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authorJordan Henderson <jhenderson@hdfgroup.org>2017-07-06 19:21:26 (GMT)
committerJordan Henderson <jhenderson@hdfgroup.org>2017-07-06 19:21:26 (GMT)
commit104047e13b2a1b726af3a907caef947d359fa34a (patch)
treecf38112804da0f600a9490ebca551ffe9ca1805f /src/H5Dmpio.c
parent610e76c75cbd8a91cc7b8e809bf122a87d182ef7 (diff)
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Amend header comment error
Suggested fix for allocating too small of a buffer for the chunk data
Diffstat (limited to 'src/H5Dmpio.c')
-rw-r--r--src/H5Dmpio.c37
1 files changed, 18 insertions, 19 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 91a730b..e70f51e 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -2223,7 +2223,8 @@ H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_in
* Description: Callback for qsort() to compare filtered collective chunk
* io info entries's original owner fields
*
- * Return: -1, 0, 1
+ * Return: The difference between the two
+ * H5D_filtered_collective_io_info_t's original owner fields
*
* Programmer: Jordan Henderson
* Monday, Apr. 10th, 2017
@@ -2754,7 +2755,6 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty
HDassert(io_info);
HDassert(type_info);
HDassert(fm);
- HDassert(local_chunk_array);
HDassert(local_chunk_array_num_entries);
if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0)
@@ -3100,6 +3100,8 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
unsigned char *mod_data = NULL; /* Chunk modification data sent by a process to a chunk's owner */
unsigned filter_mask = 0;
hssize_t iter_nelmts; /* Number of points to iterate over for the chunk IO operation */
+ hssize_t extent_npoints;
+ hsize_t true_chunk_size;
hbool_t mem_iter_init = FALSE;
size_t buf_size;
size_t i;
@@ -3120,24 +3122,16 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
if (NULL == (chunk_info = (H5D_chunk_info_t *) H5SL_search(fm->sel_chunks, &chunk_entry->index)))
HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list")
- /* If this is a read operation or a write operation where the chunk is not being fully
- * overwritten, enough memory must be allocated to read the filtered chunk from the file.
- * If this is a write operation where the chunk is being fully overwritten, enough memory
- * must be allocated for the size of the unfiltered chunk.
- */
- if (!chunk_entry->full_overwrite || io_info->op_type == H5D_IO_OP_READ) {
- buf_size = chunk_entry->chunk_states.chunk_current.length;
- } /* end if */
- else {
- hssize_t extent_npoints;
-
- if ((extent_npoints = H5S_GET_EXTENT_NPOINTS(chunk_info->fspace)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
-
- buf_size = (hsize_t) extent_npoints * type_info->src_type_size;
- } /* end else */
+ if ((extent_npoints = H5S_GET_EXTENT_NPOINTS(chunk_info->fspace)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
+ true_chunk_size = (hsize_t) extent_npoints * type_info->src_type_size;
- chunk_entry->chunk_states.new_chunk.length = buf_size;
+ /* If the size of the filtered chunk is larger than the number of points in the
+ * chunk file space extent times the datatype size, allocate enough space to hold the
+ * whole filtered chunk. Otherwise, allocate a buffer equal to the size of the
+ * chunk so that the unfiltering operation doesn't have to grow the buffer.
+ */
+ buf_size = MAX(chunk_entry->chunk_states.chunk_current.length, true_chunk_size);
if (NULL == (chunk_entry->buf = H5MM_malloc(buf_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer")
@@ -3146,6 +3140,8 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
* read from the file and unfiltered.
*/
if (!chunk_entry->full_overwrite || io_info->op_type == H5D_IO_OP_READ) {
+ chunk_entry->chunk_states.new_chunk.length = chunk_entry->chunk_states.chunk_current.length;
+
/* XXX: Test with MPI types and collective read to improve performance */
if (H5F_block_read(io_info->dset->oloc.file, H5FD_MEM_DRAW, chunk_entry->chunk_states.chunk_current.offset,
buf_size, H5AC_rawdata_dxpl_id, chunk_entry->buf) < 0)
@@ -3156,6 +3152,9 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
(size_t *) &chunk_entry->chunk_states.new_chunk.length, &buf_size, &chunk_entry->buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying")
} /* end if */
+ else {
+ chunk_entry->chunk_states.new_chunk.length = true_chunk_size;
+ } /* end else */
/* Initialize iterator for memory selection */
if (NULL == (mem_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(*mem_iter))))