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Attached are three OpenMP-HDF5 test programs. The purpose of these tests is to
experience OpenMP parallelism with HDF5. All the tests were run on modi4 with
SGI MPISpro compiler(cc) and make. The first one is the working
program. The two following only work occasionally. I modify them directly
from hdf5/examples/h5_write.c. If you want to try them out, the quickest way
is
1. have your hdf5 program compiled,
2. go to hdf5/examples directory,
3. add -mp option to the end of the CFLAGS list in the Makefile. If you
have the compiled program in another directory, you should go to the
examples in that directory.
4. modify the hdf5/examples/h5_write.c according to the program attached
here.
5. use hdf5/tools/h5dump to examine the output file.
I. First Program
-------------------------------------------------------------------------------
/*
* This example compute the element values of an array in parallel
* by two threads. Then write this dataset into HDF file. This is
* one of the ways to do OpenMP computation with HDF. As long as
* not to do HDF I/O in parallel, it is safe to use HDF.
*
*/
#include <hdf5.h>
#include <omp.h>
#define FILE "SDS.h5"
#define DATASETNAME "IntArray"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int data[NX][NY]; /* data to write */
int i, j;
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/* Disable dynamic allocation of threads. */
omp_set_dynamic(0);
/* Allocate 2 threads */
omp_set_num_threads(2);
/* Parallel computation. Let 2 threads handle this nested for loops
* in parallel. Only one data array is computed. */
#pragma omp parallel default(shared)
{
#pragma omp for
for (j = 0; j < NX; j++) {
#pragma omp parallel shared(j, NY)
{
#pragma omp for
for (i = 0; i < NY; i++)
data[j][i] = i + j;
}
}
}
/* Write this dataset into HDF file */
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
H5Dclose(dataset);
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(file);
return 0;
}
II. Second Program
-------------------------------------------------------------------------------
/*
* This example create two threads. Each thread writes a dataset to
* the HDF5 file in parallel. This program only works occasionally.
*/
#include <hdf5.h>
#include <omp.h>
#define FILE "SDS.h5"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
void writeData(int, hid_t, hid_t, hid_t, char*);
int main (void)
{
hid_t file; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int id;
char dname[2][10] = {"Array1", "Array2"};
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/*Disable dynamic allocation of threads*/
omp_set_dynamic(0);
/*Allocate 2 threads*/
omp_set_num_threads(2);
/*Parallel Part: each thread call function writeData; id is private to
* thread while others are shared */
#pragma omp parallel shared(file, dataspace, datatype, dname) private(id)
{
id = omp_get_thread_num();
writeData(id, file, dataspace, datatype, dname[id]);
}
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(file);
return 0;
}
/*Each thread call this function to write a dataset into HDF5 file*/
void writeData(int id, hid_t file, hid_t dataspace, hid_t datatype, char *dname)
{
int data[NX][NY];
hid_t dataset;
int i, j;
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j + id;
}
dataset = H5Dcreate(file, dname, datatype, dataspace,
H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
H5Dclose(dataset);
}
III. Third Program
-------------------------------------------------------------------------------
/*
* This example compute and write two datasets into HDF file in
* parallel. It also only works occasionally.
*/
#include <hdf5.h>
#include <omp.h>
#define FILE "SDS.h5"
#define DATASETNAME "IntArray"
#define NX 5 /* dataset dimensions */
#define NY 6
#define RANK 2
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
int data[NX][NY]; /* data to write */
int i, j, id;
char dname[2][10] = {"intArray1", "intArray2"};
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
omp_set_dynamic(0);
omp_set_num_threads(2);
/* This part of program compute and write two datasets in parallel. */
#pragma omp parallel shared(file, datatype, dataspace, dname) private(id, j, i, data, dataset)
{
id = omp_get_thread_num();
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i + j + id;
}
dataset = H5Dcreate(file, dname[id], datatype, dataspace,
H5P_DEFAULT);
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
H5Dclose(dataset);
}
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Fclose(file);
return 0;
}
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