diff options
| -rw-r--r-- | doc/html/TechNotes/openmp-hdf5.c | 403 | ||||
| -rw-r--r-- | doc/html/TechNotes/openmp-hdf5.html | 406 |
2 files changed, 405 insertions, 404 deletions
diff --git a/doc/html/TechNotes/openmp-hdf5.c b/doc/html/TechNotes/openmp-hdf5.c new file mode 100644 index 0000000..6d61c38 --- /dev/null +++ b/doc/html/TechNotes/openmp-hdf5.c @@ -0,0 +1,403 @@ +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; +} + diff --git a/doc/html/TechNotes/openmp-hdf5.html b/doc/html/TechNotes/openmp-hdf5.html index 763d35b..ff13b81 100644 --- a/doc/html/TechNotes/openmp-hdf5.html +++ b/doc/html/TechNotes/openmp-hdf5.html @@ -58,412 +58,10 @@ feasibility of running OpenMP programs with this version of HDF5 Thread-safe library. -======= -Appendix A -------------------------------------------------------------------------- - 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> +<A HREF="openmp-hdf5.c">Appendix A: OpenMP-HDF5 Programs</A> -#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; -} - ---- +------- Updated: 2000/11/28 Contact: hdfhelp@ncsa.uiuc.edu </pre> |