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hdf5/testpar/testphdf5.c

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/*
* 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 */
char *filenames[]={
#ifdef HAVE_PARALLEL
"ParaEg1.h5f", "ParaEg2.h5f"
#else
"Eg1.h5f", "Eg2.h5f"
#endif
};
/* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */
#define SPACE1_DIM1 8
#define SPACE1_DIM2 12
#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;
char *fname;
int color = 0; /* used for MPI_Comm_split */
int mrc; /* mpi return code */
#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
#ifdef NO
/* split into two new communicators, one contains the originally */
/* odd rank processes, the other the even ones. */
color = myid%2;
mrc = MPI_Comm_split (MPI_COMM_WORLD, color, myid, &comm);
assert(mrc==MPI_SUCCESS);
#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(filenames[color],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);
MESG("H5Dclose1 succeed");
ret=H5Dclose(dataset2);
assert(ret != FAIL);
MESG("H5Dclose2 succeed");
/* release all IDs created */
H5Sclose(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(filenames[0],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);
}
#ifdef HAVE_PARALLEL
/*
* test file access by communicator besides COMM_WORLD.
* Split COMM_WORLD into two, one (even_comm) contains the original
* processes of even ranks. The other (odd_comm) contains the original
* processes of odd ranks. Processes in even_comm creates a file, then
* cloose it, using even_comm. Processes in old_comm just do a barrier
* using odd_comm. Then they all do a barrier using COMM_WORLD.
* If the file creation and cloose does not do correct collective action
* according to the communicator argument, the processes will freeze up
* sooner or later due to barrier mixed up.
*/
void
test_split_comm_access()
{
int numprocs, myrank;
MPI_Comm comm;
MPI_Info info = MPI_INFO_NULL;
int color, mrc;
int newrank, newprocs;
hid_t fid; /* file IDs */
hid_t acc_tpl; /* File access properties */
herr_t ret; /* generic return value */
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
color = myrank%2;
mrc = MPI_Comm_split (MPI_COMM_WORLD, color, myrank, &comm);
assert(mrc==MPI_SUCCESS);
MPI_Comm_size(comm,&newprocs);
MPI_Comm_rank(comm,&newrank);
printf("oldrank/oldprocs=%d/%d, newrank/newprocs=%d/%d\n",
myrank, numprocs, newrank, newprocs);
if (color){
/* odd-rank processes */
mrc = MPI_Barrier(comm);
assert(mrc==MPI_SUCCESS);
}else{
/* even-rank processes */
/* setup file access template */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl != FAIL);
/* set Independent Parallel access with communicator */
ret = H5Pset_mpi(acc_tpl, comm, info, H5ACC_INDEPENDENT);
assert(ret != FAIL);
printf("filenames[%d]=%s\n", color, filenames[color]);
/* create the file collectively */
fid=H5Fcreate(filenames[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
assert(fid != FAIL);
MESG("H5Fcreate succeed");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
assert(ret != FAIL);
ret=H5Fclose(fid);
assert(ret != FAIL);
}
if (myrank == 0){
mrc = MPI_File_delete(filenames[color], info);
assert(mrc==MPI_SUCCESS);
}
}
#endif
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){
#ifdef HAVE_PARALLEL
test_split_comm_access();
#endif
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);
}
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