
|
|
|
|
/*
|
|
* Example of using the parallel HDF5 library to create two extendable
|
|
* datasets in one HDF5 file with independent parallel MPIO access support.
|
|
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
|
|
* Each process controls only a slab of size DIM1 x DIM2 within each
|
|
* dataset.
|
|
*/
|
|
|
|
void
|
|
extend_writeInd(char *filename)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* File access templates */
|
|
hid_t sid; /* Dataspace ID */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
hsize_t dims[RANK] = {DIM1,DIM2}; /* dataset initial dim sizes */
|
|
hsize_t max_dims[RANK] =
|
|
{H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */
|
|
hsize_t dimslocal1[RANK] = {DIM1,DIM2}; /* local dataset dim sizes */
|
|
DATATYPE data_array1[DIM1][DIM2]; /* data buffer */
|
|
hsize_t chunk_dims[RANK] = {7, 13}; /* chunk sizes */
|
|
hid_t dataset_pl; /* dataset create prop. list */
|
|
|
|
hssize_t start[RANK]; /* for hyperslab setting */
|
|
hsize_t count[RANK]; /* for hyperslab setting */
|
|
hsize_t stride[RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
int i, j;
|
|
int mpi_size, mpi_rank;
|
|
char *fname;
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
if (verbose)
|
|
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);
|
|
|
|
/* -------------------
|
|
* START AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template with parallel IO access. */
|
|
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
|
|
VRFY((acc_tpl != FAIL), "H5Pcreate access succeeded");
|
|
/* set Parallel access with communicator */
|
|
ret = H5Pset_mpi(acc_tpl, comm, info);
|
|
VRFY((ret != FAIL), "H5Pset_mpi succeeded");
|
|
|
|
/* create the file collectively */
|
|
fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
|
|
VRFY((fid != FAIL), "H5Fcreate succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret=H5Pclose(acc_tpl);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
|
|
/* --------------------------
|
|
* Define the dimensions of the overall datasets and create them.
|
|
* ------------------------- */
|
|
|
|
/* set up dataset storage chunk sizes and creation property list */
|
|
if (verbose)
|
|
printf("chunks[]=%d,%d\n", chunk_dims[0], chunk_dims[1]);
|
|
dataset_pl = H5Pcreate(H5P_DATASET_CREATE);
|
|
VRFY((dataset_pl != FAIL), "H5Pcreate succeeded");
|
|
ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims);
|
|
VRFY((ret != FAIL), "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 != FAIL), "H5Screate_simple succeeded");
|
|
|
|
/* create an extendable dataset collectively */
|
|
dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid, dataset_pl);
|
|
VRFY((dataset1 != FAIL), "H5Dcreate succeeded");
|
|
|
|
/* create another extendable dataset collectively */
|
|
dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid, dataset_pl);
|
|
VRFY((dataset2 != FAIL), "H5Dcreate succeeded");
|
|
|
|
/* release resource */
|
|
H5Sclose(sid);
|
|
|
|
|
|
|
|
/* -------------------------
|
|
* Test writing to dataset1
|
|
* -------------------------*/
|
|
/* set up dimensions of the slab this process accesses */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, BYROW);
|
|
|
|
/* put some trivial data in the data_array */
|
|
dataset_fill(start, count, stride, &data_array1[0][0]);
|
|
MESG("data_array initialized");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* Extend its current dim sizes before writing */
|
|
dims[0] = DIM1;
|
|
dims[1] = DIM2;
|
|
ret = H5Dextend (dataset1, dims);
|
|
VRFY((ret != FAIL), "H5Dextend succeeded");
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
|
|
|
|
/* write data independently */
|
|
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
VRFY((ret != FAIL), "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, BYCOL);
|
|
|
|
/* put some trivial data in the data_array */
|
|
dataset_fill(start, count, stride, &data_array1[0][0]);
|
|
MESG("data_array initialized");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
#ifdef DISABLE
|
|
/* Try write to dataset2 without extending it first. Should fail. */
|
|
/* first turn off auto error reporting */
|
|
H5Eget_auto(&old_func, &old_client_data);
|
|
H5Eset_auto(NULL, NULL);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset2);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
|
|
|
|
/* write data independently. Should fail. */
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
VRFY((ret == FAIL), "H5Dwrite failed as expected");
|
|
|
|
/* restore auto error reporting */
|
|
H5Eset_auto(old_func, old_client_data);
|
|
H5Sclose(file_dataspace);
|
|
#else
|
|
/* Skip test because H5Dwrite is not failing as expected */
|
|
printf("Skip test of write before extend\n");
|
|
#endif
|
|
|
|
/* Extend dataset2 and try again. Should succeed. */
|
|
dims[0] = DIM1;
|
|
dims[1] = DIM2;
|
|
ret = H5Dextend (dataset2, dims);
|
|
VRFY((ret != FAIL), "H5Dextend succeeded");
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset2);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "H5Sset_hyperslab succeeded");
|
|
|
|
/* write data independently */
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
VRFY((ret != FAIL), "H5Dwrite succeeded");
|
|
|
|
/* release resource */
|
|
ret=H5Sclose(file_dataspace);
|
|
VRFY((ret != FAIL), "H5Sclose succeeded");
|
|
ret=H5Sclose(mem_dataspace);
|
|
VRFY((ret != FAIL), "H5Sclose succeeded");
|
|
|
|
|
|
/* close dataset collectively */
|
|
ret=H5Dclose(dataset1);
|
|
VRFY((ret != FAIL), "H5Dclose1 succeeded");
|
|
ret=H5Dclose(dataset2);
|
|
VRFY((ret != FAIL), "H5Dclose2 succeeded");
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
}
|
|
|
|
/* Example of using the parallel HDF5 library to read an extendable dataset */
|
|
void
|
|
extend_readInd(char *filename)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* File access templates */
|
|
hid_t sid; /* Dataspace ID */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
hsize_t dims[] = {DIM1,DIM2}; /* dataset dim sizes */
|
|
DATATYPE data_array1[DIM1][DIM2]; /* data buffer */
|
|
DATATYPE data_array2[DIM1][DIM2]; /* data buffer */
|
|
DATATYPE data_origin1[DIM1][DIM2]; /* expected data buffer */
|
|
|
|
hssize_t start[RANK]; /* for hyperslab setting */
|
|
hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
int i, j;
|
|
int mpi_size, mpi_rank;
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
if (verbose)
|
|
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);
|
|
|
|
|
|
/* setup file access template */
|
|
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
|
|
VRFY((acc_tpl != FAIL), "");
|
|
/* set Parallel access with communicator */
|
|
ret = H5Pset_mpi(acc_tpl, comm, info);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
|
|
/* open the file collectively */
|
|
fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
|
|
VRFY((fid != FAIL), "");
|
|
|
|
/* Release file-access template */
|
|
ret=H5Pclose(acc_tpl);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
/* open the dataset1 collectively */
|
|
dataset1 = H5Dopen(fid, DATASETNAME1);
|
|
VRFY((dataset1 != FAIL), "");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen(fid, DATASETNAME1);
|
|
VRFY((dataset2 != FAIL), "");
|
|
|
|
/* Try extend dataset1 which is open RDONLY. Should fail. */
|
|
/* first turn off auto error reporting */
|
|
H5Eget_auto(&old_func, &old_client_data);
|
|
H5Eset_auto(NULL, NULL);
|
|
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
VRFY((file_dataspace != FAIL), "H5Dget_space succeeded");
|
|
ret=H5Sget_dims(file_dataspace, dims, NULL);
|
|
VRFY((ret > 0), "H5Sget_dims succeeded");
|
|
dims[0]=dims[0]*2;
|
|
ret=H5Dextend(dataset1, dims);
|
|
VRFY((ret == FAIL), "H5Dextend failed as expected");
|
|
|
|
/* restore auto error reporting */
|
|
H5Eset_auto(old_func, old_client_data);
|
|
|
|
|
|
/* Read dataset1 using BYROW pattern */
|
|
/* set up dimensions of the slab this process accesses */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, BYROW);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
VRFY((file_dataspace != FAIL), "");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* fill dataset with test data */
|
|
dataset_fill(start, count, stride, &data_origin1[0][0]);
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
VRFY((ret != FAIL), "H5Dread succeeded");
|
|
|
|
/* verify the read data with original expected data */
|
|
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
|
|
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, BYCOL);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset2);
|
|
VRFY((file_dataspace != FAIL), "");
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, NULL);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, count, NULL);
|
|
VRFY((mem_dataspace != FAIL), "");
|
|
|
|
/* fill dataset with test data */
|
|
dataset_fill(start, count, stride, &data_origin1[0][0]);
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
VRFY((ret != FAIL), "H5Dread succeeded");
|
|
|
|
/* verify the read data with original expected data */
|
|
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
|
|
VRFY((ret == 0), "dataset2 read verified correct");
|
|
if (ret) nerrors++;
|
|
|
|
H5Sclose(mem_dataspace);
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* close dataset collectively */
|
|
ret=H5Dclose(dataset1);
|
|
VRFY((ret != FAIL), "");
|
|
ret=H5Dclose(dataset2);
|
|
VRFY((ret != FAIL), "");
|
|
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
}
|