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bdd7d59902
Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
2501 lines
86 KiB
C
2501 lines
86 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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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 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid,
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H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
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/* create another dataset collectively */
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dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid,
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H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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VRFY((dataset2 >= 0), "H5Dcreate2 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 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
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VRFY((dataset1 >= 0), "");
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/* open another dataset collectively */
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dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
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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 */
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ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
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H5P_DEFAULT, data_array1);
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VRFY((ret >= 0), "");
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/* verify the read data with original expected data */
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ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
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if(ret) nerrors++;
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/* 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 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
/* create another dataset collectively */
|
|
datatype = H5Tcopy(H5T_NATIVE_INT);
|
|
ret = H5Tset_order(datatype, H5T_ORDER_LE);
|
|
VRFY((ret >= 0), "H5Tset_order succeeded");
|
|
|
|
dataset2 = H5Dcreate2(fid, DATASETNAME2, datatype, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dcreate2 2 succeeded");
|
|
|
|
/* create a third dataset collectively */
|
|
dataset3 = H5Dcreate2(fid, DATASETNAME3, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset3 >= 0), "H5Dcreate2 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 = H5Dcreate2(fid, DATASETNAME4, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset4 >= 0), "H5Dcreate2 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dopen2 succeeded");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen2(fid, DATASETNAME2, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dopen2 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
/* create another extendible dataset collectively */
|
|
dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dcreate2 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 = H5Dset_extent(dataset1, dims);
|
|
VRFY((ret >= 0), "H5Dset_extent 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_auto2(H5E_DEFAULT, &old_func, &old_client_data);
|
|
H5Eset_auto2(H5E_DEFAULT, 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_auto2(H5E_DEFAULT, old_func, old_client_data);
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* Extend dataset2 and try again. Should succeed. */
|
|
dims[0] = dim0;
|
|
dims[1] = dim1;
|
|
ret = H5Dset_extent(dataset2, dims);
|
|
VRFY((ret >= 0), "H5Dset_extent 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 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, fs, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
VRFY((dataset >= 0), "H5Dcreat2e 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 = H5Dset_extent(dataset, &new_size);
|
|
VRFY((ret >= 0), "H5Dset_extent 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 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "");
|
|
|
|
/* Try extend dataset1 which is open RDONLY. Should fail. */
|
|
/* first turn off auto error reporting */
|
|
H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data);
|
|
H5Eset_auto2(H5E_DEFAULT, 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 = H5Dset_extent(dataset1, dims);
|
|
VRFY((ret < 0), "H5Dset_extent failed as expected");
|
|
|
|
/* restore auto error reporting */
|
|
H5Eset_auto2(H5E_DEFAULT, 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 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
/* create another extendible dataset collectively */
|
|
dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dcreate2 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 = H5Dset_extent(dataset1, dims);
|
|
VRFY((ret >= 0), "H5Dset_extent 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively succeeded");
|
|
}
|
|
|
|
|
|
/* Try write to dataset2 beyond its current dim sizes. Should fail. */
|
|
/* Temporary turn off auto error reporting */
|
|
H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data);
|
|
H5Eset_auto2(H5E_DEFAULT, 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_auto2(H5E_DEFAULT, old_func, old_client_data);
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* Extend dataset2 and try again. Should succeed. */
|
|
dims[0] = dim0;
|
|
dims[1] = dim1;
|
|
ret = H5Dset_extent(dataset2, dims);
|
|
VRFY((ret >= 0), "H5Dset_extent 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 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "");
|
|
|
|
/* Try extend dataset1 which is open RDONLY. Should fail. */
|
|
/* first turn off auto error reporting */
|
|
H5Eget_auto2(H5E_DEFAULT, &old_func, &old_client_data);
|
|
H5Eset_auto2(H5E_DEFAULT, 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 = H5Dset_extent(dataset1, dims);
|
|
VRFY((ret < 0), "H5Dset_extent failed as expected");
|
|
|
|
/* restore auto error reporting */
|
|
H5Eset_auto2(H5E_DEFAULT, 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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(h5_rmprefix(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 = H5Dcreate2(fid, "compressed_data", H5T_NATIVE_INT, dataspace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
VRFY((dataset > 0), "H5Dcreate2 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 = H5Dopen2(fid, "compressed_data", H5P_DEFAULT);
|
|
VRFY((dataset > 0), "H5Dopen2 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");
|
|
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
|
|
ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO);
|
|
VRFY((ret>= 0),"set independent IO collectively 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 */
|
|
|
|
/*
|
|
* Part 4--Non-selection for chunked dataset
|
|
*/
|
|
|
|
/*
|
|
* Example of using the parallel HDF5 library to create chunked
|
|
* dataset in one HDF5 file with collective and independent parallel
|
|
* MPIO access support. The Datasets are of sizes dim0 x dim1.
|
|
* Each process controls only a slab of size dim0 x dim1 within the
|
|
* dataset with the exception that one processor selects no element.
|
|
*/
|
|
|
|
void
|
|
none_selection_chunk(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 */
|
|
DATATYPE *data_origin = NULL; /* data buffer */
|
|
DATATYPE *data_array = 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 */
|
|
hsize_t mstart[RANK]; /* for data buffer in memory */
|
|
|
|
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;
|
|
|
|
/* -------------------
|
|
* 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 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 */
|
|
dims[0] = dim0;
|
|
dims[1] = dim1;
|
|
sid = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((sid >= 0), "H5Screate_simple succeeded");
|
|
|
|
/* create an extendible dataset collectively */
|
|
dataset1 = H5Dcreate2(fid, DATASETNAME1, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
/* create another extendible dataset collectively */
|
|
dataset2 = H5Dcreate2(fid, DATASETNAME2, H5T_NATIVE_INT, sid, H5P_DEFAULT, dataset_pl, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
/* release resource */
|
|
H5Sclose(sid);
|
|
H5Pclose(dataset_pl);
|
|
|
|
/* -------------------------
|
|
* Test collective writing to dataset1
|
|
* -------------------------*/
|
|
/* set up dimensions of the slab this process accesses */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
/* allocate memory for data buffer. Only allocate enough buffer for
|
|
* each processor's data. */
|
|
if(mpi_rank) {
|
|
data_origin = (DATATYPE *)malloc(block[0]*block[1]*sizeof(DATATYPE));
|
|
VRFY((data_origin != NULL), "data_origin malloc succeeded");
|
|
|
|
data_array = (DATATYPE *)malloc(block[0]*block[1]*sizeof(DATATYPE));
|
|
VRFY((data_array != NULL), "data_array malloc succeeded");
|
|
|
|
/* put some trivial data in the data_array */
|
|
mstart[0] = mstart[1] = 0;
|
|
dataset_fill(mstart, block, data_origin);
|
|
MESG("data_array initialized");
|
|
if(VERBOSE_MED){
|
|
MESG("data_array created");
|
|
dataset_print(mstart, block, data_origin);
|
|
}
|
|
}
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple (RANK, block, NULL);
|
|
VRFY((mem_dataspace >= 0), "");
|
|
|
|
/* Process 0 has no selection */
|
|
if(!mpi_rank) {
|
|
ret = H5Sselect_none(mem_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_none 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");
|
|
|
|
/* Process 0 has no selection */
|
|
if(!mpi_rank) {
|
|
ret = H5Sselect_none(file_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_none 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_origin);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* verify the read data with original expected data */
|
|
if(mpi_rank) {
|
|
ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin);
|
|
if(ret) nerrors++;
|
|
}
|
|
|
|
/* -------------------------
|
|
* Test independent writing to dataset2
|
|
* -------------------------*/
|
|
ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* write data collectively */
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
xfer_plist, data_origin);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace,
|
|
H5P_DEFAULT, data_array);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* verify the read data with original expected data */
|
|
if(mpi_rank) {
|
|
ret = dataset_vrfy(mstart, count, stride, block, data_array, data_origin);
|
|
if(ret) nerrors++;
|
|
}
|
|
|
|
/* 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_origin) free(data_origin);
|
|
if(data_array) free(data_array);
|
|
}
|