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-Appendix A: OpenMP-HDF5 Programs
--------------------------------------------------------------------------
- Program 1
--------------------------------------------------------------------------
-/*
- * This example writes 64 datasets to a HDF5 file, using multiple threads
- * (OpenMP). Each thread grab the lock while it tries to call HDF5 functions
- * to write out dataset. In this way, the HDF5 calls are serialized, while
- * the calculation part is in parallel. 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>
-#include <math.h>
-
-#define NUM_THREADS 4
-#define NUM_MDSET 16
-#define FILE "SDS.h5"
-#define NX 5 /* dataset dimensions */
-#define NY 18
-#define RANK 2
-
-void CalcWriteData(hid_t, hid_t, hid_t);
-
-/*Global variable, OpenMP lock*/
-omp_lock_t lock;
-
-
-int
-main (void)
-{
- hid_t fid; /* file and dataset handles */
- hid_t datatype, dataspace; /* handles */
- hsize_t dimsf[2]; /* dataset dimensions */
- herr_t status;
- int i;
-
- /*
- * Create a new file using H5F_ACC_TRUNC access,
- * default file creation properties, and default file
- * access properties.
- */
- fid = 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_DOUBLE);
- status = H5Tset_order(datatype, H5T_ORDER_LE);
-
- /*Disable dynamic allocation of threads*/
- omp_set_dynamic(0);
-
- /*Allocate threads*/
- omp_set_num_threads(NUM_THREADS);
-
- /*Initialize lock*/
- omp_init_lock(&lock);
-
- /*Each thread grab one iteration in the for loop and call function
- * CaclWriteData*/
- #pragma omp parallel default(shared)
- {
- #pragma omp for
- for(i=0; i<NUM_THREADS; i++) {
- CalcWriteData(fid, dataspace, datatype);
- }
- }
-
- /*Finished lock mechanism, destroy it*/
- omp_destroy_lock(&lock);
-
- /*
- * Close/release resources.
- */
- H5Sclose(dataspace);
- H5Tclose(datatype);
- H5Fclose(fid);
-
- return 0;
-}
-
-/*Each thread will call this function independantly. They calculate dataset
- *and then write it out to hdf, for NUM_MDSET times */
-void CalcWriteData(hid_t fid, hid_t dataspace, hid_t datatype)
-{
- double data[NX][NY];
- hid_t dataset;
- char dname[16];
- int tid;
- int i, j, k;
-
- tid = omp_get_thread_num();
-
- for(i=0; i<NUM_MDSET; i++) {
- /*Weird calculation to extend computing time*/
- for(j=0; j<NX; j++) {
- for(k=0; k<NY; k++)
- data[j][k] = ( pow(sin(tid), 2.0) + pow(cos(tid), 2.0) ) *
- ( tid + i ) +
- ( pow(123456789.0, 8.0) - pow(123456789.0, 8.0) );
-
- }
- sprintf(dname, "tid%d-dataset%d", tid, i);
-
- /*Serialize HDF dataset writing using OpenMP lock*/
- omp_set_lock(&lock);
-
- dataset = H5Dcreate(fid, dname, datatype, dataspace, H5P_DEFAULT);
- H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,
- data);
- H5Dclose(dataset);
-
- /*Release lock*/
- omp_unset_lock(&lock);
- }
-
-}
-
-
-
-
--------------------------------------------------------------------------
- Program 2
--------------------------------------------------------------------------
-/*
- * 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;
-}
-
-
-
--------------------------------------------------------------------------
- Program 3
--------------------------------------------------------------------------
-/*
- * 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);
-}
-
-
--------------------------------------------------------------------------
- Program 4
--------------------------------------------------------------------------
-/*
- * 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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