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authorRichard Warren <Richard.Warren@hdfgroup.org>2019-12-16 21:59:26 (GMT)
committerRichard Warren <Richard.Warren@hdfgroup.org>2019-12-16 21:59:26 (GMT)
commit4eeeda3b8669dee21867f6d1246b814b28570e3a (patch)
tree926f40b116ff5476d50536ff1861c46627ae3009 /testpar
parentf9b1805c6e87fb19c4fee64c4791f25c2587e948 (diff)
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Merge t_2Gio test into hdf5_1_12. This will eventually be refactored out after merging the test functionality into the testphdf5 test.
Diffstat (limited to 'testpar')
-rw-r--r--testpar/t_2Gio.c4954
1 files changed, 4954 insertions, 0 deletions
diff --git a/testpar/t_2Gio.c b/testpar/t_2Gio.c
new file mode 100644
index 0000000..43be819
--- /dev/null
+++ b/testpar/t_2Gio.c
@@ -0,0 +1,4954 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * 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 <stdio.h>
+#include "hdf5.h"
+#include "testphdf5.h"
+
+#include "mpi.h"
+
+
+/* For this test, we don't want to inherit the RANK definition
+ * from testphdf5.h. We'll define MAX_RANK to accomodate 3D arrays
+ * and use that definition rather than RANK.
+ */
+#ifndef MAX_RANK
+#define MAX_RANK 2
+#endif
+
+/* As with RANK vs MAX_RANK, we use BIG_X_FACTOR vs ROW_FACTOR
+ * and BIG_Y_FACTOR vs COL_FACTOR. We introduce BIG_Z_FACTOR
+ * for the 3rd dimension.
+ */
+
+#ifndef BIG_X_FACTOR
+#define BIG_X_FACTOR 1048576
+#endif
+#ifndef BIG_Y_FACTOR
+#define BIG_Y_FACTOR 32
+#endif
+#ifndef BIG_Z_FACTOR
+#define BIG_Z_FACTOR 2048
+#endif
+
+#ifndef PATH_MAX
+#define PATH_MAX 512
+#endif /* !PATH_MAX */
+
+/* global variables */
+int dim0;
+int dim1;
+int dim2;
+int chunkdim0;
+int chunkdim1;
+int nerrors = 0; /* errors count */
+int ndatasets = 300; /* number of datasets to create*/
+int ngroups = 512; /* number of groups to create in root
+ * group. */
+int facc_type = FACC_MPIO; /*Test file access type */
+int dxfer_coll_type = DXFER_COLLECTIVE_IO;
+
+H5E_auto2_t old_func; /* previous error handler */
+void *old_client_data; /* previous error handler arg.*/
+
+#define NFILENAME 3
+#define PARATESTFILE filenames[0]
+const char *FILENAME[NFILENAME]={
+ "ParaTest",
+ "Hugefile",
+ NULL};
+char filenames[NFILENAME][PATH_MAX];
+hid_t fapl; /* file access property list */
+MPI_Comm test_comm = MPI_COMM_WORLD;
+
+// static int enable_error_stack = 0; /* enable error stack; disable=0 enable=1 */
+// static const char *TestProgName = NULL;
+// static void (*TestPrivateUsage)(void) = NULL;
+// static int (*TestPrivateParser)(int ac, char *av[]) = NULL;
+
+/*
+ * The following are various utility routines used by the tests.
+ */
+
+
+/*
+ * Show command usage
+ */
+static void
+usage(void)
+{
+ HDprintf(" [-r] [-w] [-m<n_datasets>] [-n<n_groups>] "
+ "[-o] [-f <prefix>] [-d <dim0> <dim1>]\n");
+ HDprintf("\t-m<n_datasets>"
+ "\tset number of datasets for the multiple dataset test\n");
+ HDprintf("\t-n<n_groups>"
+ "\tset number of groups for the multiple group test\n");
+ HDprintf("\t-f <prefix>\tfilename prefix\n");
+ HDprintf("\t-2\t\tuse Split-file together with MPIO\n");
+ HDprintf("\t-d <factor0> <factor1>\tdataset dimensions factors. Defaults (%d,%d)\n",
+ BIG_X_FACTOR, BIG_Y_FACTOR);
+ HDprintf("\t-c <dim0> <dim1>\tdataset chunk dimensions. Defaults (dim0/10,dim1/10)\n");
+ HDprintf("\n");
+}
+
+/*
+ * parse the command line options
+ */
+static int
+parse_options(int argc, char **argv)
+{
+ int mpi_size, mpi_rank; /* mpi variables */
+
+ MPI_Comm_size(test_comm, &mpi_size);
+ MPI_Comm_rank(test_comm, &mpi_rank);
+
+ /* setup default chunk-size. Make sure sizes are > 0 */
+
+ chunkdim0 = (dim0+9)/10;
+ chunkdim1 = (dim1+9)/10;
+
+ while (--argc){
+ if (**(++argv) != '-'){
+ break;
+ }else{
+ switch(*(*argv+1)){
+ case 'm': ndatasets = atoi((*argv+1)+1);
+ if (ndatasets < 0){
+ nerrors++;
+ return(1);
+ }
+ break;
+ case 'n': ngroups = atoi((*argv+1)+1);
+ if (ngroups < 0){
+ nerrors++;
+ return(1);
+ }
+ break;
+ case 'f': if (--argc < 1) {
+ nerrors++;
+ return(1);
+ }
+ if (**(++argv) == '-') {
+ nerrors++;
+ return(1);
+ }
+ paraprefix = *argv;
+ break;
+ case '2': /* Use the split-file driver with MPIO access */
+ /* Can use $HDF5_METAPREFIX to define the */
+ /* meta-file-prefix. */
+ facc_type = FACC_MPIO | FACC_SPLIT;
+ break;
+ case 'd': /* dimensizes */
+ if (--argc < 2){
+ nerrors++;
+ return(1);
+ }
+ dim0 = atoi(*(++argv))*mpi_size;
+ argc--;
+ dim1 = atoi(*(++argv))*mpi_size;
+ /* set default chunkdim sizes too */
+ chunkdim0 = (dim0+9)/10;
+ chunkdim1 = (dim1+9)/10;
+ break;
+ case 'c': /* chunk dimensions */
+ if (--argc < 2){
+ nerrors++;
+ return(1);
+ }
+ chunkdim0 = atoi(*(++argv));
+ argc--;
+ chunkdim1 = atoi(*(++argv));
+ break;
+ case 'h': /* print help message--return with nerrors set */
+ return(1);
+ default: HDprintf("Illegal option(%s)\n", *argv);
+ nerrors++;
+ return(1);
+ }
+ }
+ } /*while*/
+
+ /* check validity of dimension and chunk sizes */
+ if (dim0 <= 0 || dim1 <= 0){
+ HDprintf("Illegal dim sizes (%d, %d)\n", dim0, dim1);
+ nerrors++;
+ return(1);
+ }
+ if (chunkdim0 <= 0 || chunkdim1 <= 0){
+ HDprintf("Illegal chunkdim sizes (%d, %d)\n", chunkdim0, chunkdim1);
+ nerrors++;
+ return(1);
+ }
+
+ /* Make sure datasets can be divided into equal portions by the processes */
+ if ((dim0 % mpi_size) || (dim1 % mpi_size)){
+ if (MAINPROCESS)
+ HDprintf("dim0(%d) and dim1(%d) must be multiples of processes(%d)\n",
+ dim0, dim1, mpi_size);
+ nerrors++;
+ return(1);
+ }
+
+ /* compose the test filenames */
+ {
+ int i, n;
+
+ n = sizeof(FILENAME)/sizeof(FILENAME[0]) - 1; /* exclude the NULL */
+
+ for (i=0; i < n; i++)
+ if (h5_fixname(FILENAME[i],fapl,filenames[i],sizeof(filenames[i]))
+ == NULL){
+ HDprintf("h5_fixname failed\n");
+ nerrors++;
+ return(1);
+ }
+
+ if (MAINPROCESS) {
+ HDprintf("Test filenames are:\n");
+ for (i=0; i < n; i++)
+ HDprintf(" %s\n", filenames[i]);
+ }
+ }
+
+ return(0);
+}
+
+/*
+ * Create the appropriate File access property list
+ */
+hid_t
+create_faccess_plist(MPI_Comm comm, MPI_Info info, int l_facc_type)
+{
+ hid_t ret_pl = -1;
+ herr_t ret; /* generic return value */
+ int mpi_rank; /* mpi variables */
+
+ /* need the rank for error checking macros */
+ MPI_Comm_rank(test_comm, &mpi_rank);
+
+ ret_pl = H5Pcreate (H5P_FILE_ACCESS);
+ VRFY((ret_pl >= 0), "H5P_FILE_ACCESS");
+
+ if (l_facc_type == FACC_DEFAULT)
+ return (ret_pl);
+
+ /* set Parallel access with communicator */
+ ret = H5Pset_fapl_mpio(ret_pl, comm, info);
+ VRFY((ret >= 0), "");
+ ret = H5Pset_all_coll_metadata_ops(ret_pl, TRUE);
+ VRFY((ret >= 0), "");
+ ret = H5Pset_coll_metadata_write(ret_pl, TRUE);
+ VRFY((ret >= 0), "");
+
+ return(ret_pl);
+}
+
+
+/*
+ * 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)
+ HDprintf("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)
+ HDprintf("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)
+ HDprintf("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)
+ HDprintf("slab_set ZCOL\n");
+ break;
+ default:
+ /* Unknown mode. Set it to cover the whole dataset. */
+ HDprintf("unknown slab_set mode (%d)\n", mode);
+ block[0] = 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)
+ HDprintf("slab_set wholeset\n");
+ break;
+ }
+ if (VERBOSE_MED) {
+ HDprintf(
+ "start[]=(%lu,%lu), count[]=(%lu,%lu), stride[]=(%lu,%lu), block[]=(%lu,%lu), total datapoints=%lu\n",
+ (unsigned long) start[0], (unsigned long) start[1],
+ (unsigned long) count[0], (unsigned long) count[1],
+ (unsigned long) stride[0], (unsigned long) stride[1],
+ (unsigned long) block[0], (unsigned long) block[1],
+ (unsigned long) (block[0] * block[1] * count[0] * count[1]));
+ }
+}
+
+/*
+ * Setup the coordinates for point selection.
+ */
+void point_set(hsize_t start[],
+ hsize_t count[],
+ hsize_t stride[],
+ hsize_t block[],
+ size_t num_points,
+ hsize_t coords[],
+ int order)
+{
+ hsize_t i,j, k = 0, m ,n, s1 ,s2;
+
+ // HDcompile_assert(MAX_RANK == 3);
+ HDcompile_assert(MAX_RANK == 2);
+
+ if(OUT_OF_ORDER == order)
+ k = (num_points * MAX_RANK) - 1;
+ else if(IN_ORDER == order)
+ k = 0;
+
+ s1 = start[0];
+ s2 = start[1];
+
+ for(i = 0 ; i < count[0]; i++)
+ for(j = 0 ; j < count[1]; j++)
+ for(m = 0 ; m < block[0]; m++)
+ for(n = 0 ; n < block[1]; n++)
+ if(OUT_OF_ORDER == order) {
+ coords[k--] = s2 + (stride[1] * j) + n;
+ coords[k--] = s1 + (stride[0] * i) + m;
+ }
+ else if(IN_ORDER == order) {
+ coords[k++] = s1 + stride[0] * i + m;
+ coords[k++] = s2 + stride[1] * j + n;
+ }
+
+ if(VERBOSE_MED) {
+ HDprintf("start[]=(%lu, %lu), count[]=(%lu, %lu), stride[]=(%lu, %lu), block[]=(%lu, %lu), total datapoints=%lu\n",
+ (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
+ (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1],
+ (unsigned long)(block[0] * block[1] * count[0] * count[1]));
+ k = 0;
+ for(i = 0; i < num_points ; i++) {
+ HDprintf("(%d, %d)\n", (int)coords[k], (int)coords[k + 1]);
+ k += 2;
+ }
+ }
+}
+
+
+/*
+ * Fill the dataset with trivial data for testing.
+ * Assume dimension rank is 2 and data is stored contiguous.
+ */
+static void
+dataset_fill(hsize_t start[], hsize_t block[], DATATYPE * dataset)
+{
+ DATATYPE *dataptr = dataset;
+ hsize_t i, j;
+
+ /* put some trivial data in the data_array */
+ for (i=0; i < block[0]; i++){
+ for (j=0; j < block[1]; j++){
+ *dataptr = (DATATYPE)((i+start[0])*100 + (j+start[1]+1));
+ dataptr++;
+ }
+ }
+}
+
+
+/*
+ * Print the content of the dataset.
+ */
+static void
+dataset_print(hsize_t start[], hsize_t block[], DATATYPE * dataset)
+{
+ DATATYPE *dataptr = dataset;
+ hsize_t i, j;
+
+ /* print the column heading */
+ HDprintf("%-8s", "Cols:");
+ for (j=0; j < block[1]; j++){
+ HDprintf("%3lu ", (unsigned long)(start[1]+j));
+ }
+ HDprintf("\n");
+
+ /* print the slab data */
+ for (i=0; i < block[0]; i++){
+ HDprintf("Row %2lu: ", (unsigned long)(i+start[0]));
+ for (j=0; j < block[1]; j++){
+ HDprintf("%03d ", *dataptr++);
+ }
+ HDprintf("\n");
+ }
+}
+
+
+/*
+ * Print the content of the dataset.
+ */
+int
+dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original)
+{
+ hsize_t i, j;
+ int vrfyerrs;
+
+ /* print it if VERBOSE_MED */
+ if(VERBOSE_MED) {
+ HDprintf("dataset_vrfy dumping:::\n");
+ HDprintf("start(%lu, %lu), count(%lu, %lu), stride(%lu, %lu), block(%lu, %lu)\n",
+ (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
+ (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1]);
+ HDprintf("original values:\n");
+ dataset_print(start, block, original);
+ HDprintf("compared values:\n");
+ dataset_print(start, block, dataset);
+ }
+
+ vrfyerrs = 0;
+ for (i=0; i < block[0]; i++){
+ for (j=0; j < block[1]; j++){
+ if(*dataset != *original){
+ if(vrfyerrs++ < MAX_ERR_REPORT || VERBOSE_MED){
+ HDprintf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n",
+ (unsigned long)i, (unsigned long)j,
+ (unsigned long)(i+start[0]), (unsigned long)(j+start[1]),
+ *(original), *(dataset));
+ }
+ dataset++;
+ original++;
+ }
+ }
+ }
+ if(vrfyerrs > MAX_ERR_REPORT && !VERBOSE_MED)
+ HDprintf("[more errors ...]\n");
+ if(vrfyerrs)
+ HDprintf("%d errors found in dataset_vrfy\n", vrfyerrs);
+ return(vrfyerrs);
+}
+
+/* NOTE: This is a memory intensive test and is only run
+ * with 2 MPI ranks and with $HDF5TestExpress == 0
+ * i.e. Exhaustive test run is allowed. Otherwise
+ * the test is skipped.
+ *
+ * Thanks to l.ferraro@cineca.it for the following test::
+ *
+ * This is a simple test case to reproduce a problem
+ * occurring on LUSTRE filesystem with the creation
+ * of a 4GB dataset using chunking with parallel HDF5.
+ * The test works correctly if disabling chunking or
+ * when the bytes assigned to each process is less
+ * that 4GB. if equal or more, either hangs or results
+ * in a PMPI_Waitall error.
+ *
+ * $> mpirun -genv I_MPI_EXTRA_FILESYSTEM on
+ * -genv I_MPI_EXTRA_FILESYSTEM_LIST gpfs
+ * -n 1 ./h5_mpi_big_dataset.x 1024 1024 1024
+ */
+
+#define H5FILE_NAME "hugefile.h5"
+#define DATASETNAME "dataset"
+
+int MpioTest2G( MPI_Comm comm, int mpi_rank )
+{
+ /*
+ * HDF5 APIs definitions
+ */
+ herr_t status;
+ hid_t dcpl_id;
+ hid_t filedataspace;
+ hid_t memorydataspace;
+ hid_t file_id, dset_id; /* file and dataset identifiers */
+ hid_t plist_id; /* property list identifier */
+ hid_t filespace; /* file and memory dataspace identifiers */
+ int *data; /* pointer to data buffer to write */
+
+ hsize_t shape[3] = {1024, 1024, 1152};
+ size_t slice_per_process, data_size, data_size_bytes;
+ size_t tot_size_bytes = sizeof(int);
+ hsize_t chunk[3] = {4, shape[1], shape[2]};
+ hsize_t h5_counts[3] = { slice_per_process, shape[1], shape[2] };
+ hsize_t h5_offsets[3] = { mpi_rank * slice_per_process, 0, 0};
+
+
+ /*
+ * MPI variables
+ */
+ int mpi_size;
+ MPI_Info info = MPI_INFO_NULL;
+
+ MPI_Comm_size(comm, &mpi_size);
+
+ if(mpi_rank == 0) {
+ HDprintf("Using %d process on dataset shape [%llu, %llu, %llu]\n",
+ mpi_size, shape[0], shape[1], shape[2]);
+ }
+
+ /*
+ * Set up file access property list with parallel I/O access
+ */
+ plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ VRFY((plist_id >= 0), "H5Pcreate file_access succeeded");
+ status = H5Pset_fapl_mpio(plist_id, comm, info);
+ VRFY((status >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /*
+ * Create a new file collectively and release property list identifier.
+ */
+ file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ VRFY((file_id >= 0), "H5Fcreate succeeded");
+
+ H5Pclose(plist_id);
+
+ /*
+ * Create the dataspace for the dataset.
+ */
+ for (int i = 0; i < 3; i++) {
+ tot_size_bytes *= shape[i];
+ }
+ if(mpi_rank == 0) {
+ HDprintf("Dataset of %llu bytes\n", tot_size_bytes);
+ }
+ filespace = H5Screate_simple(3, shape, NULL);
+ VRFY((filespace >= 0), "H5Screate_simple succeeded");
+
+ /*
+ * Select chunking
+ */
+ dcpl_id = H5Pcreate (H5P_DATASET_CREATE);
+ VRFY((dcpl_id >= 0), "H5P_DATASET_CREATE");
+ status = H5Pset_chunk(dcpl_id, 3, chunk);
+ VRFY((status >= 0), "H5Pset_chunk succeeded");
+
+ /*
+ * Create the dataset with default properties and close filespace.
+ */
+ dset_id = H5Dcreate(file_id, DATASETNAME,
+ H5T_NATIVE_INT, filespace,
+ H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
+ VRFY((dset_id >= 0), "H5Dcreate succeeded");
+ H5Sclose(filespace);
+
+ /*
+ * Create property list for collective dataset write.
+ */
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((plist_id >= 0), "H5P_DATASET_XFER");
+ status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+ VRFY((status >= 0), "");
+
+ slice_per_process = (shape[0] + mpi_size - 1) / mpi_size;
+ data_size = slice_per_process * shape[1] * shape[2];
+ data_size_bytes = sizeof(int) * data_size;
+ data = HDmalloc(data_size_bytes);
+ VRFY((data != NULL), "data HDmalloc succeeded");
+
+ for (size_t i = 0; i < data_size; i++) {
+ data[i] = mpi_rank;
+ }
+
+ filedataspace = H5Screate_simple(3, shape, NULL);
+ VRFY((filedataspace >= 0), "H5Screate_simple succeeded");
+
+ // fix reminder along first dimension multiple of chunk[0]
+ if ( h5_offsets[0] + h5_counts[0] > shape[0]) {
+ h5_counts[0] = shape[0] - h5_offsets[0];
+ }
+
+ status = H5Sselect_hyperslab(filedataspace, H5S_SELECT_SET,
+ h5_offsets, NULL, h5_counts, NULL);
+ VRFY((status >= 0), "H5Sselect_hyperslab succeeded");
+
+ memorydataspace = H5Screate_simple(3, h5_counts, NULL);
+ VRFY((memorydataspace >= 0), "H5Screate_simple succeeded");
+
+ status = H5Dwrite(dset_id, H5T_NATIVE_INT,
+ memorydataspace, filedataspace, plist_id, data);
+ VRFY((status >= 0), "H5Dwrite succeeded");
+ H5Pclose(plist_id);
+
+ /*
+ * Close/release resources.
+ */
+ H5Sclose(filedataspace);
+ H5Sclose(memorydataspace);
+ H5Dclose(dset_id);
+ H5Fclose(file_id);
+
+ free(data);
+ HDprintf("Proc %d - MpioTest2G test succeeded\n", mpi_rank, data_size_bytes);
+
+ if (mpi_rank == 0)
+ HDremove(FILENAME[1]);
+ return 0;
+}
+
+
+/*
+ * Part 1.a--Independent read/write for fixed dimension datasets.
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create two datasets
+ * in one HDF5 files with parallel MPIO access support.
+ * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within each
+ * dataset.
+ */
+
+void
+dataset_writeInd(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t sid; /* Dataspace ID */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ hsize_t dims[MAX_RANK] = {1,}; /* dataset dim sizes */
+ hsize_t data_size;
+ DATATYPE *data_array1 = NULL; /* data buffer */
+ const char *filename;
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK];
+ hsize_t stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Independent write test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* allocate memory for data buffer */
+ data_size = sizeof(DATATYPE);
+ data_size *= (hsize_t)dim0 * (hsize_t)dim1;
+ data_array1 = (DATATYPE *)HDmalloc(data_size);
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+
+ /* ----------------------------------------
+ * CREATE AN HDF5 FILE WITH PARALLEL ACCESS
+ * ---------------------------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+
+ /* ---------------------------------------------
+ * Define the dimensions of the overall datasets
+ * and the slabs local to the MPI process.
+ * ------------------------------------------- */
+ /* setup dimensionality object */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple (MAX_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 (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* write data independently */
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
+ /* write data independently */
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
+
+ /* setup dimensions again to write with zero rows for process 0 */
+ if(VERBOSE_MED)
+ HDprintf("writeInd by some with zero row\n");
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW);
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+ /* need to make mem_dataspace to match for process 0 */
+ if(MAINPROCESS){
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
+ }
+ MESG("writeInd by some with zero row");
+if((mpi_rank/2)*2 != mpi_rank){
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded");
+}
+#ifdef BARRIER_CHECKS
+MPI_Barrier(test_comm);
+#endif /* BARRIER_CHECKS */
+
+ /* release dataspace ID */
+ H5Sclose(file_dataspace);
+
+ /* close dataset collectively */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5Dclose1 succeeded");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose2 succeeded");
+
+ /* release all IDs created */
+ H5Sclose(sid);
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(data_array1) HDfree(data_array1);
+}
+
+/* Example of using the parallel HDF5 library to read a dataset */
+void
+dataset_readInd(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ DATATYPE *data_array1 = NULL; /* data buffer */
+ DATATYPE *data_origin1 = NULL; /* expected data buffer */
+ const char *filename;
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK], stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Independent read test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* allocate memory for data buffer */
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+ data_origin1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
+
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* open the file collectively */
+ fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl);
+ VRFY((fid >= 0), "");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+ /* open the dataset1 collectively */
+ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "");
+
+ /* open another dataset collectively */
+ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "");
+
+
+ /* set up dimensions of the slab this process accesses */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "");
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill dataset with test data */
+ dataset_fill(start, block, data_origin1);
+
+ /* read data independently */
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ VRFY((ret >= 0), "");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* read data independently */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ VRFY((ret >= 0), "");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* close dataset collectively */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "");
+
+ /* release all IDs created */
+ H5Sclose(file_dataspace);
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(data_array1) HDfree(data_array1);
+ if(data_origin1) HDfree(data_origin1);
+}
+
+
+/*
+ * Part 1.b--Collective read/write for fixed dimension datasets.
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create two datasets
+ * in one HDF5 file with collective parallel access support.
+ * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within each
+ * dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and
+ * each process controls a hyperslab within.]
+ */
+
+void
+dataset_writeAll(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t sid; /* Dataspace ID */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2, dataset3, dataset4; /* Dataset ID */
+ hid_t dataset5, dataset6, dataset7; /* Dataset ID */
+ hid_t datatype; /* Datatype ID */
+ hsize_t dims[MAX_RANK] = {1,}; /* dataset dim sizes */
+ DATATYPE *data_array1 = NULL; /* data buffer */
+ const char *filename;
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK];
+ hsize_t stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ size_t num_points; /* for point selection */
+ hsize_t *coords = NULL; /* for point selection */
+ hsize_t current_dims; /* for point selection */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Collective write test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* set up the coords array selection */
+ num_points = dim1;
+ coords = (hsize_t *)HDmalloc(dim1 * MAX_RANK * sizeof(hsize_t));
+ VRFY((coords != NULL), "coords malloc succeeded");
+
+ /* allocate memory for data buffer */
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+
+ /* -------------------
+ * START AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+
+ /* --------------------------
+ * Define the dimensions of the overall datasets
+ * and create the dataset
+ * ------------------------- */
+ /* setup 2-D dimensionality object */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+
+
+ /* create a dataset collectively */
+ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
+
+ /* create another dataset collectively */
+ datatype = H5Tcopy(H5T_NATIVE_INT);
+ ret = H5Tset_order(datatype, H5T_ORDER_LE);
+ VRFY((ret >= 0), "H5Tset_order succeeded");
+
+ dataset2 = H5Dcreate2(fid, DATASETNAME2, datatype, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "H5Dcreate2 2 succeeded");
+
+ /* create a third dataset collectively */
+ dataset3 = H5Dcreate2(fid, DATASETNAME3, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset3 >= 0), "H5Dcreate2 succeeded");
+
+ dataset5 = H5Dcreate2(fid, DATASETNAME7, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset5 >= 0), "H5Dcreate2 succeeded");
+ dataset6 = H5Dcreate2(fid, DATASETNAME8, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset6 >= 0), "H5Dcreate2 succeeded");
+ dataset7 = H5Dcreate2(fid, DATASETNAME9, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset7 >= 0), "H5Dcreate2 succeeded");
+
+ /* release 2-D space ID created */
+ H5Sclose(sid);
+
+ /* setup scalar dimensionality object */
+ sid = H5Screate(H5S_SCALAR);
+ VRFY((sid >= 0), "H5Screate succeeded");
+
+ /* create a fourth dataset collectively */
+ dataset4 = H5Dcreate2(fid, DATASETNAME4, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset4 >= 0), "H5Dcreate2 succeeded");
+
+ /* release scalar space ID created */
+ H5Sclose(sid);
+
+ /*
+ * Set up dimensions of the slab this process accesses.
+ */
+
+ /* Dataset1: each process takes a block of rows. */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill the local slab with some trivial data */
+ dataset_fill(start, block, data_array1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* write data collectively */
+ MESG("writeAll by Row");
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
+
+ /* setup dimensions again to writeAll with zero rows for process 0 */
+ if(VERBOSE_MED)
+ HDprintf("writeAll by some with zero row\n");
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW);
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+ /* need to make mem_dataspace to match for process 0 */
+ if(MAINPROCESS){
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
+ }
+ MESG("writeAll by some with zero row");
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded");
+
+ /* release all temporary handles. */
+ /* Could have used them for dataset2 but it is cleaner */
+ /* to create them again.*/
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /* Dataset2: each process takes a block of columns. */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
+
+ /* put some trivial data in the data_array */
+ dataset_fill(start, block, data_array1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ }
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill the local slab with some trivial data */
+ dataset_fill(start, block, data_array1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* write data independently */
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
+
+ /* setup dimensions again to writeAll with zero columns for process 0 */
+ if(VERBOSE_MED)
+ HDprintf("writeAll by some with zero col\n");
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL);
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+ /* need to make mem_dataspace to match for process 0 */
+ if(MAINPROCESS){
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
+ }
+ MESG("writeAll by some with zero col");
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset1 by ZCOL succeeded");
+
+ /* release all temporary handles. */
+ /* Could have used them for dataset3 but it is cleaner */
+ /* to create them again.*/
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+
+ /* Dataset3: each process takes a block of rows, except process zero uses "none" selection. */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset3);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ if(MAINPROCESS) {
+ ret = H5Sselect_none(file_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none file_dataspace succeeded");
+ } /* end if */
+ else {
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sselect_hyperslab succeeded");
+ } /* end else */
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+ if(MAINPROCESS) {
+ ret = H5Sselect_none(mem_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none mem_dataspace succeeded");
+ } /* end if */
+
+ /* fill the local slab with some trivial data */
+ dataset_fill(start, block, data_array1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED) {
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ } /* end if */
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* write data collectively */
+ MESG("writeAll with none");
+ ret = H5Dwrite(dataset3, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset3 succeeded");
+
+ /* write data collectively (with datatype conversion) */
+ MESG("writeAll with none");
+ ret = H5Dwrite(dataset3, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset3 succeeded");
+
+ /* release all temporary handles. */
+ /* Could have used them for dataset4 but it is cleaner */
+ /* to create them again.*/
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /* Dataset4: each process writes no data, except process zero uses "all" selection. */
+ /* Additionally, these are in a scalar dataspace */
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset4);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ if(MAINPROCESS) {
+ ret = H5Sselect_none(file_dataspace);
+ VRFY((ret >= 0), "H5Sselect_all file_dataspace succeeded");
+ } /* end if */
+ else {
+ ret = H5Sselect_all(file_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none succeeded");
+ } /* end else */
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate(H5S_SCALAR);
+ VRFY((mem_dataspace >= 0), "");
+ if(MAINPROCESS) {
+ ret = H5Sselect_none(mem_dataspace);
+ VRFY((ret >= 0), "H5Sselect_all mem_dataspace succeeded");
+ } /* end if */
+ else {
+ ret = H5Sselect_all(mem_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none succeeded");
+ } /* end else */
+
+ /* fill the local slab with some trivial data */
+ dataset_fill(start, block, data_array1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED) {
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ } /* end if */
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* write data collectively */
+ MESG("writeAll with scalar dataspace");
+ ret = H5Dwrite(dataset4, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset4 succeeded");
+
+ /* write data collectively (with datatype conversion) */
+ MESG("writeAll with scalar dataspace");
+ ret = H5Dwrite(dataset4, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset4 succeeded");
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+
+ if(data_array1) free(data_array1);
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
+
+ block[0] = 1;
+ block[1] = dim1;
+ stride[0] = 1;
+ stride[1] = dim1;
+ count[0] = 1;
+ count[1] = 1;
+ start[0] = dim0/mpi_size * mpi_rank;
+ start[1] = 0;
+
+ dataset_fill(start, block, data_array1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ }
+
+ /* Dataset5: point selection in File - Hyperslab selection in Memory*/
+ /* create a file dataspace independently */
+ point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER);
+ file_dataspace = H5Dget_space (dataset5);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ start[0] = 0;
+ start[1] = 0;
+ mem_dataspace = H5Dget_space (dataset5);
+ VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset5 succeeded");
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /* Dataset6: point selection in File - Point selection in Memory*/
+ /* create a file dataspace independently */
+ start[0] = dim0/mpi_size * mpi_rank;
+ start[1] = 0;
+ point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER);
+ file_dataspace = H5Dget_space (dataset6);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ start[0] = 0;
+ start[1] = 0;
+ point_set (start, count, stride, block, num_points, coords, IN_ORDER);
+ mem_dataspace = H5Dget_space (dataset6);
+ VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset6 succeeded");
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /* Dataset7: point selection in File - All selection in Memory*/
+ /* create a file dataspace independently */
+ start[0] = dim0/mpi_size * mpi_rank;
+ start[1] = 0;
+ point_set (start, count, stride, block, num_points, coords, IN_ORDER);
+ file_dataspace = H5Dget_space (dataset7);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ current_dims = num_points;
+ mem_dataspace = H5Screate_simple (1, &current_dims, NULL);
+ VRFY((mem_dataspace >= 0), "mem_dataspace create succeeded");
+
+ ret = H5Sselect_all(mem_dataspace);
+ VRFY((ret >= 0), "H5Sselect_all succeeded");
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dwrite dataset7 succeeded");
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /*
+ * All writes completed. Close datasets collectively
+ */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5Dclose1 succeeded");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose2 succeeded");
+ ret = H5Dclose(dataset3);
+ VRFY((ret >= 0), "H5Dclose3 succeeded");
+ ret = H5Dclose(dataset4);
+ VRFY((ret >= 0), "H5Dclose4 succeeded");
+ ret = H5Dclose(dataset5);
+ VRFY((ret >= 0), "H5Dclose5 succeeded");
+ ret = H5Dclose(dataset6);
+ VRFY((ret >= 0), "H5Dclose6 succeeded");
+ ret = H5Dclose(dataset7);
+ VRFY((ret >= 0), "H5Dclose7 succeeded");
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(coords) HDfree(coords);
+ if(data_array1) HDfree(data_array1);
+}
+
+/*
+ * Example of using the parallel HDF5 library to read two datasets
+ * in one HDF5 file with collective parallel access support.
+ * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within each
+ * dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and
+ * each process controls a hyperslab within.]
+ */
+
+void
+dataset_readAll(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2, dataset5, dataset6, dataset7; /* Dataset ID */
+ DATATYPE *data_array1 = NULL; /* data buffer */
+ DATATYPE *data_origin1 = NULL; /* expected data buffer */
+ const char *filename;
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK], stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ size_t num_points; /* for point selection */
+ hsize_t *coords = NULL; /* for point selection */
+ int i,j,k;
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Collective read test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* set up the coords array selection */
+ num_points = dim1;
+ coords = (hsize_t *)HDmalloc(dim0 * dim1 * MAX_RANK * sizeof(hsize_t));
+ VRFY((coords != NULL), "coords malloc succeeded");
+
+ /* allocate memory for data buffer */
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+ data_origin1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
+
+ /* -------------------
+ * OPEN AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* open the file collectively */
+ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
+ VRFY((fid >= 0), "H5Fopen succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+
+ /* --------------------------
+ * Open the datasets in it
+ * ------------------------- */
+ /* open the dataset1 collectively */
+ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "H5Dopen2 succeeded");
+
+ /* open another dataset collectively */
+ dataset2 = H5Dopen2(fid, DATASETNAME2, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "H5Dopen2 2 succeeded");
+
+ /* open another dataset collectively */
+ dataset5 = H5Dopen2(fid, DATASETNAME7, H5P_DEFAULT);
+ VRFY((dataset5 >= 0), "H5Dopen2 5 succeeded");
+ dataset6 = H5Dopen2(fid, DATASETNAME8, H5P_DEFAULT);
+ VRFY((dataset6 >= 0), "H5Dopen2 6 succeeded");
+ dataset7 = H5Dopen2(fid, DATASETNAME9, H5P_DEFAULT);
+ VRFY((dataset7 >= 0), "H5Dopen2 7 succeeded");
+
+ /*
+ * Set up dimensions of the slab this process accesses.
+ */
+
+ /* Dataset1: each process takes a block of columns. */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill dataset with test data */
+ dataset_fill(start, block, data_origin1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_origin1);
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* read data collectively */
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset1 succeeded");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* setup dimensions again to readAll with zero columns for process 0 */
+ if(VERBOSE_MED)
+ HDprintf("readAll by some with zero col\n");
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL);
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+ /* need to make mem_dataspace to match for process 0 */
+ if(MAINPROCESS){
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
+ }
+ MESG("readAll by some with zero col");
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset1 by ZCOL succeeded");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* release all temporary handles. */
+ /* Could have used them for dataset2 but it is cleaner */
+ /* to create them again.*/
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /* Dataset2: each process takes a block of rows. */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill dataset with test data */
+ dataset_fill(start, block, data_origin1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_origin1);
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* read data collectively */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset2 succeeded");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* setup dimensions again to readAll with zero rows for process 0 */
+ if(VERBOSE_MED)
+ HDprintf("readAll by some with zero row\n");
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW);
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+ /* need to make mem_dataspace to match for process 0 */
+ if(MAINPROCESS){
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
+ }
+ MESG("readAll by some with zero row");
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset1 by ZROW succeeded");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ if(data_array1) free(data_array1);
+ if(data_origin1) free(data_origin1);
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
+ data_origin1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
+
+ block[0] = 1;
+ block[1] = dim1;
+ stride[0] = 1;
+ stride[1] = dim1;
+ count[0] = 1;
+ count[1] = 1;
+ start[0] = dim0/mpi_size * mpi_rank;
+ start[1] = 0;
+
+ dataset_fill(start, block, data_origin1);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_origin1);
+ }
+
+ /* Dataset5: point selection in memory - Hyperslab selection in file*/
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset5);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ start[0] = 0;
+ start[1] = 0;
+ point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER);
+ mem_dataspace = H5Dget_space (dataset5);
+ VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* read data collectively */
+ ret = H5Dread(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset5 succeeded");
+
+
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ if(data_array1) free(data_array1);
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
+
+ /* Dataset6: point selection in File - Point selection in Memory*/
+ /* create a file dataspace independently */
+ start[0] = dim0/mpi_size * mpi_rank;
+ start[1] = 0;
+ point_set (start, count, stride, block, num_points, coords, IN_ORDER);
+ file_dataspace = H5Dget_space (dataset6);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ start[0] = 0;
+ start[1] = 0;
+ point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER);
+ mem_dataspace = H5Dget_space (dataset6);
+ VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* read data collectively */
+ ret = H5Dread(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset6 succeeded");
+
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ if(ret) nerrors++;
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ if(data_array1) free(data_array1);
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
+
+ /* Dataset7: point selection in memory - All selection in file*/
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset7);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_all(file_dataspace);
+ VRFY((ret >= 0), "H5Sselect_all succeeded");
+
+ num_points = dim0 * dim1;
+ k=0;
+ for (i=0 ; i<dim0; i++) {
+ for (j=0 ; j<dim1; j++) {
+ coords[k++] = i;
+ coords[k++] = j;
+ }
+ }
+ mem_dataspace = H5Dget_space (dataset7);
+ VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
+ VRFY((ret >= 0), "H5Sselect_elements succeeded");
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pcreate xfer succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+ /* read data collectively */
+ ret = H5Dread(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread dataset7 succeeded");
+
+ start[0] = dim0/mpi_size * mpi_rank;
+ start[1] = 0;
+ ret = dataset_vrfy(start, count, stride, block, data_array1+(dim0/mpi_size * dim1 * mpi_rank), data_origin1);
+ if(ret) nerrors++;
+
+ /* release all temporary handles. */
+ H5Sclose(file_dataspace);
+ H5Sclose(mem_dataspace);
+ H5Pclose(xfer_plist);
+
+ /*
+ * All reads completed. Close datasets collectively
+ */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5Dclose1 succeeded");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose2 succeeded");
+ ret = H5Dclose(dataset5);
+ VRFY((ret >= 0), "H5Dclose5 succeeded");
+ ret = H5Dclose(dataset6);
+ VRFY((ret >= 0), "H5Dclose6 succeeded");
+ ret = H5Dclose(dataset7);
+ VRFY((ret >= 0), "H5Dclose7 succeeded");
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(coords) HDfree(coords);
+ if(data_array1) HDfree(data_array1);
+ if(data_origin1) HDfree(data_origin1);
+}
+
+
+/*
+ * Part 2--Independent read/write for extendible datasets.
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create two extendible
+ * datasets in one HDF5 file with independent parallel MPIO access support.
+ * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within each
+ * dataset.
+ */
+
+void
+extend_writeInd(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t sid; /* Dataspace ID */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ const char *filename;
+ hsize_t dims[MAX_RANK]; /* dataset dim sizes */
+ hsize_t max_dims[MAX_RANK] =
+ {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */
+ DATATYPE *data_array1 = NULL; /* data buffer */
+ hsize_t chunk_dims[MAX_RANK]; /* chunk sizes */
+ hid_t dataset_pl; /* dataset create prop. list */
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK]; /* for hyperslab setting */
+ hsize_t stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Extend independent write test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&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 *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+
+ /* -------------------
+ * START AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+/* Reduce the number of metadata cache slots, so that there are cache
+ * collisions during the raw data I/O on the chunked dataset. This stresses
+ * the metadata cache and tests for cache bugs. -QAK
+ */
+{
+ int mdc_nelmts;
+ size_t rdcc_nelmts;
+ size_t rdcc_nbytes;
+ double rdcc_w0;
+
+ ret = H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0);
+ VRFY((ret >= 0), "H5Pget_cache succeeded");
+ mdc_nelmts=4;
+ ret = H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0);
+ VRFY((ret >= 0), "H5Pset_cache succeeded");
+}
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+
+ /* --------------------------------------------------------------
+ * Define the dimensions of the overall datasets and create them.
+ * ------------------------------------------------------------- */
+
+ /* set up dataset storage chunk sizes and creation property list */
+ if(VERBOSE_MED)
+ HDprintf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]);
+ dataset_pl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dataset_pl >= 0), "H5Pcreate succeeded");
+ ret = H5Pset_chunk(dataset_pl, MAX_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 (MAX_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 (MAX_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 (MAX_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) HDfree(data_array1);
+}
+
+/*
+ * Example of using the parallel HDF5 library to create an extendable dataset
+ * and perform I/O on it in a way that verifies that the chunk cache is
+ * bypassed for parallel I/O.
+ */
+
+void
+extend_writeInd2(void)
+{
+ const char *filename;
+ hid_t fid; /* HDF5 file ID */
+ hid_t fapl; /* File access templates */
+ hid_t fs; /* File dataspace ID */
+ hid_t ms; /* Memory dataspace ID */
+ hid_t dataset; /* Dataset ID */
+ hsize_t orig_size=10; /* Original dataset dim size */
+ hsize_t new_size=20; /* Extended dataset dim size */
+ hsize_t one=1;
+ hsize_t max_size = H5S_UNLIMITED; /* dataset maximum dim size */
+ hsize_t chunk_size = 16384; /* chunk size */
+ hid_t dcpl; /* dataset create prop. list */
+ int written[10], /* Data to write */
+ retrieved[10]; /* Data read in */
+ int mpi_size, mpi_rank; /* MPI settings */
+ int i; /* Local index variable */
+ herr_t ret; /* Generic return value */
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Extend independent write test #2 on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* -------------------
+ * START AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ fapl = create_faccess_plist(test_comm, MPI_INFO_NULL, facc_type);
+ VRFY((fapl >= 0), "create_faccess_plist succeeded");
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(fapl);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+ /* --------------------------------------------------------------
+ * Define the dimensions of the overall datasets and create them.
+ * ------------------------------------------------------------- */
+
+ /* set up dataset storage chunk sizes and creation property list */
+ dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl >= 0), "H5Pcreate succeeded");
+ ret = H5Pset_chunk(dcpl, 1, &chunk_size);
+ VRFY((ret >= 0), "H5Pset_chunk succeeded");
+
+ /* setup dimensionality object */
+ fs = H5Screate_simple (1, &orig_size, &max_size);
+ VRFY((fs >= 0), "H5Screate_simple succeeded");
+
+ /* create an extendible dataset collectively */
+ dataset = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, fs, H5P_DEFAULT, dcpl, H5P_DEFAULT);
+ VRFY((dataset >= 0), "H5Dcreat2e succeeded");
+
+ /* release resource */
+ ret = H5Pclose(dcpl);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+ /* -------------------------
+ * Test writing to dataset
+ * -------------------------*/
+ /* create a memory dataspace independently */
+ ms = H5Screate_simple(1, &orig_size, &max_size);
+ VRFY((ms >= 0), "H5Screate_simple succeeded");
+
+ /* put some trivial data in the data_array */
+ for(i = 0; i < (int)orig_size; i++)
+ written[i] = i;
+ MESG("data array initialized");
+ if(VERBOSE_MED) {
+ MESG("writing at offset zero: ");
+ for(i = 0; i < (int)orig_size; i++)
+ HDprintf("%s%d", i?", ":"", written[i]);
+ HDprintf("\n");
+ }
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* -------------------------
+ * Read initial data from dataset.
+ * -------------------------*/
+ ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved);
+ VRFY((ret >= 0), "H5Dread succeeded");
+ for (i=0; i<(int)orig_size; i++)
+ if(written[i]!=retrieved[i]) {
+ HDprintf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__,
+ i,written[i], i,retrieved[i]);
+ nerrors++;
+ }
+ if(VERBOSE_MED){
+ MESG("read at offset zero: ");
+ for (i=0; i<(int)orig_size; i++)
+ HDprintf("%s%d", i?", ":"", retrieved[i]);
+ HDprintf("\n");
+ }
+
+ /* -------------------------
+ * Extend the dataset & retrieve new dataspace
+ * -------------------------*/
+ ret = H5Dset_extent(dataset, &new_size);
+ VRFY((ret >= 0), "H5Dset_extent succeeded");
+ ret = H5Sclose(fs);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ fs = H5Dget_space(dataset);
+ VRFY((fs >= 0), "H5Dget_space succeeded");
+
+ /* -------------------------
+ * Write to the second half of the dataset
+ * -------------------------*/
+ 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++)
+ HDprintf("%s%d", i?", ":"", written[i]);
+ HDprintf("\n");
+ }
+ ret = H5Sselect_hyperslab(fs, H5S_SELECT_SET, &orig_size, NULL, &one, &orig_size);
+ VRFY((ret >= 0), "H5Sselect_hyperslab succeeded");
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* -------------------------
+ * Read the new data
+ * -------------------------*/
+ ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved);
+ VRFY((ret >= 0), "H5Dread succeeded");
+ for (i=0; i<(int)orig_size; i++)
+ if(written[i]!=retrieved[i]) {
+ HDprintf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__,
+ i,written[i], i,retrieved[i]);
+ nerrors++;
+ }
+ if(VERBOSE_MED){
+ MESG("read at offset 10: ");
+ for (i=0; i<(int)orig_size; i++)
+ HDprintf("%s%d", i?", ":"", retrieved[i]);
+ HDprintf("\n");
+ }
+
+
+ /* Close dataset collectively */
+ ret = H5Dclose(dataset);
+ VRFY((ret >= 0), "H5Dclose succeeded");
+
+ /* Close the file collectively */
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded");
+}
+
+/* Example of using the parallel HDF5 library to read an extendible dataset */
+void
+extend_readInd(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ hsize_t dims[MAX_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[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK], stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Extend independent read test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* allocate memory for data buffer */
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+ data_array2 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded");
+ data_origin1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
+
+ /* -------------------
+ * OPEN AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* open the file collectively */
+ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
+ VRFY((fid >= 0), "");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+ /* open the dataset1 collectively */
+ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "");
+
+ /* open another dataset collectively */
+ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "");
+
+ /* Try extend dataset1 which is open RDONLY. Should fail. */
+ /* 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 (MAX_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 (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill dataset with test data */
+ dataset_fill(start, block, data_origin1);
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ }
+
+ /* read data independently */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array1);
+ VRFY((ret >= 0), "H5Dread succeeded");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ VRFY((ret == 0), "dataset2 read verified correct");
+ if(ret) nerrors++;
+
+ H5Sclose(mem_dataspace);
+ H5Sclose(file_dataspace);
+
+ /* close dataset collectively */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "");
+
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(data_array1) HDfree(data_array1);
+ if(data_array2) HDfree(data_array2);
+ if(data_origin1) HDfree(data_origin1);
+}
+
+/*
+ * Part 3--Collective read/write for extendible datasets.
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create two extendible
+ * datasets in one HDF5 file with collective parallel MPIO access support.
+ * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within each
+ * dataset.
+ */
+
+void
+extend_writeAll(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t sid; /* Dataspace ID */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ const char *filename;
+ hsize_t dims[MAX_RANK]; /* dataset dim sizes */
+ hsize_t max_dims[MAX_RANK] =
+ {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */
+ DATATYPE *data_array1 = NULL; /* data buffer */
+ hsize_t chunk_dims[MAX_RANK]; /* chunk sizes */
+ hid_t dataset_pl; /* dataset create prop. list */
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK]; /* for hyperslab setting */
+ hsize_t stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Extend independent write test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&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 *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+
+ /* -------------------
+ * START AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+/* Reduce the number of metadata cache slots, so that there are cache
+ * collisions during the raw data I/O on the chunked dataset. This stresses
+ * the metadata cache and tests for cache bugs. -QAK
+ */
+{
+ int mdc_nelmts;
+ size_t rdcc_nelmts;
+ size_t rdcc_nbytes;
+ double rdcc_w0;
+
+ ret = H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0);
+ VRFY((ret >= 0), "H5Pget_cache succeeded");
+ mdc_nelmts=4;
+ ret = H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0);
+ VRFY((ret >= 0), "H5Pset_cache succeeded");
+}
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+
+ /* --------------------------------------------------------------
+ * Define the dimensions of the overall datasets and create them.
+ * ------------------------------------------------------------- */
+
+ /* set up dataset storage chunk sizes and creation property list */
+ if(VERBOSE_MED)
+ HDprintf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]);
+ dataset_pl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dataset_pl >= 0), "H5Pcreate succeeded");
+ ret = H5Pset_chunk(dataset_pl, MAX_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 (MAX_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 (MAX_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 (MAX_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) HDfree(data_array1);
+}
+
+/* Example of using the parallel HDF5 library to read an extendible dataset */
+void
+extend_readAll(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ const char *filename;
+ hsize_t dims[MAX_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[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK], stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Extend independent read test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ /* allocate memory for data buffer */
+ data_array1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
+ data_array2 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded");
+ data_origin1 = (DATATYPE *)HDmalloc(dim0*dim1*sizeof(DATATYPE));
+ VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
+
+ /* -------------------
+ * OPEN AN HDF5 FILE
+ * -------------------*/
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* open the file collectively */
+ fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
+ VRFY((fid >= 0), "");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+ /* open the dataset1 collectively */
+ dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "");
+
+ /* open another dataset collectively */
+ dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "");
+
+ /* Try extend dataset1 which is open RDONLY. Should fail. */
+ /* 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 (MAX_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 (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* fill dataset with test data */
+ dataset_fill(start, block, data_origin1);
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(start, block, data_array1);
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* read data collectively */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_array1);
+ VRFY((ret >= 0), "H5Dread succeeded");
+
+ /* verify the read data with original expected data */
+ ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
+ VRFY((ret == 0), "dataset2 read verified correct");
+ if(ret) nerrors++;
+
+ H5Sclose(mem_dataspace);
+ H5Sclose(file_dataspace);
+ H5Pclose(xfer_plist);
+
+ /* close dataset collectively */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "");
+
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(data_array1) HDfree(data_array1);
+ if(data_array2) HDfree(data_array2);
+ if(data_origin1) HDfree(data_origin1);
+}
+
+/*
+ * Example of using the parallel HDF5 library to read a compressed
+ * dataset in an HDF5 file with collective parallel access support.
+ */
+#ifdef H5_HAVE_FILTER_DEFLATE
+void
+compress_readAll(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t dcpl; /* Dataset creation property list */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t dataspace; /* Dataspace ID */
+ hid_t dataset; /* Dataset ID */
+ int rank=1; /* Dataspace rank */
+ hsize_t dim=dim0; /* Dataspace dimensions */
+ unsigned u; /* Local index variable */
+ unsigned chunk_opts; /* Chunk options */
+ unsigned disable_partial_chunk_filters; /* Whether filters are disabled on partial chunks */
+ DATATYPE *data_read = NULL; /* data buffer */
+ DATATYPE *data_orig = NULL; /* expected data buffer */
+ const char *filename;
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+ int mpi_size, mpi_rank;
+ herr_t ret; /* Generic return value */
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Collective chunked dataset read test on file %s\n", filename);
+
+ /* Retrieve MPI parameters */
+ MPI_Comm_size(comm,&mpi_size);
+ MPI_Comm_rank(comm,&mpi_rank);
+
+ /* Allocate data buffer */
+ data_orig = (DATATYPE *)HDmalloc((size_t)dim*sizeof(DATATYPE));
+ VRFY((data_orig != NULL), "data_origin1 HDmalloc succeeded");
+ data_read = (DATATYPE *)HDmalloc((size_t)dim*sizeof(DATATYPE));
+ VRFY((data_read != NULL), "data_array1 HDmalloc succeeded");
+
+ /* Initialize data buffers */
+ for(u=0; u<dim;u++)
+ data_orig[u]=u;
+
+ /* Run test both with and without filters disabled on partial chunks */
+ for(disable_partial_chunk_filters = 0; disable_partial_chunk_filters <= 1;
+ disable_partial_chunk_filters++) {
+ /* Process zero creates the file with a compressed, chunked dataset */
+ if(mpi_rank==0) {
+ hsize_t chunk_dim; /* Chunk dimensions */
+
+ /* Create the file */
+ fid = H5Fcreate(h5_rmprefix(filename), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((fid > 0), "H5Fcreate succeeded");
+
+ /* Create property list for chunking and compression */
+ dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl > 0), "H5Pcreate succeeded");
+
+ ret = H5Pset_layout(dcpl, H5D_CHUNKED);
+ VRFY((ret >= 0), "H5Pset_layout succeeded");
+
+ /* Use eight chunks */
+ chunk_dim = dim / 8;
+ ret = H5Pset_chunk(dcpl, rank, &chunk_dim);
+ VRFY((ret >= 0), "H5Pset_chunk succeeded");
+
+ /* Set chunk options appropriately */
+ if(disable_partial_chunk_filters) {
+ ret = H5Pget_chunk_opts(dcpl, &chunk_opts);
+ VRFY((ret>=0),"H5Pget_chunk_opts succeeded");
+
+ chunk_opts |= H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS;
+
+ ret = H5Pset_chunk_opts(dcpl, chunk_opts);
+ VRFY((ret>=0),"H5Pset_chunk_opts succeeded");
+ } /* end if */
+
+ ret = H5Pset_deflate(dcpl, 9);
+ VRFY((ret >= 0), "H5Pset_deflate succeeded");
+
+ /* Create dataspace */
+ dataspace = H5Screate_simple(rank, &dim, NULL);
+ VRFY((dataspace > 0), "H5Screate_simple succeeded");
+
+ /* Create dataset */
+ dataset = H5Dcreate2(fid, "compressed_data", H5T_NATIVE_INT, dataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
+ VRFY((dataset > 0), "H5Dcreate2 succeeded");
+
+ /* Write compressed data */
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_orig);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* Close objects */
+ ret = H5Pclose(dcpl);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+ ret = H5Sclose(dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret = H5Dclose(dataset);
+ VRFY((ret >= 0), "H5Dclose succeeded");
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded");
+ }
+
+ /* Wait for file to be created */
+ MPI_Barrier(comm);
+
+ /* -------------------
+ * OPEN AN HDF5 FILE
+ * -------------------*/
+
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* open the file collectively */
+ fid=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl);
+ VRFY((fid > 0), "H5Fopen succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+ /* Open dataset with compressed chunks */
+ dataset = H5Dopen2(fid, "compressed_data", H5P_DEFAULT);
+ VRFY((dataset > 0), "H5Dopen2 succeeded");
+
+ /* Try reading & writing data */
+ if(dataset>0) {
+ /* Create dataset transfer property list */
+ xfer_plist = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((xfer_plist > 0), "H5Pcreate succeeded");
+
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
+ ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
+ VRFY((ret>= 0),"set independent IO collectively succeeded");
+ }
+
+
+ /* Try reading the data */
+ ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read);
+ VRFY((ret >= 0), "H5Dread succeeded");
+
+ /* Verify data read */
+ for(u=0; u<dim; u++)
+ if(data_orig[u]!=data_read[u]) {
+ HDprintf("Line #%d: written!=retrieved: data_orig[%u]=%d, data_read[%u]=%d\n",__LINE__,
+ (unsigned)u,data_orig[u],(unsigned)u,data_read[u]);
+ nerrors++;
+ }
+
+#if MPI_VERSION >= 3
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+#endif
+
+ ret = H5Pclose(xfer_plist);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+ ret = H5Dclose(dataset);
+ VRFY((ret >= 0), "H5Dclose succeeded");
+ } /* end if */
+
+ /* Close file */
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded");
+ } /* end for */
+
+ /* release data buffers */
+ if(data_read) HDfree(data_read);
+ if(data_orig) HDfree(data_orig);
+}
+#endif /* H5_HAVE_FILTER_DEFLATE */
+
+/*
+ * Part 4--Non-selection for chunked dataset
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create chunked
+ * dataset in one HDF5 file with collective and independent parallel
+ * MPIO access support. The Datasets are of sizes dim0 x dim1.
+ * Each process controls only a slab of size dim0 x dim1 within the
+ * dataset with the exception that one processor selects no element.
+ */
+
+void
+none_selection_chunk(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t xfer_plist; /* Dataset transfer properties list */
+ hid_t sid; /* Dataspace ID */
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* memory dataspace ID */
+ hid_t dataset1, dataset2; /* Dataset ID */
+ const char *filename;
+ hsize_t dims[MAX_RANK]; /* dataset dim sizes */
+ DATATYPE *data_origin = NULL; /* data buffer */
+ DATATYPE *data_array = NULL; /* data buffer */
+ hsize_t chunk_dims[MAX_RANK]; /* chunk sizes */
+ hid_t dataset_pl; /* dataset create prop. list */
+
+ hsize_t start[MAX_RANK]; /* for hyperslab setting */
+ hsize_t count[MAX_RANK]; /* for hyperslab setting */
+ hsize_t stride[MAX_RANK]; /* for hyperslab setting */
+ hsize_t block[MAX_RANK]; /* for hyperslab setting */
+ hsize_t mstart[MAX_RANK]; /* for data buffer in memory */
+
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ filename = GetTestParameters();
+ if(VERBOSE_MED)
+ HDprintf("Extend independent write test on file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&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);
+ VRFY((acc_tpl >= 0), "");
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "");
+
+ /* --------------------------------------------------------------
+ * Define the dimensions of the overall datasets and create them.
+ * ------------------------------------------------------------- */
+
+ /* set up dataset storage chunk sizes and creation property list */
+ if(VERBOSE_MED)
+ HDprintf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]);
+ dataset_pl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dataset_pl >= 0), "H5Pcreate succeeded");
+ ret = H5Pset_chunk(dataset_pl, MAX_RANK, chunk_dims);
+ VRFY((ret >= 0), "H5Pset_chunk succeeded");
+
+ /* setup dimensionality object */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple(MAX_RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+
+ /* create an extendible dataset collectively */
+ dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
+
+ /* create another extendible dataset collectively */
+ dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "H5Dcreate2 succeeded");
+
+ /* release resource */
+ H5Sclose(sid);
+ H5Pclose(dataset_pl);
+
+ /* -------------------------
+ * Test collective writing to dataset1
+ * -------------------------*/
+ /* set up dimensions of the slab this process accesses */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ /* allocate memory for data buffer. Only allocate enough buffer for
+ * each processor's data. */
+ if(mpi_rank) {
+ data_origin = (DATATYPE *)HDmalloc(block[0]*block[1]*sizeof(DATATYPE));
+ VRFY((data_origin != NULL), "data_origin HDmalloc succeeded");
+
+ data_array = (DATATYPE *)HDmalloc(block[0]*block[1]*sizeof(DATATYPE));
+ VRFY((data_array != NULL), "data_array HDmalloc succeeded");
+
+ /* put some trivial data in the data_array */
+ mstart[0] = mstart[1] = 0;
+ dataset_fill(mstart, block, data_origin);
+ MESG("data_array initialized");
+ if(VERBOSE_MED){
+ MESG("data_array created");
+ dataset_print(mstart, block, data_origin);
+ }
+ }
+
+ /* create a memory dataspace independently */
+ mem_dataspace = H5Screate_simple (MAX_RANK, block, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ /* Process 0 has no selection */
+ if(!mpi_rank) {
+ ret = H5Sselect_none(mem_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none succeeded");
+ }
+
+ /* create a file dataspace independently */
+ file_dataspace = H5Dget_space (dataset1);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* Process 0 has no selection */
+ if(!mpi_rank) {
+ ret = H5Sselect_none(file_dataspace);
+ VRFY((ret >= 0), "H5Sselect_none succeeded");
+ }
+
+ /* set up the collective transfer properties list */
+ xfer_plist = H5Pcreate (H5P_DATASET_XFER);
+ VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_origin);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* read data independently */
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array);
+ VRFY((ret >= 0), "");
+
+ /* verify the read data with original expected data */
+ if(mpi_rank) {
+ ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin);
+ if(ret) nerrors++;
+ }
+
+ /* -------------------------
+ * Test independent writing to dataset2
+ * -------------------------*/
+ ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* write data collectively */
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ xfer_plist, data_origin);
+ VRFY((ret >= 0), "H5Dwrite succeeded");
+
+ /* read data independently */
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, data_array);
+ VRFY((ret >= 0), "");
+
+ /* verify the read data with original expected data */
+ if(mpi_rank) {
+ ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin);
+ if(ret) nerrors++;
+ }
+
+ /* release resource */
+ ret = H5Sclose(file_dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret = H5Sclose(mem_dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret = H5Pclose(xfer_plist);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+
+ /* close dataset collectively */
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5Dclose1 succeeded");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose2 succeeded");
+
+ /* close the file collectively */
+ H5Fclose(fid);
+
+ /* release data buffers */
+ if(data_origin) HDfree(data_origin);
+ if(data_array) HDfree(data_array);
+}
+
+
+/* Function: test_actual_io_mode
+ *
+ * Purpose: tests one specific case of collective I/O and checks that the
+ * actual_chunk_opt_mode property and the actual_io_mode
+ * properties in the DXPL have the correct values.
+ *
+ * Input: selection_mode: changes the way processes select data from the space, as well
+ * as some dxpl flags to get collective I/O to break in different ways.
+ *
+ * The relevant I/O function and expected response for each mode:
+ * TEST_ACTUAL_IO_MULTI_CHUNK_IND:
+ * H5D_mpi_chunk_collective_io, each process reports independent I/O
+ *
+ * TEST_ACTUAL_IO_MULTI_CHUNK_COL:
+ * H5D_mpi_chunk_collective_io, each process reports collective I/O
+ *
+ * TEST_ACTUAL_IO_MULTI_CHUNK_MIX:
+ * H5D_mpi_chunk_collective_io, each process reports mixed I/O
+ *
+ * TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE:
+ * H5D_mpi_chunk_collective_io, processes disagree. The root reports
+ * collective, the rest report independent I/O
+ *
+ * TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND:
+ * Same test TEST_ACTUAL_IO_MULTI_CHUNK_IND.
+ * Set directly go to multi-chunk-io without num threshold calc.
+ * TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL:
+ * Same test TEST_ACTUAL_IO_MULTI_CHUNK_COL.
+ * Set directly go to multi-chunk-io without num threshold calc.
+ *
+ * TEST_ACTUAL_IO_LINK_CHUNK:
+ * H5D_link_chunk_collective_io, processes report linked chunk I/O
+ *
+ * TEST_ACTUAL_IO_CONTIGUOUS:
+ * H5D__contig_collective_write or H5D__contig_collective_read
+ * each process reports contiguous collective I/O
+ *
+ * TEST_ACTUAL_IO_NO_COLLECTIVE:
+ * Simple independent I/O. This tests that the defaults are properly set.
+ *
+ * TEST_ACTUAL_IO_RESET:
+ * Perfroms collective and then independent I/O wit hthe same dxpl to
+ * make sure the peroperty is correctly reset to the default on each use.
+ * Specifically, this test runs TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE
+ * (The most complex case that works on all builds) and then performs
+ * an independent read and write with the same dxpls.
+ *
+ * Note: DIRECT_MULTI_CHUNK_MIX and DIRECT_MULTI_CHUNK_MIX_DISAGREE
+ * is not needed as they are covered by DIRECT_CHUNK_MIX and
+ * MULTI_CHUNK_MIX_DISAGREE cases. _DIRECT_ cases are only for testing
+ * path way to multi-chunk-io by H5FD_MPIO_CHUNK_MULTI_IO insted of num-threshold.
+ *
+ * Modification:
+ * - Refctore to remove multi-chunk-without-opimization test and update for
+ * testing direct to multi-chunk-io
+ * Programmer: Jonathan Kim
+ * Date: 2012-10-10
+ *
+ *
+ * Programmer: Jacob Gruber
+ * Date: 2011-04-06
+ */
+static void
+test_actual_io_mode(int selection_mode) {
+ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_write = -1;
+ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_read = -1;
+ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_expected = -1;
+ H5D_mpio_actual_io_mode_t actual_io_mode_write = -1;
+ H5D_mpio_actual_io_mode_t actual_io_mode_read = -1;
+ H5D_mpio_actual_io_mode_t actual_io_mode_expected = -1;
+ const char * filename;
+ const char * test_name;
+ hbool_t direct_multi_chunk_io;
+ hbool_t multi_chunk_io;
+ hbool_t is_chunked;
+ hbool_t is_collective;
+ int mpi_size = -1;
+ int mpi_rank = -1;
+ int length;
+ int * buffer;
+ int i;
+ MPI_Comm mpi_comm = MPI_COMM_NULL;
+ MPI_Info mpi_info = MPI_INFO_NULL;
+ hid_t fid = -1;
+ hid_t sid = -1;
+ hid_t dataset = -1;
+ hid_t data_type = H5T_NATIVE_INT;
+ hid_t fapl = -1;
+ hid_t mem_space = -1;
+ hid_t file_space = -1;
+ hid_t dcpl = -1;
+ hid_t dxpl_write = -1;
+ hid_t dxpl_read = -1;
+ hsize_t dims[MAX_RANK];
+ hsize_t chunk_dims[MAX_RANK];
+ hsize_t start[MAX_RANK];
+ hsize_t stride[MAX_RANK];
+ hsize_t count[MAX_RANK];
+ hsize_t block[MAX_RANK];
+ char message[256];
+ herr_t ret;
+
+ /* Set up some flags to make some future if statements slightly more readable */
+ direct_multi_chunk_io = (
+ selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND ||
+ selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL );
+
+ /* Note: RESET performs the same tests as MULTI_CHUNK_MIX_DISAGREE and then
+ * tests independent I/O
+ */
+ multi_chunk_io = (
+ selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_IND ||
+ selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_COL ||
+ selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX ||
+ selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE ||
+ selection_mode == TEST_ACTUAL_IO_RESET );
+
+ is_chunked = (
+ selection_mode != TEST_ACTUAL_IO_CONTIGUOUS &&
+ selection_mode != TEST_ACTUAL_IO_NO_COLLECTIVE);
+
+ is_collective = selection_mode != TEST_ACTUAL_IO_NO_COLLECTIVE;
+
+ /* Set up MPI parameters */
+ MPI_Comm_size(test_comm, &mpi_size);
+ MPI_Comm_rank(test_comm, &mpi_rank);
+
+ MPI_Barrier(test_comm);
+
+ HDassert(mpi_size >= 1);
+
+ mpi_comm = test_comm;
+ mpi_info = MPI_INFO_NULL;
+
+ filename = (const char *)GetTestParameters();
+ HDassert(filename != NULL);
+
+ /* Setup the file access template */
+ fapl = create_faccess_plist(mpi_comm, mpi_info, facc_type);
+ VRFY((fapl >= 0), "create_faccess_plist() succeeded");
+
+ /* Create the file */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Create the basic Space */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+
+ /* Create the dataset creation plist */
+ dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl >= 0), "dataset creation plist created successfully");
+
+ /* If we are not testing contiguous datasets */
+ if(is_chunked) {
+ /* Set up chunk information. */
+ chunk_dims[0] = dims[0]/mpi_size;
+ chunk_dims[1] = dims[1];
+ ret = H5Pset_chunk(dcpl, 2, chunk_dims);
+ VRFY((ret >= 0),"chunk creation property list succeeded");
+ }
+
+ /* Create the dataset */
+ dataset = H5Dcreate2(fid, "actual_io", data_type, sid, H5P_DEFAULT,
+ dcpl, H5P_DEFAULT);
+ VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded");
+
+ /* Create the file dataspace */
+ file_space = H5Dget_space(dataset);
+ VRFY((file_space >= 0), "H5Dget_space succeeded");
+
+ /* Choose a selection method based on the type of I/O we want to occur,
+ * and also set up some selection-dependeent test info. */
+ switch(selection_mode) {
+
+ /* Independent I/O with optimization */
+ case TEST_ACTUAL_IO_MULTI_CHUNK_IND:
+ case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND:
+ /* Since the dataset is chunked by row and each process selects a row,
+ * each process writes to a different chunk. This forces all I/O to be
+ * independent.
+ */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ test_name = "Multi Chunk - Independent";
+ actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
+ actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT;
+ break;
+
+ /* Collective I/O with optimization */
+ case TEST_ACTUAL_IO_MULTI_CHUNK_COL:
+ case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL:
+ /* The dataset is chunked by rows, so each process takes a column which
+ * spans all chunks. Since the processes write non-overlapping regular
+ * selections to each chunk, the operation is purely collective.
+ */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
+
+ test_name = "Multi Chunk - Collective";
+ actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
+ if(mpi_size > 1)
+ actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
+ else
+ actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT;
+ break;
+
+ /* Mixed I/O with optimization */
+ case TEST_ACTUAL_IO_MULTI_CHUNK_MIX:
+ /* A chunk will be assigned collective I/O only if it is selected by each
+ * process. To get mixed I/O, have the root select all chunks and each
+ * subsequent process select the first and nth chunk. The first chunk,
+ * accessed by all, will be assigned collective I/O while each other chunk
+ * will be accessed only by the root and the nth procecess and will be
+ * assigned independent I/O. Each process will access one chunk collectively
+ * and at least one chunk independently, reporting mixed I/O.
+ */
+
+ if(mpi_rank == 0) {
+ /* Select the first column */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
+ } else {
+ /* Select the first and the nth chunk in the nth column */
+ block[0] = dim0 / mpi_size;
+ block[1] = dim1 / mpi_size;
+ count[0] = 2;
+ count[1] = 1;
+ stride[0] = mpi_rank * block[0];
+ stride[1] = 1;
+ start[0] = 0;
+ start[1] = mpi_rank*block[1];
+ }
+
+ test_name = "Multi Chunk - Mixed";
+ actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
+ actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED;
+ break;
+
+ /* RESET tests that the properties are properly reset to defaults each time I/O is
+ * performed. To acheive this, we have RESET perform collective I/O (which would change
+ * the values from the defaults) followed by independent I/O (which should report the
+ * default values). RESET doesn't need to have a unique selection, so we reuse
+ * MULTI_CHUMK_MIX_DISAGREE, which was chosen because it is a complex case that works
+ * on all builds. The independent section of RESET can be found at the end of this function.
+ */
+ case TEST_ACTUAL_IO_RESET:
+
+ /* Mixed I/O with optimization and internal disagreement */
+ case TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE:
+ /* A chunk will be assigned collective I/O only if it is selected by each
+ * process. To get mixed I/O with disagreement, assign process n to the
+ * first chunk and the nth chunk. The first chunk, selected by all, is
+ * assgigned collective I/O, while each other process gets independent I/O.
+ * Since the root process with only access the first chunk, it will report
+ * collective I/O. The subsequent processes will access the first chunk
+ * collectively, and their other chunk indpendently, reporting mixed I/O.
+ */
+
+ if(mpi_rank == 0) {
+ /* Select the first chunk in the first column */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
+ block[0] = block[0] / mpi_size;
+ } else {
+ /* Select the first and the nth chunk in the nth column */
+ block[0] = dim0 / mpi_size;
+ block[1] = dim1 / mpi_size;
+ count[0] = 2;
+ count[1] = 1;
+ stride[0] = mpi_rank * block[0];
+ stride[1] = 1;
+ start[0] = 0;
+ start[1] = mpi_rank*block[1];
+ }
+
+ /* If the testname was not already set by the RESET case */
+ if (selection_mode == TEST_ACTUAL_IO_RESET)
+ test_name = "RESET";
+ else
+ test_name = "Multi Chunk - Mixed (Disagreement)";
+
+ actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
+ if(mpi_size > 1) {
+ if(mpi_rank == 0)
+ actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
+ else
+ actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED;
+ }
+ else
+ actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT;
+
+ break;
+
+ /* Linked Chunk I/O */
+ case TEST_ACTUAL_IO_LINK_CHUNK:
+ /* Nothing special; link chunk I/O is forced in the dxpl settings. */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ test_name = "Link Chunk";
+ actual_chunk_opt_mode_expected = H5D_MPIO_LINK_CHUNK;
+ actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
+ break;
+
+ /* Contiguous Dataset */
+ case TEST_ACTUAL_IO_CONTIGUOUS:
+ /* A non overlapping, regular selection in a contiguous dataset leads to
+ * collective I/O */
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ test_name = "Contiguous";
+ actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
+ actual_io_mode_expected = H5D_MPIO_CONTIGUOUS_COLLECTIVE;
+ break;
+
+ case TEST_ACTUAL_IO_NO_COLLECTIVE:
+ slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
+
+ test_name = "Independent";
+ actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
+ actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE;
+ break;
+
+ default:
+ test_name = "Undefined Selection Mode";
+ actual_chunk_opt_mode_expected = -1;
+ actual_io_mode_expected = -1;
+ break;
+ }
+
+ ret = H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* Create a memory dataspace mirroring the dataset and select the same hyperslab
+ * as in the file space.
+ */
+ mem_space = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((mem_space >= 0), "mem_space created");
+
+ ret = H5Sselect_hyperslab(mem_space, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* Get the number of elements in the selection */
+ length = dim0 * dim1;
+
+ /* Allocate and initialize the buffer */
+ buffer = (int *)HDmalloc(sizeof(int) * length);
+ VRFY((buffer != NULL), "HDmalloc of buffer succeeded");
+ for(i = 0; i < length; i++)
+ buffer[i] = i;
+
+ /* Set up the dxpl for the write */
+ dxpl_write = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((dxpl_write >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded");
+
+ /* Set collective I/O properties in the dxpl. */
+ if(is_collective) {
+ /* Request collective I/O */
+ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* Set the threshold number of processes per chunk to twice mpi_size.
+ * This will prevent the threshold from ever being met, thus forcing
+ * multi chunk io instead of link chunk io.
+ * This is via deault.
+ */
+ if(multi_chunk_io) {
+ /* force multi-chunk-io by threshold */
+ ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl_write, (unsigned) mpi_size*2);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_num succeeded");
+
+ /* set this to manipulate testing senario about allocating processes
+ * to chunks */
+ ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl_write, (unsigned) 99);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_ratio succeeded");
+ }
+
+ /* Set directly go to multi-chunk-io without threshold calc. */
+ if(direct_multi_chunk_io) {
+ /* set for multi chunk io by property*/
+ ret = H5Pset_dxpl_mpio_chunk_opt(dxpl_write, H5FD_MPIO_CHUNK_MULTI_IO);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ }
+ }
+
+ /* Make a copy of the dxpl to test the read operation */
+ dxpl_read = H5Pcopy(dxpl_write);
+ VRFY((dxpl_read >= 0), "H5Pcopy succeeded");
+
+ /* Write */
+ ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl_write, buffer);
+ if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout);
+ VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
+
+ /* Retreive Actual io valuess */
+ ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write);
+ VRFY((ret >= 0), "retriving actual io mode suceeded" );
+
+ ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write);
+ VRFY((ret >= 0), "retriving actual chunk opt mode succeeded" );
+
+ /* Read */
+ ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl_read, buffer);
+ if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout);
+ VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded");
+
+ /* Retreive Actual io values */
+ ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read);
+ VRFY((ret >= 0), "retriving actual io mode succeeded" );
+
+ ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read);
+ VRFY((ret >= 0), "retriving actual chunk opt mode succeeded" );
+
+ /* Check write vs read */
+ VRFY((actual_io_mode_read == actual_io_mode_write),
+ "reading and writing are the same for actual_io_mode");
+ VRFY((actual_chunk_opt_mode_read == actual_chunk_opt_mode_write),
+ "reading and writing are the same for actual_chunk_opt_mode");
+
+ /* Test values */
+ if(actual_chunk_opt_mode_expected != (H5D_mpio_actual_chunk_opt_mode_t) -1 && actual_io_mode_expected != (H5D_mpio_actual_io_mode_t) -1) {
+ HDsprintf(message, "Actual Chunk Opt Mode has the correct value for %s.\n",test_name);
+ VRFY((actual_chunk_opt_mode_write == actual_chunk_opt_mode_expected), message);
+ HDsprintf(message, "Actual IO Mode has the correct value for %s.\n",test_name);
+ VRFY((actual_io_mode_write == actual_io_mode_expected), message);
+ } else {
+ HDfprintf(stderr, "%s %d -> (%d,%d)\n", test_name, mpi_rank,
+ actual_chunk_opt_mode_write, actual_io_mode_write);
+ }
+
+ /* To test that the property is succesfully reset to the default, we perform some
+ * independent I/O after the collective I/O
+ */
+ if (selection_mode == TEST_ACTUAL_IO_RESET) {
+ if (mpi_rank == 0) {
+ /* Switch to independent io */
+ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_INDEPENDENT);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ ret = H5Pset_dxpl_mpio(dxpl_read, H5FD_MPIO_INDEPENDENT);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* Write */
+ ret = H5Dwrite(dataset, data_type, H5S_ALL, H5S_ALL, dxpl_write, buffer);
+ VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
+
+ /* Check Properties */
+ ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write);
+ VRFY( (ret >= 0), "retriving actual io mode succeeded" );
+ ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write);
+ VRFY( (ret >= 0), "retriving actual chunk opt mode succeeded" );
+
+ VRFY(actual_chunk_opt_mode_write == H5D_MPIO_NO_CHUNK_OPTIMIZATION,
+ "actual_chunk_opt_mode has correct value for reset write (independent)");
+ VRFY(actual_io_mode_write == H5D_MPIO_NO_COLLECTIVE,
+ "actual_io_mode has correct value for reset write (independent)");
+
+ /* Read */
+ ret = H5Dread(dataset, data_type, H5S_ALL, H5S_ALL, dxpl_read, buffer);
+ VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
+
+ /* Check Properties */
+ ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read);
+ VRFY( (ret >= 0), "retriving actual io mode succeeded" );
+ ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read);
+ VRFY( (ret >= 0), "retriving actual chunk opt mode succeeded" );
+
+ VRFY(actual_chunk_opt_mode_read == H5D_MPIO_NO_CHUNK_OPTIMIZATION,
+ "actual_chunk_opt_mode has correct value for reset read (independent)");
+ VRFY(actual_io_mode_read == H5D_MPIO_NO_COLLECTIVE,
+ "actual_io_mode has correct value for reset read (independent)");
+ }
+ }
+
+ /* Release some resources */
+ ret = H5Sclose(sid);
+ ret = H5Pclose(fapl);
+ ret = H5Pclose(dcpl);
+ ret = H5Pclose(dxpl_write);
+ ret = H5Pclose(dxpl_read);
+ ret = H5Dclose(dataset);
+ ret = H5Sclose(mem_space);
+ ret = H5Sclose(file_space);
+ ret = H5Fclose(fid);
+ HDfree(buffer);
+ return;
+}
+
+
+/* Function: actual_io_mode_tests
+ *
+ * Purpose: Tests all possible cases of the actual_io_mode property.
+ *
+ * Programmer: Jacob Gruber
+ * Date: 2011-04-06
+ */
+void
+actual_io_mode_tests(void) {
+ int mpi_size = -1;
+ int mpi_rank = -1;
+ MPI_Comm_size(test_comm, &mpi_size);
+ MPI_Comm_size(test_comm, &mpi_rank);
+
+ test_actual_io_mode(TEST_ACTUAL_IO_NO_COLLECTIVE);
+
+ /*
+ * Test multi-chunk-io via proc_num threshold
+ */
+ test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_IND);
+ test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_COL);
+
+ /* The Multi Chunk Mixed test requires atleast three processes. */
+ if (mpi_size > 2)
+ test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX);
+ else
+ HDfprintf(stdout, "Multi Chunk Mixed test requires 3 proceses minimum\n");
+
+ test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE);
+
+ /*
+ * Test multi-chunk-io via setting direct property
+ */
+ test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND);
+ test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL);
+
+ test_actual_io_mode(TEST_ACTUAL_IO_LINK_CHUNK);
+ test_actual_io_mode(TEST_ACTUAL_IO_CONTIGUOUS);
+
+ test_actual_io_mode(TEST_ACTUAL_IO_RESET);
+ return;
+}
+
+/*
+ * Function: test_no_collective_cause_mode
+ *
+ * Purpose:
+ * tests cases for broken collective I/O and checks that the
+ * H5Pget_mpio_no_collective_cause properties in the DXPL have the correct values.
+ *
+ * Input:
+ * selection_mode: various mode to cause broken collective I/O
+ * Note: Originally, each TEST case is supposed to be used alone.
+ * After some discussion, this is updated to take multiple TEST cases
+ * with '|'. However there is no error check for any of combined
+ * test cases, so a tester is responsible to understand and feed
+ * proper combination of TESTs if needed.
+ *
+ *
+ * TEST_COLLECTIVE:
+ * Test for regular collective I/O without cause of breaking.
+ * Just to test normal behavior.
+ *
+ * TEST_SET_INDEPENDENT:
+ * Test for Independent I/O as the cause of breaking collective I/O.
+ *
+ * TEST_DATATYPE_CONVERSION:
+ * Test for Data Type Conversion as the cause of breaking collective I/O.
+ *
+ * TEST_DATA_TRANSFORMS:
+ * Test for Data Transfrom feature as the cause of breaking collective I/O.
+ *
+ * TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES:
+ * Test for NULL dataspace as the cause of breaking collective I/O.
+ *
+ * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT:
+ * Test for Compact layout as the cause of breaking collective I/O.
+ *
+ * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL:
+ * Test for Externl-File storage as the cause of breaking collective I/O.
+ *
+ * TEST_FILTERS:
+ * Test for using filter (checksum) as the cause of breaking collective I/O.
+ * Note: TEST_FILTERS mode will not work until H5Dcreate and H5write is supported for mpio and filter feature. Use test_no_collective_cause_mode_filter() function instead.
+ *
+ *
+ * Programmer: Jonathan Kim
+ * Date: Aug, 2012
+ */
+#define DSET_NOCOLCAUSE "nocolcause"
+#define NELM 2
+#define FILE_EXTERNAL "nocolcause_extern.data"
+static void
+test_no_collective_cause_mode(int selection_mode)
+{
+ uint32_t no_collective_cause_local_write = 0;
+ uint32_t no_collective_cause_local_read = 0;
+ uint32_t no_collective_cause_local_expected = 0;
+ uint32_t no_collective_cause_global_write = 0;
+ uint32_t no_collective_cause_global_read = 0;
+ uint32_t no_collective_cause_global_expected = 0;
+ // hsize_t coord[NELM][MAX_RANK];
+
+ const char * filename;
+ const char * test_name;
+ hbool_t is_chunked=1;
+ hbool_t is_independent=0;
+ int mpi_size = -1;
+ int mpi_rank = -1;
+ int length;
+ int * buffer;
+ int i;
+ MPI_Comm mpi_comm;
+ MPI_Info mpi_info;
+ hid_t fid = -1;
+ hid_t sid = -1;
+ hid_t dataset = -1;
+ hid_t data_type = H5T_NATIVE_INT;
+ hid_t fapl = -1;
+ hid_t dcpl = -1;
+ hid_t dxpl_write = -1;
+ hid_t dxpl_read = -1;
+ hsize_t dims[MAX_RANK];
+ hid_t mem_space = -1;
+ hid_t file_space = -1;
+ hsize_t chunk_dims[MAX_RANK];
+ herr_t ret;
+#ifdef LATER /* fletcher32 */
+ H5Z_filter_t filter_info;
+#endif /* LATER */
+ /* set to global value as default */
+ int l_facc_type = facc_type;
+ char message[256];
+
+ /* Set up MPI parameters */
+ MPI_Comm_size(test_comm, &mpi_size);
+ MPI_Comm_rank(test_comm, &mpi_rank);
+
+ MPI_Barrier(test_comm);
+
+ HDassert(mpi_size >= 1);
+
+ mpi_comm = test_comm;
+ mpi_info = MPI_INFO_NULL;
+
+ /* Create the dataset creation plist */
+ dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl >= 0), "dataset creation plist created successfully");
+
+ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT) {
+ ret = H5Pset_layout (dcpl, H5D_COMPACT);
+ VRFY((ret >= 0),"set COMPACT layout succeeded");
+ is_chunked = 0;
+ }
+
+ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) {
+ ret = H5Pset_external (dcpl, FILE_EXTERNAL, (off_t) 0, H5F_UNLIMITED);
+ VRFY((ret >= 0),"set EXTERNAL file layout succeeded");
+ is_chunked = 0;
+ }
+
+#ifdef LATER /* fletcher32 */
+ if (selection_mode & TEST_FILTERS) {
+ ret = H5Zfilter_avail(H5Z_FILTER_FLETCHER32);
+ VRFY ((ret >=0 ), "Fletcher32 filter is available.\n");
+
+ ret = H5Zget_filter_info (H5Z_FILTER_FLETCHER32, &filter_info);
+ VRFY ( ( (filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) || (filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED) ) , "Fletcher32 filter encoding and decoding available.\n");
+
+ ret = H5Pset_fletcher32(dcpl);
+ VRFY((ret >= 0),"set filter (flecher32) succeeded");
+ }
+#endif /* LATER */
+
+ if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) {
+ sid = H5Screate(H5S_NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+ is_chunked = 0;
+ }
+ else {
+ /* Create the basic Space */
+ /* if this is a compact dataset, create a small dataspace that does not exceed 64K */
+ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT) {
+ dims[0] = BIG_X_FACTOR * 6;
+ dims[1] = BIG_Y_FACTOR * 6;
+ }
+ else {
+ dims[0] = dim0;
+ dims[1] = dim1;
+ }
+ sid = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+ }
+
+
+ filename = (const char *)GetTestParameters();
+ HDassert(filename != NULL);
+
+ /* Setup the file access template */
+ fapl = create_faccess_plist(mpi_comm, mpi_info, l_facc_type);
+ VRFY((fapl >= 0), "create_faccess_plist() succeeded");
+
+ /* Create the file */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
+
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* If we are not testing contiguous datasets */
+ if(is_chunked) {
+ /* Set up chunk information. */
+ chunk_dims[0] = dims[0]/mpi_size;
+ chunk_dims[1] = dims[1];
+ ret = H5Pset_chunk(dcpl, 2, chunk_dims);
+ VRFY((ret >= 0),"chunk creation property list succeeded");
+ }
+
+
+ /* Create the dataset */
+ dataset = H5Dcreate2(fid, "nocolcause", data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
+ VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded");
+
+
+ /*
+ * Set expected causes and some tweaks based on the type of test
+ */
+ if (selection_mode & TEST_DATATYPE_CONVERSION) {
+ test_name = "Broken Collective I/O - Datatype Conversion";
+ no_collective_cause_local_expected |= H5D_MPIO_DATATYPE_CONVERSION;
+ no_collective_cause_global_expected |= H5D_MPIO_DATATYPE_CONVERSION;
+ /* set different sign to trigger type conversion */
+ data_type = H5T_NATIVE_UINT;
+ }
+
+ if (selection_mode & TEST_DATA_TRANSFORMS) {
+ test_name = "Broken Collective I/O - DATA Transfroms";
+ no_collective_cause_local_expected |= H5D_MPIO_DATA_TRANSFORMS;
+ no_collective_cause_global_expected |= H5D_MPIO_DATA_TRANSFORMS;
+ }
+
+ if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) {
+ test_name = "Broken Collective I/O - No Simple or Scalar DataSpace";
+ no_collective_cause_local_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES;
+ no_collective_cause_global_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES;
+ }
+
+ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT ||
+ selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) {
+ test_name = "Broken Collective I/O - No CONTI or CHUNKED Dataset";
+ no_collective_cause_local_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
+ no_collective_cause_global_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
+ }
+
+#ifdef LATER /* fletcher32 */
+ if (selection_mode & TEST_FILTERS) {
+ test_name = "Broken Collective I/O - Filter is required";
+ no_collective_cause_local_expected |= H5D_MPIO_FILTERS;
+ no_collective_cause_global_expected |= H5D_MPIO_FILTERS;
+ }
+#endif /* LATER */
+
+ if (selection_mode & TEST_COLLECTIVE) {
+ test_name = "Broken Collective I/O - Not Broken";
+ no_collective_cause_local_expected = H5D_MPIO_COLLECTIVE;
+ no_collective_cause_global_expected = H5D_MPIO_COLLECTIVE;
+ }
+
+ if (selection_mode & TEST_SET_INDEPENDENT) {
+ test_name = "Broken Collective I/O - Independent";
+ no_collective_cause_local_expected = H5D_MPIO_SET_INDEPENDENT;
+ no_collective_cause_global_expected = H5D_MPIO_SET_INDEPENDENT;
+ /* switch to independent io */
+ is_independent = 1;
+ }
+
+ /* use all spaces for certain tests */
+ if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES ||
+ selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) {
+ file_space = H5S_ALL;
+ mem_space = H5S_ALL;
+ }
+ else {
+ /* Get the file dataspace */
+ file_space = H5Dget_space(dataset);
+ VRFY((file_space >= 0), "H5Dget_space succeeded");
+
+ /* Create the memory dataspace */
+ mem_space = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((mem_space >= 0), "mem_space created");
+ }
+
+ /* Get the number of elements in the selection */
+ length = dims[0] * dims[1];
+
+ /* Allocate and initialize the buffer */
+ buffer = (int *)HDmalloc(sizeof(int) * length);
+ VRFY((buffer != NULL), "HDmalloc of buffer succeeded");
+ for(i = 0; i < length; i++)
+ buffer[i] = i;
+
+ /* Set up the dxpl for the write */
+ dxpl_write = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((dxpl_write >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded");
+
+ if(is_independent) {
+ /* Set Independent I/O */
+ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_INDEPENDENT);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ }
+ else {
+ /* Set Collective I/O */
+ ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ }
+
+ if (selection_mode & TEST_DATA_TRANSFORMS) {
+ ret = H5Pset_data_transform (dxpl_write, "x+1");
+ VRFY((ret >= 0), "H5Pset_data_transform succeeded");
+ }
+
+ /*---------------------
+ * Test Write access
+ *---------------------*/
+
+ /* Write */
+ ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl_write, buffer);
+ if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout);
+ VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
+
+
+ /* Get the cause of broken collective I/O */
+ ret = H5Pget_mpio_no_collective_cause (dxpl_write, &no_collective_cause_local_write, &no_collective_cause_global_write);
+ VRFY((ret >= 0), "retriving no collective cause succeeded" );
+
+
+ /*---------------------
+ * Test Read access
+ *---------------------*/
+
+ /* Make a copy of the dxpl to test the read operation */
+ dxpl_read = H5Pcopy(dxpl_write);
+ VRFY((dxpl_read >= 0), "H5Pcopy succeeded");
+
+ /* Read */
+ ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl_read, buffer);
+
+ if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout);
+ VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded");
+
+ /* Get the cause of broken collective I/O */
+ ret = H5Pget_mpio_no_collective_cause (dxpl_read, &no_collective_cause_local_read, &no_collective_cause_global_read);
+ VRFY((ret >= 0), "retriving no collective cause succeeded" );
+
+ /* Check write vs read */
+ VRFY((no_collective_cause_local_read == no_collective_cause_local_write),
+ "reading and writing are the same for local cause of Broken Collective I/O");
+ VRFY((no_collective_cause_global_read == no_collective_cause_global_write),
+ "reading and writing are the same for global cause of Broken Collective I/O");
+
+ /* Test values */
+ HDmemset (message, 0, sizeof (message));
+ HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n",test_name);
+ VRFY((no_collective_cause_local_write == no_collective_cause_local_expected), message);
+ HDmemset (message, 0, sizeof (message));
+ HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n",test_name);
+ VRFY((no_collective_cause_global_write == no_collective_cause_global_expected), message);
+
+ /* Release some resources */
+ if (sid)
+ H5Sclose(sid);
+ if (fapl)
+ H5Pclose(fapl);
+ if (dcpl)
+ H5Pclose(dcpl);
+ if (dxpl_write)
+ H5Pclose(dxpl_write);
+ if (dxpl_read)
+ H5Pclose(dxpl_read);
+ if (dataset)
+ H5Dclose(dataset);
+ if (mem_space)
+ H5Sclose(mem_space);
+ if (file_space)
+ H5Sclose(file_space);
+ if (fid)
+ H5Fclose(fid);
+ HDfree(buffer);
+
+ /* clean up external file */
+ if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL)
+ HDremove(FILE_EXTERNAL);
+
+ return;
+}
+
+
+#if 0
+/*
+ * Function: test_no_collective_cause_mode_filter
+ *
+ * Purpose:
+ * Test specific for using filter as a caus of broken collective I/O and
+ * checks that the H5Pget_mpio_no_collective_cause properties in the DXPL
+ * have the correct values.
+ *
+ * NOTE:
+ * This is a temporary function.
+ * test_no_collective_cause_mode(TEST_FILTERS) will replace this when
+ * H5Dcreate and H5write support for mpio and filter feature.
+ *
+ * Input:
+ * TEST_FILTERS_READ:
+ * Test for using filter (checksum) as the cause of breaking collective I/O.
+ *
+ * Programmer: Jonathan Kim
+ * Date: Aug, 2012
+ */
+static void
+test_no_collective_cause_mode_filter(int selection_mode)
+{
+ uint32_t no_collective_cause_local_read = 0;
+ uint32_t no_collective_cause_local_expected = 0;
+ uint32_t no_collective_cause_global_read = 0;
+ uint32_t no_collective_cause_global_expected = 0;
+
+ const char * filename;
+ const char * test_name;
+ hbool_t is_chunked=1;
+ int mpi_size = -1;
+ int mpi_rank = -1;
+ int length;
+ int * buffer;
+ int i;
+ MPI_Comm mpi_comm = MPI_COMM_NULL;
+ MPI_Info mpi_info = MPI_INFO_NULL;
+ hid_t fid = -1;
+ hid_t sid = -1;
+ hid_t dataset = -1;
+ hid_t data_type = H5T_NATIVE_INT;
+ hid_t fapl_write = -1;
+ hid_t fapl_read = -1;
+ hid_t dcpl = -1;
+ hid_t dxpl = -1;
+ hsize_t dims[MAX_RANK];
+ hid_t mem_space = -1;
+ hid_t file_space = -1;
+ hsize_t chunk_dims[MAX_RANK];
+ herr_t ret;
+#ifdef LATER /* fletcher32 */
+ H5Z_filter_t filter_info;
+#endif /* LATER */
+ char message[256];
+
+ /* Set up MPI parameters */
+ MPI_Comm_size(test_comm, &mpi_size);
+ MPI_Comm_rank(test_comm, &mpi_rank);
+
+ MPI_Barrier(test_comm);
+
+ HDassert(mpi_size >= 1);
+
+ mpi_comm = test_comm;
+ mpi_info = MPI_INFO_NULL;
+
+ /* Create the dataset creation plist */
+ dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ VRFY((dcpl >= 0), "dataset creation plist created successfully");
+
+ if (selection_mode == TEST_FILTERS_READ ) {
+#ifdef LATER /* fletcher32 */
+ ret = H5Zfilter_avail(H5Z_FILTER_FLETCHER32);
+ VRFY ((ret >=0 ), "Fletcher32 filter is available.\n");
+
+ ret = H5Zget_filter_info (H5Z_FILTER_FLETCHER32, (unsigned int *) &filter_info);
+ VRFY ( ( (filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED) || (filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED) ) , "Fletcher32 filter encoding and decoding available.\n");
+
+ ret = H5Pset_fletcher32(dcpl);
+ VRFY((ret >= 0),"set filter (flecher32) succeeded");
+#endif /* LATER */
+ }
+ else {
+ VRFY(0, "Unexpected mode, only test for TEST_FILTERS_READ.");
+ }
+
+ /* Create the basic Space */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+
+
+ filename = (const char *)GetTestParameters();
+ HDassert(filename != NULL);
+
+ /* Setup the file access template */
+ fapl_write = create_faccess_plist(mpi_comm, mpi_info, FACC_DEFAULT);
+ VRFY((fapl_write >= 0), "create_faccess_plist() succeeded");
+
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_write);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* If we are not testing contiguous datasets */
+ if(is_chunked) {
+ /* Set up chunk information. */
+ chunk_dims[0] = dims[0]/mpi_size;
+ chunk_dims[1] = dims[1];
+ ret = H5Pset_chunk(dcpl, 2, chunk_dims);
+ VRFY((ret >= 0),"chunk creation property list succeeded");
+ }
+
+
+ /* Create the dataset */
+ dataset = H5Dcreate2(fid, DSET_NOCOLCAUSE, data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
+ VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded");
+
+#ifdef LATER /* fletcher32 */
+ /* Set expected cause */
+ test_name = "Broken Collective I/O - Filter is required";
+ no_collective_cause_local_expected = H5D_MPIO_FILTERS;
+ no_collective_cause_global_expected = H5D_MPIO_FILTERS;
+#endif /* LATER */
+
+ /* Get the file dataspace */
+ file_space = H5Dget_space(dataset);
+ VRFY((file_space >= 0), "H5Dget_space succeeded");
+
+ /* Create the memory dataspace */
+ mem_space = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((mem_space >= 0), "mem_space created");
+
+ /* Get the number of elements in the selection */
+ length = dim0 * dim1;
+
+ /* Allocate and initialize the buffer */
+ buffer = (int *)HDmalloc(sizeof(int) * length);
+ VRFY((buffer != NULL), "HDmalloc of buffer succeeded");
+ for(i = 0; i < length; i++)
+ buffer[i] = i;
+
+ /* Set up the dxpl for the write */
+ dxpl = H5Pcreate(H5P_DATASET_XFER);
+ VRFY((dxpl >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded");
+
+ if (selection_mode == TEST_FILTERS_READ) {
+ /* To test read in collective I/O mode , write in independent mode
+ * because write fails with mpio + filter */
+ ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_INDEPENDENT);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ }
+ else {
+ /* To test write in collective I/O mode. */
+ ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+ }
+
+
+ /* Write */
+ ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl, buffer);
+
+ if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout);
+ VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
+
+
+ /* Make a copy of the dxpl to test the read operation */
+ dxpl = H5Pcopy(dxpl);
+ VRFY((dxpl >= 0), "H5Pcopy succeeded");
+
+ if (dataset)
+ H5Dclose(dataset);
+ if (fapl_write)
+ H5Pclose(fapl_write);
+ if (fid)
+ H5Fclose(fid);
+
+
+ /*---------------------
+ * Test Read access
+ *---------------------*/
+
+ /* Setup the file access template */
+ fapl_read = create_faccess_plist(mpi_comm, mpi_info, facc_type);
+ VRFY((fapl_read >= 0), "create_faccess_plist() succeeded");
+
+ fid = H5Fopen (filename, H5F_ACC_RDONLY, fapl_read);
+ dataset = H5Dopen2 (fid, DSET_NOCOLCAUSE, H5P_DEFAULT);
+
+ /* Set collective I/O properties in the dxpl. */
+ ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
+ VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
+
+ /* Read */
+ ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl, buffer);
+
+ if(ret < 0) H5Eprint2(H5E_DEFAULT, stdout);
+ VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded");
+
+ /* Get the cause of broken collective I/O */
+ ret = H5Pget_mpio_no_collective_cause (dxpl, &no_collective_cause_local_read, &no_collective_cause_global_read);
+ VRFY((ret >= 0), "retriving no collective cause succeeded" );
+
+ /* Test values */
+ HDmemset (message, 0, sizeof (message));
+ HDsprintf(message, "Local cause of Broken Collective I/O has the correct value for %s.\n",test_name);
+ VRFY((no_collective_cause_local_read == (uint32_t)no_collective_cause_local_expected), message);
+ HDmemset (message, 0, sizeof (message));
+ HDsprintf(message, "Global cause of Broken Collective I/O has the correct value for %s.\n",test_name);
+ VRFY((no_collective_cause_global_read == (uint32_t)no_collective_cause_global_expected), message);
+
+ /* Release some resources */
+ if (sid)
+ H5Sclose(sid);
+ if (fapl_read)
+ H5Pclose(fapl_read);
+ if (dcpl)
+ H5Pclose(dcpl);
+ if (dxpl)
+ H5Pclose(dxpl);
+ if (dataset)
+ H5Dclose(dataset);
+ if (mem_space)
+ H5Sclose(mem_space);
+ if (file_space)
+ H5Sclose(file_space);
+ if (fid)
+ H5Fclose(fid);
+ HDfree(buffer);
+ return;
+}
+#endif
+
+/* Function: no_collective_cause_tests
+ *
+ * Purpose: Tests cases for broken collective IO.
+ *
+ * Programmer: Jonathan Kim
+ * Date: Aug, 2012
+ */
+void
+no_collective_cause_tests(void)
+{
+ /*
+ * Test individual cause
+ */
+ test_no_collective_cause_mode (TEST_COLLECTIVE);
+ test_no_collective_cause_mode (TEST_SET_INDEPENDENT);
+ test_no_collective_cause_mode (TEST_DATATYPE_CONVERSION);
+ test_no_collective_cause_mode (TEST_DATA_TRANSFORMS);
+ test_no_collective_cause_mode (TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES);
+ test_no_collective_cause_mode (TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT);
+ test_no_collective_cause_mode (TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL);
+#ifdef LATER /* fletcher32 */
+ /* TODO: use this instead of below TEST_FILTERS_READ when H5Dcreate and
+ * H5Dwrite is ready for mpio + filter feature.
+ */
+ /* test_no_collective_cause_mode (TEST_FILTERS); */
+ test_no_collective_cause_mode_filter (TEST_FILTERS_READ);
+#endif /* LATER */
+
+ /*
+ * Test combined causes
+ */
+ test_no_collective_cause_mode (TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL | TEST_DATATYPE_CONVERSION);
+ test_no_collective_cause_mode (TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS);
+ test_no_collective_cause_mode (TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL | TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS);
+
+ return;
+}
+
+/*
+ * Test consistency semantics of atomic mode
+ */
+
+/*
+ * Example of using the parallel HDF5 library to create a dataset,
+ * where process 0 writes and the other processes read at the same
+ * time. If atomic mode is set correctly, the other processes should
+ * read the old values in the dataset or the new ones.
+ */
+
+void
+dataset_atomicity(void)
+{
+ hid_t fid; /* HDF5 file ID */
+ hid_t acc_tpl; /* File access templates */
+ hid_t sid; /* Dataspace ID */
+ hid_t dataset1; /* Dataset IDs */
+ hsize_t dims[MAX_RANK]; /* dataset dim sizes */
+ int *write_buf = NULL; /* data buffer */
+ int *read_buf = NULL; /* data buffer */
+ int buf_size;
+ hid_t dataset2;
+ hid_t file_dataspace; /* File dataspace ID */
+ hid_t mem_dataspace; /* Memory dataspace ID */
+ hsize_t start[MAX_RANK];
+ hsize_t stride[MAX_RANK];
+ hsize_t count[MAX_RANK];
+ hsize_t block[MAX_RANK];
+ const char *filename;
+ herr_t ret; /* Generic return value */
+ int mpi_size, mpi_rank;
+ int i, j, k;
+ hbool_t atomicity = FALSE;
+ MPI_Comm comm = test_comm;
+ MPI_Info info = MPI_INFO_NULL;
+
+ dim0 = 64; dim1 = 32;
+ filename = GetTestParameters();
+ if (facc_type != FACC_MPIO) {
+ HDprintf("Atomicity tests will not work without the MPIO VFD\n");
+ return;
+ }
+ if(VERBOSE_MED)
+ HDprintf("atomic writes to file %s\n", filename);
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ buf_size = dim0 * dim1;
+ /* allocate memory for data buffer */
+ write_buf = (int *)HDcalloc(buf_size, sizeof(int));
+ VRFY((write_buf != NULL), "write_buf HDcalloc succeeded");
+ /* allocate memory for data buffer */
+ read_buf = (int *)HDcalloc(buf_size, sizeof(int));
+ VRFY((read_buf != NULL), "read_buf HDcalloc succeeded");
+
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* create the file collectively */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+ /* setup dimensionality object */
+ dims[0] = dim0;
+ dims[1] = dim1;
+ sid = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded");
+
+ /* create datasets */
+ dataset1 = H5Dcreate2(fid, DATASETNAME5, H5T_NATIVE_INT, sid,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
+
+ dataset2 = H5Dcreate2(fid, DATASETNAME6, H5T_NATIVE_INT, sid,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "H5Dcreate2 succeeded");
+
+ /* initialize datasets to 0s */
+ if (0 == mpi_rank) {
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, write_buf);
+ VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
+
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, write_buf);
+ VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
+ }
+
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5Dclose succeeded");
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose succeeded");
+ ret = H5Sclose(sid);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded");
+
+ MPI_Barrier (comm);
+
+ /* make sure setting atomicity fails on a serial file ID */
+ /* file locking allows only one file open (serial) for writing */
+ if(MAINPROCESS){
+ fid=H5Fopen(filename,H5F_ACC_RDWR,H5P_DEFAULT);
+ VRFY((fid >= 0), "H5Fopen succeeed");
+ }
+
+ /* should fail */
+ ret = H5Fset_mpi_atomicity(fid , TRUE);
+ VRFY((ret == FAIL), "H5Fset_mpi_atomicity failed");
+
+ if(MAINPROCESS){
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded");
+ }
+
+ MPI_Barrier (comm);
+
+ /* setup file access template */
+ acc_tpl = create_faccess_plist(comm, info, facc_type);
+ VRFY((acc_tpl >= 0), "");
+
+ /* open the file collectively */
+ fid=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl);
+ VRFY((fid >= 0), "H5Fopen succeeded");
+
+ /* Release file-access template */
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "H5Pclose succeeded");
+
+ ret = H5Fset_mpi_atomicity(fid , TRUE);
+ VRFY((ret >= 0), "H5Fset_mpi_atomicity succeeded");
+
+ /* open dataset1 (contiguous case) */
+ dataset1 = H5Dopen2(fid, DATASETNAME5, H5P_DEFAULT);
+ VRFY((dataset1 >= 0), "H5Dopen2 succeeded");
+
+ if (0 == mpi_rank) {
+ for (i=0 ; i<buf_size ; i++) {
+ write_buf[i] = 5;
+ }
+ }
+ else {
+ for (i=0 ; i<buf_size ; i++) {
+ read_buf[i] = 8;
+ }
+ }
+
+ /* check that the atomicity flag is set */
+ ret = H5Fget_mpi_atomicity(fid , &atomicity);
+ VRFY((ret >= 0), "atomcity get failed");
+ VRFY((atomicity == TRUE), "atomcity set failed");
+
+ MPI_Barrier (comm);
+
+ /* Process 0 writes contiguously to the entire dataset */
+ if (0 == mpi_rank) {
+ ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
+ VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
+ }
+ /* The other processes read the entire dataset */
+ else {
+ ret = H5Dread(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, read_buf);
+ VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
+ }
+
+ if(VERBOSE_MED) {
+ i=0;j=0;k=0;
+ for (i=0 ; i<dim0 ; i++) {
+ HDprintf ("\n");
+ for (j=0 ; j<dim1 ; j++)
+ HDprintf ("%d ", read_buf[k++]);
+ }
+ }
+
+ /* The processes that read the dataset must either read all values
+ as 0 (read happened before process 0 wrote to dataset 1), or 5
+ (read happened after process 0 wrote to dataset 1) */
+ if (0 != mpi_rank) {
+ int compare = read_buf[0];
+
+ VRFY((compare == 0 || compare == 5),
+ "Atomicity Test Failed Process %d: Value read should be 0 or 5\n");
+ for (i=1; i<buf_size; i++) {
+ if (read_buf[i] != compare) {
+ HDprintf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, i, read_buf[i], compare);
+ nerrors ++;
+ }
+ }
+ }
+
+ ret = H5Dclose(dataset1);
+ VRFY((ret >= 0), "H5D close succeeded");
+
+ /* release data buffers */
+ if(write_buf) HDfree(write_buf);
+ if(read_buf) HDfree(read_buf);
+
+ /* open dataset2 (non-contiguous case) */
+ dataset2 = H5Dopen2(fid, DATASETNAME6, H5P_DEFAULT);
+ VRFY((dataset2 >= 0), "H5Dopen2 succeeded");
+
+ /* allocate memory for data buffer */
+ write_buf = (int *)HDcalloc(buf_size, sizeof(int));
+ VRFY((write_buf != NULL), "write_buf HDcalloc succeeded");
+ /* allocate memory for data buffer */
+ read_buf = (int *)HDcalloc(buf_size, sizeof(int));
+ VRFY((read_buf != NULL), "read_buf HDcalloc succeeded");
+
+ for (i=0 ; i<buf_size ; i++) {
+ write_buf[i] = 5;
+ }
+ for (i=0 ; i<buf_size ; i++) {
+ read_buf[i] = 8;
+ }
+
+ atomicity = FALSE;
+ /* check that the atomicity flag is set */
+ ret = H5Fget_mpi_atomicity(fid , &atomicity);
+ VRFY((ret >= 0), "atomcity get failed");
+ VRFY((atomicity == TRUE), "atomcity set failed");
+
+
+ block[0] = dim0/mpi_size - 1;
+ block[1] = dim1/mpi_size - 1;
+ stride[0] = block[0] + 1;
+ stride[1] = block[1] + 1;
+ count[0] = mpi_size;
+ count[1] = mpi_size;
+ start[0] = 0;
+ start[1] = 0;
+
+ /* create a file dataspace */
+ file_dataspace = H5Dget_space (dataset2);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ /* create a memory dataspace */
+ mem_dataspace = H5Screate_simple (MAX_RANK, dims, NULL);
+ VRFY((mem_dataspace >= 0), "");
+
+ ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
+
+ MPI_Barrier (comm);
+
+ /* Process 0 writes to the dataset */
+ if (0 == mpi_rank) {
+ ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, write_buf);
+ VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
+ }
+ /* All processes wait for the write to finish. This works because
+ atomicity is set to true */
+ MPI_Barrier (comm);
+ /* The other processes read the entire dataset */
+ if (0 != mpi_rank) {
+ ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
+ H5P_DEFAULT, read_buf);
+ VRFY((ret >= 0), "H5Dread dataset2 succeeded");
+ }
+
+ if(VERBOSE_MED) {
+ if (mpi_rank == 1) {
+ i=0;j=0;k=0;
+ for (i=0 ; i<dim0 ; i++) {
+ HDprintf ("\n");
+ for (j=0 ; j<dim1 ; j++)
+ HDprintf ("%d ", read_buf[k++]);
+ }
+ HDprintf ("\n");
+ }
+ }
+
+ /* The processes that read the dataset must either read all values
+ as 5 (read happened after process 0 wrote to dataset 1) */
+ if (0 != mpi_rank) {
+ int compare;
+ i=0;j=0;k=0;
+
+ compare = 5;
+
+ for (i=0 ; i<dim0 ; i++) {
+ if ((hsize_t)i >= mpi_rank*(block[0]+1)) {
+ break;
+ }
+ if ((i+1)%(block[0]+1)==0) {
+ k += dim1;
+ continue;
+ }
+ for (j=0 ; j<dim1 ; j++) {
+ if ((hsize_t)j >= mpi_rank*(block[1]+1)) {
+ k += dim1 - mpi_rank*(block[1]+1);
+ break;
+ }
+ if ((j+1)%(block[1]+1)==0) {
+ k++;
+ continue;
+ }
+ else if (compare != read_buf[k]) {
+ HDprintf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, k, read_buf[k], compare);
+ nerrors++;
+ }
+ k ++;
+ }
+ }
+ }
+
+ ret = H5Dclose(dataset2);
+ VRFY((ret >= 0), "H5Dclose succeeded");
+ ret = H5Sclose(file_dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+ ret = H5Sclose(mem_dataspace);
+ VRFY((ret >= 0), "H5Sclose succeeded");
+
+ /* release data buffers */
+ if(write_buf) HDfree(write_buf);
+ if(read_buf) HDfree(read_buf);
+
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded");
+
+}
+
+/* Function: dense_attr_test
+ *
+ * Purpose: Test cases for writing dense attributes in parallel
+ *
+ * Programmer: Quincey Koziol
+ * Date: April, 2013
+ */
+void
+test_dense_attr(void)
+{
+ int mpi_size, mpi_rank;
+ hid_t fpid, fid;
+ hid_t gid, gpid;
+ hid_t atFileSpace, atid;
+ hsize_t atDims[1] = {10000};
+ herr_t status;
+ const char *filename;
+
+ /* get filename */
+ filename = (const char *)GetTestParameters();
+ HDassert( filename != NULL );
+
+ /* set up MPI parameters */
+ MPI_Comm_size(test_comm,&mpi_size);
+ MPI_Comm_rank(test_comm,&mpi_rank);
+
+ fpid = H5Pcreate(H5P_FILE_ACCESS);
+ VRFY((fpid > 0), "H5Pcreate succeeded");
+ status = H5Pset_libver_bounds(fpid, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
+ VRFY((status >= 0), "H5Pset_libver_bounds succeeded");
+ status = H5Pset_fapl_mpio(fpid, test_comm, MPI_INFO_NULL);
+ VRFY((status >= 0), "H5Pset_fapl_mpio succeeded");
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fpid);
+ VRFY((fid > 0), "H5Fcreate succeeded");
+ status = H5Pclose(fpid);
+ VRFY((status >= 0), "H5Pclose succeeded");
+
+ gpid = H5Pcreate(H5P_GROUP_CREATE);
+ VRFY((gpid > 0), "H5Pcreate succeeded");
+ status = H5Pset_attr_phase_change(gpid, 0, 0);
+ VRFY((status >= 0), "H5Pset_attr_phase_change succeeded");
+ gid = H5Gcreate2(fid, "foo", H5P_DEFAULT, gpid, H5P_DEFAULT);
+ VRFY((gid > 0), "H5Gcreate2 succeeded");
+ status = H5Pclose(gpid);
+ VRFY((status >= 0), "H5Pclose succeeded");
+
+ atFileSpace = H5Screate_simple(1, atDims, NULL);
+ VRFY((atFileSpace > 0), "H5Screate_simple succeeded");
+ atid = H5Acreate2(gid, "bar", H5T_STD_U64LE, atFileSpace, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((atid > 0), "H5Acreate succeeded");
+ status = H5Sclose(atFileSpace);
+ VRFY((status >= 0), "H5Sclose succeeded");
+
+ status = H5Aclose(atid);
+ VRFY((status >= 0), "H5Aclose succeeded");
+
+ status = H5Gclose(gid);
+ VRFY((status >= 0), "H5Gclose succeeded");
+ status = H5Fclose(fid);
+ VRFY((status >= 0), "H5Fclose succeeded");
+
+ return;
+}
+
+
+int
+main(int argc, char **argv)
+{
+ int express_test;
+ int mpi_size, mpi_rank; /* mpi variables */
+ hsize_t oldsize, newsize = 1048576;
+
+#ifndef H5_HAVE_WIN32_API
+ /* Un-buffer the stdout and stderr */
+ HDsetbuf(stderr, NULL);
+ HDsetbuf(stdout, NULL);
+#endif
+
+
+ MPI_Init(&argc, &argv);
+ MPI_Comm_size(test_comm, &mpi_size);
+ MPI_Comm_rank(test_comm, &mpi_rank);
+
+ dim0 = BIG_X_FACTOR;
+ dim1 = BIG_Y_FACTOR;
+ dim2 = BIG_Z_FACTOR;
+
+ if (MAINPROCESS){
+ HDprintf("===================================\n");
+ HDprintf("2 GByte IO TESTS START\n");
+ HDprintf("2 MPI ranks will run the tests...\n");
+ HDprintf("===================================\n");
+ h5_show_hostname();
+ }
+
+ H5open();
+ /* Set the internal transition size to allow use of derived datatypes
+ * without having to actually read or write large datasets (>2GB).
+ */
+ oldsize = H5_mpi_set_bigio_count(newsize);
+
+ if (mpi_size > 2) {
+ int rank_color = 0;
+ if (mpi_rank >= 2) rank_color = 1;
+ if (MPI_Comm_split(test_comm, rank_color, mpi_rank, &test_comm) != MPI_SUCCESS) {
+ HDprintf("MPI returned an error. Exiting\n");
+ }
+ }
+
+ /* Initialize testing framework */
+ if (mpi_rank < 2) {
+ TestInit(argv[0], usage, parse_options);
+
+ /* Parse command line arguments */
+ TestParseCmdLine(argc, argv);
+
+ AddTest("idsetw", dataset_writeInd, NULL,
+ "dataset independent write", PARATESTFILE);
+
+ AddTest("idsetr", dataset_readInd, NULL,
+ "dataset independent read", PARATESTFILE);
+
+ AddTest("cdsetw", dataset_writeAll, NULL,
+ "dataset collective write", PARATESTFILE);
+
+ AddTest("cdsetr", dataset_readAll, NULL,
+ "dataset collective read", PARATESTFILE);
+
+ AddTest("eidsetw2", extend_writeInd2, NULL,
+ "extendible dataset independent write #2", PARATESTFILE);
+
+ AddTest("selnone", none_selection_chunk, NULL,
+ "chunked dataset with none-selection", PARATESTFILE);
+
+#ifdef H5_HAVE_FILTER_DEFLATE
+ AddTest("cmpdsetr", compress_readAll, NULL,
+ "compressed dataset collective read", PARATESTFILE);
+#endif /* H5_HAVE_FILTER_DEFLATE */
+
+ /* Display testing information */
+ if (MAINPROCESS)
+ TestInfo(argv[0]);
+
+ /* setup file access property list */
+ fapl = H5Pcreate (H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(fapl, test_comm, MPI_INFO_NULL);
+
+ /* Perform requested testing */
+ PerformTests();
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD);
+
+ /* Restore the default bigio setting */
+ H5_mpi_set_bigio_count(oldsize);
+
+ express_test = GetTestExpress();
+ if ((express_test == 0) && (mpi_rank < 2)) {
+ MpioTest2G(test_comm, mpi_rank);
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD);
+
+ if (mpi_rank == 0)
+ HDremove(FILENAME[0]);
+
+ H5close();
+ if (test_comm != MPI_COMM_WORLD) {
+ MPI_Comm_free(&test_comm);
+ }
+ MPI_Finalize();
+ return 0;
+}