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authorJordan Henderson <jhenderson@hdfgroup.org>2017-02-03 19:21:10 (GMT)
committerJordan Henderson <jhenderson@hdfgroup.org>2017-02-03 19:21:10 (GMT)
commitb458565918a878d84d619ecbfce917102945ead0 (patch)
tree6699783e1e38a5e35deab966b8c17b59f10199be /src/H5Dmpio.c
parentaf3227fe4ea83a42f3d35b26a86898943107bf6f (diff)
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Fix bug where data doesn't write correctly when MEMSPACE isnt the same
as FILESPACE
Diffstat (limited to 'src/H5Dmpio.c')
-rw-r--r--src/H5Dmpio.c40
1 files changed, 33 insertions, 7 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index c1d044f..20b6d08 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -1945,7 +1945,6 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i
/* Gather the new chunk sizes to all processes for a collective re-allocation
* of the chunks in the file
*/
- /* XXX: May access unavailable memory on processes with no selection */
if (H5D__mpio_array_gather(io_info, &chunk_list[i], have_chunk_to_process ? 1 : 0, sizeof(*chunk_list),
(void **) &collective_chunk_list, &collective_chunk_list_num_entries, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes")
@@ -3148,6 +3147,8 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
size_t buf_size;
size_t mod_data_alloced_bytes = 0;
H5S_t *dataspace = NULL; /* Other process' dataspace for the chunk */
+ void *tmp_gath_buf = NULL; /* Temporary gather buffer for owner of the chunk to gather into from
+ application write buffer before scattering out to the chunk data buffer */
herr_t ret_value = SUCCEED;
FUNC_ENTER_STATIC
@@ -3241,13 +3242,36 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
break;
case H5D_IO_OP_WRITE:
- /* Update the chunk data with the modifications from the current (owning) process */
+ if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer")
+
+ /* Gather modification data from the application write buffer into a temporary buffer */
if (!H5D__gather_mem(io_info->u.wbuf, chunk_entry->chunk_info.mspace, mem_iter,
- (size_t) iter_nelmts, io_info->dxpl_cache, chunk_entry->buf))
+ (size_t) iter_nelmts, io_info->dxpl_cache, tmp_gath_buf))
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't gather from write buffer")
- if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+ if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
+ mem_iter_init = FALSE;
+
+ /* Initialize iterator for file selection */
+ if (H5S_select_iter_init(mem_iter, chunk_entry->chunk_info.fspace, type_info->dst_type_size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information")
+ mem_iter_init = TRUE;
+
+ if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_entry->chunk_info.fspace)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
+
+ /* Scatter the owner's modification data into the chunk data buffer according to
+ * the file space.
+ */
+ if (H5D__scatter_mem(tmp_gath_buf, chunk_entry->chunk_info.fspace, mem_iter,
+ (size_t) iter_nelmts, io_info->dxpl_cache, chunk_entry->buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to chunk data buffer")
+
+ if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
+ mem_iter_init = FALSE;
/* Update the chunk data with any modifications from other processes */
while (chunk_entry->num_writers > 1) {
@@ -3336,14 +3360,14 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
chunk_entry->num_writers--;
- if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+ if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
+ mem_iter_init = FALSE;
if (dataspace) {
if (H5S_close(dataspace) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace")
dataspace = NULL;
}
- mem_iter_init = FALSE;
} /* end while */
@@ -3374,11 +3398,13 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
break;
default:
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "invalid I/O operation")
- }
+ } /* end switch */
done:
if (mod_data)
H5MM_free(mod_data);
+ if (tmp_gath_buf)
+ H5MM_free(tmp_gath_buf);
if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
if (mem_iter)