[svn-r3012] Purpose:

    New doc and update
Description:
    The original openmp-hdf5.html contains a bunch of C source code.
    HTML does not like source code, especially C-code that contained
    <...>.  It gobbled it badly.
Solution:
    Moved the source code to a new file, openmp-hdf5.c and make a
    reference to it from openmp-hdf5.html.
Platforms tested:
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1 files changed, 403 insertions, 0 deletions

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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;
+}     
+