mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-12-03 02:32:04 +08:00
f96b4b79a0
Added #define FAIL patch due to confusion that API's are still defined to return FAIL while FAIL has been undefined from public.h.
359 lines
9.8 KiB
C
359 lines
9.8 KiB
C
|
|
/*
|
|
* Example of using the parallel HDF5 library to access datasets.
|
|
*
|
|
* This program contains two parts. In the first part, the mpi processes
|
|
* collectively create a new parallel HDF5 file and create two fixed
|
|
* dimension datasets in it. Then each process writes a hyperslab into
|
|
* each dataset in an independent mode. All processes collectively
|
|
* close the datasets and the file.
|
|
* In the second part, the processes collectively open the created file
|
|
* and the two datasets in it. Then each process reads a hyperslab from
|
|
* each dataset in an independent mode and prints them out.
|
|
* All processes collectively close the datasets and the file.
|
|
*/
|
|
|
|
#include <assert.h>
|
|
#include <hdf5.h>
|
|
#include <mpi.h>
|
|
#include <mpio.h>
|
|
|
|
/* Temporary source code */
|
|
#include <phdf5sup.c>
|
|
/* temporary code end */
|
|
|
|
/* Constants definitions */
|
|
#ifdef HAVE_PARALLEL
|
|
#define FILE1 "ufs:ParaEg1.h5"
|
|
#define FILE2 "ufs:ParaEg2.h5"
|
|
#else
|
|
#define FILE1 "Eg1.h5"
|
|
#define FILE2 "Eg2.h5"
|
|
#endif
|
|
|
|
/* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */
|
|
#define SPACE1_DIM1 24
|
|
#define SPACE1_DIM2 20
|
|
#define SPACE1_RANK 2
|
|
#define DATASETNAME1 "Data1"
|
|
#define DATASETNAME2 "Data2"
|
|
#define DATASETNAME3 "Data3"
|
|
|
|
#define FAIL -1
|
|
|
|
/* Example of using the parallel HDF5 library to create a dataset */
|
|
void
|
|
phdf5write()
|
|
{
|
|
hid_t fid1, fid2; /* HDF5 file IDs */
|
|
hid_t acc_tpl1; /* File access templates */
|
|
hid_t sid1,sid2; /* Dataspace ID */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
int rank = SPACE1_RANK; /* Logical rank of dataspace */
|
|
size_t dims1[SPACE1_RANK] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
|
|
int data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
|
|
|
|
int start[SPACE1_RANK]; /* for hyperslab setting */
|
|
size_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
int i, j;
|
|
int numprocs, myid;
|
|
#ifdef HAVE_PARALLEL
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
/* set up MPI parameters */
|
|
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
|
|
MPI_Comm_rank(MPI_COMM_WORLD,&myid);
|
|
#else
|
|
numprocs = 1;
|
|
myid = 0;
|
|
#endif
|
|
|
|
|
|
/* setup file access template */
|
|
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
|
|
assert(acc_tpl1 != FAIL);
|
|
MESG("H5Pcreate access succeed");
|
|
#ifdef HAVE_PARALLEL
|
|
/* set Independent Parallel access with communicator */
|
|
ret = H5Pset_mpi(acc_tpl1, comm, info, H5ACC_INDEPENDENT);
|
|
assert(ret != FAIL);
|
|
MESG("H5Pset_mpi succeed");
|
|
#endif
|
|
|
|
/* create the file collectively */
|
|
fid1=H5Fcreate(FILE1,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
|
|
assert(fid1 != FAIL);
|
|
MESG("H5Fcreate succeed");
|
|
|
|
/* Release file-access template */
|
|
ret=H5Mclose(acc_tpl1);
|
|
assert(ret != FAIL);
|
|
|
|
|
|
/* setup dimensionality object */
|
|
sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL);
|
|
assert (sid1 != FAIL);
|
|
MESG("H5Screate_simple succeed");
|
|
|
|
|
|
/* create a dataset collectively */
|
|
dataset1 = H5Dcreate(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1,
|
|
H5P_DEFAULT);
|
|
assert(dataset1 != FAIL);
|
|
MESG("H5Dcreate succeed");
|
|
|
|
/* create another dataset collectively */
|
|
dataset2 = H5Dcreate(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1,
|
|
H5P_DEFAULT);
|
|
assert(dataset2 != FAIL);
|
|
MESG("H5Dcreate succeed");
|
|
|
|
|
|
|
|
/* set up dimensions of the slab this process accesses */
|
|
start[0] = myid*SPACE1_DIM1/numprocs;
|
|
start[1] = 0;
|
|
count[0] = SPACE1_DIM1/numprocs;
|
|
count[1] = SPACE1_DIM2;
|
|
stride[0] = 1;
|
|
stride[1] =1;
|
|
printf("start[]=(%d,%d), count[]=(%lu,%lu), total datapoints=%lu\n",
|
|
start[0], start[1], count[0], count[1], count[0]*count[1]);
|
|
|
|
/* put some trivial data in the data_array */
|
|
for (i=0; i < count[0]; i++){
|
|
for (j=0; j < count[1]; j++){
|
|
data_array1[i][j] = (i+start[0])*100 + (j+1);
|
|
}
|
|
}
|
|
MESG("data_array initialized");
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
assert(file_dataspace != FAIL);
|
|
MESG("H5Dget_space succeed");
|
|
ret=H5Sset_hyperslab(file_dataspace, start, count, stride);
|
|
assert(ret != FAIL);
|
|
MESG("H5Sset_hyperslab succeed");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
|
|
assert (mem_dataspace != FAIL);
|
|
|
|
/* write data independently */
|
|
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
assert(ret != FAIL);
|
|
MESG("H5Dwrite succeed");
|
|
|
|
/* write data independently */
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
assert(ret != FAIL);
|
|
MESG("H5Dwrite succeed");
|
|
|
|
/* release dataspace ID */
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* close dataset collectively */
|
|
ret=H5Dclose(dataset1);
|
|
assert(ret != FAIL);
|
|
ret=H5Dclose(dataset2);
|
|
assert(ret != FAIL);
|
|
|
|
/* release all IDs created */
|
|
H5Dclose(sid1);
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid1);
|
|
}
|
|
|
|
/* Example of using the parallel HDF5 library to read a dataset */
|
|
void
|
|
phdf5read()
|
|
{
|
|
hid_t fid1, fid2; /* HDF5 file IDs */
|
|
hid_t acc_tpl1; /* File access templates */
|
|
hid_t sid1,sid2; /* Dataspace ID */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
int rank = SPACE1_RANK; /* Logical rank of dataspace */
|
|
size_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
|
|
int data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
|
|
|
|
int start[SPACE1_RANK]; /* for hyperslab setting */
|
|
size_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
int i, j;
|
|
int numprocs, myid;
|
|
#ifdef HAVE_PARALLEL
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
/* set up MPI parameters */
|
|
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
|
|
MPI_Comm_rank(MPI_COMM_WORLD,&myid);
|
|
#else
|
|
numprocs = 1;
|
|
myid = 0;
|
|
#endif
|
|
|
|
|
|
/* setup file access template */
|
|
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
|
|
assert(acc_tpl1 != FAIL);
|
|
#ifdef HAVE_PARALLEL
|
|
/* set Independent Parallel access with communicator */
|
|
ret = H5Pset_mpi(acc_tpl1, comm, info, H5ACC_INDEPENDENT);
|
|
assert(ret != FAIL);
|
|
#endif
|
|
|
|
|
|
/* open the file collectively */
|
|
fid1=H5Fopen(FILE1,H5F_ACC_RDWR,acc_tpl1);
|
|
assert(fid1 != FAIL);
|
|
|
|
/* Release file-access template */
|
|
ret=H5Mclose(acc_tpl1);
|
|
assert(ret != FAIL);
|
|
|
|
/* open the dataset1 collectively */
|
|
dataset1 = H5Dopen(fid1, DATASETNAME1);
|
|
assert(dataset1 != FAIL);
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen(fid1, DATASETNAME1);
|
|
assert(dataset2 != FAIL);
|
|
|
|
|
|
/* set up dimensions of the slab this process accesses */
|
|
start[0] = myid*SPACE1_DIM1/numprocs;
|
|
start[1] = 0;
|
|
count[0] = SPACE1_DIM1/numprocs;
|
|
count[1] = SPACE1_DIM2;
|
|
stride[0] = 1;
|
|
stride[1] =1;
|
|
printf("start[]=(%d,%d), count[]=(%lu,%lu), total datapoints=%lu\n",
|
|
start[0], start[1], count[0], count[1], count[0]*count[1]);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset1);
|
|
assert(file_dataspace != FAIL);
|
|
ret=H5Sset_hyperslab(file_dataspace, start, count, stride);
|
|
assert(ret != FAIL);
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
|
|
assert (mem_dataspace != FAIL);
|
|
|
|
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
assert(ret != FAIL);
|
|
|
|
/* print the slab read */
|
|
for (i=0; i < count[0]; i++){
|
|
printf("Row %d: ", i+start[0]);
|
|
for (j=0; j < count[1]; j++){
|
|
printf("%d ", data_array1[i][j]);
|
|
}
|
|
printf("\n");
|
|
}
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array1);
|
|
assert(ret != FAIL);
|
|
|
|
/* print the slab read */
|
|
for (i=0; i < count[0]; i++){
|
|
printf("Row %d: ", i+start[0]);
|
|
for (j=0; j < count[1]; j++){
|
|
printf("%d ", data_array1[i][j]);
|
|
}
|
|
printf("\n");
|
|
}
|
|
|
|
/* close dataset collectively */
|
|
ret=H5Dclose(dataset1);
|
|
assert(ret != FAIL);
|
|
ret=H5Dclose(dataset2);
|
|
assert(ret != FAIL);
|
|
|
|
/* release all IDs created */
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid1);
|
|
}
|
|
|
|
void
|
|
usage()
|
|
{
|
|
printf("Usage: testphdf5 [-r] [-w]\n");
|
|
printf("\t-r\b\bno read\n");
|
|
printf("\t-w\b\bno write\n");
|
|
printf("\tdefault do write then read\n");
|
|
printf("\n");
|
|
}
|
|
|
|
main(int argc, char **argv)
|
|
{
|
|
int numprocs, myid, namelen;
|
|
char processor_name[MPI_MAX_PROCESSOR_NAME];
|
|
int doread=1; /* read test */
|
|
int dowrite=1; /* write test */
|
|
|
|
void usage();
|
|
#ifdef HAVE_PARALLEL
|
|
MPI_Init(&argc,&argv);
|
|
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
|
|
MPI_Comm_rank(MPI_COMM_WORLD,&myid);
|
|
MPI_Get_processor_name(processor_name,&namelen);
|
|
pause_proc(MPI_COMM_WORLD, myid, processor_name, namelen, argc, argv);
|
|
#endif
|
|
|
|
/* parse option */
|
|
while (--argc){
|
|
if (**(++argv) != '-'){
|
|
break;
|
|
}else{
|
|
switch(*(*argv+1)){
|
|
case 'r': doread = 0; break;
|
|
case 'w': dowrite = 0; break;
|
|
default: usage(); break;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (dowrite){
|
|
MPI_BANNER("testing PHDF5 writing dataset ...");
|
|
phdf5write();
|
|
}
|
|
if (doread){
|
|
MPI_BANNER("testing PHDF5 reading dataset ...");
|
|
phdf5read();
|
|
}
|
|
|
|
if (!(dowrite || doread))
|
|
usage();
|
|
else
|
|
MPI_BANNER("PHDF5 tests finished");
|
|
|
|
#ifdef HAVE_PARALLEL
|
|
MPI_Finalize();
|
|
#endif
|
|
|
|
return(0);
|
|
}
|
|
|