path: root/doc/html/TechNotes/openmp-hdf5.html

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		    Using HDF5 with OpenMP
		    ----------------------


I.    Introduction to OpenMP

    - For shared-memory parallelism
    - A combination of library and directives
    - Available for C/C++ and Fortran
    - SGI leading effort
    - Information at http://www.openmp.org and 
      http://www.sgi.com/software/openmp

II.   Programming(SGI MPISpro compiler and C language)

    - Turn on compiler '-mp' option
    - Include 'omp.h' library in program
    - Use library functions, directives and environment variables


III.  Sample Programs

Attached are four 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 two are 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 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);
    }

}




		II.  Second 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;
}     



		III.  Third 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);
}


		IV.  Fourth 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
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