mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2024-11-27 02:10:55 +08:00
Code Issues Packages Projects Releases Wiki Activity
b5cf422799
hdf5/testpar/t_coll_md_read.c
kmu 838d4ec56b squash cast warning fix
2020-01-23 15:12:00 -06:00

507 lines
21 KiB
C
Raw Blame History

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* A test suite to test HDF5's collective metadata read capabilities, as enabled
* by making a call to H5Pset_all_coll_metadata_ops().
*/
#include "testphdf5.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/*
* Define the non-participating process as the "last"
* rank to avoid any weirdness potentially caused by
* an if (mpi_rank == 0) check.
*/
#define PARTIAL_NO_SELECTION_NO_SEL_PROCESS (mpi_rank == mpi_size - 1)
#define PARTIAL_NO_SELECTION_DATASET_NAME "partial_no_selection_dset"
#define PARTIAL_NO_SELECTION_DATASET_NDIMS 2
#define PARTIAL_NO_SELECTION_Y_DIM_SCALE 5
#define PARTIAL_NO_SELECTION_X_DIM_SCALE 5
#define MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS 2
#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue"
#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE 20000
#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE 1
#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1
/*
* A test for issue HDFFV-10501. A parallel hang was reported which occurred
* in linked-chunk I/O when collective metadata reads are enabled and some ranks
* do not have any selection in a dataset's dataspace, while others do. The ranks
* which have no selection during the read/write operation called H5D__chunk_addrmap()
* to retrieve the lowest chunk address, since we require that the read/write be done
* in strictly non-decreasing order of chunk address. For version 1 and 2 B-trees,
* this caused the non-participating ranks to issue a collective MPI_Bcast() call
* which the other ranks did not issue, thus causing a hang.
*
* However, since these ranks are not actually reading/writing anything, this call
* can simply be removed and the address used for the read/write can be set to an
* arbitrary number (0 was chosen).
*/
void test_partial_no_selection_coll_md_read(void)
{
const char *filename;
hsize_t *dataset_dims = NULL;
hsize_t max_dataset_dims[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hsize_t sel_dims[1];
hsize_t chunk_dims[PARTIAL_NO_SELECTION_DATASET_NDIMS] = { PARTIAL_NO_SELECTION_Y_DIM_SCALE, PARTIAL_NO_SELECTION_X_DIM_SCALE };
hsize_t start[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hsize_t stride[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hsize_t count[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hsize_t block[PARTIAL_NO_SELECTION_DATASET_NDIMS];
hid_t file_id = H5I_INVALID_HID;
hid_t fapl_id = H5I_INVALID_HID;
hid_t dset_id = H5I_INVALID_HID;
hid_t dcpl_id = H5I_INVALID_HID;
hid_t dxpl_id = H5I_INVALID_HID;
hid_t fspace_id = H5I_INVALID_HID;
hid_t mspace_id = H5I_INVALID_HID;
int mpi_rank, mpi_size;
void *data = NULL;
void *read_buf = NULL;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
filename = GetTestParameters();
fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
/*
* Even though the testphdf5 framework currently sets collective metadata reads
* on the FAPL, we call it here just to be sure this is futureproof, since
* demonstrating this issue relies upon it.
*/
VRFY((H5Pset_all_coll_metadata_ops(fapl_id, true) >= 0), "Set collective metadata reads succeeded");
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
dataset_dims = HDmalloc(PARTIAL_NO_SELECTION_DATASET_NDIMS * sizeof(*dataset_dims));
VRFY((dataset_dims != NULL), "malloc succeeded");
dataset_dims[0] = (hsize_t)PARTIAL_NO_SELECTION_Y_DIM_SCALE * (hsize_t)mpi_size;
dataset_dims[1] = (hsize_t)PARTIAL_NO_SELECTION_X_DIM_SCALE * (hsize_t)mpi_size;
max_dataset_dims[0] = H5S_UNLIMITED;
max_dataset_dims[1] = H5S_UNLIMITED;
fspace_id = H5Screate_simple(PARTIAL_NO_SELECTION_DATASET_NDIMS, dataset_dims, max_dataset_dims);
VRFY((fspace_id >= 0), "H5Screate_simple succeeded");
/*
* Set up chunking on the dataset in order to reproduce the problem.
*/
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
VRFY((H5Pset_chunk(dcpl_id, PARTIAL_NO_SELECTION_DATASET_NDIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
dset_id = H5Dcreate2(file_id, PARTIAL_NO_SELECTION_DATASET_NAME, H5T_NATIVE_INT, fspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
/*
* Setup hyperslab selection to split the dataset among the ranks.
*
* The ranks will write rows across the dataset.
*/
start[0] = (hsize_t)PARTIAL_NO_SELECTION_Y_DIM_SCALE * (hsize_t)mpi_rank;
start[1] = 0;
stride[0] = PARTIAL_NO_SELECTION_Y_DIM_SCALE;
stride[1] = PARTIAL_NO_SELECTION_X_DIM_SCALE;
count[0] = 1;
count[1] = (hsize_t)mpi_size;
block[0] = PARTIAL_NO_SELECTION_Y_DIM_SCALE;
block[1] = PARTIAL_NO_SELECTION_X_DIM_SCALE;
VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
sel_dims[0] = count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE);
mspace_id = H5Screate_simple(1, sel_dims, NULL);
VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
data = HDcalloc(1, count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
VRFY((data != NULL), "calloc succeeded");
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl_id >= 0), "H5Pcreate succeeded");
/*
* Enable collective access for the data transfer.
*/
VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded");
VRFY((H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, data) >= 0), "H5Dwrite succeeded");
VRFY((H5Fflush(file_id, H5F_SCOPE_GLOBAL) >= 0), "H5Fflush succeeded");
/*
* Ensure that linked-chunk I/O is performed since this is
* the particular code path where the issue lies and we don't
* want the library doing multi-chunk I/O behind our backs.
*/
VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_ONE_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
read_buf = HDmalloc(count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int));
VRFY((read_buf != NULL), "malloc succeeded");
/*
* Make sure to call H5Sselect_none() on the non-participating process.
*/
if (PARTIAL_NO_SELECTION_NO_SEL_PROCESS) {
VRFY((H5Sselect_none(fspace_id) >= 0), "H5Sselect_none succeeded");
VRFY((H5Sselect_none(mspace_id) >= 0), "H5Sselect_none succeeded");
}
/*
* Finally have each rank read their section of data back from the dataset.
*/
VRFY((H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, read_buf) >= 0), "H5Dread succeeded");
/*
* Check data integrity just to be sure.
*/
if (!PARTIAL_NO_SELECTION_NO_SEL_PROCESS) {
VRFY((!HDmemcmp(data, read_buf, count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) * sizeof(int))), "memcmp succeeded");
}
if (dataset_dims) {
HDfree(dataset_dims);
dataset_dims = NULL;
}
if (data) {
HDfree(data);
data = NULL;
}
if (read_buf) {
HDfree(read_buf);
read_buf = NULL;
}
VRFY((H5Sclose(fspace_id) >= 0), "H5Sclose succeeded");
VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded");
VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Dclose(dset_id) >= 0), "H5Dclose succeeded");
VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
}
/*
* A test for HDFFV-10562 which attempts to verify that using multi-chunk
* I/O with collective metadata reads enabled doesn't causes issues due to
* collective metadata reads being made only by process 0 in H5D__chunk_addrmap().
*
* Failure in this test may either cause a hang, or, due to how the MPI calls
* pertaining to this issue might mistakenly match up, may cause an MPI error
* message similar to:
*
* #008: H5Dmpio.c line 2546 in H5D__obtain_mpio_mode(): MPI_BCast failed
* major: Internal error (too specific to document in detail)
* minor: Some MPI function failed
* #009: H5Dmpio.c line 2546 in H5D__obtain_mpio_mode(): Message truncated, error stack:
*PMPI_Bcast(1600)..................: MPI_Bcast(buf=0x1df98e0, count=18, MPI_BYTE, root=0, comm=0x84000006) failed
*MPIR_Bcast_impl(1452).............:
*MPIR_Bcast(1476)..................:
*MPIR_Bcast_intra(1249)............:
*MPIR_SMP_Bcast(1088)..............:
*MPIR_Bcast_binomial(239)..........:
*MPIDI_CH3U_Receive_data_found(131): Message from rank 0 and tag 2 truncated; 2616 bytes received but buffer size is 18
* major: Internal error (too specific to document in detail)
* minor: MPI Error String
*
*/
void test_multi_chunk_io_addrmap_issue(void)
{
const char *filename;
hsize_t start[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
hsize_t stride[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
hsize_t count[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
hsize_t block[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS];
hsize_t dims[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS] = {10, 5};
hsize_t chunk_dims[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS] = {5, 5};
hsize_t max_dims[MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS] = {H5S_UNLIMITED, H5S_UNLIMITED};
hid_t file_id = H5I_INVALID_HID;
hid_t fapl_id = H5I_INVALID_HID;
hid_t dset_id = H5I_INVALID_HID;
hid_t dcpl_id = H5I_INVALID_HID;
hid_t dxpl_id = H5I_INVALID_HID;
hid_t space_id = H5I_INVALID_HID;
void *read_buf = NULL;
int mpi_rank;
int data[5][5] = { {0, 1, 2, 3, 4},
{0, 1, 2, 3, 4},
{0, 1, 2, 3, 4},
{0, 1, 2, 3, 4},
{0, 1, 2, 3, 4} };
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
filename = GetTestParameters();
fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
/*
* Even though the testphdf5 framework currently sets collective metadata reads
* on the FAPL, we call it here just to be sure this is futureproof, since
* demonstrating this issue relies upon it.
*/
VRFY((H5Pset_all_coll_metadata_ops(fapl_id, true) >= 0), "Set collective metadata reads succeeded");
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
space_id = H5Screate_simple(MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS, dims, max_dims);
VRFY((space_id >= 0), "H5Screate_simple succeeded");
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
VRFY((H5Pset_chunk(dcpl_id, MULTI_CHUNK_IO_ADDRMAP_ISSUE_DIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
dset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_INT, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl_id >= 0), "H5Pcreate succeeded");
VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded");
VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_MULTI_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
start[1] = 0;
stride[0] = stride[1] = 1;
count[0] = count[1] = 5;
block[0] = block[1] = 1;
if (mpi_rank == 0)
start[0] = 0;
else
start[0] = 5;
VRFY((H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
if (mpi_rank != 0)
VRFY((H5Sselect_none(space_id) >= 0), "H5Sselect_none succeeded");
VRFY((H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, space_id, dxpl_id, data) >= 0), "H5Dwrite succeeded");
VRFY((H5Fflush(file_id, H5F_SCOPE_GLOBAL) >= 0), "H5Fflush succeeded");
read_buf = HDmalloc(50 * sizeof(int));
VRFY((read_buf != NULL), "malloc succeeded");
VRFY((H5Dread(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl_id, read_buf) >= 0), "H5Dread succeeded");
if (read_buf) {
HDfree(read_buf);
read_buf = NULL;
}
VRFY((H5Sclose(space_id) >= 0), "H5Sclose succeeded");
VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Dclose(dset_id) >= 0), "H5Dclose succeeded");
VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
}
/*
* A test for HDFFV-10562 which attempts to verify that using linked-chunk
* I/O with collective metadata reads enabled doesn't cause issues due to
* collective metadata reads being made only by process 0 in H5D__sort_chunk().
*
* NOTE: Due to the way that the threshold value which pertains to this test
* is currently calculated within HDF5, there are several conditions that this
* test must maintain. Refer to the function H5D__sort_chunk in H5Dmpio.c for
* a better idea of why.
*
* Condition 1: We need to make sure that the test always selects every single
* chunk in the dataset. It is fine if the selection is split up among multiple
* ranks, but their combined selection must cover the whole dataset.
*
* Condition 2: The number of chunks in the dataset divided by the number of MPI
* ranks must exceed or equal 10000. In other words, each MPI rank must be
* responsible for 10000 or more unique chunks.
*
* Condition 3: This test will currently only be reliably reproducable for 2 or 3
* MPI ranks. The threshold value calculated reduces to a constant 100 / mpi_size,
* and is compared against a default value of 30%.
*
* Failure in this test may either cause a hang, or, due to how the MPI calls
* pertaining to this issue might mistakenly match up, may cause an MPI error
* message similar to:
*
* #008: H5Dmpio.c line 2338 in H5D__sort_chunk(): MPI_BCast failed
* major: Internal error (too specific to document in detail)
* minor: Some MPI function failed
* #009: H5Dmpio.c line 2338 in H5D__sort_chunk(): Other MPI error, error stack:
*PMPI_Bcast(1600)........: MPI_Bcast(buf=0x7eae610, count=320000, MPI_BYTE, root=0, comm=0x84000006) failed
*MPIR_Bcast_impl(1452)...:
*MPIR_Bcast(1476)........:
*MPIR_Bcast_intra(1249)..:
*MPIR_SMP_Bcast(1088)....:
*MPIR_Bcast_binomial(250): message sizes do not match across processes in the collective routine: Received 2096 but expected 320000
* major: Internal error (too specific to document in detail)
* minor: MPI Error String
*/
void test_link_chunk_io_sort_chunk_issue(void)
{
const char *filename;
hsize_t *dataset_dims = NULL;
hsize_t max_dataset_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hsize_t sel_dims[1];
hsize_t chunk_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS] = { LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS };
hsize_t start[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hsize_t stride[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hsize_t count[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hsize_t block[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hid_t file_id = H5I_INVALID_HID;
hid_t fapl_id = H5I_INVALID_HID;
hid_t dset_id = H5I_INVALID_HID;
hid_t dcpl_id = H5I_INVALID_HID;
hid_t dxpl_id = H5I_INVALID_HID;
hid_t fspace_id = H5I_INVALID_HID;
hid_t mspace_id = H5I_INVALID_HID;
int mpi_rank, mpi_size;
void *data = NULL;
void *read_buf = NULL;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
filename = GetTestParameters();
fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
/*
* Even though the testphdf5 framework currently sets collective metadata reads
* on the FAPL, we call it here just to be sure this is futureproof, since
* demonstrating this issue relies upon it.
*/
VRFY((H5Pset_all_coll_metadata_ops(fapl_id, true) >= 0), "Set collective metadata reads succeeded");
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
dataset_dims = HDmalloc(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS * sizeof(*dataset_dims));
VRFY((dataset_dims != NULL), "malloc succeeded");
dataset_dims[0] = (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE * (hsize_t)mpi_size * (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_Y_DIM_SCALE;
max_dataset_dims[0] = H5S_UNLIMITED;
fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, max_dataset_dims);
VRFY((fspace_id >= 0), "H5Screate_simple succeeded");
/*
* Set up chunking on the dataset in order to reproduce the problem.
*/
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
VRFY((H5Pset_chunk(dcpl_id, LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
dset_id = H5Dcreate2(file_id, LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME, H5T_NATIVE_INT, fspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
/*
* Setup hyperslab selection to split the dataset among the ranks.
*
* The ranks will write rows across the dataset.
*/
stride[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE;
count[0] = (dataset_dims[0] / LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) / (hsize_t)mpi_size;
start[0] = count[0] * (hsize_t)mpi_rank;
block[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE;
VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE);
mspace_id = H5Screate_simple(1, sel_dims, NULL);
VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
data = HDcalloc(1, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int));
VRFY((data != NULL), "calloc succeeded");
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl_id >= 0), "H5Pcreate succeeded");
/*
* Enable collective access for the data transfer.
*/
VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) >= 0), "H5Pset_dxpl_mpio succeeded");
VRFY((H5Dwrite(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, data) >= 0), "H5Dwrite succeeded");
VRFY((H5Fflush(file_id, H5F_SCOPE_GLOBAL) >= 0), "H5Fflush succeeded");
/*
* Ensure that linked-chunk I/O is performed since this is
* the particular code path where the issue lies and we don't
* want the library doing multi-chunk I/O behind our backs.
*/
VRFY((H5Pset_dxpl_mpio_chunk_opt(dxpl_id, H5FD_MPIO_CHUNK_ONE_IO) >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
read_buf = HDmalloc(count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int));
VRFY((read_buf != NULL), "malloc succeeded");
VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0), "H5Sselect_hyperslab succeeded");
sel_dims[0] = count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE);
VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded");
mspace_id = H5Screate_simple(1, sel_dims, NULL);
VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
read_buf = HDrealloc(read_buf, count[0] * (LINK_CHUNK_IO_SORT_CHUNK_ISSUE_CHUNK_SIZE) * sizeof(int));
VRFY((read_buf != NULL), "realloc succeeded");
/*
* Finally have each rank read their section of data back from the dataset.
*/
VRFY((H5Dread(dset_id, H5T_NATIVE_INT, mspace_id, fspace_id, dxpl_id, read_buf) >= 0), "H5Dread succeeded");
if (dataset_dims) {
HDfree(dataset_dims);
dataset_dims = NULL;
}
if (data) {
HDfree(data);
data = NULL;
}
if (read_buf) {
HDfree(read_buf);
read_buf = NULL;
}
VRFY((H5Sclose(fspace_id) >= 0), "H5Sclose succeeded");
VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded");
VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Dclose(dset_id) >= 0), "H5Dclose succeeded");
VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
}
Reference in New Issue View Git Blame Copy Permalink