/* Read and verify attribute for group or dataset. */
int read_attribute(hid_t obj_id, int this_type, int num)
{
    hid_t aid;
    hsize_t group_block[2]={1,1}, dset_block[2]={1, 8};
    int  i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0;
    char attr_name[32];

    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);

    if(this_type == is_group) {
        sprintf(attr_name, "Group Attribute %d", num);
        aid = H5Aopen_name(obj_id, attr_name);
        if(MAINPROCESS) {
            H5Aread(aid, H5T_NATIVE_INT, &in_num);
            vrfy_errors =  dataset_vrfy(NULL, NULL, NULL, group_block,
                                        &in_num, &num);
	}
        H5Aclose(aid);
    }
    else if(this_type == is_dset) {
        sprintf(attr_name, "Dataset Attribute %d", num);
        for(i=0; i<8; i++)
            out_data[i] = i;
        aid = H5Aopen_name(obj_id, attr_name);
        if(MAINPROCESS) {
            H5Aread(aid, H5T_NATIVE_INT, in_data);
            vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data,
                                       out_data);
	}
        H5Aclose(aid);
    }

    return vrfy_errors;
}
Exemple #2
0
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, DATASETNAME2, 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);
}
Exemple #3
0
/* 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);
}