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hdf5/testpar/t_dset.c
Albert Cheng 651c4b1064 [svn-r4582] Purpose: 
New test feature
Description:
    Added create_faccess_plist() that create just MPIO or split+MPIO
    file-access property list.  This in turn can run parallel tests
    with just MPIO or with Split-file VFD too.
    Added -s option for split-file Plus MPIO tests.
    For testphdf5.c: removed a bunch of old debug code that got left
    in by mistake.
Platforms tested:
    Modi4 and eirene parallel.
    But it has uncovered errors in the library.  The test program
    is correct though.  Checking the test program in so that it won't
    get lost and can be used for debugging.  Also, the -s is not used
    by default during test.  At least it won't abort "make check".
2001-11-02 10:21:51 -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)
{
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 */
acc_tpl = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 0), "");
/* 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");
/* setup dimensions again to write with zero rows for process 0 */
if (verbose)
printf("writeInd 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("writeInd by some with zero row");
if ((mpi_rank/2)*2 != mpi_rank){
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
H5P_DEFAULT, data_array1);
VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded");
}
MPI_Barrier(MPI_COMM_WORLD);
/* 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 = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 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 */
acc_tpl = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 0), "");
/* 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_DATASET_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 */
if (verbose)
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_DATASET_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 */
if (verbose)
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 */
acc_tpl = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 0), "");
/* 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_DATASET_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 */
if (verbose)
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_DATASET_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 */
if (verbose)
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 */
acc_tpl = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 0), "");
/* 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);
H5Pclose(dataset_pl);
/* -------------------------
* 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), "");
/* 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);
/* 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 = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 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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