summaryrefslogtreecommitdiffstats
path: root/doc/html/TechNotes
diff options
context:
space:
mode:
authorRaymond Lu <songyulu@hdfgroup.org>2000-11-22 19:20:35 (GMT)
committerRaymond Lu <songyulu@hdfgroup.org>2000-11-22 19:20:35 (GMT)
commit97763c1071e2d6626bf1aac9476e9de97e6e9703 (patch)
treea13fe79e49df9729e9902648c45c91de7b8fab0b /doc/html/TechNotes
parentc19e71dd3e02dc3b21f1822cbdaa05dbbac4bf56 (diff)
downloadhdf5-97763c1071e2d6626bf1aac9476e9de97e6e9703.zip
hdf5-97763c1071e2d6626bf1aac9476e9de97e6e9703.tar.gz
hdf5-97763c1071e2d6626bf1aac9476e9de97e6e9703.tar.bz2
[svn-r2997]
Purpose: Update Description: Added a new testing program into this file. It shows the way that does parallel computation and serialized I/O.
Diffstat (limited to 'doc/html/TechNotes')
-rw-r--r--doc/html/TechNotes/openmp-hdf5.html141
1 files changed, 136 insertions, 5 deletions
diff --git a/doc/html/TechNotes/openmp-hdf5.html b/doc/html/TechNotes/openmp-hdf5.html
index 3902927..decf1de 100644
--- a/doc/html/TechNotes/openmp-hdf5.html
+++ b/doc/html/TechNotes/openmp-hdf5.html
@@ -21,9 +21,9 @@ II. Programming(SGI MPISpro compiler and C language)
III. Sample Programs
-Attached are three OpenMP-HDF5 test programs. The purpose of these tests is to
+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 one is the working
+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
@@ -38,7 +38,138 @@ is
- I. First Program
+ 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
@@ -130,7 +261,7 @@ main (void)
- II. Second Program
+ III. Third Program
-------------------------------------------------------------------------------
/*
* This example create two threads. Each thread writes a dataset to
@@ -225,7 +356,7 @@ void writeData(int id, hid_t file, hid_t dataspace, hid_t datatype, char *dname)
}
- III. Third Program
+ IV. Fourth Program
-------------------------------------------------------------------------------
/*
* This example compute and write two datasets into HDF file in