[svn-r2727]

Purpose:
    This file describes the experiencing of OpenMP with hdf5.
Description:
    All detailed description is in the file.
Solution:
    [details about the changes, algorithm, etc...]
    [Please as detail as you can since your own explanation is
    better than others guessing it from the code.]
Platforms tested:
    Everything was done on modi4.

1 files changed, 285 insertions, 0 deletions

diff --git a/doc/html/TechNotes/openmp-test.txt b/doc/html/TechNotes/openmp-test.txt
new file mode 100644
index 0000000..686e647
--- /dev/null
+++ b/doc/html/TechNotes/openmp-test.txt
@@ -0,0 +1,285 @@
+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;
+}     
+
+