diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 188 |
1 files changed, 117 insertions, 71 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 189d9f1..bcb90a0 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -44,6 +44,12 @@ #define H5D_DEFAULT_SKIPLIST_HEIGHT 8 +/* Macros for iterating over chunks to operate on */ +#define H5D_CHUNK_GET_FIRST_NODE(map) (map.use_single ? (H5SL_node_t *)(1) : H5SL_first(map.sel_chunks)) +#define H5D_CHUNK_GET_NODE_INFO(map, node) (map.use_single ? map.single_chunk_info : (H5D_chunk_info_t *)H5SL_item(node)) +#define H5D_CHUNK_GET_NEXT_NODE(map, node) (map.use_single ? (H5SL_node_t *)NULL : H5SL_next(node)) + + /******************/ /* Local Typedefs */ /******************/ @@ -119,7 +125,7 @@ static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims, H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage the H5D_chunk_info_t struct */ -H5FL_DEFINE_STATIC(H5D_chunk_info_t); +H5FL_DEFINE(H5D_chunk_info_t); /* Declare a free list to manage sequences of size_t */ H5FL_SEQ_DEFINE_STATIC(size_t); @@ -1412,13 +1418,13 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, else {/* sequential or independent read */ #endif /* Get first node in chunk skip list */ - chunk_node = H5SL_first(fm.sel_chunks); + chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm); while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list node */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node); + chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* Pass in chunk's coordinates in a union. */ store.chunk.offset = chunk_info->coords; @@ -1446,7 +1452,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, } /* end if */ /* Advance to next chunk in list */ - chunk_node = H5SL_next(chunk_node); + chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node); } /* end while */ #ifdef H5_HAVE_PARALLEL } @@ -1521,14 +1527,14 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, /* Loop over all the chunks, performing I/O on each */ /* Get first node in chunk skip list */ - chunk_node=H5SL_first(fm.sel_chunks); + chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm); /* Iterate through chunks to be operated on */ while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list nodes */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node); + chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, src_type_size) < 0) @@ -1671,7 +1677,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, } /* end if */ /* Get the next chunk node in the skip list */ - chunk_node=H5SL_next(chunk_node); + chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node); } /* end while */ done: @@ -1810,13 +1816,13 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, else {/* sequential or independent write */ #endif /* H5_HAVE_PARALLEL */ /* Get first node in chunk skip list */ - chunk_node=H5SL_first(fm.sel_chunks); + chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm); while(chunk_node) { H5D_chunk_info_t *chunk_info; /* Chunk information */ /* Get the actual chunk information from the skip list node */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node); + chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* Pass in chunk's coordinates in a union. */ store.chunk.offset = chunk_info->coords; @@ -1850,7 +1856,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, relax = TRUE; /* Advance to next chunk in list */ - chunk_node = H5SL_next(chunk_node); + chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node); } /* end while */ #ifdef H5_HAVE_PARALLEL } @@ -1928,14 +1934,14 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, /* Loop over all the chunks, performing I/O on each */ /* Get first node in chunk skip list */ - chunk_node=H5SL_first(fm.sel_chunks); + chunk_node = H5D_CHUNK_GET_FIRST_NODE(fm); /* Iterate through chunks to be operated on */ while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list node */ - chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node); + chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, dst_type_size) < 0) @@ -2083,7 +2089,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, } /* end if */ /* Get the next chunk node in the skip list */ - chunk_node=H5SL_next(chunk_node); + chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node); } /* end while */ done: @@ -2412,14 +2418,6 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info, #endif /* H5_HAVE_PARALLEL */ - /* Initialize skip list for chunk selections */ - if(NULL == dataset->shared->cache.chunk.sel_chunks) { - if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_DEFAULT_SKIPLIST_HEIGHT))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections") - } /* end if */ - fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks; - HDassert(fm->sel_chunks); - /* Initialize "last chunk" information */ fm->last_index = (hsize_t)-1; fm->last_chunk_info = NULL; @@ -2430,7 +2428,40 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info, /* Special case for only one element in selection */ /* (usually appending a record) */ - if(nelmts == 1) { + if(nelmts == 1 +#ifdef H5_HAVE_PARALLEL + && !(io_info->using_mpi_vfd) +#endif /* H5_HAVE_PARALLEL */ + ) { + /* Initialize skip list for chunk selections */ + fm->sel_chunks = NULL; + fm->use_single = TRUE; + + /* Initialize single chunk dataspace */ + if(NULL == dataset->shared->cache.chunk.single_space) { + /* Make a copy of the dataspace for the dataset */ + if((dataset->shared->cache.chunk.single_space = H5S_copy(file_space, TRUE, FALSE)) == NULL) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space") + + /* Resize chunk's dataspace dimensions to size of chunk */ + if(H5S_set_extent_real(dataset->shared->cache.chunk.single_space, fm->chunk_dim) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't adjust chunk dimensions") + + /* Set the single chunk dataspace to 'all' selection */ + if(H5S_select_all(dataset->shared->cache.chunk.single_space, TRUE) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to set all selection") + } /* end if */ + fm->single_space = dataset->shared->cache.chunk.single_space; + HDassert(fm->single_space); + + /* Allocate the single chunk information */ + if(NULL == dataset->shared->cache.chunk.single_chunk_info) { + if(NULL == (dataset->shared->cache.chunk.single_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") + } /* end if */ + fm->single_chunk_info = dataset->shared->cache.chunk.single_chunk_info; + HDassert(fm->single_chunk_info); + /* Reset chunk template information */ fm->mchunk_tmpl = NULL; @@ -2439,6 +2470,17 @@ H5D_create_chunk_map(H5D_chunk_map_t *fm, const H5D_io_info_t *io_info, HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element") } /* end if */ else { + /* Initialize skip list for chunk selections */ + if(NULL == dataset->shared->cache.chunk.sel_chunks) { + if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, 0.5, (size_t)H5D_DEFAULT_SKIPLIST_HEIGHT))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk selections") + } /* end if */ + fm->sel_chunks = dataset->shared->cache.chunk.sel_chunks; + HDassert(fm->sel_chunks); + + /* We are not using single element mode */ + fm->use_single = FALSE; + /* Get type of selection on disk & in memory */ if((fsel_type = H5S_GET_SELECT_TYPE(file_space)) < H5S_SEL_NONE) HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection") @@ -2596,7 +2638,7 @@ done: RETURNS No return value DESCRIPTION - Releases all the memory for a chunk info node. Called by H5SL_iterate + Releases all the memory for a chunk info node. Called by H5SL_free GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES @@ -2605,21 +2647,24 @@ done: static herr_t H5D_free_chunk_info(void *item, void UNUSED *key, void UNUSED *opdata) { - H5D_chunk_info_t *chunk_info=(H5D_chunk_info_t *)item; + H5D_chunk_info_t *chunk_info = (H5D_chunk_info_t *)item; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info) - assert(chunk_info); + HDassert(chunk_info); - /* Close the chunk's file dataspace */ - (void)H5S_close(chunk_info->fspace); + /* Close the chunk's file dataspace, if it's not shared */ + if(!chunk_info->fspace_shared) + (void)H5S_close(chunk_info->fspace); + else + H5S_select_all(chunk_info->fspace, TRUE); /* Close the chunk's memory dataspace, if it's not shared */ if(!chunk_info->mspace_shared) (void)H5S_close(chunk_info->mspace); /* Free the actual chunk info */ - H5FL_FREE(H5D_chunk_info_t,chunk_info); + H5FL_FREE(H5D_chunk_info_t, chunk_info); FUNC_LEAVE_NOAPI(0); } /* H5D_free_chunk_info() */ @@ -2644,10 +2689,23 @@ H5D_destroy_chunk_map(const H5D_chunk_map_t *fm) FUNC_ENTER_NOAPI_NOINIT(H5D_destroy_chunk_map) - /* Release the nodes on the list of selected chunks */ - if(fm->sel_chunks) - if(H5SL_free(fm->sel_chunks, H5D_free_chunk_info, NULL) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTNEXT, FAIL, "can't iterate over chunks") + /* Single element I/O vs. multiple element I/O cleanup */ + if(fm->use_single) { + /* Sanity checks */ + HDassert(fm->sel_chunks == NULL); + HDassert(fm->single_chunk_info); + HDassert(fm->single_chunk_info->fspace_shared); + HDassert(fm->single_chunk_info->mspace_shared); + + /* Reset the selection for the single element I/O */ + H5S_select_all(fm->single_space, TRUE); + } /* end if */ + else { + /* Release the nodes on the list of selected chunks */ + if(fm->sel_chunks) + if(H5SL_free(fm->sel_chunks, H5D_free_chunk_info, NULL) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTNEXT, FAIL, "can't iterate over chunks") + } /* end else */ /* Free the memory chunk dataspace template */ if(fm->mchunk_tmpl) @@ -2682,8 +2740,7 @@ H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t #endif /* H5_HAVE_PARALLEL */ *io_info) { - H5S_t *tmp_fchunk = NULL; /* Temporary file dataspace */ - H5D_chunk_info_t *new_chunk_info = NULL; /* chunk information to insert into skip list */ + H5D_chunk_info_t *chunk_info; /* Chunk information to insert into skip list */ hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ unsigned u; /* Local index variable */ @@ -2698,62 +2755,49 @@ H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") - /* Allocate the file & memory chunk information */ - if(NULL == (new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") - new_chunk_info->chunk_points = 1; + /* Initialize the 'single chunk' file & memory chunk information */ + chunk_info = fm->single_chunk_info; + chunk_info->chunk_points = 1; /* Set chunk location & hyperslab size */ for(u = 0; u < fm->f_ndims; u++) { HDassert(sel_start[u] == sel_end[u]); - new_chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u]; + chunk_info->coords[u] = (sel_start[u] / fm->layout->u.chunk.dim[u]) * fm->layout->u.chunk.dim[u]; } /* end for */ - new_chunk_info->coords[fm->f_ndims] = 0; + chunk_info->coords[fm->f_ndims] = 0; /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims, new_chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &new_chunk_info->index) < 0) + if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") - /* Create chunk dataspace for selection operations (copy file space) */ - if((tmp_fchunk = H5S_copy(fm->file_space, FALSE, FALSE)) == NULL) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") - - /* Resize chunk's dataspace dimensions to size of chunk */ - if(H5S_set_extent_real(tmp_fchunk, fm->chunk_dim) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions") + /* Copy selection for file's dataspace into chunk dataspace */ + if(H5S_select_copy(fm->single_space, fm->file_space, FALSE) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file selection") /* Move selection back to have correct offset in chunk */ - if(H5S_SELECT_ADJUST_U(tmp_fchunk, new_chunk_info->coords) < 0) + if(H5S_SELECT_ADJUST_U(fm->single_space, chunk_info->coords) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") #ifdef H5_HAVE_PARALLEL /* store chunk selection information */ if(io_info->using_mpi_vfd) - fm->select_chunk[new_chunk_info->index] = TRUE; + fm->select_chunk[chunk_info->index] = TRUE; #endif /* H5_HAVE_PARALLEL */ - /* Set the file chunk dataspace */ - new_chunk_info->fspace = tmp_fchunk; + /* Set the file dataspace for the chunk to the shared 'single' dataspace */ + chunk_info->fspace = fm->single_space; + + /* Indicate that the chunk's file dataspace is shared */ + chunk_info->fspace_shared = TRUE; /* Just point at the memory dataspace & selection */ /* (Casting away const OK -QAK) */ - new_chunk_info->mspace = (H5S_t *)fm->mem_space; + chunk_info->mspace = (H5S_t *)fm->mem_space; - /* Indicate that the chunk's memory space is shared */ - new_chunk_info->mspace_shared = 1; - - /* Insert the new chunk into the skip list */ - if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list") + /* Indicate that the chunk's memory dataspace is shared */ + chunk_info->mspace_shared = TRUE; done: - if(ret_value < 0) { - if(new_chunk_info) - (void)H5D_free_chunk_info(new_chunk_info, NULL, NULL); - if(tmp_fchunk) - (void)H5S_close(tmp_fchunk); - } /* end if */ - FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create_chunk_map_single() */ @@ -2870,11 +2914,12 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t #endif /* H5_HAVE_PARALLEL */ /* Set the file chunk dataspace */ - new_chunk_info->fspace=tmp_fchunk; + new_chunk_info->fspace = tmp_fchunk; + new_chunk_info->fspace_shared = FALSE; /* Set the memory chunk dataspace */ new_chunk_info->mspace=NULL; - new_chunk_info->mspace_shared=0; + new_chunk_info->mspace_shared = FALSE; /* Copy the chunk's coordinates */ for(u=0; u<fm->f_ndims; u++) @@ -2988,7 +3033,7 @@ H5D_create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) chunk_info->mspace=(H5S_t *)fm->mem_space; /* Indicate that the chunk's memory space is shared */ - chunk_info->mspace_shared=1; + chunk_info->mspace_shared = TRUE; } /* end if */ else { /* Get bounding box for file selection */ @@ -3117,11 +3162,12 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const } /* end if */ /* Set the file chunk dataspace */ - chunk_info->fspace=fspace; + chunk_info->fspace = fspace; + chunk_info->fspace_shared = FALSE; /* Set the memory chunk dataspace */ chunk_info->mspace=NULL; - chunk_info->mspace_shared=0; + chunk_info->mspace_shared = FALSE; /* Set the number of selected elements in chunk to zero */ chunk_info->chunk_points=0; |