Hi all,
I am having trouble with the following piece of code (I hacked apart one of
the parallel HDF5 tutorial examples and changed the API to 1.8.4).
I am trying get each process to write to a different data set simultaneously
(but all data sets are in the same file) using independent I/O. I suspect
this may not be possible, but the documentation seems to say otherwise (see
http://www.hdfgroup.org/HDF5/Tutor/pprog.html, at the bottom it says "Each
process writes to a individual dataset.").
I have enforced that the data sets are created collectively, but the
simultaneous write fails.
Do you all know why this does not work?
The code is listed below.
Cheers,
Matt
/*
* This example writes data to the HDF5 file.
* Number of processes is assumed to be 1 or multiples of 2 (up to 8)
*/
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <assert.h>
#include <mpi.h>
#include <hdf5.h>
#define H5FILE_NAME "SDS.h5"
#define DATASETNAME "IntArray"
#define NX 8 /* dataset dimensions */
#define NY 5
#define RANK 2
int main (int argc, char **argv)
{
/*
* HDF5 APIs definitions
*/
hid_t file_id, dset_id, group_id; /* file and dataset
identifiers */
hid_t filespace; /* file and memory dataspace identifiers */
hsize_t dimsf[] = {NX, NY}; /* dataset dimensions */
int *data; /* pointer to data buffer to write
*/
hid_t plist_id; /* property list identifier */
int i;
herr_t status;
char name[500];
/*
* MPI variables
*/
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
/*
* Initialize MPI
*/
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
/*
* Initialize data buffer
*/
data = (int *) malloc(sizeof(int)*dimsf[0]*
dimsf[1]);
for (i=0; i < dimsf[0]*dimsf[1]; i++) {
data[i] = mpi_rank;
}
/*
* Set up file access property list with parallel I/O access
*/
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, comm, info);
/*
* Create a new file collectively and release property list identifier.
*/
file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
H5Pclose(plist_id);
/*
* Create property list for collective dataset write.
*/
plist_id = H5Pcreate(H5P_DATASET_XFER);
//H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
/*
* Create the dataspace for the dataset.
*/
filespace = H5Screate_simple(RANK, dimsf, NULL);
for(i=0;i<mpi_size;++i)
{
MPI_Barrier(MPI_COMM_WORLD);
sprintf(name,"node%d",i);
dset_id = H5Dcreate(file_id, name, H5T_NATIVE_INT, filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dclose(dset_id);
MPI_Barrier(MPI_COMM_WORLD);
}
MPI_Barrier(MPI_COMM_WORLD);
sprintf(name,"node%d",i);
dset_id = H5Dopen(file_id, name, H5P_DEFAULT);
status = H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, plist_id,
data);
H5Dclose(dset_id);
free(data);
/*
* Close/release resources.
*/
H5Sclose(filespace);
H5Pclose(plist_id);
H5Fclose(file_id);
MPI_Finalize();
return 0;
}