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authorAlbert Cheng <acheng@hdfgroup.org>2000-10-31 15:40:57 (GMT)
committerAlbert Cheng <acheng@hdfgroup.org>2000-10-31 15:40:57 (GMT)
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[svn-r2756] Purpose:
"New" document Description: Raymond has prepared and added a new document reporting his experience of using HDF5 with OpenMP. It was checked in as a .txt file but browsers could not display it properly, at least not for the MS-IE. Solution: I renamed the file from openmp-test.txt to openmp-hdf5.html, added in simple mind html control statement (<pre>), added an entry to the TechNote.html so that it can be found with other technical notes. Platforms tested: Viewed by MS-IE.
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+<pre>
+ Using HDF5 with OpenMP
+ ----------------------
+
+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;
+}
+
+---
+Updated: 2000/10/31
+Contact: hdfhelp@ncsa.uiuc.edu
+</pre>