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hdf5/testpar/t_2Gio.c
luzpaz 174505ca3c
Fix typos found in the rest of the hdf5 code-base (#1985) 
* Fix typos found in the rest of the hdf5 code-base

* Typo in tool.cmake

* Revert "Typo in tool.cmake"

This reverts commit 06b8403d99.

* Fix clang-format styling
2022-08-10 13:57:26 -07:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* 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 accommodate 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];
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 'i': /* Collective MPI-IO access with independent IO */
dxfer_coll_type = DXFER_INDEPENDENT_IO;
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], PATH_MAX) == 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);
if (l_facc_type == FACC_MPIO) {
/* 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);
}
if (l_facc_type == (FACC_MPIO | FACC_SPLIT)) {
hid_t mpio_pl;
mpio_pl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((mpio_pl >= 0), "");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(mpio_pl, comm, info);
VRFY((ret >= 0), "");
/* setup file access template */
ret_pl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((ret_pl >= 0), "");
/* set Parallel access with communicator */
ret = H5Pset_fapl_split(ret_pl, ".meta", mpio_pl, ".raw", mpio_pl);
VRFY((ret >= 0), "H5Pset_fapl_split succeeded");
H5Pclose(mpio_pl);
return (ret_pl);
}
/* unknown file access types */
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] = (hsize_t)dim0 / (hsize_t)mpi_size;
block[1] = (hsize_t)dim1;
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = (hsize_t)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] = (hsize_t)dim0;
block[1] = (hsize_t)dim1 / (hsize_t)mpi_size;
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = 0;
start[1] = (hsize_t)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] = (hsize_t)(mpi_rank ? dim0 / mpi_size : 0);
block[1] = (hsize_t)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] = (hsize_t)(mpi_rank ? (hsize_t)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] = (hsize_t)dim0;
block[1] = (hsize_t)(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] = (hsize_t)(mpi_rank ? (hsize_t)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] = (hsize_t)dim0;
block[1] = (hsize_t)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 a testing express level
* of 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"
static int
MpioTest2G(MPI_Comm comm)
{
/*
* HDF5 APIs definitions
*/
herr_t status;
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 */
size_t tot_size_bytes;
hid_t dcpl_id;
hid_t memorydataspace;
hid_t filedataspace;
size_t slice_per_process;
size_t data_size;
size_t data_size_bytes;
hsize_t chunk[3];
hsize_t h5_counts[3];
hsize_t h5_offsets[3];
hsize_t shape[3] = {1024, 1024, 1152};
/*
* MPI variables
*/
int mpi_size, mpi_rank;
MPI_Info info = MPI_INFO_NULL;
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
if (mpi_rank == 0) {
HDprintf("Using %d process on dataset shape "
"[%" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE "]\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.
*/
tot_size_bytes = sizeof(int);
for (int i = 0; i < 3; i++) {
tot_size_bytes *= shape[i];
}
if (mpi_rank == 0) {
HDprintf("Dataset of %zu 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");
chunk[0] = 4;
chunk[1] = shape[1];
chunk[2] = shape[2];
status = H5Pset_chunk(dcpl_id, 3, chunk);
VRFY((status >= 0), "H5Pset_chunk succeeded");
/*
* Create the dataset with default properties and close filespace.
*/
dset_id = H5Dcreate2(file_id, DATASETNAME, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate2 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), "");
H5_CHECKED_ASSIGN(slice_per_process, size_t, (shape[0] + (hsize_t)mpi_size - 1) / (hsize_t)mpi_size,
hsize_t);
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;
}
h5_counts[0] = slice_per_process;
h5_counts[1] = shape[1];
h5_counts[2] = shape[2];
h5_offsets[0] = (size_t)mpi_rank * slice_per_process;
h5_offsets[1] = 0;
h5_offsets[2] = 0;
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);
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] = (hsize_t)dim0;
dims[1] = (hsize_t)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((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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 = (size_t)dim1;
coords = (hsize_t *)HDmalloc((size_t)dim1 * (size_t)MAX_RANK * sizeof(hsize_t));
VRFY((coords != NULL), "coords malloc succeeded");
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
block[0] = 1;
block[1] = (hsize_t)dim1;
stride[0] = 1;
stride[1] = (hsize_t)dim1;
count[0] = 1;
count[1] = 1;
start[0] = (hsize_t)dim0 / (hsize_t)mpi_size * (hsize_t)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] = (hsize_t)dim0 / (hsize_t)mpi_size * (hsize_t)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] = (hsize_t)dim0 / (hsize_t)mpi_size * (hsize_t)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 = (size_t)dim1;
coords = (hsize_t *)HDmalloc((size_t)dim0 * (size_t)dim1 * MAX_RANK * sizeof(hsize_t));
VRFY((coords != NULL), "coords malloc succeeded");
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
block[0] = 1;
block[1] = (hsize_t)dim1;
stride[0] = 1;
stride[1] = (hsize_t)dim1;
count[0] = 1;
count[1] = 1;
start[0] = (hsize_t)dim0 / (hsize_t)mpi_size * (hsize_t)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((size_t)dim0 * (size_t)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] = (hsize_t)dim0 / (hsize_t)mpi_size * (hsize_t)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((size_t)dim0 * (size_t)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 = (size_t)dim0 * (size_t)dim1;
k = 0;
for (i = 0; i < dim0; i++) {
for (j = 0; j < dim1; j++) {
coords[k++] = (hsize_t)i;
coords[k++] = (hsize_t)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] = (hsize_t)dim0 / (hsize_t)mpi_size * (hsize_t)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] = (hsize_t)chunkdim0;
chunk_dims[1] = (hsize_t)chunkdim1;
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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_id; /* 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_id = create_faccess_plist(test_comm, MPI_INFO_NULL, facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
/* create the file collectively */
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((fid >= 0), "H5Fcreate succeeded");
/* Release file-access template */
ret = H5Pclose(fapl_id);
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++)
H5_CHECKED_ASSIGN(written[i], int, orig_size + (hsize_t)i, hsize_t);
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((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
data_array2 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded");
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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] = (hsize_t)chunkdim0;
chunk_dims[1] = (hsize_t)chunkdim1;
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
data_array2 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded");
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)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 = (hsize_t)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] = (DATATYPE)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++;
}
#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES
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] = (hsize_t)chunkdim0;
chunk_dims[1] = (hsize_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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:
* Performs collective and then independent I/O with the 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 instead 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 = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_read = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
H5D_mpio_actual_io_mode_t actual_io_mode_write = H5D_MPIO_NO_COLLECTIVE;
H5D_mpio_actual_io_mode_t actual_io_mode_read = H5D_MPIO_NO_COLLECTIVE;
H5D_mpio_actual_io_mode_t actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE;
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_id = -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_id = create_faccess_plist(mpi_comm, mpi_info, facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist() succeeded");
/* Create the file */
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((fid >= 0), "H5Fcreate succeeded");
/* Create the basic Space */
dims[0] = (hsize_t)dim0;
dims[1] = (hsize_t)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] / (hsize_t)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 process 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] = (hsize_t)(dim0 / mpi_size);
block[1] = (hsize_t)(dim1 / mpi_size);
count[0] = 2;
count[1] = 1;
stride[0] = (hsize_t)mpi_rank * block[0];
stride[1] = 1;
start[0] = 0;
start[1] = (hsize_t)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 achieve 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 independently, 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] / (hsize_t)mpi_size;
}
else {
/* Select the first and the nth chunk in the nth column */
block[0] = (hsize_t)(dim0 / mpi_size);
block[1] = (hsize_t)(dim1 / mpi_size);
count[0] = 2;
count[1] = 1;
stride[0] = (hsize_t)mpi_rank * block[0];
stride[1] = 1;
start[0] = 0;
start[1] = (hsize_t)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 = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE;
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) * (size_t)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 default.
*/
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 scenario 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");
/* Retrieve Actual io values */
ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write);
VRFY((ret >= 0), "retrieving actual io mode succeeded");
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write);
VRFY((ret >= 0), "retrieving 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");
/* Retrieve Actual io values */
ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read);
VRFY((ret >= 0), "retrieving actual io mode succeeded");
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read);
VRFY((ret >= 0), "retrieving 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) {
HDsnprintf(message, sizeof(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);
HDsnprintf(message, sizeof(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 successfully 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), "retrieving actual io mode succeeded");
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write);
VRFY((ret >= 0), "retrieving 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), "retrieving actual io mode succeeded");
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read);
VRFY((ret >= 0), "retrieving 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_id);
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 at least 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 processes 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 Transform 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.
*
* Programmer: Jonathan Kim
* Date: Aug, 2012
*/
#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_id = -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;
/* 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;
}
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] = (hsize_t)dim0;
dims[1] = (hsize_t)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_id = create_faccess_plist(mpi_comm, mpi_info, l_facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist() succeeded");
/* Create the file */
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((fid >= 0), "H5Fcreate succeeded");
/* If we are not testing contiguous datasets */
if (is_chunked) {
/* Set up chunk information. */
chunk_dims[0] = dims[0] / (hsize_t)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 Transforms";
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;
}
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 */
H5_CHECKED_ASSIGN(length, int, dims[0] * dims[1], hsize_t);
/* Allocate and initialize the buffer */
buffer = (int *)HDmalloc(sizeof(int) * (size_t)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), "retrieving 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), "retrieving 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));
HDsnprintf(message, sizeof(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));
HDsnprintf(message, sizeof(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_id)
H5Pclose(fapl_id);
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;
}
/* 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);
/*
* 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((size_t)buf_size, sizeof(int));
VRFY((write_buf != NULL), "write_buf HDcalloc succeeded");
/* allocate memory for data buffer */
read_buf = (int *)HDcalloc((size_t)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] = (hsize_t)dim0;
dims[1] = (hsize_t)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 succeeded");
}
/* 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((size_t)buf_size, sizeof(int));
VRFY((write_buf != NULL), "write_buf HDcalloc succeeded");
/* allocate memory for data buffer */
read_buf = (int *)HDcalloc((size_t)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] = (hsize_t)(dim0 / mpi_size) - 1;
block[1] = (hsize_t)(dim1 / mpi_size) - 1;
stride[0] = block[0] + 1;
stride[1] = block[1] + 1;
count[0] = (hsize_t)mpi_size;
count[1] = (hsize_t)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 >= (hsize_t)mpi_rank * (block[0] + 1)) {
break;
}
if (((hsize_t)i + 1) % (block[0] + 1) == 0) {
k += dim1;
continue;
}
for (j = 0; j < dim1; j++) {
if ((hsize_t)j >= (hsize_t)mpi_rank * (block[1] + 1)) {
H5_CHECKED_ASSIGN(k, int, (hsize_t)dim1 - (hsize_t)mpi_rank * (block[1] + 1) + (hsize_t)k,
hsize_t);
break;
}
if (((hsize_t)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);
HDmemset(filenames, 0, sizeof(filenames));
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();
}
if (H5dont_atexit() < 0) {
HDprintf("Failed to turn off atexit processing. Continue.\n");
};
H5open();
HDmemset(filenames, 0, sizeof(filenames));
for (int i = 0; i < NFILENAME; i++) {
if (NULL == (filenames[i] = HDmalloc(PATH_MAX))) {
HDprintf("couldn't allocate filename array\n");
MPI_Abort(MPI_COMM_WORLD, -1);
}
}
/* 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_Barrier(MPI_COMM_WORLD);
if (mpi_rank == 0)
HDremove(FILENAME[0]);
for (int i = 0; i < NFILENAME; i++) {
HDfree(filenames[i]);
filenames[i] = NULL;
}
H5close();
if (test_comm != MPI_COMM_WORLD) {
MPI_Comm_free(&test_comm);
}
MPI_Finalize();
return 0;
}
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