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hdf5/doc/html/ph5example.c
Albert Cheng 27994b9321 [svn-r3848] Purpose: 
updated to v1.4 API.
Platforms tested:
    Eyeballed modi4.
2001-04-24 15:38:45 -05:00

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/*
* Example of using the parallel HDF5 library to access datasets.
* Last revised: April 24, 2001.
*
* 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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