mirror of
https://github.com/HDFGroup/hdf5.git
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174505ca3c
* Fix typos found in the rest of the hdf5 code-base
* Typo in tool.cmake
* Revert "Typo in tool.cmake"
This reverts commit 06b8403d99.
* Fix clang-format styling
4149 lines
156 KiB
C
4149 lines
156 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 COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* 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[], hsize_t stride[], hsize_t block[],
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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] = (hsize_t)(dim0 / mpi_size);
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block[1] = (hsize_t)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] = (hsize_t)mpi_rank * block[0];
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start[1] = 0;
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if (VERBOSE_MED)
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HDprintf("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] = (hsize_t)dim0;
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block[1] = (hsize_t)(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] = (hsize_t)mpi_rank * block[1];
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if (VERBOSE_MED)
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HDprintf("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] = (hsize_t)(mpi_rank ? dim0 / mpi_size : 0);
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block[1] = (hsize_t)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 ? (hsize_t)mpi_rank * block[0] : 0);
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start[1] = 0;
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if (VERBOSE_MED)
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HDprintf("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] = (hsize_t)dim0;
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block[1] = (hsize_t)(mpi_rank ? dim1 / mpi_size : 0);
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stride[0] = block[0];
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stride[1] = (hsize_t)(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 ? (hsize_t)mpi_rank * block[1] : 0);
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if (VERBOSE_MED)
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HDprintf("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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HDprintf("unknown slab_set mode (%d)\n", mode);
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block[0] = (hsize_t)dim0;
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block[1] = (hsize_t)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)
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HDprintf("slab_set wholeset\n");
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break;
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}
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if (VERBOSE_MED) {
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HDprintf("start[]=(%lu,%lu), count[]=(%lu,%lu), stride[]=(%lu,%lu), block[]=(%lu,%lu), total "
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"datapoints=%lu\n",
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(unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0],
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(unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1],
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(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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* Setup the coordinates for point selection.
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*/
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void
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point_set(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], size_t num_points,
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hsize_t coords[], int order)
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{
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hsize_t i, j, k = 0, m, n, s1, s2;
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HDcompile_assert(RANK == 2);
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if (OUT_OF_ORDER == order)
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k = (num_points * RANK) - 1;
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else if (IN_ORDER == order)
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k = 0;
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s1 = start[0];
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s2 = start[1];
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for (i = 0; i < count[0]; i++)
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for (j = 0; j < count[1]; j++)
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for (m = 0; m < block[0]; m++)
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for (n = 0; n < block[1]; n++)
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if (OUT_OF_ORDER == order) {
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coords[k--] = s2 + (stride[1] * j) + n;
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coords[k--] = s1 + (stride[0] * i) + m;
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}
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else if (IN_ORDER == order) {
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coords[k++] = s1 + stride[0] * i + m;
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coords[k++] = s2 + stride[1] * j + n;
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}
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if (VERBOSE_MED) {
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HDprintf("start[]=(%lu, %lu), count[]=(%lu, %lu), stride[]=(%lu, %lu), block[]=(%lu, %lu), total "
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"datapoints=%lu\n",
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(unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0],
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(unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1],
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(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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k = 0;
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for (i = 0; i < num_points; i++) {
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HDprintf("(%d, %d)\n", (int)coords[k], (int)coords[k + 1]);
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k += 2;
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}
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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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HDprintf("%-8s", "Cols:");
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for (j = 0; j < block[1]; j++) {
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HDprintf("%3lu ", (unsigned long)(start[1] + j));
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}
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HDprintf("\n");
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/* print the slab data */
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for (i = 0; i < block[0]; i++) {
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HDprintf("Row %2lu: ", (unsigned long)(i + start[0]));
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for (j = 0; j < block[1]; j++) {
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HDprintf("%03d ", *dataptr++);
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}
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HDprintf("\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,
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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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HDprintf("dataset_vrfy dumping:::\n");
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HDprintf("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],
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(unsigned long)count[1], (unsigned long)stride[0], (unsigned long)stride[1],
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(unsigned long)block[0], (unsigned long)block[1]);
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HDprintf("original values:\n");
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dataset_print(start, block, original);
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HDprintf("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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HDprintf("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, (unsigned long)(i + start[0]),
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(unsigned long)(j + start[1]), *(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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HDprintf("[more errors ...]\n");
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if (vrfyerrs)
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HDprintf("%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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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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HDprintf("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 *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
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VRFY((data_array1 != NULL), "data_array1 HDmalloc 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);
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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] = (hsize_t)dim0;
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dims[1] = (hsize_t)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, 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, 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, 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, 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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HDprintf("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, 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)
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HDfree(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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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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HDprintf("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 *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
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VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
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|
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
|
|
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* open the file collectively */
|
|
fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl);
|
|
VRFY((fid >= 0), "");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* open the dataset1 collectively */
|
|
dataset1 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "");
|
|
|
|
/* open another dataset collectively */
|
|
dataset2 = H5Dopen2(fid, DATASETNAME1, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "");
|
|
|
|
/* set up dimensions of the slab this process accesses */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space(dataset1);
|
|
VRFY((file_dataspace >= 0), "");
|
|
ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* create a memory dataspace independently */
|
|
mem_dataspace = H5Screate_simple(RANK, block, NULL);
|
|
VRFY((mem_dataspace >= 0), "");
|
|
|
|
/* fill dataset with test data */
|
|
dataset_fill(start, block, data_origin1);
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* verify the read data with original expected data */
|
|
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
|
|
if (ret)
|
|
nerrors++;
|
|
|
|
/* read data independently */
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* verify the read data with original expected data */
|
|
ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1);
|
|
if (ret)
|
|
nerrors++;
|
|
|
|
/* close dataset collectively */
|
|
ret = H5Dclose(dataset1);
|
|
VRFY((ret >= 0), "");
|
|
ret = H5Dclose(dataset2);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* release all IDs created */
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
|
|
/* release data buffers */
|
|
if (data_array1)
|
|
HDfree(data_array1);
|
|
if (data_origin1)
|
|
HDfree(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 dataset5, dataset6, dataset7; /* Dataset ID */
|
|
hid_t datatype; /* Datatype ID */
|
|
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 */
|
|
|
|
size_t num_points; /* for point selection */
|
|
hsize_t *coords = NULL; /* for point selection */
|
|
hsize_t current_dims; /* for point selection */
|
|
|
|
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)
|
|
HDprintf("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);
|
|
|
|
/* set up the coords array selection */
|
|
num_points = (size_t)dim1;
|
|
coords = (hsize_t *)HDmalloc((size_t)dim1 * (size_t)RANK * sizeof(hsize_t));
|
|
VRFY((coords != NULL), "coords malloc succeeded");
|
|
|
|
/* allocate memory for data buffer */
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
|
|
|
|
/* -------------------
|
|
* START AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* create the file collectively */
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
|
|
VRFY((fid >= 0), "H5Fcreate succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* --------------------------
|
|
* Define the dimensions of the overall datasets
|
|
* and create the dataset
|
|
* ------------------------- */
|
|
/* setup 2-D dimensionality object */
|
|
dims[0] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)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");
|
|
|
|
dataset5 = H5Dcreate2(fid, DATASETNAME7, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset5 >= 0), "H5Dcreate2 succeeded");
|
|
dataset6 = H5Dcreate2(fid, DATASETNAME8, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset6 >= 0), "H5Dcreate2 succeeded");
|
|
dataset7 = H5Dcreate2(fid, DATASETNAME9, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset7 >= 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)
|
|
HDprintf("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)
|
|
HDprintf("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);
|
|
|
|
if (data_array1)
|
|
free(data_array1);
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
|
|
|
|
block[0] = 1;
|
|
block[1] = (hsize_t)dim1;
|
|
stride[0] = 1;
|
|
stride[1] = (hsize_t)dim1;
|
|
count[0] = 1;
|
|
count[1] = 1;
|
|
start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank);
|
|
start[1] = 0;
|
|
|
|
dataset_fill(start, block, data_array1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_array1);
|
|
}
|
|
|
|
/* Dataset5: point selection in File - Hyperslab selection in Memory*/
|
|
/* create a file dataspace independently */
|
|
point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER);
|
|
file_dataspace = H5Dget_space(dataset5);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
start[0] = 0;
|
|
start[1] = 0;
|
|
mem_dataspace = H5Dget_space(dataset5);
|
|
VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_hyperslab(mem_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), "");
|
|
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 */
|
|
ret = H5Dwrite(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset5 succeeded");
|
|
|
|
/* release all temporary handles. */
|
|
H5Sclose(file_dataspace);
|
|
H5Sclose(mem_dataspace);
|
|
H5Pclose(xfer_plist);
|
|
|
|
/* Dataset6: point selection in File - Point selection in Memory*/
|
|
/* create a file dataspace independently */
|
|
start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank);
|
|
start[1] = 0;
|
|
point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER);
|
|
file_dataspace = H5Dget_space(dataset6);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
start[0] = 0;
|
|
start[1] = 0;
|
|
point_set(start, count, stride, block, num_points, coords, IN_ORDER);
|
|
mem_dataspace = H5Dget_space(dataset6);
|
|
VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
/* 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 */
|
|
ret = H5Dwrite(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset6 succeeded");
|
|
|
|
/* release all temporary handles. */
|
|
H5Sclose(file_dataspace);
|
|
H5Sclose(mem_dataspace);
|
|
H5Pclose(xfer_plist);
|
|
|
|
/* Dataset7: point selection in File - All selection in Memory*/
|
|
/* create a file dataspace independently */
|
|
start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank);
|
|
start[1] = 0;
|
|
point_set(start, count, stride, block, num_points, coords, IN_ORDER);
|
|
file_dataspace = H5Dget_space(dataset7);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
current_dims = num_points;
|
|
mem_dataspace = H5Screate_simple(1, ¤t_dims, NULL);
|
|
VRFY((mem_dataspace >= 0), "mem_dataspace create succeeded");
|
|
|
|
ret = H5Sselect_all(mem_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_all succeeded");
|
|
|
|
/* 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 */
|
|
ret = H5Dwrite(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dwrite dataset7 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), "H5Dclose4 succeeded");
|
|
ret = H5Dclose(dataset5);
|
|
VRFY((ret >= 0), "H5Dclose5 succeeded");
|
|
ret = H5Dclose(dataset6);
|
|
VRFY((ret >= 0), "H5Dclose6 succeeded");
|
|
ret = H5Dclose(dataset7);
|
|
VRFY((ret >= 0), "H5Dclose7 succeeded");
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
|
|
/* release data buffers */
|
|
if (coords)
|
|
HDfree(coords);
|
|
if (data_array1)
|
|
HDfree(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, dataset5, dataset6, dataset7; /* Dataset ID */
|
|
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 */
|
|
|
|
size_t num_points; /* for point selection */
|
|
hsize_t *coords = NULL; /* for point selection */
|
|
int i, j, k;
|
|
|
|
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)
|
|
HDprintf("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);
|
|
|
|
/* set up the coords array selection */
|
|
num_points = (size_t)dim1;
|
|
coords = (hsize_t *)HDmalloc((size_t)dim0 * (size_t)dim1 * RANK * sizeof(hsize_t));
|
|
VRFY((coords != NULL), "coords malloc succeeded");
|
|
|
|
/* allocate memory for data buffer */
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
|
|
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
|
|
|
|
/* -------------------
|
|
* OPEN AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* open the file collectively */
|
|
fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl);
|
|
VRFY((fid >= 0), "H5Fopen succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* --------------------------
|
|
* Open the datasets in it
|
|
* ------------------------- */
|
|
/* open the dataset1 collectively */
|
|
dataset1 = 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");
|
|
|
|
/* open another dataset collectively */
|
|
dataset5 = H5Dopen2(fid, DATASETNAME7, H5P_DEFAULT);
|
|
VRFY((dataset5 >= 0), "H5Dopen2 5 succeeded");
|
|
dataset6 = H5Dopen2(fid, DATASETNAME8, H5P_DEFAULT);
|
|
VRFY((dataset6 >= 0), "H5Dopen2 6 succeeded");
|
|
dataset7 = H5Dopen2(fid, DATASETNAME9, H5P_DEFAULT);
|
|
VRFY((dataset7 >= 0), "H5Dopen2 7 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)
|
|
HDprintf("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)
|
|
HDprintf("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);
|
|
|
|
if (data_array1)
|
|
free(data_array1);
|
|
if (data_origin1)
|
|
free(data_origin1);
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
|
|
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded");
|
|
|
|
block[0] = 1;
|
|
block[1] = (hsize_t)dim1;
|
|
stride[0] = 1;
|
|
stride[1] = (hsize_t)dim1;
|
|
count[0] = 1;
|
|
count[1] = 1;
|
|
start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank);
|
|
start[1] = 0;
|
|
|
|
dataset_fill(start, block, data_origin1);
|
|
MESG("data_array initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("data_array created");
|
|
dataset_print(start, block, data_origin1);
|
|
}
|
|
|
|
/* Dataset5: point selection in memory - Hyperslab selection in file*/
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space(dataset5);
|
|
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");
|
|
|
|
start[0] = 0;
|
|
start[1] = 0;
|
|
point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER);
|
|
mem_dataspace = H5Dget_space(dataset5);
|
|
VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
/* 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(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dread dataset5 succeeded");
|
|
|
|
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);
|
|
|
|
if (data_array1)
|
|
free(data_array1);
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
|
|
|
|
/* Dataset6: point selection in File - Point selection in Memory*/
|
|
/* create a file dataspace independently */
|
|
start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank);
|
|
start[1] = 0;
|
|
point_set(start, count, stride, block, num_points, coords, IN_ORDER);
|
|
file_dataspace = H5Dget_space(dataset6);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
start[0] = 0;
|
|
start[1] = 0;
|
|
point_set(start, count, stride, block, num_points, coords, OUT_OF_ORDER);
|
|
mem_dataspace = H5Dget_space(dataset6);
|
|
VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
/* 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(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dread dataset6 succeeded");
|
|
|
|
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);
|
|
|
|
if (data_array1)
|
|
free(data_array1);
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 malloc succeeded");
|
|
|
|
/* Dataset7: point selection in memory - All selection in file*/
|
|
/* create a file dataspace independently */
|
|
file_dataspace = H5Dget_space(dataset7);
|
|
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_all(file_dataspace);
|
|
VRFY((ret >= 0), "H5Sselect_all succeeded");
|
|
|
|
num_points = (size_t)(dim0 * dim1);
|
|
k = 0;
|
|
for (i = 0; i < dim0; i++) {
|
|
for (j = 0; j < dim1; j++) {
|
|
coords[k++] = (hsize_t)i;
|
|
coords[k++] = (hsize_t)j;
|
|
}
|
|
}
|
|
mem_dataspace = H5Dget_space(dataset7);
|
|
VRFY((mem_dataspace >= 0), "H5Dget_space succeeded");
|
|
ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords);
|
|
VRFY((ret >= 0), "H5Sselect_elements succeeded");
|
|
|
|
/* 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(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
VRFY((ret >= 0), "H5Dread dataset7 succeeded");
|
|
|
|
start[0] = (hsize_t)(dim0 / mpi_size * mpi_rank);
|
|
start[1] = 0;
|
|
ret = dataset_vrfy(start, count, stride, block, data_array1 + (dim0 / mpi_size * dim1 * mpi_rank),
|
|
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");
|
|
ret = H5Dclose(dataset5);
|
|
VRFY((ret >= 0), "H5Dclose5 succeeded");
|
|
ret = H5Dclose(dataset6);
|
|
VRFY((ret >= 0), "H5Dclose6 succeeded");
|
|
ret = H5Dclose(dataset7);
|
|
VRFY((ret >= 0), "H5Dclose7 succeeded");
|
|
|
|
/* close the file collectively */
|
|
H5Fclose(fid);
|
|
|
|
/* release data buffers */
|
|
if (coords)
|
|
HDfree(coords);
|
|
if (data_array1)
|
|
HDfree(data_array1);
|
|
if (data_origin1)
|
|
HDfree(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 */
|
|
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)
|
|
HDprintf("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] = (hsize_t)chunkdim0;
|
|
chunk_dims[1] = (hsize_t)chunkdim1;
|
|
|
|
/* allocate memory for data buffer */
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
|
|
|
|
/* -------------------
|
|
* START AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
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)
|
|
HDprintf("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] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)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. */
|
|
|
|
/* 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. */
|
|
H5E_BEGIN_TRY
|
|
{
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, data_array1);
|
|
}
|
|
H5E_END_TRY
|
|
VRFY((ret < 0), "H5Dwrite failed as expected");
|
|
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* Extend dataset2 and try again. Should succeed. */
|
|
dims[0] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)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)
|
|
HDfree(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 */
|
|
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)
|
|
HDprintf("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);
|
|
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++)
|
|
HDprintf("%s%d", i ? ", " : "", written[i]);
|
|
HDprintf("\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]) {
|
|
HDprintf("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++)
|
|
HDprintf("%s%d", i ? ", " : "", retrieved[i]);
|
|
HDprintf("\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
|
|
* -------------------------*/
|
|
H5_CHECK_OVERFLOW(orig_size, hsize_t, int);
|
|
for (i = 0; i < (int)orig_size; i++)
|
|
written[i] = (int)orig_size + i;
|
|
MESG("data array re-initialized");
|
|
if (VERBOSE_MED) {
|
|
MESG("writing at offset 10: ");
|
|
for (i = 0; i < (int)orig_size; i++)
|
|
HDprintf("%s%d", i ? ", " : "", written[i]);
|
|
HDprintf("\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]) {
|
|
HDprintf("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++)
|
|
HDprintf("%s%d", i ? ", " : "", retrieved[i]);
|
|
HDprintf("\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 */
|
|
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)
|
|
HDprintf("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 *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
|
|
data_array2 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded");
|
|
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
|
|
|
|
/* -------------------
|
|
* OPEN AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* open the file collectively */
|
|
fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl);
|
|
VRFY((fid >= 0), "");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* open the dataset1 collectively */
|
|
dataset1 = 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. */
|
|
|
|
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]++;
|
|
H5E_BEGIN_TRY
|
|
{
|
|
ret = H5Dset_extent(dataset1, dims);
|
|
}
|
|
H5E_END_TRY
|
|
VRFY((ret < 0), "H5Dset_extent failed as expected");
|
|
|
|
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)
|
|
HDfree(data_array1);
|
|
if (data_array2)
|
|
HDfree(data_array2);
|
|
if (data_origin1)
|
|
HDfree(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 */
|
|
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)
|
|
HDprintf("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] = (hsize_t)chunkdim0;
|
|
chunk_dims[1] = (hsize_t)chunkdim1;
|
|
|
|
/* allocate memory for data buffer */
|
|
data_array1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
|
|
|
|
/* -------------------
|
|
* START AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
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)
|
|
HDprintf("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] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)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. */
|
|
|
|
/* 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. */
|
|
H5E_BEGIN_TRY
|
|
{
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1);
|
|
}
|
|
H5E_END_TRY
|
|
VRFY((ret < 0), "H5Dwrite failed as expected");
|
|
|
|
H5Sclose(file_dataspace);
|
|
|
|
/* Extend dataset2 and try again. Should succeed. */
|
|
dims[0] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)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)
|
|
HDfree(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 */
|
|
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)
|
|
HDprintf("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 *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array1 != NULL), "data_array1 HDmalloc succeeded");
|
|
data_array2 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_array2 != NULL), "data_array2 HDmalloc succeeded");
|
|
data_origin1 = (DATATYPE *)HDmalloc((size_t)dim0 * (size_t)dim1 * sizeof(DATATYPE));
|
|
VRFY((data_origin1 != NULL), "data_origin1 HDmalloc succeeded");
|
|
|
|
/* -------------------
|
|
* OPEN AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* open the file collectively */
|
|
fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl);
|
|
VRFY((fid >= 0), "");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* open the dataset1 collectively */
|
|
dataset1 = 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. */
|
|
|
|
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]++;
|
|
H5E_BEGIN_TRY
|
|
{
|
|
ret = H5Dset_extent(dataset1, dims);
|
|
}
|
|
H5E_END_TRY
|
|
VRFY((ret < 0), "H5Dset_extent failed as expected");
|
|
|
|
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)
|
|
HDfree(data_array1);
|
|
if (data_array2)
|
|
HDfree(data_array2);
|
|
if (data_origin1)
|
|
HDfree(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 = (hsize_t)dim0; /* Dataspace dimensions */
|
|
unsigned u; /* Local index variable */
|
|
unsigned chunk_opts; /* Chunk options */
|
|
unsigned disable_partial_chunk_filters; /* Whether filters are disabled on partial chunks */
|
|
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)
|
|
HDprintf("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 HDmalloc succeeded");
|
|
data_read = (DATATYPE *)HDmalloc((size_t)dim * sizeof(DATATYPE));
|
|
VRFY((data_read != NULL), "data_array1 HDmalloc succeeded");
|
|
|
|
/* Initialize data buffers */
|
|
for (u = 0; u < dim; u++)
|
|
data_orig[u] = (DATATYPE)u;
|
|
|
|
/* Run test both with and without filters disabled on partial chunks */
|
|
for (disable_partial_chunk_filters = 0; disable_partial_chunk_filters <= 1;
|
|
disable_partial_chunk_filters++) {
|
|
/* 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");
|
|
|
|
/* Set chunk options appropriately */
|
|
if (disable_partial_chunk_filters) {
|
|
ret = H5Pget_chunk_opts(dcpl, &chunk_opts);
|
|
VRFY((ret >= 0), "H5Pget_chunk_opts succeeded");
|
|
|
|
chunk_opts |= H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS;
|
|
|
|
ret = H5Pset_chunk_opts(dcpl, chunk_opts);
|
|
VRFY((ret >= 0), "H5Pset_chunk_opts succeeded");
|
|
} /* end if */
|
|
|
|
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);
|
|
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), "H5Dread succeeded");
|
|
|
|
/* Verify data read */
|
|
for (u = 0; u < dim; u++)
|
|
if (data_orig[u] != data_read[u]) {
|
|
HDprintf("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++;
|
|
}
|
|
|
|
#ifdef H5_HAVE_PARALLEL_FILTERED_WRITES
|
|
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, xfer_plist, data_read);
|
|
VRFY((ret >= 0), "H5Dwrite succeeded");
|
|
#endif
|
|
|
|
ret = H5Pclose(xfer_plist);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret = H5Dclose(dataset);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
} /* end if */
|
|
|
|
/* Close file */
|
|
ret = H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
} /* end for */
|
|
|
|
/* 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 */
|
|
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)
|
|
HDprintf("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] = (hsize_t)chunkdim0;
|
|
chunk_dims[1] = (hsize_t)chunkdim1;
|
|
|
|
/* -------------------
|
|
* START AN HDF5 FILE
|
|
* -------------------*/
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* create the file collectively */
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
|
|
VRFY((fid >= 0), "H5Fcreate succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "");
|
|
|
|
/* --------------------------------------------------------------
|
|
* Define the dimensions of the overall datasets and create them.
|
|
* ------------------------------------------------------------- */
|
|
|
|
/* set up dataset storage chunk sizes and creation property list */
|
|
if (VERBOSE_MED)
|
|
HDprintf("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] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)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 *)HDmalloc(block[0] * block[1] * sizeof(DATATYPE));
|
|
VRFY((data_origin != NULL), "data_origin HDmalloc succeeded");
|
|
|
|
data_array = (DATATYPE *)HDmalloc(block[0] * block[1] * sizeof(DATATYPE));
|
|
VRFY((data_array != NULL), "data_array HDmalloc 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)
|
|
HDfree(data_origin);
|
|
if (data_array)
|
|
HDfree(data_array);
|
|
}
|
|
|
|
/* Function: test_actual_io_mode
|
|
*
|
|
* Purpose: tests one specific case of collective I/O and checks that the
|
|
* actual_chunk_opt_mode property and the actual_io_mode
|
|
* properties in the DXPL have the correct values.
|
|
*
|
|
* Input: selection_mode: changes the way processes select data from the space, as well
|
|
* as some dxpl flags to get collective I/O to break in different ways.
|
|
*
|
|
* The relevant I/O function and expected response for each mode:
|
|
* TEST_ACTUAL_IO_MULTI_CHUNK_IND:
|
|
* H5D_mpi_chunk_collective_io, each process reports independent I/O
|
|
*
|
|
* TEST_ACTUAL_IO_MULTI_CHUNK_COL:
|
|
* H5D_mpi_chunk_collective_io, each process reports collective I/O
|
|
*
|
|
* TEST_ACTUAL_IO_MULTI_CHUNK_MIX:
|
|
* H5D_mpi_chunk_collective_io, each process reports mixed I/O
|
|
*
|
|
* TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE:
|
|
* H5D_mpi_chunk_collective_io, processes disagree. The root reports
|
|
* collective, the rest report independent I/O
|
|
*
|
|
* TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND:
|
|
* Same test TEST_ACTUAL_IO_MULTI_CHUNK_IND.
|
|
* Set directly go to multi-chunk-io without num threshold calc.
|
|
* TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL:
|
|
* Same test TEST_ACTUAL_IO_MULTI_CHUNK_COL.
|
|
* Set directly go to multi-chunk-io without num threshold calc.
|
|
*
|
|
* TEST_ACTUAL_IO_LINK_CHUNK:
|
|
* H5D_link_chunk_collective_io, processes report linked chunk I/O
|
|
*
|
|
* TEST_ACTUAL_IO_CONTIGUOUS:
|
|
* H5D__contig_collective_write or H5D__contig_collective_read
|
|
* each process reports contiguous collective I/O
|
|
*
|
|
* TEST_ACTUAL_IO_NO_COLLECTIVE:
|
|
* Simple independent I/O. This tests that the defaults are properly set.
|
|
*
|
|
* TEST_ACTUAL_IO_RESET:
|
|
* Performs collective and then independent I/O with hthe same dxpl to
|
|
* make sure the peroperty is correctly reset to the default on each use.
|
|
* Specifically, this test runs TEST_ACTUAL_IO_MULTI_CHUNK_NO_OPT_MIX_DISAGREE
|
|
* (The most complex case that works on all builds) and then performs
|
|
* an independent read and write with the same dxpls.
|
|
*
|
|
* Note: DIRECT_MULTI_CHUNK_MIX and DIRECT_MULTI_CHUNK_MIX_DISAGREE
|
|
* is not needed as they are covered by DIRECT_CHUNK_MIX and
|
|
* MULTI_CHUNK_MIX_DISAGREE cases. _DIRECT_ cases are only for testing
|
|
* path way to multi-chunk-io by H5FD_MPIO_CHUNK_MULTI_IO instead of num-threshold.
|
|
*
|
|
* Modification:
|
|
* - Refctore to remove multi-chunk-without-opimization test and update for
|
|
* testing direct to multi-chunk-io
|
|
* Programmer: Jonathan Kim
|
|
* Date: 2012-10-10
|
|
*
|
|
*
|
|
* Programmer: Jacob Gruber
|
|
* Date: 2011-04-06
|
|
*/
|
|
static void
|
|
test_actual_io_mode(int selection_mode)
|
|
{
|
|
H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_write = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
|
|
H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_read = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
|
|
H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
|
|
H5D_mpio_actual_io_mode_t actual_io_mode_write = H5D_MPIO_NO_COLLECTIVE;
|
|
H5D_mpio_actual_io_mode_t actual_io_mode_read = H5D_MPIO_NO_COLLECTIVE;
|
|
H5D_mpio_actual_io_mode_t actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE;
|
|
const char *filename;
|
|
const char *test_name;
|
|
hbool_t direct_multi_chunk_io;
|
|
hbool_t multi_chunk_io;
|
|
hbool_t is_chunked;
|
|
hbool_t is_collective;
|
|
int mpi_size = -1;
|
|
int mpi_rank = -1;
|
|
int length;
|
|
int *buffer;
|
|
int i;
|
|
MPI_Comm mpi_comm = MPI_COMM_NULL;
|
|
MPI_Info mpi_info = MPI_INFO_NULL;
|
|
hid_t fid = -1;
|
|
hid_t sid = -1;
|
|
hid_t dataset = -1;
|
|
hid_t data_type = H5T_NATIVE_INT;
|
|
hid_t fapl = -1;
|
|
hid_t mem_space = -1;
|
|
hid_t file_space = -1;
|
|
hid_t dcpl = -1;
|
|
hid_t dxpl_write = -1;
|
|
hid_t dxpl_read = -1;
|
|
hsize_t dims[RANK];
|
|
hsize_t chunk_dims[RANK];
|
|
hsize_t start[RANK];
|
|
hsize_t stride[RANK];
|
|
hsize_t count[RANK];
|
|
hsize_t block[RANK];
|
|
char message[256];
|
|
herr_t ret;
|
|
|
|
/* Set up some flags to make some future if statements slightly more readable */
|
|
direct_multi_chunk_io = (selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND ||
|
|
selection_mode == TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL);
|
|
|
|
/* Note: RESET performs the same tests as MULTI_CHUNK_MIX_DISAGREE and then
|
|
* tests independent I/O
|
|
*/
|
|
multi_chunk_io =
|
|
(selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_IND ||
|
|
selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_COL ||
|
|
selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX ||
|
|
selection_mode == TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE || selection_mode == TEST_ACTUAL_IO_RESET);
|
|
|
|
is_chunked =
|
|
(selection_mode != TEST_ACTUAL_IO_CONTIGUOUS && selection_mode != TEST_ACTUAL_IO_NO_COLLECTIVE);
|
|
|
|
is_collective = selection_mode != TEST_ACTUAL_IO_NO_COLLECTIVE;
|
|
|
|
/* Set up MPI parameters */
|
|
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
|
|
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
|
|
|
|
MPI_Barrier(MPI_COMM_WORLD);
|
|
|
|
HDassert(mpi_size >= 1);
|
|
|
|
mpi_comm = MPI_COMM_WORLD;
|
|
mpi_info = MPI_INFO_NULL;
|
|
|
|
filename = (const char *)GetTestParameters();
|
|
HDassert(filename != NULL);
|
|
|
|
/* Setup the file access template */
|
|
fapl = create_faccess_plist(mpi_comm, mpi_info, facc_type);
|
|
VRFY((fapl >= 0), "create_faccess_plist() succeeded");
|
|
|
|
/* Create the file */
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
|
|
VRFY((fid >= 0), "H5Fcreate succeeded");
|
|
|
|
/* Create the basic Space */
|
|
dims[0] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)dim1;
|
|
sid = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((sid >= 0), "H5Screate_simple succeeded");
|
|
|
|
/* Create the dataset creation plist */
|
|
dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
|
VRFY((dcpl >= 0), "dataset creation plist created successfully");
|
|
|
|
/* If we are not testing contiguous datasets */
|
|
if (is_chunked) {
|
|
/* Set up chunk information. */
|
|
chunk_dims[0] = dims[0] / (hsize_t)mpi_size;
|
|
chunk_dims[1] = dims[1];
|
|
ret = H5Pset_chunk(dcpl, 2, chunk_dims);
|
|
VRFY((ret >= 0), "chunk creation property list succeeded");
|
|
}
|
|
|
|
/* Create the dataset */
|
|
dataset = H5Dcreate2(fid, "actual_io", data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded");
|
|
|
|
/* Create the file dataspace */
|
|
file_space = H5Dget_space(dataset);
|
|
VRFY((file_space >= 0), "H5Dget_space succeeded");
|
|
|
|
/* Choose a selection method based on the type of I/O we want to occur,
|
|
* and also set up some selection-dependeent test info. */
|
|
switch (selection_mode) {
|
|
|
|
/* Independent I/O with optimization */
|
|
case TEST_ACTUAL_IO_MULTI_CHUNK_IND:
|
|
case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND:
|
|
/* Since the dataset is chunked by row and each process selects a row,
|
|
* each process writes to a different chunk. This forces all I/O to be
|
|
* independent.
|
|
*/
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
test_name = "Multi Chunk - Independent";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT;
|
|
break;
|
|
|
|
/* Collective I/O with optimization */
|
|
case TEST_ACTUAL_IO_MULTI_CHUNK_COL:
|
|
case TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL:
|
|
/* The dataset is chunked by rows, so each process takes a column which
|
|
* spans all chunks. Since the processes write non-overlapping regular
|
|
* selections to each chunk, the operation is purely collective.
|
|
*/
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
|
|
|
|
test_name = "Multi Chunk - Collective";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
|
|
if (mpi_size > 1)
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
|
|
else
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT;
|
|
break;
|
|
|
|
/* Mixed I/O with optimization */
|
|
case TEST_ACTUAL_IO_MULTI_CHUNK_MIX:
|
|
/* A chunk will be assigned collective I/O only if it is selected by each
|
|
* process. To get mixed I/O, have the root select all chunks and each
|
|
* subsequent process select the first and nth chunk. The first chunk,
|
|
* accessed by all, will be assigned collective I/O while each other chunk
|
|
* will be accessed only by the root and the nth process and will be
|
|
* assigned independent I/O. Each process will access one chunk collectively
|
|
* and at least one chunk independently, reporting mixed I/O.
|
|
*/
|
|
|
|
if (mpi_rank == 0) {
|
|
/* Select the first column */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
|
|
}
|
|
else {
|
|
/* Select the first and the nth chunk in the nth column */
|
|
block[0] = (hsize_t)(dim0 / mpi_size);
|
|
block[1] = (hsize_t)(dim1 / mpi_size);
|
|
count[0] = 2;
|
|
count[1] = 1;
|
|
stride[0] = (hsize_t)mpi_rank * block[0];
|
|
stride[1] = 1;
|
|
start[0] = 0;
|
|
start[1] = (hsize_t)mpi_rank * block[1];
|
|
}
|
|
|
|
test_name = "Multi Chunk - Mixed";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED;
|
|
break;
|
|
|
|
/* RESET tests that the properties are properly reset to defaults each time I/O is
|
|
* performed. To achieve this, we have RESET perform collective I/O (which would change
|
|
* the values from the defaults) followed by independent I/O (which should report the
|
|
* default values). RESET doesn't need to have a unique selection, so we reuse
|
|
* MULTI_CHUMK_MIX_DISAGREE, which was chosen because it is a complex case that works
|
|
* on all builds. The independent section of RESET can be found at the end of this function.
|
|
*/
|
|
case TEST_ACTUAL_IO_RESET:
|
|
|
|
/* Mixed I/O with optimization and internal disagreement */
|
|
case TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE:
|
|
/* A chunk will be assigned collective I/O only if it is selected by each
|
|
* process. To get mixed I/O with disagreement, assign process n to the
|
|
* first chunk and the nth chunk. The first chunk, selected by all, is
|
|
* assgigned collective I/O, while each other process gets independent I/O.
|
|
* Since the root process with only access the first chunk, it will report
|
|
* collective I/O. The subsequent processes will access the first chunk
|
|
* collectively, and their other chunk independently, reporting mixed I/O.
|
|
*/
|
|
|
|
if (mpi_rank == 0) {
|
|
/* Select the first chunk in the first column */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL);
|
|
block[0] = block[0] / (hsize_t)mpi_size;
|
|
}
|
|
else {
|
|
/* Select the first and the nth chunk in the nth column */
|
|
block[0] = (hsize_t)(dim0 / mpi_size);
|
|
block[1] = (hsize_t)(dim1 / mpi_size);
|
|
count[0] = 2;
|
|
count[1] = 1;
|
|
stride[0] = (hsize_t)mpi_rank * block[0];
|
|
stride[1] = 1;
|
|
start[0] = 0;
|
|
start[1] = (hsize_t)mpi_rank * block[1];
|
|
}
|
|
|
|
/* If the testname was not already set by the RESET case */
|
|
if (selection_mode == TEST_ACTUAL_IO_RESET)
|
|
test_name = "RESET";
|
|
else
|
|
test_name = "Multi Chunk - Mixed (Disagreement)";
|
|
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_MULTI_CHUNK;
|
|
if (mpi_size > 1) {
|
|
if (mpi_rank == 0)
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
|
|
else
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_MIXED;
|
|
}
|
|
else
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_INDEPENDENT;
|
|
|
|
break;
|
|
|
|
/* Linked Chunk I/O */
|
|
case TEST_ACTUAL_IO_LINK_CHUNK:
|
|
/* Nothing special; link chunk I/O is forced in the dxpl settings. */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
test_name = "Link Chunk";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_LINK_CHUNK;
|
|
actual_io_mode_expected = H5D_MPIO_CHUNK_COLLECTIVE;
|
|
break;
|
|
|
|
/* Contiguous Dataset */
|
|
case TEST_ACTUAL_IO_CONTIGUOUS:
|
|
/* A non overlapping, regular selection in a contiguous dataset leads to
|
|
* collective I/O */
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
test_name = "Contiguous";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
|
|
actual_io_mode_expected = H5D_MPIO_CONTIGUOUS_COLLECTIVE;
|
|
break;
|
|
|
|
case TEST_ACTUAL_IO_NO_COLLECTIVE:
|
|
slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW);
|
|
|
|
test_name = "Independent";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
|
|
actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE;
|
|
break;
|
|
|
|
default:
|
|
test_name = "Undefined Selection Mode";
|
|
actual_chunk_opt_mode_expected = H5D_MPIO_NO_CHUNK_OPTIMIZATION;
|
|
actual_io_mode_expected = H5D_MPIO_NO_COLLECTIVE;
|
|
break;
|
|
}
|
|
|
|
ret = H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, stride, count, block);
|
|
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
|
|
|
|
/* Create a memory dataspace mirroring the dataset and select the same hyperslab
|
|
* as in the file space.
|
|
*/
|
|
mem_space = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((mem_space >= 0), "mem_space created");
|
|
|
|
ret = H5Sselect_hyperslab(mem_space, H5S_SELECT_SET, start, stride, count, block);
|
|
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
|
|
|
|
/* Get the number of elements in the selection */
|
|
length = dim0 * dim1;
|
|
|
|
/* Allocate and initialize the buffer */
|
|
buffer = (int *)HDmalloc(sizeof(int) * (size_t)length);
|
|
VRFY((buffer != NULL), "HDmalloc of buffer succeeded");
|
|
for (i = 0; i < length; i++)
|
|
buffer[i] = i;
|
|
|
|
/* Set up the dxpl for the write */
|
|
dxpl_write = H5Pcreate(H5P_DATASET_XFER);
|
|
VRFY((dxpl_write >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded");
|
|
|
|
/* Set collective I/O properties in the dxpl. */
|
|
if (is_collective) {
|
|
/* Request collective I/O */
|
|
ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* Set the threshold number of processes per chunk to twice mpi_size.
|
|
* This will prevent the threshold from ever being met, thus forcing
|
|
* multi chunk io instead of link chunk io.
|
|
* This is via default.
|
|
*/
|
|
if (multi_chunk_io) {
|
|
/* force multi-chunk-io by threshold */
|
|
ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl_write, (unsigned)mpi_size * 2);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_num succeeded");
|
|
|
|
/* set this to manipulate testing scenario about allocating processes
|
|
* to chunks */
|
|
ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl_write, (unsigned)99);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_ratio succeeded");
|
|
}
|
|
|
|
/* Set directly go to multi-chunk-io without threshold calc. */
|
|
if (direct_multi_chunk_io) {
|
|
/* set for multi chunk io by property*/
|
|
ret = H5Pset_dxpl_mpio_chunk_opt(dxpl_write, H5FD_MPIO_CHUNK_MULTI_IO);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
}
|
|
}
|
|
|
|
/* Make a copy of the dxpl to test the read operation */
|
|
dxpl_read = H5Pcopy(dxpl_write);
|
|
VRFY((dxpl_read >= 0), "H5Pcopy succeeded");
|
|
|
|
/* Write */
|
|
ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl_write, buffer);
|
|
if (ret < 0)
|
|
H5Eprint2(H5E_DEFAULT, stdout);
|
|
VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
|
|
|
|
/* Retrieve Actual io values */
|
|
ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write);
|
|
VRFY((ret >= 0), "retrieving actual io mode succeeded");
|
|
|
|
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write);
|
|
VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded");
|
|
|
|
/* Read */
|
|
ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl_read, buffer);
|
|
if (ret < 0)
|
|
H5Eprint2(H5E_DEFAULT, stdout);
|
|
VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded");
|
|
|
|
/* Retrieve Actual io values */
|
|
ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read);
|
|
VRFY((ret >= 0), "retrieving actual io mode succeeded");
|
|
|
|
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read);
|
|
VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded");
|
|
|
|
/* Check write vs read */
|
|
VRFY((actual_io_mode_read == actual_io_mode_write),
|
|
"reading and writing are the same for actual_io_mode");
|
|
VRFY((actual_chunk_opt_mode_read == actual_chunk_opt_mode_write),
|
|
"reading and writing are the same for actual_chunk_opt_mode");
|
|
|
|
/* Test values */
|
|
if (actual_chunk_opt_mode_expected != (H5D_mpio_actual_chunk_opt_mode_t)-1 &&
|
|
actual_io_mode_expected != (H5D_mpio_actual_io_mode_t)-1) {
|
|
HDsnprintf(message, sizeof(message), "Actual Chunk Opt Mode has the correct value for %s.\n",
|
|
test_name);
|
|
VRFY((actual_chunk_opt_mode_write == actual_chunk_opt_mode_expected), message);
|
|
HDsnprintf(message, sizeof(message), "Actual IO Mode has the correct value for %s.\n", test_name);
|
|
VRFY((actual_io_mode_write == actual_io_mode_expected), message);
|
|
}
|
|
else {
|
|
HDfprintf(stderr, "%s %d -> (%d,%d)\n", test_name, mpi_rank, actual_chunk_opt_mode_write,
|
|
actual_io_mode_write);
|
|
}
|
|
|
|
/* To test that the property is successfully reset to the default, we perform some
|
|
* independent I/O after the collective I/O
|
|
*/
|
|
if (selection_mode == TEST_ACTUAL_IO_RESET) {
|
|
if (mpi_rank == 0) {
|
|
/* Switch to independent io */
|
|
ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_INDEPENDENT);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
ret = H5Pset_dxpl_mpio(dxpl_read, H5FD_MPIO_INDEPENDENT);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
|
|
/* Write */
|
|
ret = H5Dwrite(dataset, data_type, H5S_ALL, H5S_ALL, dxpl_write, buffer);
|
|
VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
|
|
|
|
/* Check Properties */
|
|
ret = H5Pget_mpio_actual_io_mode(dxpl_write, &actual_io_mode_write);
|
|
VRFY((ret >= 0), "retrieving actual io mode succeeded");
|
|
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_write, &actual_chunk_opt_mode_write);
|
|
VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded");
|
|
|
|
VRFY(actual_chunk_opt_mode_write == H5D_MPIO_NO_CHUNK_OPTIMIZATION,
|
|
"actual_chunk_opt_mode has correct value for reset write (independent)");
|
|
VRFY(actual_io_mode_write == H5D_MPIO_NO_COLLECTIVE,
|
|
"actual_io_mode has correct value for reset write (independent)");
|
|
|
|
/* Read */
|
|
ret = H5Dread(dataset, data_type, H5S_ALL, H5S_ALL, dxpl_read, buffer);
|
|
VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
|
|
|
|
/* Check Properties */
|
|
ret = H5Pget_mpio_actual_io_mode(dxpl_read, &actual_io_mode_read);
|
|
VRFY((ret >= 0), "retrieving actual io mode succeeded");
|
|
ret = H5Pget_mpio_actual_chunk_opt_mode(dxpl_read, &actual_chunk_opt_mode_read);
|
|
VRFY((ret >= 0), "retrieving actual chunk opt mode succeeded");
|
|
|
|
VRFY(actual_chunk_opt_mode_read == H5D_MPIO_NO_CHUNK_OPTIMIZATION,
|
|
"actual_chunk_opt_mode has correct value for reset read (independent)");
|
|
VRFY(actual_io_mode_read == H5D_MPIO_NO_COLLECTIVE,
|
|
"actual_io_mode has correct value for reset read (independent)");
|
|
}
|
|
}
|
|
|
|
/* Release some resources */
|
|
ret = H5Sclose(sid);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
ret = H5Pclose(fapl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret = H5Pclose(dcpl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret = H5Pclose(dxpl_write);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret = H5Pclose(dxpl_read);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
ret = H5Dclose(dataset);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
ret = H5Sclose(mem_space);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
ret = H5Sclose(file_space);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
ret = H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
HDfree(buffer);
|
|
return;
|
|
}
|
|
|
|
/* Function: actual_io_mode_tests
|
|
*
|
|
* Purpose: Tests all possible cases of the actual_io_mode property.
|
|
*
|
|
* Programmer: Jacob Gruber
|
|
* Date: 2011-04-06
|
|
*/
|
|
void
|
|
actual_io_mode_tests(void)
|
|
{
|
|
int mpi_size = -1;
|
|
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
|
|
|
|
/* Only run these tests if selection I/O is not being used - selection I/O
|
|
* bypasses this IO mode decision - it's effectively always multi chunk
|
|
* currently */
|
|
if (!H5_use_selection_io_g) {
|
|
test_actual_io_mode(TEST_ACTUAL_IO_NO_COLLECTIVE);
|
|
|
|
/*
|
|
* Test multi-chunk-io via proc_num threshold
|
|
*/
|
|
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_IND);
|
|
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_COL);
|
|
|
|
/* The Multi Chunk Mixed test requires at least three processes. */
|
|
if (mpi_size > 2)
|
|
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX);
|
|
else
|
|
HDfprintf(stdout, "Multi Chunk Mixed test requires 3 processes minimum\n");
|
|
|
|
test_actual_io_mode(TEST_ACTUAL_IO_MULTI_CHUNK_MIX_DISAGREE);
|
|
|
|
/*
|
|
* Test multi-chunk-io via setting direct property
|
|
*/
|
|
test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_IND);
|
|
test_actual_io_mode(TEST_ACTUAL_IO_DIRECT_MULTI_CHUNK_COL);
|
|
|
|
test_actual_io_mode(TEST_ACTUAL_IO_LINK_CHUNK);
|
|
test_actual_io_mode(TEST_ACTUAL_IO_CONTIGUOUS);
|
|
|
|
test_actual_io_mode(TEST_ACTUAL_IO_RESET);
|
|
}
|
|
|
|
return;
|
|
}
|
|
|
|
/*
|
|
* Function: test_no_collective_cause_mode
|
|
*
|
|
* Purpose:
|
|
* tests cases for broken collective I/O and checks that the
|
|
* H5Pget_mpio_no_collective_cause properties in the DXPL have the correct values.
|
|
*
|
|
* Input:
|
|
* selection_mode: various mode to cause broken collective I/O
|
|
* Note: Originally, each TEST case is supposed to be used alone.
|
|
* After some discussion, this is updated to take multiple TEST cases
|
|
* with '|'. However there is no error check for any of combined
|
|
* test cases, so a tester is responsible to understand and feed
|
|
* proper combination of TESTs if needed.
|
|
*
|
|
*
|
|
* TEST_COLLECTIVE:
|
|
* Test for regular collective I/O without cause of breaking.
|
|
* Just to test normal behavior.
|
|
*
|
|
* TEST_SET_INDEPENDENT:
|
|
* Test for Independent I/O as the cause of breaking collective I/O.
|
|
*
|
|
* TEST_DATATYPE_CONVERSION:
|
|
* Test for Data Type Conversion as the cause of breaking collective I/O.
|
|
*
|
|
* TEST_DATA_TRANSFORMS:
|
|
* Test for Data Transform feature as the cause of breaking collective I/O.
|
|
*
|
|
* TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES:
|
|
* Test for NULL dataspace as the cause of breaking collective I/O.
|
|
*
|
|
* TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT:
|
|
* Test for Compact layout as the cause of breaking collective I/O.
|
|
*
|
|
* TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL:
|
|
* Test for Externl-File storage as the cause of breaking collective I/O.
|
|
*
|
|
* Programmer: Jonathan Kim
|
|
* Date: Aug, 2012
|
|
*/
|
|
#ifdef LATER
|
|
#define DSET_NOCOLCAUSE "nocolcause"
|
|
#endif
|
|
#define FILE_EXTERNAL "nocolcause_extern.data"
|
|
static void
|
|
test_no_collective_cause_mode(int selection_mode)
|
|
{
|
|
uint32_t no_collective_cause_local_write = 0;
|
|
uint32_t no_collective_cause_local_read = 0;
|
|
uint32_t no_collective_cause_local_expected = 0;
|
|
uint32_t no_collective_cause_global_write = 0;
|
|
uint32_t no_collective_cause_global_read = 0;
|
|
uint32_t no_collective_cause_global_expected = 0;
|
|
|
|
const char *filename;
|
|
const char *test_name;
|
|
hbool_t is_chunked = 1;
|
|
hbool_t is_independent = 0;
|
|
int mpi_size = -1;
|
|
int mpi_rank = -1;
|
|
int length;
|
|
int *buffer;
|
|
int i;
|
|
MPI_Comm mpi_comm;
|
|
MPI_Info mpi_info;
|
|
hid_t fid = -1;
|
|
hid_t sid = -1;
|
|
hid_t dataset = -1;
|
|
hid_t data_type = H5T_NATIVE_INT;
|
|
hid_t fapl = -1;
|
|
hid_t dcpl = -1;
|
|
hid_t dxpl_write = -1;
|
|
hid_t dxpl_read = -1;
|
|
hsize_t dims[RANK];
|
|
hid_t mem_space = -1;
|
|
hid_t file_space = -1;
|
|
hsize_t chunk_dims[RANK];
|
|
herr_t ret;
|
|
/* set to global value as default */
|
|
int l_facc_type = facc_type;
|
|
char message[256];
|
|
|
|
/* Set up MPI parameters */
|
|
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
|
|
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
|
|
|
|
MPI_Barrier(MPI_COMM_WORLD);
|
|
|
|
HDassert(mpi_size >= 1);
|
|
|
|
mpi_comm = MPI_COMM_WORLD;
|
|
mpi_info = MPI_INFO_NULL;
|
|
|
|
/* Create the dataset creation plist */
|
|
dcpl = H5Pcreate(H5P_DATASET_CREATE);
|
|
VRFY((dcpl >= 0), "dataset creation plist created successfully");
|
|
|
|
if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT) {
|
|
ret = H5Pset_layout(dcpl, H5D_COMPACT);
|
|
VRFY((ret >= 0), "set COMPACT layout succeeded");
|
|
is_chunked = 0;
|
|
}
|
|
|
|
if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) {
|
|
ret = H5Pset_external(dcpl, FILE_EXTERNAL, (off_t)0, H5F_UNLIMITED);
|
|
VRFY((ret >= 0), "set EXTERNAL file layout succeeded");
|
|
is_chunked = 0;
|
|
}
|
|
|
|
if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) {
|
|
sid = H5Screate(H5S_NULL);
|
|
VRFY((sid >= 0), "H5Screate_simple succeeded");
|
|
is_chunked = 0;
|
|
}
|
|
else {
|
|
/* Create the basic Space */
|
|
/* if this is a compact dataset, create a small dataspace that does not exceed 64K */
|
|
if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT) {
|
|
dims[0] = ROW_FACTOR * 6;
|
|
dims[1] = COL_FACTOR * 6;
|
|
}
|
|
else {
|
|
dims[0] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)dim1;
|
|
}
|
|
sid = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((sid >= 0), "H5Screate_simple succeeded");
|
|
}
|
|
|
|
filename = (const char *)GetTestParameters();
|
|
HDassert(filename != NULL);
|
|
|
|
/* Setup the file access template */
|
|
fapl = create_faccess_plist(mpi_comm, mpi_info, l_facc_type);
|
|
VRFY((fapl >= 0), "create_faccess_plist() succeeded");
|
|
|
|
/* Create the file */
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
|
|
|
|
VRFY((fid >= 0), "H5Fcreate succeeded");
|
|
|
|
/* If we are not testing contiguous datasets */
|
|
if (is_chunked) {
|
|
/* Set up chunk information. */
|
|
chunk_dims[0] = dims[0] / (hsize_t)mpi_size;
|
|
chunk_dims[1] = dims[1];
|
|
ret = H5Pset_chunk(dcpl, 2, chunk_dims);
|
|
VRFY((ret >= 0), "chunk creation property list succeeded");
|
|
}
|
|
|
|
/* Create the dataset */
|
|
dataset = H5Dcreate2(fid, "nocolcause", data_type, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
|
|
VRFY((dataset >= 0), "H5Dcreate2() dataset succeeded");
|
|
|
|
/*
|
|
* Set expected causes and some tweaks based on the type of test
|
|
*/
|
|
if (selection_mode & TEST_DATATYPE_CONVERSION) {
|
|
test_name = "Broken Collective I/O - Datatype Conversion";
|
|
no_collective_cause_local_expected |= H5D_MPIO_DATATYPE_CONVERSION;
|
|
no_collective_cause_global_expected |= H5D_MPIO_DATATYPE_CONVERSION;
|
|
/* set different sign to trigger type conversion */
|
|
data_type = H5T_NATIVE_UINT;
|
|
}
|
|
|
|
if (selection_mode & TEST_DATA_TRANSFORMS) {
|
|
test_name = "Broken Collective I/O - DATA Transforms";
|
|
no_collective_cause_local_expected |= H5D_MPIO_DATA_TRANSFORMS;
|
|
no_collective_cause_global_expected |= H5D_MPIO_DATA_TRANSFORMS;
|
|
}
|
|
|
|
if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES) {
|
|
test_name = "Broken Collective I/O - No Simple or Scalar DataSpace";
|
|
no_collective_cause_local_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES;
|
|
no_collective_cause_global_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES;
|
|
}
|
|
|
|
if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT ||
|
|
selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) {
|
|
test_name = "Broken Collective I/O - No CONTI or CHUNKED Dataset";
|
|
no_collective_cause_local_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
|
|
no_collective_cause_global_expected |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
|
|
}
|
|
|
|
if (selection_mode & TEST_COLLECTIVE) {
|
|
test_name = "Broken Collective I/O - Not Broken";
|
|
no_collective_cause_local_expected = H5D_MPIO_COLLECTIVE;
|
|
no_collective_cause_global_expected = H5D_MPIO_COLLECTIVE;
|
|
}
|
|
|
|
if (selection_mode & TEST_SET_INDEPENDENT) {
|
|
test_name = "Broken Collective I/O - Independent";
|
|
no_collective_cause_local_expected = H5D_MPIO_SET_INDEPENDENT;
|
|
no_collective_cause_global_expected = H5D_MPIO_SET_INDEPENDENT;
|
|
/* switch to independent io */
|
|
is_independent = 1;
|
|
}
|
|
|
|
/* use all spaces for certain tests */
|
|
if (selection_mode & TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES ||
|
|
selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) {
|
|
file_space = H5S_ALL;
|
|
mem_space = H5S_ALL;
|
|
}
|
|
else {
|
|
/* Get the file dataspace */
|
|
file_space = H5Dget_space(dataset);
|
|
VRFY((file_space >= 0), "H5Dget_space succeeded");
|
|
|
|
/* Create the memory dataspace */
|
|
mem_space = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((mem_space >= 0), "mem_space created");
|
|
}
|
|
|
|
/* Get the number of elements in the selection */
|
|
H5_CHECKED_ASSIGN(length, int, dims[0] * dims[1], uint64_t);
|
|
|
|
/* Allocate and initialize the buffer */
|
|
buffer = (int *)HDmalloc(sizeof(int) * (size_t)length);
|
|
VRFY((buffer != NULL), "HDmalloc of buffer succeeded");
|
|
for (i = 0; i < length; i++)
|
|
buffer[i] = i;
|
|
|
|
/* Set up the dxpl for the write */
|
|
dxpl_write = H5Pcreate(H5P_DATASET_XFER);
|
|
VRFY((dxpl_write >= 0), "H5Pcreate(H5P_DATASET_XFER) succeeded");
|
|
|
|
if (is_independent) {
|
|
/* Set Independent I/O */
|
|
ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_INDEPENDENT);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
}
|
|
else {
|
|
/* Set Collective I/O */
|
|
ret = H5Pset_dxpl_mpio(dxpl_write, H5FD_MPIO_COLLECTIVE);
|
|
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
|
|
}
|
|
|
|
if (selection_mode & TEST_DATA_TRANSFORMS) {
|
|
ret = H5Pset_data_transform(dxpl_write, "x+1");
|
|
VRFY((ret >= 0), "H5Pset_data_transform succeeded");
|
|
}
|
|
|
|
/*---------------------
|
|
* Test Write access
|
|
*---------------------*/
|
|
|
|
/* Write */
|
|
ret = H5Dwrite(dataset, data_type, mem_space, file_space, dxpl_write, buffer);
|
|
if (ret < 0)
|
|
H5Eprint2(H5E_DEFAULT, stdout);
|
|
VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
|
|
|
|
/* Get the cause of broken collective I/O */
|
|
ret = H5Pget_mpio_no_collective_cause(dxpl_write, &no_collective_cause_local_write,
|
|
&no_collective_cause_global_write);
|
|
VRFY((ret >= 0), "retrieving no collective cause succeeded");
|
|
|
|
/*---------------------
|
|
* Test Read access
|
|
*---------------------*/
|
|
|
|
/* Make a copy of the dxpl to test the read operation */
|
|
dxpl_read = H5Pcopy(dxpl_write);
|
|
VRFY((dxpl_read >= 0), "H5Pcopy succeeded");
|
|
|
|
/* Read */
|
|
ret = H5Dread(dataset, data_type, mem_space, file_space, dxpl_read, buffer);
|
|
|
|
if (ret < 0)
|
|
H5Eprint2(H5E_DEFAULT, stdout);
|
|
VRFY((ret >= 0), "H5Dread() dataset multichunk read succeeded");
|
|
|
|
/* Get the cause of broken collective I/O */
|
|
ret = H5Pget_mpio_no_collective_cause(dxpl_read, &no_collective_cause_local_read,
|
|
&no_collective_cause_global_read);
|
|
VRFY((ret >= 0), "retrieving no collective cause succeeded");
|
|
|
|
/* Check write vs read */
|
|
VRFY((no_collective_cause_local_read == no_collective_cause_local_write),
|
|
"reading and writing are the same for local cause of Broken Collective I/O");
|
|
VRFY((no_collective_cause_global_read == no_collective_cause_global_write),
|
|
"reading and writing are the same for global cause of Broken Collective I/O");
|
|
|
|
/* Test values */
|
|
HDmemset(message, 0, sizeof(message));
|
|
HDsnprintf(message, sizeof(message),
|
|
"Local cause of Broken Collective I/O has the correct value for %s.\n", test_name);
|
|
VRFY((no_collective_cause_local_write == no_collective_cause_local_expected), message);
|
|
HDmemset(message, 0, sizeof(message));
|
|
HDsnprintf(message, sizeof(message),
|
|
"Global cause of Broken Collective I/O has the correct value for %s.\n", test_name);
|
|
VRFY((no_collective_cause_global_write == no_collective_cause_global_expected), message);
|
|
|
|
/* Release some resources */
|
|
if (sid)
|
|
H5Sclose(sid);
|
|
if (fapl)
|
|
H5Pclose(fapl);
|
|
if (dcpl)
|
|
H5Pclose(dcpl);
|
|
if (dxpl_write)
|
|
H5Pclose(dxpl_write);
|
|
if (dxpl_read)
|
|
H5Pclose(dxpl_read);
|
|
if (dataset)
|
|
H5Dclose(dataset);
|
|
if (mem_space)
|
|
H5Sclose(mem_space);
|
|
if (file_space)
|
|
H5Sclose(file_space);
|
|
if (fid)
|
|
H5Fclose(fid);
|
|
HDfree(buffer);
|
|
|
|
/* clean up external file */
|
|
if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL)
|
|
HDremove(FILE_EXTERNAL);
|
|
|
|
return;
|
|
}
|
|
|
|
/* Function: no_collective_cause_tests
|
|
*
|
|
* Purpose: Tests cases for broken collective IO.
|
|
*
|
|
* Programmer: Jonathan Kim
|
|
* Date: Aug, 2012
|
|
*/
|
|
void
|
|
no_collective_cause_tests(void)
|
|
{
|
|
/*
|
|
* Test individual cause
|
|
*/
|
|
test_no_collective_cause_mode(TEST_COLLECTIVE);
|
|
test_no_collective_cause_mode(TEST_SET_INDEPENDENT);
|
|
test_no_collective_cause_mode(TEST_DATATYPE_CONVERSION);
|
|
test_no_collective_cause_mode(TEST_DATA_TRANSFORMS);
|
|
test_no_collective_cause_mode(TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES);
|
|
test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT);
|
|
test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL);
|
|
|
|
/*
|
|
* Test combined causes
|
|
*/
|
|
test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL | TEST_DATATYPE_CONVERSION);
|
|
test_no_collective_cause_mode(TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS);
|
|
test_no_collective_cause_mode(TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL | TEST_DATATYPE_CONVERSION |
|
|
TEST_DATA_TRANSFORMS);
|
|
|
|
return;
|
|
}
|
|
|
|
/*
|
|
* Test consistency semantics of atomic mode
|
|
*/
|
|
|
|
/*
|
|
* Example of using the parallel HDF5 library to create a dataset,
|
|
* where process 0 writes and the other processes read at the same
|
|
* time. If atomic mode is set correctly, the other processes should
|
|
* read the old values in the dataset or the new ones.
|
|
*/
|
|
|
|
void
|
|
dataset_atomicity(void)
|
|
{
|
|
hid_t fid; /* HDF5 file ID */
|
|
hid_t acc_tpl; /* File access templates */
|
|
hid_t sid; /* Dataspace ID */
|
|
hid_t dataset1; /* Dataset IDs */
|
|
hsize_t dims[RANK]; /* dataset dim sizes */
|
|
int *write_buf = NULL; /* data buffer */
|
|
int *read_buf = NULL; /* data buffer */
|
|
int buf_size;
|
|
hid_t dataset2;
|
|
hid_t file_dataspace; /* File dataspace ID */
|
|
hid_t mem_dataspace; /* Memory dataspace ID */
|
|
hsize_t start[RANK];
|
|
hsize_t stride[RANK];
|
|
hsize_t count[RANK];
|
|
hsize_t block[RANK];
|
|
const char *filename;
|
|
herr_t ret; /* Generic return value */
|
|
int mpi_size, mpi_rank;
|
|
int i, j, k;
|
|
hbool_t atomicity = FALSE;
|
|
MPI_Comm comm = MPI_COMM_WORLD;
|
|
MPI_Info info = MPI_INFO_NULL;
|
|
|
|
dim0 = 64;
|
|
dim1 = 32;
|
|
filename = GetTestParameters();
|
|
if (facc_type != FACC_MPIO) {
|
|
HDprintf("Atomicity tests will not work without the MPIO VFD\n");
|
|
return;
|
|
}
|
|
if (VERBOSE_MED)
|
|
HDprintf("atomic writes to file %s\n", filename);
|
|
|
|
/* set up MPI parameters */
|
|
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
|
|
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
|
|
|
|
buf_size = dim0 * dim1;
|
|
/* allocate memory for data buffer */
|
|
write_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int));
|
|
VRFY((write_buf != NULL), "write_buf HDcalloc succeeded");
|
|
/* allocate memory for data buffer */
|
|
read_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int));
|
|
VRFY((read_buf != NULL), "read_buf HDcalloc succeeded");
|
|
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* create the file collectively */
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
|
|
VRFY((fid >= 0), "H5Fcreate succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
|
|
/* setup dimensionality object */
|
|
dims[0] = (hsize_t)dim0;
|
|
dims[1] = (hsize_t)dim1;
|
|
sid = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((sid >= 0), "H5Screate_simple succeeded");
|
|
|
|
/* create datasets */
|
|
dataset1 = H5Dcreate2(fid, DATASETNAME5, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
dataset2 = H5Dcreate2(fid, DATASETNAME6, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dcreate2 succeeded");
|
|
|
|
/* initialize datasets to 0s */
|
|
if (0 == mpi_rank) {
|
|
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
|
|
VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
|
|
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
|
|
VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
|
|
}
|
|
|
|
ret = H5Dclose(dataset1);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
ret = H5Dclose(dataset2);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
ret = H5Sclose(sid);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
ret = H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
|
|
MPI_Barrier(comm);
|
|
|
|
/* make sure setting atomicity fails on a serial file ID */
|
|
/* file locking allows only one file open (serial) for writing */
|
|
if (MAINPROCESS) {
|
|
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
|
|
VRFY((fid >= 0), "H5Fopen succeeded");
|
|
|
|
/* should fail */
|
|
H5E_BEGIN_TRY
|
|
{
|
|
ret = H5Fset_mpi_atomicity(fid, TRUE);
|
|
}
|
|
H5E_END_TRY
|
|
VRFY((ret == FAIL), "H5Fset_mpi_atomicity failed");
|
|
|
|
ret = H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
}
|
|
|
|
MPI_Barrier(comm);
|
|
|
|
/* setup file access template */
|
|
acc_tpl = create_faccess_plist(comm, info, facc_type);
|
|
VRFY((acc_tpl >= 0), "");
|
|
|
|
/* open the file collectively */
|
|
fid = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl);
|
|
VRFY((fid >= 0), "H5Fopen succeeded");
|
|
|
|
/* Release file-access template */
|
|
ret = H5Pclose(acc_tpl);
|
|
VRFY((ret >= 0), "H5Pclose succeeded");
|
|
|
|
ret = H5Fset_mpi_atomicity(fid, TRUE);
|
|
VRFY((ret >= 0), "H5Fset_mpi_atomicity succeeded");
|
|
|
|
/* open dataset1 (contiguous case) */
|
|
dataset1 = H5Dopen2(fid, DATASETNAME5, H5P_DEFAULT);
|
|
VRFY((dataset1 >= 0), "H5Dopen2 succeeded");
|
|
|
|
if (0 == mpi_rank) {
|
|
for (i = 0; i < buf_size; i++) {
|
|
write_buf[i] = 5;
|
|
}
|
|
}
|
|
else {
|
|
for (i = 0; i < buf_size; i++) {
|
|
read_buf[i] = 8;
|
|
}
|
|
}
|
|
|
|
/* check that the atomicity flag is set */
|
|
ret = H5Fget_mpi_atomicity(fid, &atomicity);
|
|
VRFY((ret >= 0), "atomcity get failed");
|
|
VRFY((atomicity == TRUE), "atomcity set failed");
|
|
|
|
MPI_Barrier(comm);
|
|
|
|
/* Process 0 writes contiguously to the entire dataset */
|
|
if (0 == mpi_rank) {
|
|
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
|
|
VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
|
|
}
|
|
/* The other processes read the entire dataset */
|
|
else {
|
|
ret = H5Dread(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, read_buf);
|
|
VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
|
|
}
|
|
|
|
if (VERBOSE_MED) {
|
|
i = 0;
|
|
j = 0;
|
|
k = 0;
|
|
for (i = 0; i < dim0; i++) {
|
|
HDprintf("\n");
|
|
for (j = 0; j < dim1; j++)
|
|
HDprintf("%d ", read_buf[k++]);
|
|
}
|
|
}
|
|
|
|
/* The processes that read the dataset must either read all values
|
|
as 0 (read happened before process 0 wrote to dataset 1), or 5
|
|
(read happened after process 0 wrote to dataset 1) */
|
|
if (0 != mpi_rank) {
|
|
int compare = read_buf[0];
|
|
|
|
VRFY((compare == 0 || compare == 5),
|
|
"Atomicity Test Failed Process %d: Value read should be 0 or 5\n");
|
|
for (i = 1; i < buf_size; i++) {
|
|
if (read_buf[i] != compare) {
|
|
HDprintf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, i,
|
|
read_buf[i], compare);
|
|
nerrors++;
|
|
}
|
|
}
|
|
}
|
|
|
|
ret = H5Dclose(dataset1);
|
|
VRFY((ret >= 0), "H5D close succeeded");
|
|
|
|
/* release data buffers */
|
|
if (write_buf)
|
|
HDfree(write_buf);
|
|
if (read_buf)
|
|
HDfree(read_buf);
|
|
|
|
/* open dataset2 (non-contiguous case) */
|
|
dataset2 = H5Dopen2(fid, DATASETNAME6, H5P_DEFAULT);
|
|
VRFY((dataset2 >= 0), "H5Dopen2 succeeded");
|
|
|
|
/* allocate memory for data buffer */
|
|
write_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int));
|
|
VRFY((write_buf != NULL), "write_buf HDcalloc succeeded");
|
|
/* allocate memory for data buffer */
|
|
read_buf = (int *)HDcalloc((size_t)buf_size, sizeof(int));
|
|
VRFY((read_buf != NULL), "read_buf HDcalloc succeeded");
|
|
|
|
for (i = 0; i < buf_size; i++) {
|
|
write_buf[i] = 5;
|
|
}
|
|
for (i = 0; i < buf_size; i++) {
|
|
read_buf[i] = 8;
|
|
}
|
|
|
|
atomicity = FALSE;
|
|
/* check that the atomicity flag is set */
|
|
ret = H5Fget_mpi_atomicity(fid, &atomicity);
|
|
VRFY((ret >= 0), "atomcity get failed");
|
|
VRFY((atomicity == TRUE), "atomcity set failed");
|
|
|
|
block[0] = (hsize_t)(dim0 / mpi_size - 1);
|
|
block[1] = (hsize_t)(dim1 / mpi_size - 1);
|
|
stride[0] = block[0] + 1;
|
|
stride[1] = block[1] + 1;
|
|
count[0] = (hsize_t)mpi_size;
|
|
count[1] = (hsize_t)mpi_size;
|
|
start[0] = 0;
|
|
start[1] = 0;
|
|
|
|
/* create a file dataspace */
|
|
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");
|
|
|
|
/* create a memory dataspace */
|
|
mem_dataspace = H5Screate_simple(RANK, dims, NULL);
|
|
VRFY((mem_dataspace >= 0), "");
|
|
|
|
ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
|
|
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
|
|
|
|
MPI_Barrier(comm);
|
|
|
|
/* Process 0 writes to the dataset */
|
|
if (0 == mpi_rank) {
|
|
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, write_buf);
|
|
VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
|
|
}
|
|
/* All processes wait for the write to finish. This works because
|
|
atomicity is set to true */
|
|
MPI_Barrier(comm);
|
|
/* The other processes read the entire dataset */
|
|
if (0 != mpi_rank) {
|
|
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, read_buf);
|
|
VRFY((ret >= 0), "H5Dread dataset2 succeeded");
|
|
}
|
|
|
|
if (VERBOSE_MED) {
|
|
if (mpi_rank == 1) {
|
|
i = 0;
|
|
j = 0;
|
|
k = 0;
|
|
for (i = 0; i < dim0; i++) {
|
|
HDprintf("\n");
|
|
for (j = 0; j < dim1; j++)
|
|
HDprintf("%d ", read_buf[k++]);
|
|
}
|
|
HDprintf("\n");
|
|
}
|
|
}
|
|
|
|
/* The processes that read the dataset must either read all values
|
|
as 5 (read happened after process 0 wrote to dataset 1) */
|
|
if (0 != mpi_rank) {
|
|
int compare;
|
|
i = 0;
|
|
j = 0;
|
|
k = 0;
|
|
|
|
compare = 5;
|
|
|
|
H5_CHECK_OVERFLOW(block[0], hsize_t, int);
|
|
H5_CHECK_OVERFLOW(block[1], hsize_t, int);
|
|
for (i = 0; i < dim0; i++) {
|
|
if (i >= mpi_rank * ((int)block[0] + 1)) {
|
|
break;
|
|
}
|
|
if ((i + 1) % ((int)block[0] + 1) == 0) {
|
|
k += dim1;
|
|
continue;
|
|
}
|
|
for (j = 0; j < dim1; j++) {
|
|
if (j >= mpi_rank * ((int)block[1] + 1)) {
|
|
k += dim1 - mpi_rank * ((int)block[1] + 1);
|
|
break;
|
|
}
|
|
if ((j + 1) % ((int)block[1] + 1) == 0) {
|
|
k++;
|
|
continue;
|
|
}
|
|
else if (compare != read_buf[k]) {
|
|
HDprintf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank,
|
|
k, read_buf[k], compare);
|
|
nerrors++;
|
|
}
|
|
k++;
|
|
}
|
|
}
|
|
}
|
|
|
|
ret = H5Dclose(dataset2);
|
|
VRFY((ret >= 0), "H5Dclose succeeded");
|
|
ret = H5Sclose(file_dataspace);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
ret = H5Sclose(mem_dataspace);
|
|
VRFY((ret >= 0), "H5Sclose succeeded");
|
|
|
|
/* release data buffers */
|
|
if (write_buf)
|
|
HDfree(write_buf);
|
|
if (read_buf)
|
|
HDfree(read_buf);
|
|
|
|
ret = H5Fclose(fid);
|
|
VRFY((ret >= 0), "H5Fclose succeeded");
|
|
}
|
|
|
|
/* Function: dense_attr_test
|
|
*
|
|
* Purpose: Test cases for writing dense attributes in parallel
|
|
*
|
|
* Programmer: Quincey Koziol
|
|
* Date: April, 2013
|
|
*/
|
|
void
|
|
test_dense_attr(void)
|
|
{
|
|
int mpi_size, mpi_rank;
|
|
hid_t fpid, fid;
|
|
hid_t gid, gpid;
|
|
hid_t atFileSpace, atid;
|
|
hsize_t atDims[1] = {10000};
|
|
herr_t status;
|
|
const char *filename;
|
|
|
|
/* get filename */
|
|
filename = (const char *)GetTestParameters();
|
|
HDassert(filename != NULL);
|
|
|
|
/* set up MPI parameters */
|
|
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
|
|
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
|
|
|
|
fpid = H5Pcreate(H5P_FILE_ACCESS);
|
|
VRFY((fpid > 0), "H5Pcreate succeeded");
|
|
status = H5Pset_libver_bounds(fpid, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
|
|
VRFY((status >= 0), "H5Pset_libver_bounds succeeded");
|
|
status = H5Pset_fapl_mpio(fpid, MPI_COMM_WORLD, MPI_INFO_NULL);
|
|
VRFY((status >= 0), "H5Pset_fapl_mpio succeeded");
|
|
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fpid);
|
|
VRFY((fid > 0), "H5Fcreate succeeded");
|
|
status = H5Pclose(fpid);
|
|
VRFY((status >= 0), "H5Pclose succeeded");
|
|
|
|
gpid = H5Pcreate(H5P_GROUP_CREATE);
|
|
VRFY((gpid > 0), "H5Pcreate succeeded");
|
|
status = H5Pset_attr_phase_change(gpid, 0, 0);
|
|
VRFY((status >= 0), "H5Pset_attr_phase_change succeeded");
|
|
gid = H5Gcreate2(fid, "foo", H5P_DEFAULT, gpid, H5P_DEFAULT);
|
|
VRFY((gid > 0), "H5Gcreate2 succeeded");
|
|
status = H5Pclose(gpid);
|
|
VRFY((status >= 0), "H5Pclose succeeded");
|
|
|
|
atFileSpace = H5Screate_simple(1, atDims, NULL);
|
|
VRFY((atFileSpace > 0), "H5Screate_simple succeeded");
|
|
atid = H5Acreate2(gid, "bar", H5T_STD_U64LE, atFileSpace, H5P_DEFAULT, H5P_DEFAULT);
|
|
VRFY((atid > 0), "H5Acreate succeeded");
|
|
status = H5Sclose(atFileSpace);
|
|
VRFY((status >= 0), "H5Sclose succeeded");
|
|
|
|
status = H5Aclose(atid);
|
|
VRFY((status >= 0), "H5Aclose succeeded");
|
|
|
|
status = H5Gclose(gid);
|
|
VRFY((status >= 0), "H5Gclose succeeded");
|
|
status = H5Fclose(fid);
|
|
VRFY((status >= 0), "H5Fclose succeeded");
|
|
|
|
return;
|
|
}
|