diff options
| -rw-r--r-- | src/H5Dmpio.c | 40 |
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) |