mirror of
https://github.com/HDFGroup/hdf5.git
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427ff7da28
Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
2232 lines
76 KiB
C
2232 lines
76 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Parallel tests for datasets
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*/
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/*
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* Example of using the parallel HDF5 library to access datasets.
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*
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* This program contains three major parts. Part 1 tests fixed dimension
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* datasets, for both independent and collective transfer modes.
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* Part 2 tests extendible datasets, for independent transfer mode
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* only.
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* Part 3 tests extendible datasets, for collective transfer mode
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* only.
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*/
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#include "testphdf5.h"
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/*
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* The following are various utility routines used by the tests.
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*/
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/*
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* Setup the dimensions of the hyperslab.
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* Two modes--by rows or by columns.
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* Assume dimension rank is 2.
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* BYROW divide into slabs of rows
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* BYCOL divide into blocks of columns
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* ZROW same as BYROW except process 0 gets 0 rows
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* ZCOL same as BYCOL except process 0 gets 0 columns
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*/
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static void
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slab_set(int mpi_rank, int mpi_size, hsize_t start[], hsize_t count[],
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hsize_t stride[], hsize_t block[], int mode)
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{
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switch (mode){
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case BYROW:
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/* Each process takes a slabs of rows. */
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block[0] = dim0/mpi_size;
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block[1] = dim1;
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stride[0] = block[0];
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stride[1] = block[1];
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count[0] = 1;
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count[1] = 1;
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start[0] = mpi_rank*block[0];
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start[1] = 0;
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if (VERBOSE_MED) printf("slab_set BYROW\n");
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break;
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case BYCOL:
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/* Each process takes a block of columns. */
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block[0] = dim0;
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block[1] = dim1/mpi_size;
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stride[0] = block[0];
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stride[1] = block[1];
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count[0] = 1;
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count[1] = 1;
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start[0] = 0;
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start[1] = mpi_rank*block[1];
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if (VERBOSE_MED) printf("slab_set BYCOL\n");
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break;
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case ZROW:
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/* Similar to BYROW except process 0 gets 0 row */
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block[0] = (mpi_rank ? dim0/mpi_size : 0);
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block[1] = dim1;
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stride[0] = (mpi_rank ? block[0] : 1); /* avoid setting stride to 0 */
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stride[1] = block[1];
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count[0] = 1;
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count[1] = 1;
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start[0] = (mpi_rank? mpi_rank*block[0] : 0);
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start[1] = 0;
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if (VERBOSE_MED) printf("slab_set ZROW\n");
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break;
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case ZCOL:
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/* Similar to BYCOL except process 0 gets 0 column */
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block[0] = dim0;
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block[1] = (mpi_rank ? dim1/mpi_size : 0);
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stride[0] = block[0];
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stride[1] = (mpi_rank ? block[1] : 1); /* avoid setting stride to 0 */
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count[0] = 1;
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count[1] = 1;
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start[0] = 0;
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start[1] = (mpi_rank? mpi_rank*block[1] : 0);
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if (VERBOSE_MED) printf("slab_set ZCOL\n");
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break;
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default:
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/* Unknown mode. Set it to cover the whole dataset. */
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printf("unknown slab_set mode (%d)\n", mode);
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block[0] = dim0;
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block[1] = dim1;
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stride[0] = block[0];
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stride[1] = block[1];
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count[0] = 1;
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count[1] = 1;
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start[0] = 0;
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start[1] = 0;
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if (VERBOSE_MED) printf("slab_set wholeset\n");
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break;
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}
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if (VERBOSE_MED){
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printf("start[]=(%lu,%lu), count[]=(%lu,%lu), stride[]=(%lu,%lu), block[]=(%lu,%lu), total datapoints=%lu\n",
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(unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
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(unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1],
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(unsigned long)(block[0]*block[1]*count[0]*count[1]));
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}
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}
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/*
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* Fill the dataset with trivial data for testing.
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* Assume dimension rank is 2 and data is stored contiguous.
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*/
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static void
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dataset_fill(hsize_t start[], hsize_t block[], DATATYPE * dataset)
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{
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DATATYPE *dataptr = dataset;
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hsize_t i, j;
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/* put some trivial data in the data_array */
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for (i=0; i < block[0]; i++){
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for (j=0; j < block[1]; j++){
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*dataptr = (DATATYPE)((i+start[0])*100 + (j+start[1]+1));
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dataptr++;
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}
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}
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}
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/*
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* Print the content of the dataset.
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*/
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static void
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dataset_print(hsize_t start[], hsize_t block[], DATATYPE * dataset)
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{
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DATATYPE *dataptr = dataset;
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hsize_t i, j;
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/* print the column heading */
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printf("%-8s", "Cols:");
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for (j=0; j < block[1]; j++){
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printf("%3lu ", (unsigned long)(start[1]+j));
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}
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printf("\n");
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/* print the slab data */
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for (i=0; i < block[0]; i++){
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printf("Row %2lu: ", (unsigned long)(i+start[0]));
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for (j=0; j < block[1]; j++){
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printf("%03d ", *dataptr++);
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}
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printf("\n");
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}
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}
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/*
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* Print the content of the dataset.
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*/
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int
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dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original)
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{
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hsize_t i, j;
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int vrfyerrs;
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/* print it if VERBOSE_MED */
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if (VERBOSE_MED) {
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printf("dataset_vrfy dumping:::\n");
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printf("start(%lu, %lu), count(%lu, %lu), stride(%lu, %lu), block(%lu, %lu)\n",
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(unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1],
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(unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1]);
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printf("original values:\n");
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dataset_print(start, block, original);
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printf("compared values:\n");
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dataset_print(start, block, dataset);
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}
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vrfyerrs = 0;
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for (i=0; i < block[0]; i++){
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for (j=0; j < block[1]; j++){
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if (*dataset != *original){
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if (vrfyerrs++ < MAX_ERR_REPORT || VERBOSE_MED){
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printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n",
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(unsigned long)i, (unsigned long)j,
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(unsigned long)(i+start[0]), (unsigned long)(j+start[1]),
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*(original), *(dataset));
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}
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dataset++;
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original++;
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}
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}
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}
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if (vrfyerrs > MAX_ERR_REPORT && !VERBOSE_MED)
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printf("[more errors ...]\n");
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if (vrfyerrs)
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printf("%d errors found in dataset_vrfy\n", vrfyerrs);
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return(vrfyerrs);
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}
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/*
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* Part 1.a--Independent read/write for fixed dimension datasets.
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*/
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/*
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* Example of using the parallel HDF5 library to create two datasets
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* in one HDF5 files with parallel MPIO access support.
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* The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1.
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* Each process controls only a slab of size dim0 x dim1 within each
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* dataset.
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*/
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void
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dataset_writeInd(void)
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{
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hid_t fid; /* HDF5 file ID */
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hid_t acc_tpl; /* File access templates */
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hid_t sid; /* Dataspace ID */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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hbool_t use_gpfs = FALSE; /* Use GPFS hints */
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hsize_t dims[RANK]; /* dataset dim sizes */
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DATATYPE *data_array1 = NULL; /* data buffer */
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const char *filename;
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hsize_t start[RANK]; /* for hyperslab setting */
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hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
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hsize_t block[RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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int mpi_size, mpi_rank;
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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filename = GetTestParameters();
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if (VERBOSE_MED)
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printf("Independent write test on file %s\n", filename);
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/* set up MPI parameters */
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MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
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MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
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/* allocate memory for data buffer */
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data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
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VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
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/* ----------------------------------------
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* CREATE AN HDF5 FILE WITH PARALLEL ACCESS
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* ---------------------------------------*/
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/* setup file access template */
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acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs);
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VRFY((acc_tpl >= 0), "");
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/* create the file collectively */
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fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);
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VRFY((fid >= 0), "H5Fcreate succeeded");
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/* Release file-access template */
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ret=H5Pclose(acc_tpl);
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VRFY((ret >= 0), "");
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/* ---------------------------------------------
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* Define the dimensions of the overall datasets
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* and the slabs local to the MPI process.
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* ------------------------------------------- */
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/* setup dimensionality object */
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dims[0] = dim0;
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dims[1] = dim1;
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sid = H5Screate_simple (RANK, dims, NULL);
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VRFY((sid >= 0), "H5Screate_simple succeeded");
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/* create a dataset collectively */
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dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid,
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H5P_DEFAULT);
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VRFY((dataset1 >= 0), "H5Dcreate succeeded");
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/* create another dataset collectively */
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dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid,
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H5P_DEFAULT);
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VRFY((dataset2 >= 0), "H5Dcreate succeeded");
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/*
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* To test the independent orders of writes between processes, all
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* even number processes write to dataset1 first, then dataset2.
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* All odd number processes write to dataset2 first, then dataset1.
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*/
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/* set up dimensions of the slab this process accesses */
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slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
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/* put some trivial data in the data_array */
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dataset_fill(start, block, data_array1);
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MESG("data_array initialized");
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
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VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (RANK, block, NULL);
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VRFY((mem_dataspace >= 0), "");
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/* write data independently */
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ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
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/* write data independently */
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ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
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/* setup dimensions again to write with zero rows for process 0 */
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if (VERBOSE_MED)
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printf("writeInd by some with zero row\n");
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slab_set(mpi_rank, mpi_size, start, count, stride, block, ZROW);
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
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VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
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/* need to make mem_dataspace to match for process 0 */
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if (MAINPROCESS){
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ret=H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
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VRFY((ret >= 0), "H5Sset_hyperslab mem_dataspace succeeded");
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}
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MESG("writeInd by some with zero row");
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if ((mpi_rank/2)*2 != mpi_rank){
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ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret >= 0), "H5Dwrite dataset1 by ZROW succeeded");
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}
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#ifdef BARRIER_CHECKS
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MPI_Barrier(MPI_COMM_WORLD);
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#endif /* BARRIER_CHECKS */
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/* release dataspace ID */
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H5Sclose(file_dataspace);
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/* close dataset collectively */
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ret=H5Dclose(dataset1);
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VRFY((ret >= 0), "H5Dclose1 succeeded");
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ret=H5Dclose(dataset2);
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VRFY((ret >= 0), "H5Dclose2 succeeded");
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/* release all IDs created */
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H5Sclose(sid);
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/* close the file collectively */
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H5Fclose(fid);
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/* release data buffers */
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if (data_array1) free(data_array1);
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}
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/* Example of using the parallel HDF5 library to read a dataset */
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void
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dataset_readInd(void)
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{
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hid_t fid; /* HDF5 file ID */
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hid_t acc_tpl; /* File access templates */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset1, dataset2; /* Dataset ID */
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hbool_t use_gpfs = FALSE; /* Use GPFS hints */
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DATATYPE *data_array1 = NULL; /* data buffer */
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DATATYPE *data_origin1 = NULL; /* expected data buffer */
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const char *filename;
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hsize_t start[RANK]; /* for hyperslab setting */
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hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */
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hsize_t block[RANK]; /* for hyperslab setting */
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herr_t ret; /* Generic return value */
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int mpi_size, mpi_rank;
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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filename = GetTestParameters();
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if (VERBOSE_MED)
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printf("Independent read test on file %s\n", filename);
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/* set up MPI parameters */
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MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
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MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
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/* allocate memory for data buffer */
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data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
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VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
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data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE));
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VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
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/* setup file access template */
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acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs);
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VRFY((acc_tpl >= 0), "");
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/* open the file collectively */
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fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl);
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VRFY((fid >= 0), "");
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/* Release file-access template */
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ret=H5Pclose(acc_tpl);
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VRFY((ret >= 0), "");
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/* open the dataset1 collectively */
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dataset1 = H5Dopen(fid, DATASETNAME1);
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VRFY((dataset1 >= 0), "");
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/* open another dataset collectively */
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dataset2 = H5Dopen(fid, DATASETNAME1);
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VRFY((dataset2 >= 0), "");
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/* set up dimensions of the slab this process accesses */
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slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
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/* create a file dataspace independently */
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file_dataspace = H5Dget_space (dataset1);
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VRFY((file_dataspace >= 0), "");
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
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VRFY((ret >= 0), "");
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/* create a memory dataspace independently */
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mem_dataspace = H5Screate_simple (RANK, block, NULL);
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VRFY((mem_dataspace >= 0), "");
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/* fill dataset with test data */
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dataset_fill(start, block, data_origin1);
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/* 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(void)
|
|
{
|
|
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, dataset3, dataset4; /* Dataset ID */
|
|
hid_t datatype; /* Datatype ID */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
hsize_t dims[RANK]; /* dataset dim sizes */
|
|
DATATYPE *data_array1 = NULL; /* data buffer */
|
|
const char *filename;
|
|
|
|
hsize_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;
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
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, use_gpfs);
|
|
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 2-D 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");
|
|
|
|
/* create a third dataset collectively */
|
|
dataset3 = H5Dcreate(fid, DATASETNAME3, H5T_NATIVE_INT, sid, H5P_DEFAULT);
|
|
VRFY((dataset3 >= 0), "H5Dcreate succeeded");
|
|
|
|
/* release 2-D space ID created */
|
|
H5Sclose(sid);
|
|
|
|
/* setup scalar dimensionality object */
|
|
sid = H5Screate(H5S_SCALAR);
|
|
VRFY((sid >= 0), "H5Screate succeeded");
|
|
|
|
/* create a fourth dataset collectively */
|
|
dataset4 = H5Dcreate(fid, DATASETNAME4, H5T_NATIVE_INT, sid, H5P_DEFAULT);
|
|
VRFY((dataset4 >= 0), "H5Dcreate succeeded");
|
|
|
|
/* release scalar space ID created */
|
|
H5Sclose(sid);
|
|
|
|
/*
|
|
* 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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
|
|
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio 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_MED)
|
|
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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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_MED)
|
|
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. */
|
|
/* Could have used them for dataset3 but it is cleaner */
|
|
/* to create them again.*/
|
|
H5Sclose(file_dataspace);
|
|
H5Sclose(mem_dataspace);
|
|
H5Pclose(xfer_plist);
|
|
|
|
|
|
/* Dataset3: each process takes a block of rows, except process zero uses "none" selection. */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset3);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
if (MAINPROCESS) {
|
|
ret=H5Sselect_none(file_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_none file_dataspace succeeded");
|
|
} /* end if */
|
|
else {
|
|
ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
|
|
VRFY((ret >= 0), "H5Sselect_hyperslab succeeded");
|
|
} /* end else */
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, block, NULL);
|
|
VRFY((mem_dataspace >= 0), "");
|
|
if (MAINPROCESS) {
|
|
ret=H5Sselect_none(mem_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_none mem_dataspace succeeded");
|
|
} /* end if */
|
|
|
|
/* fill the local slab with some trivial data */
|
|
dataset_fill(start, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
} /* end if */
|
|
|
|
/* 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 with none");
|
|
ret = H5Dwrite(dataset3, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset3 succeeded");
|
|
|
|
/* write data collectively (with datatype conversion) */
|
|
MESG("writeAll with none");
|
|
ret = H5Dwrite(dataset3, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset3 succeeded");
|
|
|
|
/* release all temporary handles. */
|
|
/* Could have used them for dataset4 but it is cleaner */
|
|
/* to create them again.*/
|
|
H5Sclose(file_dataspace);
|
|
H5Sclose(mem_dataspace);
|
|
H5Pclose(xfer_plist);
|
|
|
|
/* Dataset4: each process writes no data, except process zero uses "all" selection. */
|
|
/* Additionally, these are in a scalar dataspace */
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space (dataset4);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
if (MAINPROCESS) {
|
|
ret=H5Sselect_none(file_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_all file_dataspace succeeded");
|
|
} /* end if */
|
|
else {
|
|
ret=H5Sselect_all(file_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_none succeeded");
|
|
} /* end else */
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate(H5S_SCALAR);
|
|
VRFY((mem_dataspace >= 0), "");
|
|
if (MAINPROCESS) {
|
|
ret=H5Sselect_none(mem_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_all mem_dataspace succeeded");
|
|
} /* end if */
|
|
else {
|
|
ret=H5Sselect_all(mem_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_none succeeded");
|
|
} /* end else */
|
|
|
|
/* fill the local slab with some trivial data */
|
|
dataset_fill(start, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
} /* end if */
|
|
|
|
/* 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 with scalar dataspace");
|
|
ret = H5Dwrite(dataset4, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset4 succeeded");
|
|
|
|
/* write data collectively (with datatype conversion) */
|
|
MESG("writeAll with scalar dataspace");
|
|
ret = H5Dwrite(dataset4, H5T_NATIVE_UCHAR, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset4 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");
|
|
ret=H5Dclose(dataset3);
|
|
VRFY((ret >= 0), "H5Dclose3 succeeded");
|
|
ret=H5Dclose(dataset4);
|
|
VRFY((ret >= 0), "H5Dclose3 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 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(void)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* 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 */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
DATATYPE *data_array1 = NULL; /* data buffer */
|
|
DATATYPE *data_origin1 = NULL; /* expected data buffer */
|
|
const char *filename;
|
|
|
|
hsize_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;
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
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, use_gpfs);
|
|
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, block, data_origin1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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_MED)
|
|
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, block, data_origin1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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_MED)
|
|
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(void)
|
|
{
|
|
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 */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
const char *filename;
|
|
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 */
|
|
|
|
hsize_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 mpi_size, mpi_rank;
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
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, use_gpfs);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* Reduce the number of metadata cache slots, so that there are cache
|
|
* collisions during the raw data I/O on the chunked dataset. This stresses
|
|
* the metadata cache and tests for cache bugs. -QAK
|
|
*/
|
|
{
|
|
int mdc_nelmts;
|
|
size_t rdcc_nelmts;
|
|
size_t rdcc_nbytes;
|
|
double rdcc_w0;
|
|
|
|
ret=H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0);
|
|
VRFY((ret >= 0), "H5Pget_cache succeeded");
|
|
mdc_nelmts=4;
|
|
ret=H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0);
|
|
VRFY((ret >= 0), "H5Pset_cache 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_MED)
|
|
printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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 create an extendable dataset
|
|
* and perform I/O on it in a way that verifies that the chunk cache is
|
|
* bypassed for parallel I/O.
|
|
*/
|
|
|
|
void
|
|
extend_writeInd2(void)
|
|
{
|
|
const char *filename;
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t fapl; /* File access templates */
|
|
hid_t fs; /* File dataspace ID */
|
|
hid_t ms; /* Memory dataspace ID */
|
|
hid_t dataset; /* Dataset ID */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
hsize_t orig_size=10; /* Original dataset dim size */
|
|
hsize_t new_size=20; /* Extended dataset dim size */
|
|
hsize_t one=1;
|
|
hsize_t max_size = H5S_UNLIMITED; /* dataset maximum dim size */
|
|
hsize_t chunk_size = 16384; /* chunk size */
|
|
hid_t dcpl; /* dataset create prop. list */
|
|
int written[10], /* Data to write */
|
|
retrieved[10]; /* Data read in */
|
|
int mpi_size, mpi_rank; /* MPI settings */
|
|
int i; /* Local index variable */
|
|
herr_t ret; /* Generic return value */
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
printf("Extend independent write test #2 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);
|
|
|
|
/* -------------------
|
|
* START AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
|
|
VRFY((fapl >= 0), "create_faccess_plist succeeded");
|
|
|
|
/* create the file collectively */
|
|
fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,fapl);
|
|
VRFY((fid >= 0), "H5Fcreate succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret=H5Pclose(fapl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
|
|
|
|
/* --------------------------------------------------------------
|
|
* Define the dimensions of the overall datasets and create them.
|
|
* ------------------------------------------------------------- */
|
|
|
|
/* set up dataset storage chunk sizes and creation property list */
|
|
dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
|
VRFY((dcpl >= 0), "H5Pcreate succeeded");
|
|
ret = H5Pset_chunk(dcpl, 1, &chunk_size);
|
|
VRFY((ret >= 0), "H5Pset_chunk succeeded");
|
|
|
|
/* setup dimensionality object */
|
|
fs = H5Screate_simple (1, &orig_size, &max_size);
|
|
VRFY((fs >= 0), "H5Screate_simple succeeded");
|
|
|
|
/* create an extendible dataset collectively */
|
|
dataset = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, fs, dcpl);
|
|
VRFY((dataset >= 0), "H5Dcreate succeeded");
|
|
|
|
/* release resource */
|
|
ret=H5Pclose(dcpl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
|
|
|
|
/* -------------------------
|
|
* Test writing to dataset
|
|
* -------------------------*/
|
|
/* create a memory dataspace independently */
|
|
ms = H5Screate_simple(1, &orig_size, &max_size);
|
|
VRFY((ms >= 0), "H5Screate_simple succeeded");
|
|
|
|
/* put some trivial data in the data_array */
|
|
for (i=0; i<(int)orig_size; i++)
|
|
written[i] = i;
|
|
MESG("data array initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("writing at offset zero: ");
|
|
for (i=0; i<(int)orig_size; i++)
|
|
printf("%s%d", i?", ":"", written[i]);
|
|
printf("\n");
|
|
}
|
|
ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
|
|
/* -------------------------
|
|
* Read initial data from dataset.
|
|
* -------------------------*/
|
|
ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved);
|
|
VRFY((ret >= 0), "H5Dread succeeded");
|
|
for (i=0; i<(int)orig_size; i++)
|
|
if(written[i]!=retrieved[i]) {
|
|
printf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__,
|
|
i,written[i], i,retrieved[i]);
|
|
nerrors++;
|
|
}
|
|
if (VERBOSE_MED){
|
|
MESG("read at offset zero: ");
|
|
for (i=0; i<(int)orig_size; i++)
|
|
printf("%s%d", i?", ":"", retrieved[i]);
|
|
printf("\n");
|
|
}
|
|
|
|
/* -------------------------
|
|
* Extend the dataset & retrieve new dataspace
|
|
* -------------------------*/
|
|
ret =H5Dextend(dataset, &new_size);
|
|
VRFY((ret >= 0), "H5Dextend succeeded");
|
|
ret=H5Sclose(fs);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
fs = H5Dget_space(dataset);
|
|
VRFY((fs >= 0), "H5Dget_space succeeded");
|
|
|
|
/* -------------------------
|
|
* Write to the second half of the dataset
|
|
* -------------------------*/
|
|
for (i=0; i<(int)orig_size; i++)
|
|
written[i] = orig_size + i;
|
|
MESG("data array re-initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("writing at offset 10: ");
|
|
for (i=0; i<(int)orig_size; i++)
|
|
printf("%s%d", i?", ":"", written[i]);
|
|
printf("\n");
|
|
}
|
|
ret = H5Sselect_hyperslab(fs, H5S_SELECT_SET, &orig_size, NULL, &one, &orig_size);
|
|
VRFY((ret >= 0), "H5Sselect_hyperslab succeeded");
|
|
ret = H5Dwrite(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, written);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
|
|
/* -------------------------
|
|
* Read the new data
|
|
* -------------------------*/
|
|
ret = H5Dread(dataset, H5T_NATIVE_INT, ms, fs, H5P_DEFAULT, retrieved);
|
|
VRFY((ret >= 0), "H5Dread succeeded");
|
|
for (i=0; i<(int)orig_size; i++)
|
|
if(written[i]!=retrieved[i]) {
|
|
printf("Line #%d: written!=retrieved: written[%d]=%d, retrieved[%d]=%d\n",__LINE__,
|
|
i,written[i], i,retrieved[i]);
|
|
nerrors++;
|
|
}
|
|
if (VERBOSE_MED){
|
|
MESG("read at offset 10: ");
|
|
for (i=0; i<(int)orig_size; i++)
|
|
printf("%s%d", i?", ":"", retrieved[i]);
|
|
printf("\n");
|
|
}
|
|
|
|
|
|
/* Close dataset collectively */
|
|
ret=H5Dclose(dataset);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
|
|
/* Close the file collectively */
|
|
ret = H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
}
|
|
|
|
/* Example of using the parallel HDF5 library to read an extendible dataset */
|
|
void
|
|
extend_readInd(void)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* File access templates */
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* memory dataspace ID */
|
|
hid_t dataset1, dataset2; /* Dataset ID */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
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 */
|
|
const char *filename;
|
|
|
|
hsize_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;
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
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, use_gpfs);
|
|
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, block, data_origin1);
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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, block, data_origin1);
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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);
|
|
}
|
|
|
|
/*
|
|
* Part 3--Collective read/write for extendible datasets.
|
|
*/
|
|
|
|
/*
|
|
* Example of using the parallel HDF5 library to create two extendible
|
|
* datasets in one HDF5 file with collective 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_writeAll(void)
|
|
{
|
|
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 */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
const char *filename;
|
|
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 */
|
|
|
|
hsize_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 mpi_size, mpi_rank;
|
|
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
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, use_gpfs);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* Reduce the number of metadata cache slots, so that there are cache
|
|
* collisions during the raw data I/O on the chunked dataset. This stresses
|
|
* the metadata cache and tests for cache bugs. -QAK
|
|
*/
|
|
{
|
|
int mdc_nelmts;
|
|
size_t rdcc_nelmts;
|
|
size_t rdcc_nbytes;
|
|
double rdcc_w0;
|
|
|
|
ret=H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0);
|
|
VRFY((ret >= 0), "H5Pget_cache succeeded");
|
|
mdc_nelmts=4;
|
|
ret=H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0);
|
|
VRFY((ret >= 0), "H5Pset_cache 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_MED)
|
|
printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, 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");
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
|
|
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* write data collectively */
|
|
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
|
|
/* release resource */
|
|
H5Sclose(file_dataspace);
|
|
H5Sclose(mem_dataspace);
|
|
H5Pclose(xfer_plist);
|
|
|
|
|
|
/* -------------------------
|
|
* 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, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
}
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, block, NULL);
|
|
VRFY((mem_dataspace >= 0), "");
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
|
|
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* 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,
|
|
xfer_plist, 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,
|
|
xfer_plist, 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");
|
|
ret=H5Pclose(xfer_plist);
|
|
VRFY((ret >= 0), "H5Pclose 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_readAll(void)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* 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 */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
const char *filename;
|
|
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 */
|
|
|
|
hsize_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;
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
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, use_gpfs);
|
|
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, block, data_origin1);
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
|
|
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* read data collectively */
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, 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);
|
|
H5Pclose(xfer_plist);
|
|
|
|
|
|
/* 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, block, data_origin1);
|
|
if (VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
}
|
|
|
|
/* set up the collective transfer properties list */
|
|
xfer_plist = H5Pcreate (H5P_DATASET_XFER);
|
|
VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded");
|
|
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* read data collectively */
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, 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);
|
|
H5Pclose(xfer_plist);
|
|
|
|
/* 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);
|
|
}
|
|
|
|
/*
|
|
* Example of using the parallel HDF5 library to read a compressed
|
|
* dataset in an HDF5 file with collective parallel access support.
|
|
*/
|
|
|
|
#ifdef H5_HAVE_FILTER_DEFLATE
|
|
void
|
|
compress_readAll(void)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* File access templates */
|
|
hid_t dcpl; /* Dataset creation property list */
|
|
hid_t xfer_plist; /* Dataset transfer properties list */
|
|
hid_t dataspace; /* Dataspace ID */
|
|
hid_t dataset; /* Dataset ID */
|
|
int rank=1; /* Dataspace rank */
|
|
hsize_t dim=dim0; /* Dataspace dimensions */
|
|
unsigned u; /* Local index variable */
|
|
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
|
|
DATATYPE *data_read = NULL; /* data buffer */
|
|
DATATYPE *data_orig = NULL; /* expected data buffer */
|
|
const char *filename;
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
int mpi_size, mpi_rank;
|
|
herr_t ret; /* Generic return value */
|
|
|
|
filename = GetTestParameters();
|
|
if (VERBOSE_MED)
|
|
printf("Collective chunked dataset read test on file %s\n", filename);
|
|
|
|
/* Retrieve MPI parameters */
|
|
MPI_Comm_size(comm,&mpi_size);
|
|
MPI_Comm_rank(comm,&mpi_rank);
|
|
|
|
/* Allocate data buffer */
|
|
data_orig = (DATATYPE *)HDmalloc((size_t)dim*sizeof(DATATYPE));
|
|
VRFY((data_orig != NULL), "data_origin1 malloc succeeded");
|
|
data_read = (DATATYPE *)HDmalloc((size_t)dim*sizeof(DATATYPE));
|
|
VRFY((data_read != NULL), "data_array1 malloc succeeded");
|
|
|
|
/* Initialize data buffers */
|
|
for(u=0; u<dim;u++)
|
|
data_orig[u]=u;
|
|
|
|
/* Process zero creates the file with a compressed, chunked dataset */
|
|
if(mpi_rank==0) {
|
|
hsize_t chunk_dim; /* Chunk dimensions */
|
|
|
|
/* Create the file */
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((fid > 0), "H5Fcreate succeeded");
|
|
|
|
/* Create property list for chunking and compression */
|
|
dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
|
VRFY((dcpl > 0), "H5Pcreate succeeded");
|
|
|
|
ret=H5Pset_layout(dcpl, H5D_CHUNKED);
|
|
VRFY((ret >= 0), "H5Pset_layout succeeded");
|
|
|
|
/* Use eight chunks */
|
|
chunk_dim=dim/8;
|
|
ret=H5Pset_chunk(dcpl, rank, &chunk_dim);
|
|
VRFY((ret >= 0), "H5Pset_chunk succeeded");
|
|
|
|
ret=H5Pset_deflate(dcpl, 9);
|
|
VRFY((ret >= 0), "H5Pset_deflate succeeded");
|
|
|
|
/* Create dataspace */
|
|
dataspace = H5Screate_simple(rank, &dim, NULL);
|
|
VRFY((dataspace > 0), "H5Screate_simple succeeded");
|
|
|
|
/* Create dataset */
|
|
dataset = H5Dcreate(fid, "compressed_data", H5T_NATIVE_INT, dataspace, dcpl);
|
|
VRFY((dataset > 0), "H5Screate_simple succeeded");
|
|
|
|
/* Write compressed data */
|
|
ret=H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_orig);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
|
|
/* Close objects */
|
|
ret=H5Pclose(dcpl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret=H5Sclose(dataspace);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
ret=H5Dclose(dataset);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
ret=H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
}
|
|
|
|
/* Wait for file to be created */
|
|
MPI_Barrier(comm);
|
|
|
|
/* -------------------
|
|
* OPEN AN HDF5 FILE
|
|
* -------------------*/
|
|
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* open the file collectively */
|
|
fid=H5Fopen(filename,H5F_ACC_RDWR,acc_tpl);
|
|
VRFY((fid > 0), "H5Fopen succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret=H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
|
|
|
|
/* Open dataset with compressed chunks */
|
|
dataset = H5Dopen(fid, "compressed_data");
|
|
VRFY((dataset > 0), "H5Dopen succeeded");
|
|
|
|
/* Try reading & writing data */
|
|
if(dataset>0) {
|
|
/* Create dataset transfer property list */
|
|
xfer_plist = H5Pcreate(H5P_DATASET_XFER);
|
|
VRFY((xfer_plist > 0), "H5Pcreate succeeded");
|
|
|
|
ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* Try reading the data */
|
|
ret=H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* Verify data read */
|
|
for(u=0; u<dim; u++)
|
|
if(data_orig[u]!=data_read[u]) {
|
|
printf("Line #%d: written!=retrieved: data_orig[%u]=%d, data_read[%u]=%d\n",__LINE__,
|
|
(unsigned)u,data_orig[u],(unsigned)u,data_read[u]);
|
|
nerrors++;
|
|
}
|
|
|
|
/* Writing to the compressed, chunked dataset in parallel should fail */
|
|
H5E_BEGIN_TRY {
|
|
ret=H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read);
|
|
} H5E_END_TRY;
|
|
VRFY((ret < 0), "H5Dwrite failed");
|
|
|
|
ret=H5Pclose(xfer_plist);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret=H5Dclose(dataset);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
} /* end if */
|
|
|
|
ret=H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
|
|
/* release data buffers */
|
|
if (data_read) HDfree(data_read);
|
|
if (data_orig) HDfree(data_orig);
|
|
}
|
|
#endif /* H5_HAVE_FILTER_DEFLATE */
|
|
|