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diff --git a/doc/html/TechNotes/openmp-hdf5.html b/doc/html/TechNotes/openmp-hdf5.html new file mode 100644 index 0000000..c404e85 --- /dev/null +++ b/doc/html/TechNotes/openmp-hdf5.html @@ -0,0 +1,292 @@ +<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> |