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hdf5/testpar/t_coll_md.c

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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://www.hdfgroup.org/licenses. *
* 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 and write capabilities,
* as enabled by making a call to H5Pset_all_coll_metadata_ops() and/or
* H5Pset_coll_metadata_write().
*/
#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_COLL_THRESH_NUM 10000
#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DATASET_NAME "linked_chunk_io_sort_chunk_issue"
#define LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS 1
#define COLL_GHEAP_WRITE_ATTR_NELEMS 10
#define COLL_GHEAP_WRITE_ATTR_NAME "coll_gheap_write_attr"
#define COLL_GHEAP_WRITE_ATTR_DIMS 1
#define COLL_IO_IND_MD_WRITE_NDIMS 2
#define COLL_IO_IND_MD_WRITE_CHUNK0 4
#define COLL_IO_IND_MD_WRITE_CHUNK1 256
#define COLL_IO_IND_MD_WRITE_NCHUNK1 16384
/*
* 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 = malloc(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 = calloc(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 = malloc(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((!memcmp(data, read_buf,
count[1] * (PARTIAL_NO_SELECTION_Y_DIM_SCALE * PARTIAL_NO_SELECTION_X_DIM_SCALE) *
sizeof(int))),
"memcmp succeeded");
}
if (dataset_dims) {
free(dataset_dims);
dataset_dims = NULL;
}
if (data) {
free(data);
data = NULL;
}
if (read_buf) {
free(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 = malloc(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) {
free(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().
*
* 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[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hsize_t sel_dims[LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS];
hsize_t chunk_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");
/*
* Create a one-dimensional dataset of exactly LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM
* chunks, where every rank writes to a piece of every single chunk to keep utilization high.
*/
dataset_dims[0] = (hsize_t)mpi_size * (hsize_t)LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM;
fspace_id = H5Screate_simple(LINK_CHUNK_IO_SORT_CHUNK_ISSUE_DIMS, dataset_dims, NULL);
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");
/* Chunk size is equal to MPI size since each rank writes to a piece of every chunk */
chunk_dims[0] = (hsize_t)mpi_size;
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.
*/
start[0] = (hsize_t)mpi_rank;
stride[0] = (hsize_t)mpi_size;
count[0] = LINK_CHUNK_IO_SORT_CHUNK_ISSUE_COLL_THRESH_NUM;
block[0] = 1;
VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, start, stride, count, block) >= 0),
"H5Sselect_hyperslab succeeded");
sel_dims[0] = count[0];
mspace_id = H5Screate_simple(1, sel_dims, NULL);
VRFY((mspace_id >= 0), "H5Screate_simple succeeded");
data = calloc(1, count[0] * 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 = malloc(count[0] * 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];
VRFY((H5Sclose(mspace_id) >= 0), "H5Sclose succeeded");
mspace_id = H5Screate_simple(1, sel_dims, NULL);
VRFY((mspace_id >= 0), "H5Screate_simple 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 (data) {
free(data);
data = NULL;
}
if (read_buf) {
free(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 GitHub issue #2433 which causes a collective metadata write
* of global heap data. This test is meant to ensure that global heap data
* gets correctly mapped as raw data during a collective metadata write
* using vector I/O.
*
* An assertion exists in the library that should be triggered if global
* heap data is not correctly mapped as raw data.
*/
void
test_collective_global_heap_write(void)
{
const char *filename;
hsize_t attr_dims[COLL_GHEAP_WRITE_ATTR_DIMS];
hid_t file_id = H5I_INVALID_HID;
hid_t fapl_id = H5I_INVALID_HID;
hid_t attr_id = H5I_INVALID_HID;
hid_t vl_type = H5I_INVALID_HID;
hid_t fspace_id = H5I_INVALID_HID;
hvl_t vl_data;
int mpi_rank, mpi_size;
int data_buf[COLL_GHEAP_WRITE_ATTR_NELEMS];
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
* writes on the FAPL, we call it here just to be sure this is futureproof,
* since demonstrating this issue relies upon it.
*/
VRFY((H5Pset_coll_metadata_write(fapl_id, true) >= 0), "Set collective metadata writes succeeded");
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
attr_dims[0] = 1;
fspace_id = H5Screate_simple(COLL_GHEAP_WRITE_ATTR_DIMS, attr_dims, NULL);
VRFY((fspace_id >= 0), "H5Screate_simple succeeded");
vl_type = H5Tvlen_create(H5T_NATIVE_INT);
VRFY((vl_type >= 0), "H5Tvlen_create succeeded");
vl_data.len = COLL_GHEAP_WRITE_ATTR_NELEMS;
vl_data.p = data_buf;
/*
* Create a variable-length attribute that will get written to the global heap
*/
attr_id = H5Acreate2(file_id, COLL_GHEAP_WRITE_ATTR_NAME, vl_type, fspace_id, H5P_DEFAULT, H5P_DEFAULT);
VRFY((attr_id >= 0), "H5Acreate2 succeeded");
for (size_t i = 0; i < COLL_GHEAP_WRITE_ATTR_NELEMS; i++)
data_buf[i] = (int)i;
VRFY((H5Awrite(attr_id, vl_type, &vl_data) >= 0), "H5Awrite succeeded");
VRFY((H5Sclose(fspace_id) >= 0), "H5Sclose succeeded");
VRFY((H5Tclose(vl_type) >= 0), "H5Sclose succeeded");
VRFY((H5Aclose(attr_id) >= 0), "H5Aclose succeeded");
VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
}
/*
* A test to ensure that hangs don't occur when collective I/O
* is requested at the interface level (by a call to
* H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE)), while
* collective metadata writes are NOT requested.
*/
void
test_coll_io_ind_md_write(void)
{
const char *filename;
long long *data = NULL;
hsize_t dset_dims[COLL_IO_IND_MD_WRITE_NDIMS];
hsize_t chunk_dims[COLL_IO_IND_MD_WRITE_NDIMS];
hsize_t sel_dims[COLL_IO_IND_MD_WRITE_NDIMS];
hsize_t offset[COLL_IO_IND_MD_WRITE_NDIMS];
hid_t file_id = H5I_INVALID_HID;
hid_t fapl_id = H5I_INVALID_HID;
hid_t dset_id = H5I_INVALID_HID;
hid_t dset_id2 = H5I_INVALID_HID;
hid_t dcpl_id = H5I_INVALID_HID;
hid_t dxpl_id = H5I_INVALID_HID;
hid_t fspace_id = H5I_INVALID_HID;
int mpi_rank, mpi_size;
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");
VRFY((H5Pset_all_coll_metadata_ops(fapl_id, false) >= 0), "Unset collective metadata reads succeeded");
VRFY((H5Pset_coll_metadata_write(fapl_id, false) >= 0), "Unset collective metadata writes succeeded");
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
dset_dims[0] = (hsize_t)(mpi_size * COLL_IO_IND_MD_WRITE_CHUNK0);
dset_dims[1] = (hsize_t)(COLL_IO_IND_MD_WRITE_CHUNK1 * COLL_IO_IND_MD_WRITE_NCHUNK1);
fspace_id = H5Screate_simple(COLL_IO_IND_MD_WRITE_NDIMS, dset_dims, NULL);
VRFY((fspace_id >= 0), "H5Screate_simple succeeded");
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
chunk_dims[0] = (hsize_t)(COLL_IO_IND_MD_WRITE_CHUNK0);
chunk_dims[1] = (hsize_t)(COLL_IO_IND_MD_WRITE_CHUNK1);
VRFY((H5Pset_chunk(dcpl_id, COLL_IO_IND_MD_WRITE_NDIMS, chunk_dims) >= 0), "H5Pset_chunk succeeded");
VRFY((H5Pset_shuffle(dcpl_id) >= 0), "H5Pset_shuffle succeeded");
dset_id = H5Dcreate2(file_id, "dset1", H5T_NATIVE_LLONG, fspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
sel_dims[0] = (hsize_t)(COLL_IO_IND_MD_WRITE_CHUNK0);
sel_dims[1] = (hsize_t)(COLL_IO_IND_MD_WRITE_CHUNK1 * COLL_IO_IND_MD_WRITE_NCHUNK1);
offset[0] = (hsize_t)mpi_rank * sel_dims[0];
offset[1] = 0;
VRFY((H5Sselect_hyperslab(fspace_id, H5S_SELECT_SET, offset, NULL, sel_dims, NULL) >= 0),
"H5Sselect_hyperslab 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");
data = malloc(sel_dims[0] * sel_dims[1] * sizeof(long long));
for (size_t i = 0; i < sel_dims[0] * sel_dims[1]; i++)
data[i] = rand();
VRFY((H5Dwrite(dset_id, H5T_NATIVE_LLONG, H5S_BLOCK, fspace_id, dxpl_id, data) >= 0),
"H5Dwrite succeeded");
dset_id2 = H5Dcreate2(file_id, "dset2", H5T_NATIVE_LLONG, fspace_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id2 >= 0), "H5Dcreate2 succeeded");
for (size_t i = 0; i < sel_dims[0] * sel_dims[1]; i++)
data[i] = rand();
VRFY((H5Dwrite(dset_id2, H5T_NATIVE_LLONG, H5S_BLOCK, fspace_id, dxpl_id, data) >= 0),
"H5Dwrite succeeded");
free(data);
VRFY((H5Sclose(fspace_id) >= 0), "H5Sclose succeeded");
VRFY((H5Dclose(dset_id) >= 0), "H5Dclose succeeded");
VRFY((H5Dclose(dset_id2) >= 0), "H5Dclose succeeded");
VRFY((H5Pclose(dcpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Pclose(dxpl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Pclose(fapl_id) >= 0), "H5Pclose succeeded");
VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded");
}
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