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Partial fix for HDFFV-10792

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This commit is contained in:
Jordan Henderson 2019-10-07 16:00:44 -05:00
parent f32e70895e
commit c4f785bc93
2 changed files with 58 additions and 4 deletions
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13
release_docs/RELEASE.txt
View File

@ -370,6 +370,19 @@ Bug Fixes since HDF5-1.10.3 release
Library
-------
- Fixed an assertion failure in the parallel library when collectively
filling chunks. As it is required that chunks be written in
monotonically non-decreasing order of offset in the file, this assertion
was being triggered when the list of chunk file space allocations being
passed to the collective chunk filling routine was not sorted according
to this particular requirement.
The addition of a sort of the out of order chunks trades a bit of
performance for the elimination of this assertion and of any complaints
from MPI implementations about the file offsets used being out of order.
(JTH - 2019/10/07)
- Fixed the iteration error in test_versionbounds() in test/dtypes.c
The test was supposed to loop through all valid combinations of

49
src/H5Dchunk.c
View File

@ -323,6 +323,7 @@ static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfil
#ifdef H5_HAVE_PARALLEL
static herr_t H5D__chunk_collective_fill(const H5D_t *dset,
H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf);
static int H5D__chunk_cmp_addr(const void *addr1, const void *addr2);
#endif /* H5_HAVE_PARALLEL */
static int
@ -4977,6 +4978,7 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
MPI_Datatype mem_type, file_type;
H5FD_mpio_xfer_t prev_xfer_mode; /* Previous data xfer mode */
hbool_t have_xfer_mode = FALSE; /* Whether the previous xffer mode has been retrieved */
hbool_t need_addr_sort = FALSE;
int i; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
@ -5025,19 +5027,28 @@ H5D__chunk_collective_fill(const H5D_t *dset, H5D_chunk_coll_info_t *chunk_info,
/* make sure that the addresses in the datatype are
monotonically non decreasing */
if(i)
HDassert(chunk_disp_array[i] > chunk_disp_array[i - 1]);
} /* end if */
if(i && (chunk_disp_array[i] < chunk_disp_array[i - 1]))
need_addr_sort = TRUE;
} /* end for */
/* calculate if there are any leftover blocks after evenly
distributing. If there are, then round robin the distribution
to processes 0 -> leftover. */
if(leftover && leftover > mpi_rank) {
chunk_disp_array[blocks] = (MPI_Aint)chunk_info->addr[blocks*mpi_size + mpi_rank];
chunk_disp_array[blocks] = (MPI_Aint)chunk_info->addr[blocks*mpi_size + mpi_rank];
if(blocks && (chunk_disp_array[blocks] < chunk_disp_array[blocks - 1]))
need_addr_sort = TRUE;
block_lens[blocks] = block_len;
blocks++;
}
/*
* Ensure that the blocks are sorted in monotonically non-decreasing
* order of offset in the file.
*/
if(need_addr_sort)
HDqsort(chunk_disp_array, blocks, sizeof(MPI_Aint), H5D__chunk_cmp_addr);
/* MSC
* should use this if MPI_type_create_hindexed block is working
* mpi_code = MPI_Type_create_hindexed_block(blocks, block_len, chunk_disp_array, MPI_BYTE, &file_type);
@ -5093,6 +5104,36 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_collective_fill() */
static int
H5D__chunk_cmp_addr(const void *addr1, const void *addr2)
{
MPI_Aint _addr1 = (MPI_Aint)0, _addr2 = (MPI_Aint)0;
int ret_value = 0;
FUNC_ENTER_STATIC_NOERR
_addr1 = *((const MPI_Aint *) addr1);
_addr2 = *((const MPI_Aint *) addr2);
#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1
{
MPI_Aint diff = MPI_Aint_diff(_addr1, _addr2);
if(diff < (MPI_Aint)0)
ret_value = -1;
else if(diff > (MPI_Aint)0)
ret_value = 1;
else
ret_value = 0;
}
#else
ret_value = (_addr1 > _addr2) - (_addr1 < _addr2);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_cmp_addr() */
#endif /* H5_HAVE_PARALLEL */