diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 13 | ||||
| -rw-r--r-- | src/H5Dchunk.c | 49 |
2 files changed, 58 insertions, 4 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index c2f2ebe..2a0dc8e 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -380,6 +380,19 @@ 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 diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 53ca7d1..09fb709 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -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 */ |