Hi Matt,
On Mar 2, 2010, at 8:38 PM, Matthew Becker wrote:
> Hi Mark and all,
>
> Sorry for the spam. This was a simple bug. It works with both mpio and
> mpiposix io. I still have a question.
>
> I have been through the tutorials, but it still is not clear to me.
>
> Does the function H5Dopen need to be called collectively? The code below (or
> above) seems to indicate that H5Dcreate must be called collectively (it
> doesn't work for me if it is not...), but that H5Dopen does *not* need to be
> called collectively?
>
> What is the logic here?
Here's a link with some information about which routines need to be
called collectively.
http://www.hdfgroup.org/HDF5/faq/parallel-apis.html#coll
Quincey
>
> Cheers,
> Matt
>
>
>
>
>
> On Tue, Mar 2, 2010 at 6:01 PM, Mark Howison <[email protected]> wrote:
> Hi Matthew, have you tried using the MPI-POSIX VFD instead? Mark
>
> On Tue, Mar 2, 2010 at 3:56 PM, Matthew Becker <[email protected]> wrote:
> > 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;
> > }
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
> > [email protected]
> > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> >
> >
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
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