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hdf5/examples/ph5example.c

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[svn-r3842] Purpose: New feature Description: Added a parallel HDF5 example. make check knows how to run it in serial mode but not in parallel mode since the current makefile has no provision for parallel code execution. One would have to do it by hand (e.g., mpirun -np 2 ./ph4example) Platforms tested: modi4 (serial and parallel)
2001-04-25 04:06:02 +08:00
/*
* Example of using the parallel HDF5 library to access datasets.
[svn-r3846] Description: updated revision date. Platforms tested: modi4 (serial and parallel)
2001-04-25 04:34:57 +08:00
* Last revised: April 24, 2001.
[svn-r3842] Purpose: New feature Description: Added a parallel HDF5 example. make check knows how to run it in serial mode but not in parallel mode since the current makefile has no provision for parallel code execution. One would have to do it by hand (e.g., mpirun -np 2 ./ph4example) Platforms tested: modi4 (serial and parallel)
2001-04-25 04:06:02 +08:00
*
* 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>
#ifdef H5_HAVE_PARALLEL
/* Temporary source code */
#define FAIL -1
/* temporary code end */
/* Define some handy debugging shorthands, routines, ... */
/* debugging tools */
#define MESG(x)\
if (verbose) printf("%s\n", x);\
#define MPI_BANNER(mesg)\
{printf("--------------------------------\n");\
printf("Proc %d: ", mpi_rank); \
printf("*** %s\n", mesg);\
printf("--------------------------------\n");}
#define SYNC(comm)\
{MPI_BANNER("doing a SYNC"); MPI_Barrier(comm); MPI_BANNER("SYNC DONE");}
/* End of Define some handy debugging shorthands, routines, ... */
/* Constants definitions */
/* 24 is a multiple of 2, 3, 4, 6, 8, 12. Neat for parallel tests. */
#define SPACE1_DIM1 24
#define SPACE1_DIM2 24
#define SPACE1_RANK 2
#define DATASETNAME1 "Data1"
#define DATASETNAME2 "Data2"
#define DATASETNAME3 "Data3"
/* hyperslab layout styles */
#define BYROW 1 /* divide into slabs of rows */
#define BYCOL 2 /* divide into blocks of columns */
/* dataset data type. Int's can be easily octo dumped. */
typedef int DATATYPE;
/* global variables */
int nerrors = 0; /* errors count */
int mpi_size, mpi_rank; /* mpi variables */
/* option flags */
int verbose = 0; /* verbose, default as no. */
int doread=1; /* read test */
int dowrite=1; /* write test */
/*
* Setup the dimensions of the hyperslab.
* Two modes--by rows or by columns.
* Assume dimension rank is 2.
*/
void
slab_set(hssize_t start[], hsize_t count[], hsize_t stride[], int mode)
{
switch (mode){
case BYROW:
/* Each process takes a slabs of rows. */
stride[0] = 1;
stride[1] = 1;
count[0] = SPACE1_DIM1/mpi_size;
count[1] = SPACE1_DIM2;
start[0] = mpi_rank*count[0];
start[1] = 0;
break;
case BYCOL:
/* Each process takes a block of columns. */
stride[0] = 1;
stride[1] = 1;
count[0] = SPACE1_DIM1;
count[1] = SPACE1_DIM2/mpi_size;
start[0] = 0;
start[1] = mpi_rank*count[1];
break;
default:
/* Unknown mode. Set it to cover the whole dataset. */
printf("unknown slab_set mode (%d)\n", mode);
stride[0] = 1;
stride[1] = 1;
count[0] = SPACE1_DIM1;
count[1] = SPACE1_DIM2;
start[0] = 0;
start[1] = 0;
break;
}
}
/*
* Fill the dataset with trivial data for testing.
* Assume dimension rank is 2 and data is stored contiguous.
*/
void
dataset_fill(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
{
DATATYPE *dataptr = dataset;
int i, j;
/* put some trivial data in the data_array */
for (i=0; i < count[0]; i++){
for (j=0; j < count[1]; j++){
*dataptr++ = (i*stride[0]+start[0])*100 + (j*stride[1]+start[1]+1);
}
}
}
/*
* Print the content of the dataset.
*/
void dataset_print(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE * dataset)
{
DATATYPE *dataptr = dataset;
int i, j;
/* print the slab read */
for (i=0; i < count[0]; i++){
printf("Row %d: ", (int)(i*stride[0]+start[0]));
for (j=0; j < count[1]; j++){
printf("%03d ", *dataptr++);
}
printf("\n");
}
}
/*
* Print the content of the dataset.
*/
int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original)
{
#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */
DATATYPE *dataptr = dataset;
DATATYPE *originptr = original;
int i, j, nerrors;
/* print it if verbose */
if (verbose)
dataset_print(start, count, stride, dataset);
nerrors = 0;
for (i=0; i < count[0]; i++){
for (j=0; j < count[1]; j++){
if (*dataset++ != *original++){
nerrors++;
if (nerrors <= MAX_ERR_REPORT){
printf("Dataset Verify failed at [%d][%d](row %d, col %d): expect %d, got %d\n",
i, j,
(int)(i*stride[0]+start[0]), (int)(j*stride[1]+start[1]),
*(dataset-1), *(original-1));
}
}
}
}
if (nerrors > MAX_ERR_REPORT)
printf("[more errors ...]\n");
if (nerrors)
printf("%d errors found in dataset_vrfy\n", nerrors);
return(nerrors);
}
/*
* Example of using the parallel HDF5 library to create two datasets
* in one HDF5 files with parallel MPIO access support.
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
* Each process controls only a slab of size DIM1 x DIM2 within each
* dataset.
*/
void
phdf5writeInd(char *filename)
{
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 */
hsize_t dims1[SPACE1_RANK] =
{SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
hsize_t dimslocal1[SPACE1_RANK] =
{SPACE1_DIM1,SPACE1_DIM2}; /* local dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int mpi_size, mpi_rank;
char *fname;
int mrc; /* mpi return code */
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Independent write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* -------------------
* START AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
MESG("H5Pcreate access succeed");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
assert(ret != FAIL);
MESG("H5Pset_fapl_mpio succeed");
/* create the file collectively */
fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
assert(fid1 != FAIL);
MESG("H5Fcreate succeed");
/* Release file-access template */
ret=H5Pclose(acc_tpl1);
assert(ret != FAIL);
/* --------------------------
* Define the dimensions of the overall datasets
* and the slabs local to the MPI process.
* ------------------------- */
/* 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] = mpi_rank*SPACE1_DIM1/mpi_size;
start[1] = 0;
count[0] = SPACE1_DIM1/mpi_size;
count[1] = SPACE1_DIM2;
stride[0] = 1;
stride[1] =1;
if (verbose)
printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\n",
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
assert(file_dataspace != FAIL);
MESG("H5Dget_space succeed");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
count, NULL);
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
phdf5readInd(char *filename)
{
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 */
hsize_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Independent read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* setup file access template */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
assert(ret != FAIL);
/* open the file collectively */
fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1);
assert(fid1 != FAIL);
/* Release file-access template */
ret=H5Pclose(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] = mpi_rank*SPACE1_DIM1/mpi_size;
start[1] = 0;
count[0] = SPACE1_DIM1/mpi_size;
count[1] = SPACE1_DIM2;
stride[0] = 1;
stride[1] =1;
if (verbose)
printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\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=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
count, NULL);
assert(ret != FAIL);
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill dataset with test data */
dataset_fill(start, count, stride, &data_origin1[0][0]);
/* read data independently */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
assert(ret != FAIL);
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret != FAIL);
/* read data independently */
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
assert(ret != FAIL);
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret == 0);
/* 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);
}
/*
* Example of using the parallel HDF5 library to create two datasets
* in one HDF5 file with collective parallel access support.
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
* Each process controls only a slab of size DIM1 x DIM2 within each
* dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and
* each process controls a hyperslab within.]
*/
void
phdf5writeAll(char *filename)
{
hid_t fid1, fid2; /* HDF5 file IDs */
hid_t acc_tpl1; /* File access templates */
hid_t xfer_plist; /* Dataset transfer properties list */
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 */
hsize_t dims1[SPACE1_RANK] =
{SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Collective write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* -------------------
* START AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
MESG("H5Pcreate access succeed");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
assert(ret != FAIL);
MESG("H5Pset_fapl_mpio succeed");
/* create the file collectively */
fid1=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl1);
assert(fid1 != FAIL);
MESG("H5Fcreate succeed");
/* Release file-access template */
ret=H5Pclose(acc_tpl1);
assert(ret != FAIL);
/* --------------------------
* Define the dimensions of the overall datasets
* and create the dataset
* ------------------------- */
/* 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 2 succeed");
/*
* Set up dimensions of the slab this process accesses.
*/
/* Dataset1: each process takes a block of rows. */
slab_set(start, count, stride, BYROW);
if (verbose)
printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\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);
MESG("H5Dget_space succeed");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
count, NULL);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill the local slab with some trivial data */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* write data collectively */
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dwrite succeed");
/* release all temporary handles. */
/* Could have used them for dataset2 but it is cleaner */
/* to create them again.*/
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/* Dataset2: each process takes a block of columns. */
slab_set(start, count, stride, BYCOL);
if (verbose)
printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\n",
start[0], start[1], count[0], count[1], count[0]*count[1]);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
assert(file_dataspace != FAIL);
MESG("H5Dget_space succeed");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
count, NULL);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill the local slab with some trivial data */
dataset_fill(start, count, stride, &data_array1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* write data independently */
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dwrite succeed");
/* release all temporary handles. */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/*
* All writes completed. Close datasets 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 two datasets
* in one HDF5 file with collective parallel access support.
* The Datasets are of sizes (number-of-mpi-processes x DIM1) x DIM2.
* Each process controls only a slab of size DIM1 x DIM2 within each
* dataset. [Note: not so yet. Datasets are of sizes DIM1xDIM2 and
* each process controls a hyperslab within.]
*/
void
phdf5readAll(char *filename)
{
hid_t fid1, fid2; /* HDF5 file IDs */
hid_t acc_tpl1; /* File access templates */
hid_t xfer_plist; /* Dataset transfer properties list */
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 */
hsize_t dims1[] = {SPACE1_DIM1,SPACE1_DIM2}; /* dataspace dim sizes */
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
hssize_t start[SPACE1_RANK]; /* for hyperslab setting */
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Collective read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* -------------------
* OPEN AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl1 = H5Pcreate (H5P_FILE_ACCESS);
assert(acc_tpl1 != FAIL);
MESG("H5Pcreate access succeed");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl1, comm, info);
assert(ret != FAIL);
MESG("H5Pset_fapl_mpio succeed");
/* open the file collectively */
fid1=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl1);
assert(fid1 != FAIL);
MESG("H5Fopen succeed");
/* Release file-access template */
ret=H5Pclose(acc_tpl1);
assert(ret != FAIL);
/* --------------------------
* Open the datasets in it
* ------------------------- */
/* open the dataset1 collectively */
dataset1 = H5Dopen(fid1, DATASETNAME1);
assert(dataset1 != FAIL);
MESG("H5Dopen succeed");
/* open another dataset collectively */
dataset2 = H5Dopen(fid1, DATASETNAME1);
assert(dataset2 != FAIL);
MESG("H5Dopen 2 succeed");
/*
* Set up dimensions of the slab this process accesses.
*/
/* Dataset1: each process takes a block of columns. */
slab_set(start, count, stride, BYCOL);
if (verbose)
printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\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);
MESG("H5Dget_space succeed");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
count, NULL);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill dataset with test data */
dataset_fill(start, count, stride, &data_origin1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* read data collectively */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dread succeed");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret != FAIL);
/* release all temporary handles. */
/* Could have used them for dataset2 but it is cleaner */
/* to create them again.*/
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/* Dataset2: each process takes a block of rows. */
slab_set(start, count, stride, BYROW);
if (verbose)
printf("start[]=(%d,%d), count[]=(%d,%d), total datapoints=%d\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);
MESG("H5Dget_space succeed");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride,
count, NULL);
assert(ret != FAIL);
MESG("H5Sset_hyperslab succeed");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (SPACE1_RANK, count, NULL);
assert (mem_dataspace != FAIL);
/* fill dataset with test data */
dataset_fill(start, count, stride, &data_origin1[0][0]);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, &data_array1[0][0]);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
assert(xfer_plist != FAIL);
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
assert(ret != FAIL);
MESG("H5Pcreate xfer succeed");
/* read data independently */
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
assert(ret != FAIL);
MESG("H5Dread succeed");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, &data_array1[0][0], &data_origin1[0][0]);
assert(ret != FAIL);
/* release all temporary handles. */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/*
* All reads completed. Close datasets collectively
*/
ret=H5Dclose(dataset1);
assert(ret != FAIL);
MESG("H5Dclose1 succeed");
ret=H5Dclose(dataset2);
assert(ret != FAIL);
MESG("H5Dclose2 succeed");
/* close the file collectively */
H5Fclose(fid1);
}
/*
* 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(char *filenames[])
{
int mpi_size, 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 */
if (verbose)
printf("Independent write test on file %s %s\n",
filenames[0], filenames[1]);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
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);
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 Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
assert(ret != FAIL);
/* 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);
}
}
/*
* Show command usage
*/
void
usage()
{
printf("Usage: testphdf5 [-r] [-w] [-v]\n");
printf("\t-r\tno read\n");
printf("\t-w\tno write\n");
printf("\t-v\tverbose on\n");
printf("\tdefault do write then read\n");
printf("\n");
}
/*
* parse the command line options
*/
int
parse_options(int argc, char **argv){
while (--argc){
if (**(++argv) != '-'){
break;
}else{
switch(*(*argv+1)){
case 'r': doread = 0;
break;
case 'w': dowrite = 0;
break;
case 'v': verbose = 1;
break;
default: usage();
nerrors++;
return(1);
}
}
}
return(0);
}
int
main(int argc, char **argv)
{
char *filenames[]={ "ParaEg1.h5f", "ParaEg2.h5f" };
int mpi_namelen;
char mpi_name[MPI_MAX_PROCESSOR_NAME];
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
MPI_Get_processor_name(mpi_name,&mpi_namelen);
/* Make sure datasets can be divided into equal chunks by the processes */
if ((SPACE1_DIM1 % mpi_size) || (SPACE1_DIM2 % mpi_size)){
printf("DIM1(%d) and DIM2(%d) must be multiples of processes (%d)\n",
SPACE1_DIM1, SPACE1_DIM2, mpi_size);
nerrors++;
goto finish;
}
if (parse_options(argc, argv) != 0)
goto finish;
if (dowrite){
MPI_BANNER("testing PHDF5 dataset using split communicators...");
test_split_comm_access(filenames);
MPI_BANNER("testing PHDF5 dataset independent write...");
phdf5writeInd(filenames[0]);
MPI_BANNER("testing PHDF5 dataset collective write...");
phdf5writeAll(filenames[1]);
}
if (doread){
MPI_BANNER("testing PHDF5 dataset independent read...");
phdf5readInd(filenames[0]);
MPI_BANNER("testing PHDF5 dataset collective read...");
phdf5readAll(filenames[1]);
}
if (!(dowrite || doread)){
usage();
nerrors++;
}
finish:
if (mpi_rank == 0){ /* only process 0 reports */
if (nerrors)
printf("***PHDF5 tests detected %d errors***\n", nerrors);
else{
printf("===================================\n");
printf("PHDF5 tests finished with no errors\n");
printf("===================================\n");
}
}
MPI_Finalize();
return(nerrors);
}
#else /* H5_HAVE_PARALLEL */
/* dummy program since H5_HAVE_PARALLE is not configured in */
int
main()
{
printf("No PHDF5 example because parallel is not configured in\n");
return(0);
}
#endif /* H5_HAVE_PARALLEL */
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