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hdf5/testpar/t_dset.c
Albert Cheng c6e0eb1bd4 [svn-r2993] Purpose: 
New feature
Description:
    Added tests to make sure collective read or write works correctly
    even if some process has no data to transfer.
    ZROW--process 0 asks for zero rows of data while other processes ask
	for a slab of rows.
    ZCOL--process 0 asks for zero columns of data while other processes ask
	for a slab of columns.
Platforms tested:
    IRIX64 parallel (-64,-n32).
cvS: ----------------------------------------------------------------------
2000-11-21 18:08:54 -05:00

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/* $Id$ */
/*
* Parallel tests for datasets
*/
/*
* Example of using the parallel HDF5 library to access datasets.
*
* This program contains two major parts. Part 1 tests fixed dimension
* datasets, for both independent and collective transfer modes.
* Part 2 tests extendible datasets, for independent transfer mode
* only. Collective mode for extendible datasets are not supported yet.
*/
#include <testphdf5.h>
/*
* The following are various utility routines used by the tests.
*/
/*
* Setup the dimensions of the hyperslab.
* Two modes--by rows or by columns.
* Assume dimension rank is 2.
* BYROW divide into slabs of rows
* BYCOL divide into blocks of columns
* ZROW same as BYROW except process 0 gets 0 rows
* ZCOL same as BYCOL except process 0 gets 0 columns
*/
void
slab_set(int mpi_rank, int mpi_size, hssize_t start[], hsize_t count[],
hsize_t stride[], hsize_t block[], int mode)
{
switch (mode){
case BYROW:
/* Each process takes a slabs of rows. */
block[0] = dim0/mpi_size;
block[1] = dim1;
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = mpi_rank*block[0];
start[1] = 0;
if (verbose) printf("slab_set BYROW\n");
break;
case BYCOL:
/* Each process takes a block of columns. */
block[0] = dim0;
block[1] = dim1/mpi_size;
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = 0;
start[1] = mpi_rank*block[1];
if (verbose) printf("slab_set BYCOL\n");
break;
case ZROW:
/* Similar to BYROW except process 0 gets 0 row */
block[0] = (mpi_rank ? dim0/mpi_size : 0);
block[1] = dim1;
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = (mpi_rank? mpi_rank*block[0] : 0);
start[1] = 0;
if (verbose) printf("slab_set ZROW\n");
break;
case ZCOL:
/* Similar to BYCOL except process 0 gets 0 column */
block[0] = dim0;
block[1] = (mpi_rank ? dim1/mpi_size : 0);
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = 0;
start[1] = (mpi_rank? mpi_rank*block[1] : 0);
if (verbose) printf("slab_set ZCOL\n");
break;
default:
/* Unknown mode. Set it to cover the whole dataset. */
printf("unknown slab_set mode (%d)\n", mode);
block[0] = dim0;
block[1] = dim1;
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = 0;
start[1] = 0;
if (verbose) printf("slab_set wholeset\n");
break;
}
if (verbose){
printf("start[]=(%ld,%ld), count[]=(%lu,%lu), stride[]=(%lu,%lu), block[]=(%lu,%lu), total datapoints=%lu\n",
start[0], start[1], count[0], count[1],
stride[0], stride[1], block[0], block[1],
block[0]*block[1]*count[0]*count[1]);
}
}
/*
* Fill the dataset with trivial data for testing.
* Assume dimension rank is 2 and data is stored contiguous.
*/
void
dataset_fill(hssize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE * dataset)
{
DATATYPE *dataptr = dataset;
int i, j;
/* put some trivial data in the data_array */
for (i=0; i < block[0]; i++){
for (j=0; j < block[1]; j++){
*dataptr = (i+start[0])*100 + (j+start[1]+1);
dataptr++;
}
}
}
/*
* Print the content of the dataset.
*/
void dataset_print(hssize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE * dataset)
{
DATATYPE *dataptr = dataset;
int i, j;
/* print the column heading */
printf("%-8s", "Cols:");
for (j=0; j < block[1]; j++){
printf("%3ld ", start[1]+j);
}
printf("\n");
/* print the slab data */
for (i=0; i < block[0]; i++){
printf("Row %2ld: ", i+start[0]);
for (j=0; j < block[1]; j++){
printf("%03d ", *dataptr++);
}
printf("\n");
}
}
/*
* Print the content of the dataset.
*/
int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original)
{
#define MAX_ERR_REPORT 10 /* Maximum number of errors reported */
DATATYPE *dataptr = dataset;
DATATYPE *originptr = original;
int i, j, vrfyerrs;
/* print it if verbose */
if (verbose) {
printf("dataset_vrfy dumping:::\n");
printf("start(%ld, %ld), count(%lu, %lu), stride(%lu, %lu), block(%lu, %lu)\n",
start[0], start[1], count[0], count[1],
stride[0], stride[1], block[0], block[1]);
printf("original values:\n");
dataset_print(start, count, stride, block, original);
printf("compared values:\n");
dataset_print(start, count, stride, block, dataset);
}
vrfyerrs = 0;
for (i=0; i < block[0]; i++){
for (j=0; j < block[1]; j++){
if (*dataset != *original){
if (vrfyerrs++ < MAX_ERR_REPORT || verbose){
printf("Dataset Verify failed at [%d][%d](row %d, col %d): expect %d, got %d\n",
i, j,
(int)(i+start[0]), (int)(j+start[1]),
*(original), *(dataset));
}
dataset++;
original++;
}
}
}
if (vrfyerrs > MAX_ERR_REPORT && !verbose)
printf("[more errors ...]\n");
if (vrfyerrs)
printf("%d errors found in dataset_vrfy\n", vrfyerrs);
return(vrfyerrs);
}
/*
* Part 1.a--Independent read/write for fixed dimension datasets.
*/
/*
* 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 dim0) x dim1.
* Each process controls only a slab of size dim0 x dim1 within each
* dataset.
*/
void
dataset_writeInd(char *filename)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t sid; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
hsize_t dims[RANK]; /* dataset dim sizes */
DATATYPE *data_array1 = NULL; /* data buffer */
hssize_t start[RANK]; /* for hyperslab setting */
hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
hsize_t block[RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int mpi_size, mpi_rank;
char *fname;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Independent write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
/* ----------------------------------------
* CREATE AN HDF5 FILE WITH PARALLEL ACCESS
* ---------------------------------------*/
/* setup file access template with parallel IO access. */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((acc_tpl >= 0), "H5Pcreate access succeeded");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
VRFY((ret >= 0), "H5Pset_fapl_mpio succeeded");
/* create the file collectively */
fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
VRFY((fid >= 0), "H5Fcreate succeeded");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
VRFY((ret >= 0), "");
/* ---------------------------------------------
* Define the dimensions of the overall datasets
* and the slabs local to the MPI process.
* ------------------------------------------- */
/* setup dimensionality object */
dims[0] = dim0;
dims[1] = dim1;
sid = H5Screate_simple (RANK, dims, NULL);
VRFY((sid >= 0), "H5Screate_simple succeeded");
/* create a dataset collectively */
dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid,
H5P_DEFAULT);
VRFY((dataset1 >= 0), "H5Dcreate succeeded");
/* create another dataset collectively */
dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid,
H5P_DEFAULT);
VRFY((dataset2 >= 0), "H5Dcreate succeeded");
/*
* To test the independent orders of writes between processes, all
* even number processes write to dataset1 first, then dataset2.
* All odd number processes write to dataset2 first, then dataset1.
*/
/* set up dimensions of the slab this process accesses */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, block, data_array1);
MESG("data_array initialized");
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* write data independently */
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
/* write data independently */
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
/* release dataspace ID */
H5Sclose(file_dataspace);
/* close dataset collectively */
ret=H5Dclose(dataset1);
VRFY((ret >= 0), "H5Dclose1 succeeded");
ret=H5Dclose(dataset2);
VRFY((ret >= 0), "H5Dclose2 succeeded");
/* release all IDs created */
H5Sclose(sid);
/* close the file collectively */
H5Fclose(fid);
/* release data buffers */
if (data_array1) free(data_array1);
}
/* Example of using the parallel HDF5 library to read a dataset */
void
dataset_readInd(char *filename)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t sid; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
DATATYPE *data_array1 = NULL; /* data buffer */
DATATYPE *data_origin1 = NULL; /* expected data buffer */
hssize_t start[RANK]; /* for hyperslab setting */
hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
hsize_t block[RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Independent read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
/* setup file access template */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((acc_tpl >= 0), "");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
VRFY((ret >= 0), "");
/* open the file collectively */
fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
VRFY((fid >= 0), "");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
VRFY((ret >= 0), "");
/* open the dataset1 collectively */
dataset1 = H5Dopen(fid, DATASETNAME1);
VRFY((dataset1 >= 0), "");
/* open another dataset collectively */
dataset2 = H5Dopen(fid, DATASETNAME1);
VRFY((dataset2 >= 0), "");
/* set up dimensions of the slab this process accesses */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill dataset with test data */
dataset_fill(start, count, stride, block, data_origin1);
/* read data independently */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
if (ret) nerrors++;
/* read data independently */
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
if (ret) nerrors++;
/* close dataset collectively */
ret=H5Dclose(dataset1);
VRFY((ret >= 0), "");
ret=H5Dclose(dataset2);
VRFY((ret >= 0), "");
/* release all IDs created */
H5Sclose(file_dataspace);
/* close the file collectively */
H5Fclose(fid);
/* release data buffers */
if (data_array1) free(data_array1);
if (data_origin1) free(data_origin1);
}
/*
* Part 1.b--Collective read/write for fixed dimension datasets.
*/
/*
* 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 dim0) x dim1.
* Each process controls only a slab of size dim0 x dim1 within each
* dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and
* each process controls a hyperslab within.]
*/
void
dataset_writeAll(char *filename)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t xfer_plist; /* Dataset transfer properties list */
hid_t sid; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
hid_t datatype; /* Datatype ID */
hsize_t dims[RANK]; /* dataset dim sizes */
DATATYPE *data_array1 = NULL; /* data buffer */
hssize_t start[RANK]; /* for hyperslab setting */
hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
hsize_t block[RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Collective write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
/* -------------------
* START AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((acc_tpl >= 0), "H5Pcreate access succeeded");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
VRFY((ret >= 0), "H5Pset_fapl_mpio succeeded");
/* create the file collectively */
fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
VRFY((fid >= 0), "H5Fcreate succeeded");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
VRFY((ret >= 0), "");
/* --------------------------
* Define the dimensions of the overall datasets
* and create the dataset
* ------------------------- */
/* setup dimensionality object */
dims[0] = dim0;
dims[1] = dim1;
sid = H5Screate_simple (RANK, dims, NULL);
VRFY((sid >= 0), "H5Screate_simple succeeded");
/* create a dataset collectively */
dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT);
VRFY((dataset1 >= 0), "H5Dcreate succeeded");
/* create another dataset collectively */
datatype = H5Tcopy(H5T_NATIVE_INT);
ret = H5Tset_order(datatype, H5T_ORDER_LE);
VRFY((ret >= 0), "H5Tset_order succeeded");
dataset2 = H5Dcreate(fid, DATASETNAME2, datatype, sid, H5P_DEFAULT);
VRFY((dataset2 >= 0), "H5Dcreate 2 succeeded");
/*
* Set up dimensions of the slab this process accesses.
*/
/* Dataset1: each process takes a block of rows. */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill the local slab with some trivial data */
dataset_fill(start, count, stride, block, data_array1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATA_XFER);
VRFY((xfer_plist >= 0), "");
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
/* write data collectively */
MESG("writeAll by Row");
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
/* setup dimensions again to writeAll with zero rows for process 0 */
printf("writeAll by some with zero row\n");
slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW);
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* need to make mem_dataspace to match for process 0 */
if (MAINPROCESS){
ret=H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
}
MESG("writeAll by some with zero row");
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded");
/* 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(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, block, data_array1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill the local slab with some trivial data */
dataset_fill(start, count, stride, block, data_array1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATA_XFER);
VRFY((xfer_plist >= 0), "");
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
/* write data independently */
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
/* setup dimensions again to writeAll with zero columns for process 0 */
printf("writeAll by some with zero col\n");
slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL);
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* need to make mem_dataspace to match for process 0 */
if (MAINPROCESS){
ret=H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
}
MESG("writeAll by some with zero col");
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset1 by ZCOL succeeded");
/* release all temporary handles. */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/*
* All writes completed. Close datasets collectively
*/
ret=H5Dclose(dataset1);
VRFY((ret >= 0), "H5Dclose1 succeeded");
ret=H5Dclose(dataset2);
VRFY((ret >= 0), "H5Dclose2 succeeded");
/* release all IDs created */
H5Sclose(sid);
/* close the file collectively */
H5Fclose(fid);
/* release data buffers */
if (data_array1) free(data_array1);
}
/*
* 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 dim0) x dim1.
* Each process controls only a slab of size dim0 x dim1 within each
* dataset. [Note: not so yet. Datasets are of sizes dim0xdim1 and
* each process controls a hyperslab within.]
*/
void
dataset_readAll(char *filename)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t xfer_plist; /* Dataset transfer properties list */
hid_t sid; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
DATATYPE *data_array1 = NULL; /* data buffer */
DATATYPE *data_origin1 = NULL; /* expected data buffer */
hssize_t start[RANK]; /* for hyperslab setting */
hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
hsize_t block[RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Collective read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
/* -------------------
* OPEN AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((acc_tpl >= 0), "H5Pcreate access succeeded");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
VRFY((ret >= 0), "H5Pset_fapl_mpio succeeded");
/* open the file collectively */
fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
VRFY((fid >= 0), "H5Fopen succeeded");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
VRFY((ret >= 0), "");
/* --------------------------
* Open the datasets in it
* ------------------------- */
/* open the dataset1 collectively */
dataset1 = H5Dopen(fid, DATASETNAME1);
VRFY((dataset1 >= 0), "H5Dopen succeeded");
/* open another dataset collectively */
dataset2 = H5Dopen(fid, DATASETNAME2);
VRFY((dataset2 >= 0), "H5Dopen 2 succeeded");
/*
* Set up dimensions of the slab this process accesses.
*/
/* Dataset1: each process takes a block of columns. */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill dataset with test data */
dataset_fill(start, count, stride, block, data_origin1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_origin1);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATA_XFER);
VRFY((xfer_plist >= 0), "");
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
/* read data collectively */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dread dataset1 succeeded");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
if (ret) nerrors++;
/* setup dimensions again to readAll with zero columns for process 0 */
printf("readAll by some with zero col\n");
slab_set(mpi_rank, mpi_size, start, count, stride, block, ZCOL);
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* need to make mem_dataspace to match for process 0 */
if (MAINPROCESS){
ret=H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
}
MESG("readAll by some with zero col");
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dread dataset1 by ZCOL succeeded");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
if (ret) nerrors++;
/* 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(mpi_rank, mpi_size, start, count, stride, block, BYROW);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill dataset with test data */
dataset_fill(start, count, stride, block, data_origin1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_origin1);
}
/* set up the collective transfer properties list */
xfer_plist = H5Pcreate (H5P_DATA_XFER);
VRFY((xfer_plist >= 0), "");
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
/* read data collectively */
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dread dataset2 succeeded");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
if (ret) nerrors++;
/* setup dimensions again to readAll with zero rows for process 0 */
printf("readAll by some with zero row\n");
slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW);
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* need to make mem_dataspace to match for process 0 */
if (MAINPROCESS){
ret=H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
}
MESG("readAll by some with zero row");
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
xfer_plist, data_array1);
VRFY((ret >= 0), "H5Dread dataset1 by ZROW succeeded");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
if (ret) nerrors++;
/* release all temporary handles. */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
H5Pclose(xfer_plist);
/*
* All reads completed. Close datasets collectively
*/
ret=H5Dclose(dataset1);
VRFY((ret >= 0), "H5Dclose1 succeeded");
ret=H5Dclose(dataset2);
VRFY((ret >= 0), "H5Dclose2 succeeded");
/* close the file collectively */
H5Fclose(fid);
/* release data buffers */
if (data_array1) free(data_array1);
if (data_origin1) free(data_origin1);
}
/*
* Part 2--Independent read/write for extendible datasets.
*/
/*
* Example of using the parallel HDF5 library to create two extendible
* datasets in one HDF5 file with independent parallel MPIO access support.
* The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
* Each process controls only a slab of size dim0 x dim1 within each
* dataset.
*/
void
extend_writeInd(char *filename)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t sid; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
hsize_t dims[RANK]; /* dataset dim sizes */
hsize_t max_dims[RANK] =
{H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */
DATATYPE *data_array1 = NULL; /* data buffer */
hsize_t chunk_dims[RANK]; /* chunk sizes */
hid_t dataset_pl; /* dataset create prop. list */
hssize_t start[RANK]; /* for hyperslab setting */
hsize_t count[RANK]; /* for hyperslab setting */
hsize_t stride[RANK]; /* for hyperslab setting */
hsize_t block[RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int mpi_size, mpi_rank;
char *fname;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Extend independent write test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* setup chunk-size. Make sure sizes are > 0 */
chunk_dims[0] = chunkdim0;
chunk_dims[1] = chunkdim1;
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
/* -------------------
* START AN HDF5 FILE
* -------------------*/
/* setup file access template with parallel IO access. */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((acc_tpl >= 0), "H5Pcreate access succeeded");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
VRFY((ret >= 0), "H5Pset_fapl_mpio succeeded");
/* create the file collectively */
fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
VRFY((fid >= 0), "H5Fcreate succeeded");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
VRFY((ret >= 0), "");
/* --------------------------------------------------------------
* Define the dimensions of the overall datasets and create them.
* ------------------------------------------------------------- */
/* set up dataset storage chunk sizes and creation property list */
if (verbose)
printf("chunks[]=%lu,%lu\n", chunk_dims[0], chunk_dims[1]);
dataset_pl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dataset_pl >= 0), "H5Pcreate succeeded");
ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims);
VRFY((ret >= 0), "H5Pset_chunk succeeded");
/* setup dimensionality object */
/* start out with no rows, extend it later. */
dims[0] = dims[1] = 0;
sid = H5Screate_simple (RANK, dims, max_dims);
VRFY((sid >= 0), "H5Screate_simple succeeded");
/* create an extendible dataset collectively */
dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid, dataset_pl);
VRFY((dataset1 >= 0), "H5Dcreate succeeded");
/* create another extendible dataset collectively */
dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid, dataset_pl);
VRFY((dataset2 >= 0), "H5Dcreate succeeded");
/* release resource */
H5Sclose(sid);
/* -------------------------
* Test writing to dataset1
* -------------------------*/
/* set up dimensions of the slab this process accesses */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, block, data_array1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* Extend its current dim sizes before writing */
dims[0] = dim0;
dims[1] = dim1;
ret = H5Dextend (dataset1, dims);
VRFY((ret >= 0), "H5Dextend succeeded");
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* write data independently */
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dwrite succeeded");
/* release resource */
H5Sclose(file_dataspace);
H5Sclose(mem_dataspace);
/* -------------------------
* Test writing to dataset2
* -------------------------*/
/* set up dimensions of the slab this process accesses */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
/* put some trivial data in the data_array */
dataset_fill(start, count, stride, block, data_array1);
MESG("data_array initialized");
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
#ifndef DISABLE
/* Try write to dataset2 beyond its current dim sizes. Should fail. */
/* Temporary turn off auto error reporting */
H5Eget_auto(&old_func, &old_client_data);
H5Eset_auto(NULL, NULL);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset2);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* write data independently. Should fail. */
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret < 0), "H5Dwrite failed as expected");
/* restore auto error reporting */
H5Eset_auto(old_func, old_client_data);
H5Sclose(file_dataspace);
#else
/* Skip test because H5Dwrite is not failing as expected */
printf("***Skip test of write-beyond-current-dim-size\n");
#endif
/* Extend dataset2 and try again. Should succeed. */
dims[0] = dim0;
dims[1] = dim1;
ret = H5Dextend (dataset2, dims);
VRFY((ret >= 0), "H5Dextend succeeded");
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset2);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* write data independently */
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dwrite succeeded");
/* release resource */
ret=H5Sclose(file_dataspace);
VRFY((ret >= 0), "H5Sclose succeeded");
ret=H5Sclose(mem_dataspace);
VRFY((ret >= 0), "H5Sclose succeeded");
/* close dataset collectively */
ret=H5Dclose(dataset1);
VRFY((ret >= 0), "H5Dclose1 succeeded");
ret=H5Dclose(dataset2);
VRFY((ret >= 0), "H5Dclose2 succeeded");
/* close the file collectively */
H5Fclose(fid);
/* release data buffers */
if (data_array1) free(data_array1);
}
/* Example of using the parallel HDF5 library to read an extendible dataset */
void
extend_readInd(char *filename)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t sid; /* Dataspace ID */
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* memory dataspace ID */
hid_t dataset1, dataset2; /* Dataset ID */
hsize_t dims[RANK]; /* dataset dim sizes */
DATATYPE *data_array1 = NULL; /* data buffer */
DATATYPE *data_array2 = NULL; /* data buffer */
DATATYPE *data_origin1 = NULL; /* expected data buffer */
hssize_t start[RANK]; /* for hyperslab setting */
hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
hsize_t block[RANK]; /* for hyperslab setting */
herr_t ret; /* Generic return value */
int i, j;
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
if (verbose)
printf("Extend independent read test on file %s\n", filename);
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
/* allocate memory for data buffer */
data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
data_array2 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_array2 != NULL), "data_array2 malloc succeeded");
data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
/* -------------------
* OPEN AN HDF5 FILE
* -------------------*/
/* setup file access template */
acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
VRFY((acc_tpl >= 0), "");
/* set Parallel access with communicator */
ret = H5Pset_fapl_mpio(acc_tpl, comm, info);
VRFY((ret >= 0), "");
/* open the file collectively */
fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
VRFY((fid >= 0), "");
/* Release file-access template */
ret=H5Pclose(acc_tpl);
VRFY((ret >= 0), "");
/* open the dataset1 collectively */
dataset1 = H5Dopen(fid, DATASETNAME1);
VRFY((dataset1 >= 0), "");
/* open another dataset collectively */
dataset2 = H5Dopen(fid, DATASETNAME1);
VRFY((dataset2 >= 0), "");
/* Try extend dataset1 which is open RDONLY. Should fail. */
/* first turn off auto error reporting */
H5Eget_auto(&old_func, &old_client_data);
H5Eset_auto(NULL, NULL);
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret=H5Sget_simple_extent_dims(file_dataspace, dims, NULL);
VRFY((ret > 0), "H5Sget_simple_extent_dims succeeded");
dims[0]++;
ret=H5Dextend(dataset1, dims);
VRFY((ret < 0), "H5Dextend failed as expected");
/* restore auto error reporting */
H5Eset_auto(old_func, old_client_data);
H5Sclose(file_dataspace);
/* Read dataset1 using BYROW pattern */
/* set up dimensions of the slab this process accesses */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset1);
VRFY((file_dataspace >= 0), "");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill dataset with test data */
dataset_fill(start, count, stride, block, data_origin1);
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* read data independently */
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dread succeeded");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
VRFY((ret == 0), "dataset1 read verified correct");
if (ret) nerrors++;
H5Sclose(mem_dataspace);
H5Sclose(file_dataspace);
/* Read dataset2 using BYCOL pattern */
/* set up dimensions of the slab this process accesses */
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
/* create a file dataspace independently */
file_dataspace = H5Dget_space (dataset2);
VRFY((file_dataspace >= 0), "");
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* fill dataset with test data */
dataset_fill(start, count, stride, block, data_origin1);
if (verbose){
MESG("data_array created");
dataset_print(start, count, stride, block, data_array1);
}
/* read data independently */
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dread succeeded");
/* verify the read data with original expected data */
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
VRFY((ret == 0), "dataset2 read verified correct");
if (ret) nerrors++;
H5Sclose(mem_dataspace);
H5Sclose(file_dataspace);
/* close dataset collectively */
ret=H5Dclose(dataset1);
VRFY((ret >= 0), "");
ret=H5Dclose(dataset2);
VRFY((ret >= 0), "");
/* close the file collectively */
H5Fclose(fid);
/* release data buffers */
if (data_array1) free(data_array1);
if (data_array2) free(data_array2);
if (data_origin1) free(data_origin1);
}
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