mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-12-27 08:01:04 +08:00
1101 lines
38 KiB
C
1101 lines
38 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
|
* Copyright by The HDF Group. *
|
|
* All rights reserved. *
|
|
* *
|
|
* This file is part of HDF5. The full HDF5 copyright notice, including *
|
|
* terms governing use, modification, and redistribution, is contained in *
|
|
* the COPYING file, which can be found at the root of the source code *
|
|
* distribution tree, or in https://www.hdfgroup.org/licenses. *
|
|
* If you do not have access to either file, you may request a copy from *
|
|
* help@hdfgroup.org. *
|
|
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
|
|
|
|
/*
|
|
* 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.
|
|
*
|
|
* The need of requirement of parallel file prefix is that in general
|
|
* the current working directory in which compiling is done, is not suitable
|
|
* for parallel I/O and there is no standard pathname for parallel file
|
|
* systems. In some cases, the parallel file name may even needs some
|
|
* parallel file type prefix such as: "pfs:/GF/...". Therefore, this
|
|
* example requires an explicit parallel file prefix. See the usage
|
|
* for more detail.
|
|
*/
|
|
|
|
#include <assert.h>
|
|
#include "hdf5.h"
|
|
#include <string.h>
|
|
#include <stdlib.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) \
|
|
do { \
|
|
if (verbose) \
|
|
printf("%s\n", x); \
|
|
} while (0)
|
|
|
|
#define MPI_BANNER(mesg) \
|
|
do { \
|
|
printf("--------------------------------\n"); \
|
|
printf("Proc %d: ", mpi_rank); \
|
|
printf("*** %s\n", mesg); \
|
|
printf("--------------------------------\n"); \
|
|
} while (0)
|
|
|
|
#define SYNC(comm) \
|
|
do { \
|
|
MPI_BANNER("doing a SYNC"); \
|
|
MPI_Barrier(comm); \
|
|
MPI_BANNER("SYNC DONE"); \
|
|
} while (0)
|
|
/* 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 */
|
|
|
|
#define PARAPREFIX "HDF5_PARAPREFIX" /* file prefix environment variable name */
|
|
|
|
/* dataset data type. Int's can be easily octo dumped. */
|
|
typedef int DATATYPE;
|
|
|
|
/* global variables */
|
|
int nerrors = 0; /* errors count */
|
|
#ifndef PATH_MAX
|
|
#define PATH_MAX 512
|
|
#endif /* !PATH_MAX */
|
|
char testfiles[2][PATH_MAX];
|
|
|
|
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 */
|
|
int docleanup = 1; /* cleanup */
|
|
|
|
/* Prototypes */
|
|
void slab_set(hsize_t start[], hsize_t count[], hsize_t stride[], int mode);
|
|
void dataset_fill(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset);
|
|
void dataset_print(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset);
|
|
int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original);
|
|
void phdf5writeInd(char *filename);
|
|
void phdf5readInd(char *filename);
|
|
void phdf5writeAll(char *filename);
|
|
void phdf5readAll(char *filename);
|
|
void test_split_comm_access(char filenames[][PATH_MAX]);
|
|
int parse_options(int argc, char **argv);
|
|
void usage(void);
|
|
int mkfilenames(char *prefix);
|
|
void cleanup(void);
|
|
|
|
/*
|
|
* Setup the dimensions of the hyperslab.
|
|
* Two modes--by rows or by columns.
|
|
* Assume dimension rank is 2.
|
|
*/
|
|
void
|
|
slab_set(hsize_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(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset)
|
|
{
|
|
DATATYPE *dataptr = dataset;
|
|
hsize_t 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(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset)
|
|
{
|
|
DATATYPE *dataptr = dataset;
|
|
hsize_t i, j;
|
|
|
|
/* print the slab read */
|
|
for (i = 0; i < count[0]; i++) {
|
|
printf("Row %lu: ", (unsigned long)(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(hsize_t start[], hsize_t count[], hsize_t stride[], DATATYPE *dataset, DATATYPE *original)
|
|
{
|
|
#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */
|
|
|
|
hsize_t i, j;
|
|
int nerr;
|
|
|
|
/* print it if verbose */
|
|
if (verbose)
|
|
dataset_print(start, count, stride, dataset);
|
|
|
|
nerr = 0;
|
|
for (i = 0; i < count[0]; i++) {
|
|
for (j = 0; j < count[1]; j++) {
|
|
if (*dataset++ != *original++) {
|
|
nerr++;
|
|
if (nerr <= MAX_ERR_REPORT) {
|
|
printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n",
|
|
(unsigned long)i, (unsigned long)j, (unsigned long)(i * stride[0] + start[0]),
|
|
(unsigned long)(j * stride[1] + start[1]), *(dataset - 1), *(original - 1));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
if (nerr > MAX_ERR_REPORT)
|
|
printf("[more errors ...]\n");
|
|
if (nerr)
|
|
printf("%d errors found in dataset_vrfy\n", nerr);
|
|
return (nerr);
|
|
}
|
|
|
|
/*
|
|
* 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; /* HDF5 file IDs */
|
|
hid_t acc_tpl1; /* File access templates */
|
|
hid_t sid1; /* Dataspace ID */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
hsize_t dims1[SPACE1_RANK] = {SPACE1_DIM1, SPACE1_DIM2}; /* dataspace dim sizes */
|
|
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
|
|
|
|
hsize_t start[SPACE1_RANK]; /* for hyperslab setting */
|
|
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
if (verbose)
|
|
printf("Independent write test on file %s\n", filename);
|
|
|
|
/* -------------------
|
|
* 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 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
assert(dataset1 != FAIL);
|
|
MESG("H5Dcreate2 succeed");
|
|
|
|
/* create another dataset collectively */
|
|
dataset2 = H5Dcreate2(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
assert(dataset2 != FAIL);
|
|
MESG("H5Dcreate2 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[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0],
|
|
(unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
|
|
(unsigned long)(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; /* HDF5 file IDs */
|
|
hid_t acc_tpl1; /* File access templates */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
|
|
DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
|
|
|
|
hsize_t start[SPACE1_RANK]; /* for hyperslab setting */
|
|
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
if (verbose)
|
|
printf("Independent read test on file %s\n", filename);
|
|
|
|
/* 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 = H5Dopen2(fid1, DATASETNAME1, H5P_DEFAULT);
|
|
assert(dataset1 != FAIL);
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen2(fid1, DATASETNAME1, H5P_DEFAULT);
|
|
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[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0],
|
|
(unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
|
|
(unsigned long)(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; /* HDF5 file IDs */
|
|
hid_t acc_tpl1; /* File access templates */
|
|
hid_t xfer_plist; /* Dataset transfer properties list */
|
|
hid_t sid1; /* Dataspace ID */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
hsize_t dims1[SPACE1_RANK] = {SPACE1_DIM1, SPACE1_DIM2}; /* dataspace dim sizes */
|
|
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
|
|
|
|
hsize_t start[SPACE1_RANK]; /* for hyperslab setting */
|
|
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
if (verbose)
|
|
printf("Collective write test on file %s\n", filename);
|
|
|
|
/* -------------------
|
|
* 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 = H5Dcreate2(fid1, DATASETNAME1, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
assert(dataset1 != FAIL);
|
|
MESG("H5Dcreate2 succeed");
|
|
|
|
/* create another dataset collectively */
|
|
dataset2 = H5Dcreate2(fid1, DATASETNAME2, H5T_NATIVE_INT, sid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
assert(dataset2 != FAIL);
|
|
MESG("H5Dcreate2 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[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0],
|
|
(unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
|
|
(unsigned long)(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[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0],
|
|
(unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
|
|
(unsigned long)(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; /* HDF5 file IDs */
|
|
hid_t acc_tpl1; /* File access templates */
|
|
hid_t xfer_plist; /* Dataset transfer properties list */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
DATATYPE data_array1[SPACE1_DIM1][SPACE1_DIM2]; /* data buffer */
|
|
DATATYPE data_origin1[SPACE1_DIM1][SPACE1_DIM2]; /* expected data buffer */
|
|
|
|
hsize_t start[SPACE1_RANK]; /* for hyperslab setting */
|
|
hsize_t count[SPACE1_RANK], stride[SPACE1_RANK]; /* for hyperslab setting */
|
|
|
|
herr_t ret; /* Generic return value */
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
if (verbose)
|
|
printf("Collective read test on file %s\n", filename);
|
|
|
|
/* -------------------
|
|
* 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 = H5Dopen2(fid1, DATASETNAME1, H5P_DEFAULT);
|
|
assert(dataset1 != FAIL);
|
|
MESG("H5Dopen2 succeed");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen2(fid1, DATASETNAME1, H5P_DEFAULT);
|
|
assert(dataset2 != FAIL);
|
|
MESG("H5Dopen2 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[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0],
|
|
(unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
|
|
(unsigned long)(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[]=(%lu,%lu), count[]=(%lu,%lu), total datapoints=%lu\n", (unsigned long)start[0],
|
|
(unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
|
|
(unsigned long)(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[][PATH_MAX])
|
|
{
|
|
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]);
|
|
|
|
color = mpi_rank % 2;
|
|
mrc = MPI_Comm_split(MPI_COMM_WORLD, color, mpi_rank, &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 (mpi_rank == 0) {
|
|
mrc = MPI_File_delete(filenames[color], info);
|
|
assert(mrc == MPI_SUCCESS);
|
|
}
|
|
MPI_Comm_free(&comm);
|
|
}
|
|
|
|
/*
|
|
* Show command usage
|
|
*/
|
|
void
|
|
usage(void)
|
|
{
|
|
printf("Usage: testphdf5 [-f <prefix>] [-r] [-w] [-v]\n");
|
|
printf("\t-f\tfile prefix for parallel test files.\n");
|
|
printf("\t \t e.g. pfs:/PFS/myname\n");
|
|
printf("\t \tcan be set via $" PARAPREFIX ".\n");
|
|
printf("\t \tDefault is current directory.\n");
|
|
printf("\t-c\tno cleanup\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");
|
|
}
|
|
|
|
/*
|
|
* compose the test filename with the prefix supplied.
|
|
* return code: 0 if no error
|
|
* 1 otherwise.
|
|
*/
|
|
int
|
|
mkfilenames(char *prefix)
|
|
{
|
|
int i, n;
|
|
size_t strsize;
|
|
|
|
/* filename will be prefix/ParaEgN.h5 where N is 0 to 9. */
|
|
/* So, string must be big enough to hold the prefix, / and 10 more chars */
|
|
/* and the terminating null. */
|
|
strsize = strlen(prefix) + 12;
|
|
if (strsize > PATH_MAX) {
|
|
printf("File prefix too long; Use a short path name.\n");
|
|
return (1);
|
|
}
|
|
n = sizeof(testfiles) / sizeof(testfiles[0]);
|
|
if (n > 9) {
|
|
printf("Warning: Too many entries in testfiles. "
|
|
"Need to adjust the code to accommodate the large size.\n");
|
|
}
|
|
for (i = 0; i < n; i++) {
|
|
snprintf(testfiles[i], PATH_MAX, "%s/ParaEg%d.h5", prefix, i);
|
|
}
|
|
return (0);
|
|
}
|
|
|
|
/*
|
|
* parse the command line options
|
|
*/
|
|
int
|
|
parse_options(int argc, char **argv)
|
|
{
|
|
int i, n;
|
|
|
|
/* initialize testfiles to nulls */
|
|
n = sizeof(testfiles) / sizeof(testfiles[0]);
|
|
for (i = 0; i < n; i++) {
|
|
testfiles[i][0] = '\0';
|
|
}
|
|
|
|
while (--argc) {
|
|
if (**(++argv) != '-') {
|
|
break;
|
|
}
|
|
else {
|
|
switch (*(*argv + 1)) {
|
|
case 'f':
|
|
++argv;
|
|
if (--argc < 1) {
|
|
usage();
|
|
nerrors++;
|
|
return (1);
|
|
}
|
|
if (mkfilenames(*argv)) {
|
|
nerrors++;
|
|
return (1);
|
|
}
|
|
break;
|
|
case 'c':
|
|
docleanup = 0; /* no cleanup */
|
|
break;
|
|
case 'r':
|
|
doread = 0;
|
|
break;
|
|
case 'w':
|
|
dowrite = 0;
|
|
break;
|
|
case 'v':
|
|
verbose = 1;
|
|
break;
|
|
default:
|
|
usage();
|
|
nerrors++;
|
|
return (1);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* check the file prefix */
|
|
if (testfiles[0][0] == '\0') {
|
|
/* try get it from environment variable HDF5_PARAPREFIX */
|
|
char *env;
|
|
char *env_default = "."; /* default to current directory */
|
|
if ((env = getenv(PARAPREFIX)) == NULL) {
|
|
env = env_default;
|
|
}
|
|
mkfilenames(env);
|
|
}
|
|
return (0);
|
|
}
|
|
|
|
/*
|
|
* cleanup test files created
|
|
*/
|
|
void
|
|
cleanup(void)
|
|
{
|
|
int i, n;
|
|
|
|
n = sizeof(testfiles) / sizeof(testfiles[0]);
|
|
for (i = 0; i < n; i++) {
|
|
MPI_File_delete(testfiles[i], MPI_INFO_NULL);
|
|
}
|
|
}
|
|
|
|
/* Main Program */
|
|
int
|
|
main(int argc, char **argv)
|
|
{
|
|
int mpi_namelen;
|
|
char mpi_name[MPI_MAX_PROCESSOR_NAME];
|
|
int i, n;
|
|
|
|
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;
|
|
|
|
/* show test file names */
|
|
if (mpi_rank == 0) {
|
|
n = sizeof(testfiles) / sizeof(testfiles[0]);
|
|
printf("Parallel test files are:\n");
|
|
for (i = 0; i < n; i++) {
|
|
printf(" %s\n", testfiles[i]);
|
|
}
|
|
}
|
|
|
|
if (dowrite) {
|
|
MPI_BANNER("testing PHDF5 dataset using split communicators...");
|
|
test_split_comm_access(testfiles);
|
|
MPI_BANNER("testing PHDF5 dataset independent write...");
|
|
phdf5writeInd(testfiles[0]);
|
|
MPI_BANNER("testing PHDF5 dataset collective write...");
|
|
phdf5writeAll(testfiles[1]);
|
|
}
|
|
if (doread) {
|
|
MPI_BANNER("testing PHDF5 dataset independent read...");
|
|
phdf5readInd(testfiles[0]);
|
|
MPI_BANNER("testing PHDF5 dataset collective read...");
|
|
phdf5readAll(testfiles[1]);
|
|
}
|
|
|
|
if (!(dowrite || doread)) {
|
|
usage();
|
|
nerrors++;
|
|
}
|
|
|
|
finish:
|
|
if (mpi_rank == 0) { /* only process 0 reports */
|
|
if (nerrors)
|
|
printf("***PHDF5 example detected %d errors***\n", nerrors);
|
|
else {
|
|
printf("=====================================\n");
|
|
printf("PHDF5 example finished with no errors\n");
|
|
printf("=====================================\n");
|
|
}
|
|
}
|
|
if (docleanup)
|
|
cleanup();
|
|
MPI_Finalize();
|
|
|
|
return (nerrors);
|
|
}
|
|
|
|
#else /* H5_HAVE_PARALLEL */
|
|
/* dummy program since H5_HAVE_PARALLE is not configured in */
|
|
int
|
|
main(void)
|
|
{
|
|
printf("No PHDF5 example because parallel is not configured in\n");
|
|
return (0);
|
|
}
|
|
#endif /* H5_HAVE_PARALLEL */
|