Hi Bruno,
On Sep 26, 2011, at 7:11 AM, Bruno Magalhaes wrote:
> Hi,
>
> We are trying to use parallel HDF5 to write data to a file.
>
> The execution seems to be going well, but the H5Fclose hangs the execution.
> I.e the following message is printed:
> "All parallel hdf5 content written, closing file...\n"
> but the
> "Done"
> never gets to be printed.
>
> Any suggestion or amendment to the following code?
Your problem is that you are modifying metadata independently (in the
"if(mpiRank == 0)" block, which is not allowed (currently). You'll need to
change that so that all the H5A/H5D calls in that block are executed
collectively, so that all the processes have the same "view" of the file's
state. (We are working to change this, but it'll be a while before it gets
implemented)
Quincey
> Thanks
>
> Bruno Magalhaes, Blue Brain Project, EPFL, Lausanne CH [+41 2169 31805]
>
>
>
>
> //------------------- BEGINNING OF SOURCE CODE --------------------
>
> #include <stdio.h>
> #include <cstdlib>
>
> #include <mpi.h>
>
> #define H5_USE_16_API 1
> #include "hdf5.h"
>
> #define NUMVALUES 19
>
> using namespace std;
>
> int main(int argc, char** argv) {
>
> MPI_Init(&argc, &argv);
>
> int mpiRank=-1, mpiSize=-1;
> MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
> MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
>
> if (mpiRank==0) printf("Writing header...\n");
>
> int numOfNeurons = 100;
>
> hid_t file_id = 0;
> herr_t status;
> hsize_t dims[2];
> char filename[1024] = "/bgscratch/bmagalha/delete.h5";
>
> //Set up file access property list with parallel I/O access
> hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
> H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL) ;
>
> //Create a new file collectively and release property list identifier.
> file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
> H5Pclose(plist_id);
>
> if (mpiRank == 0) {
> //Initialize the attribute data.
> int info_version_data = 3;
> int info_numberOfFiles_data = 1;
>
> hsize_t info_dims = 1;
> hid_t filespace_h = H5Screate_simple(0,&info_dims, NULL);
> hid_t dset_id_info = H5Dcreate(file_id, "/info", H5T_NATIVE_FLOAT,
> filespace_h, H5P_DEFAULT);
>
> //Create the data space for the attribute.
> hid_t info_dataspace_id = H5Screate_simple(1, &info_dims, NULL);
>
> //Create a dataset attribute and count of files.
> hid_t info_version_id = H5Acreate(dset_id_info, "version",
> H5T_STD_I32BE, info_dataspace_id, H5P_DEFAULT);
> hid_t info_numberOfFiles_id = H5Acreate(dset_id_info, "numberOfFiles",
> H5T_STD_I32BE, info_dataspace_id, H5P_DEFAULT);
>
> //Write the attribute and files Countdata.
> H5Awrite(info_version_id, H5T_NATIVE_INT, &info_version_data);
> H5Awrite(info_numberOfFiles_id, H5T_NATIVE_INT,
> &info_numberOfFiles_data);
>
> //Create property list for individual dataset write (default).
> plist_id = H5Pcreate(H5P_DATASET_XFER);
> H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
>
> //to write data collectively, use:
> // plist_id = H5Pcreate(H5P_DATASET_XFER);
> // H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
>
> //Close the attributes, dataspace and dataset.
> status = H5Aclose(info_version_id);
> status = H5Aclose(info_numberOfFiles_id);
> status = H5Dclose(dset_id_info);
> status = H5Sclose(info_dataspace_id);
> }
>
> if (mpiRank==0) printf("Writing body...\n");
>
> char name[512];
> float *allSynapsesSendBuff;
> for (int i = 0; i < numOfNeurons; i++) {
>
> dims[0] = 2000; // Create the dataset.
> allSynapsesSendBuff = new float[NUMVALUES * dims[0]];
>
> dims[1] = NUMVALUES;
> hid_t filespace = H5Screate_simple(2, dims, NULL);
>
> sprintf(name, "a.%d.%d", mpiRank, i);
>
> //Create dataset with default properties and close filespace
> hid_t dset_id = H5Dcreate(file_id, name, H5T_NATIVE_FLOAT, filespace,
> H5P_DEFAULT);
>
> //Create property list for independent dataset write
> hid_t plist_id = H5Pcreate(H5P_DATASET_XFER);
> H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
>
> H5Dwrite(dset_id, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, plist_id,
> allSynapsesSendBuff);
>
> // End access to the dataset and release resources used by it.
> status = H5Dclose(dset_id);
> status = H5Sclose(filespace);
> status = H5Pclose(plist_id);
> }
>
> MPI_Barrier(MPI_COMM_WORLD);
> if (mpiRank==0) printf("All parallel hdf5 content written, closing
> file...\n");
> fflush(stdout);
>
> // Terminates access to the file.
> status = H5Fclose(file_id);
> MPI_Barrier(MPI_COMM_WORLD);
>
> if (mpiRank==0) printf("Done.\n");
> MPI_Finalize();
> return 0;
> }
>
>
> //------------------- END OF SOURCE CODE --------------------
>
>
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