diff options
Diffstat (limited to 'src/H5Dchunk.c')
| -rw-r--r-- | src/H5Dchunk.c | 155 |
1 files changed, 100 insertions, 55 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 5c99c90..d210f6d 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -112,7 +112,6 @@ typedef struct H5D_chunk_it_ud1_t { const H5D_io_info_t *io_info; /* I/O info for dataset operation */ const hsize_t *dims; /* New dataset dimensions */ const hbool_t *shrunk_dims; /* Dimensions which have been shrunk */ - const hsize_t *down_chunks; /* "down" size of number of chunks in each dimension */ H5D_chunk_prune_stack_t *rm_stack; /* Stack of chunks outside the new dimensions */ H5S_t *chunk_space; /* Dataspace for a chunk */ uint32_t elmts_per_chunk;/* Elements in chunk */ @@ -122,10 +121,9 @@ typedef struct H5D_chunk_it_ud1_t { } H5D_chunk_it_ud1_t; /* Callback info for iteration to obtain chunk address and the index of the chunk for all chunks in the B-tree. */ -typedef struct H5D_chunk_id_ud2_t { +typedef struct H5D_chunk_it_ud2_t { /* down */ H5D_chunk_common_ud_t common; /* Common info for B-tree user data (must be first) */ - const hsize_t *down_chunks; /* "down chunk" element counts for chunks */ /* up */ haddr_t *chunk_addr; /* Array of chunk addresses to fill in */ @@ -270,6 +268,88 @@ H5FL_DEFINE_STATIC(H5D_chunk_prune_stack_t); /*------------------------------------------------------------------------- + * Function: H5D_chunk_set_info_real + * + * Purpose: Internal routine to set the information about chunks for a dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, June 30, 2009 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_chunk_set_info_real(H5O_layout_t *layout, unsigned ndims, const hsize_t *curr_dims) +{ + unsigned u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_chunk_set_info_real, FAIL) + + /* Sanity checks */ + HDassert(layout); + HDassert(ndims > 0); + HDassert(curr_dims); + + /* Compute the # of chunks in dataset dimensions */ + for(u = 0, layout->u.chunk.nchunks = 1; u < ndims; u++) { + /* Round up to the next integer # of chunks, to accomodate partial chunks */ + layout->u.chunk.chunks[u] = ((curr_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u]; + + /* Accumulate the # of chunks */ + layout->u.chunk.nchunks *= layout->u.chunk.chunks[u]; + } /* end for */ + + /* Get the "down" sizes for each dimension */ + if(H5V_array_down(ndims, layout->u.chunk.chunks, layout->u.chunk.down_chunks) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_chunk_set_info_real() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_set_info + * + * Purpose: Sets the information about chunks for a dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Quincey Koziol + * Tuesday, June 30, 2009 + * + *------------------------------------------------------------------------- + */ +herr_t +H5D_chunk_set_info(const H5D_t *dset) +{ + hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /* Curr. size of dataset dimensions */ + int sndims; /* Rank of dataspace */ + unsigned ndims; /* Rank of dataspace */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_chunk_set_info, FAIL) + + /* Sanity checks */ + HDassert(dset); + + /* Get the dim info for dataset */ + if((sndims = H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL)) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataspace dimensions") + H5_ASSIGN_OVERFLOW(ndims, sndims, int, unsigned); + + /* Set the layout information */ + if(H5D_chunk_set_info_real(&dset->shared->layout, ndims, curr_dims) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout's chunk info") + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_chunk_set_info() */ + + +/*------------------------------------------------------------------------- * Function: H5D_chunk_construct * * Purpose: Constructs new chunked layout information for dataset @@ -407,6 +487,10 @@ H5D_chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id) H5D_chunk_cinfo_cache_reset(&(rdcc->last)); } /* end else */ + /* Set the number of chunks in dataset */ + if(H5D_chunk_set_info(dset) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set # of chunks for dataset") + /* Compose chunked index info struct */ idx_info.f = f; idx_info.dxpl_id = dxpl_id; @@ -514,24 +598,14 @@ H5D_chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info for(u = 0; u < f_ndims; u++) { /* Keep the size of the chunk dimensions as hsize_t for various routines */ fm->chunk_dim[u] = fm->layout->u.chunk.dim[u]; - - /* Round up to the next integer # of chunks, to accomodate partial chunks */ - fm->chunks[u] = ((fm->f_dims[u] + dataset->shared->layout.u.chunk.dim[u]) - 1) / dataset->shared->layout.u.chunk.dim[u]; } /* end for */ - /* Compute the "down" size of 'chunks' information */ - if(H5V_array_down(f_ndims, fm->chunks, fm->down_chunks) < 0) - HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") - #ifdef H5_HAVE_PARALLEL /* Calculate total chunk in file map*/ fm->select_chunk = NULL; - fm->total_chunks = 1; - for(u = 0; u < fm->f_ndims; u++) - fm->total_chunks = fm->total_chunks * fm->chunks[u]; if(io_info->using_mpi_vfd) { - H5_CHECK_OVERFLOW(fm->total_chunks, hsize_t, size_t); - if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->total_chunks * sizeof(H5D_chunk_info_t *)))) + H5_CHECK_OVERFLOW(fm->layout->u.chunk.nchunks, hsize_t, size_t); + if(NULL == (fm->select_chunk = (H5D_chunk_info_t **)H5MM_calloc((size_t)fm->layout->u.chunk.nchunks * sizeof(H5D_chunk_info_t *)))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") } /* end if */ #endif /* H5_HAVE_PARALLEL */ @@ -901,7 +975,7 @@ H5D_create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t chunk_info->coords[fm->f_ndims] = 0; /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_info->index) < 0) + if(H5V_chunk_index(fm->f_ndims, chunk_info->coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_info->index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Copy selection for file's dataspace into chunk dataspace */ @@ -985,9 +1059,8 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t end[u] = (coords[u] + fm->chunk_dim[u]) - 1; } /* end for */ - /* Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0) + if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Iterate through each chunk in the dataset */ @@ -1104,8 +1177,8 @@ H5D_create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; } while(coords[curr_dim] > sel_end[curr_dim]); - /* Re-Calculate the index of this chunk */ - if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0) + /* Re-calculate the index of this chunk */ + if(H5V_chunk_index(fm->f_ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ } /* end while */ @@ -1253,7 +1326,7 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb) /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0) + if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory skip list */ @@ -1365,7 +1438,7 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb) /* Calculate the index of this chunk */ - if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->down_chunks, &chunk_index) < 0) + if(H5V_chunk_index(ndims, coords, fm->layout->u.chunk.dim, fm->layout->u.chunk.down_chunks, &chunk_index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory skip list */ @@ -3318,8 +3391,7 @@ H5D_chunk_prune_fill(const H5D_chunk_rec_t *chunk_rec, H5D_chunk_it_ud1_t *udata HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "unable to select hyperslab") /* Calculate the index of this chunk */ - if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, udata->down_chunks, - &io_info->store->chunk.index) < 0) + if(H5V_chunk_index(rank, chunk_rec->offset, layout->u.chunk.dim, layout->u.chunk.down_chunks, &io_info->store->chunk.index) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, H5_ITER_ERROR, "can't get chunk index") /* Lock the chunk into the cache, to get a pointer to the chunk buffer */ @@ -3575,8 +3647,6 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) H5D_chunk_common_ud_t idx_udata; /* User data for index removal routine */ H5S_t *chunk_space = NULL; /* Dataspace for a chunk */ hsize_t chunk_dims[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */ - hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Current number of chunks in each dimension */ - hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */ hsize_t hyper_start[H5O_LAYOUT_NDIMS]; /* Starting location of hyperslab */ uint32_t elmts_per_chunk; /* Elements in chunk */ unsigned rank; /* Current # of dimensions */ @@ -3611,16 +3681,11 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) /* (also compute the dimensions which have been shrunk) */ elmts_per_chunk = 1; for(u = 0; u < rank; u++) { - chunks[u] = ((curr_dims[u] + layout->u.chunk.dim[u]) - 1) / layout->u.chunk.dim[u]; elmts_per_chunk *= layout->u.chunk.dim[u]; chunk_dims[u] = layout->u.chunk.dim[u]; shrunk_dims[u] = curr_dims[u] < old_dims[u]; } /* end for */ - /* Get the "down" sizes for each dimension */ - if(H5V_array_down(rank, chunks, down_chunks) < 0) - HGOTO_ERROR(H5E_IO, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") - /* Create a dataspace for a chunk & set the extent */ if(NULL == (chunk_space = H5S_create_simple(rank, chunk_dims, NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") @@ -3646,7 +3711,6 @@ H5D_chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dims) udata.idx_info = &idx_info; udata.dims = curr_dims; udata.shrunk_dims = shrunk_dims; - udata.down_chunks = down_chunks; udata.elmts_per_chunk = elmts_per_chunk; udata.chunk_space = chunk_space; udata.hyper_start = hyper_start; @@ -3789,7 +3853,7 @@ H5D_chunk_addrmap_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_addrmap_cb) /* Compute the index for this chunk */ - if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->down_chunks, &chunk_index) < 0) + if(H5V_chunk_index(rank, chunk_rec->offset, udata->common.mesg->u.chunk.dim, udata->common.mesg->u.chunk.down_chunks, &chunk_index) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, H5_ITER_ERROR, "can't get chunk index") /* Set it in the userdata to return */ @@ -3814,12 +3878,11 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[], - const hsize_t down_chunks[]) +H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ - H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ + H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_addrmap, FAIL) @@ -3827,12 +3890,10 @@ H5D_chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[], HDassert(dset); HDassert(dset->shared); HDassert(chunk_addr); - HDassert(down_chunks); /* Set up user data for B-tree callback */ HDmemset(&udata, 0, sizeof(udata)); udata.common.mesg = &dset->shared->layout; - udata.down_chunks = down_chunks; udata.chunk_addr = chunk_addr; /* Compose chunked index info struct */ @@ -3926,10 +3987,6 @@ H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id) H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ unsigned rank; /*current # of dimensions */ - hsize_t curr_dims[H5O_LAYOUT_NDIMS]; /*current dataspace dimensions */ - hsize_t chunks[H5O_LAYOUT_NDIMS]; /*current number of chunks in each dimension */ - hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of elements in each dimension */ - unsigned u; /*counters */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_chunk_update_cache, FAIL) @@ -3946,18 +4003,6 @@ H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id) if(rank == 1) HGOTO_DONE(SUCCEED) - /* Go get the dimensions */ - if(H5S_get_simple_extent_dims(dset->shared->space, curr_dims, NULL) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions") - - /* Round up to the next integer # of chunks, to accomodate partial chunks */ - for(u = 0; u < rank; u++) - chunks[u] = ((curr_dims[u] + dset->shared->layout.u.chunk.dim[u]) - 1) / dset->shared->layout.u.chunk.dim[u]; - - /* Get the "down" sizes for each dimension */ - if(H5V_array_down(rank, chunks, down_chunks) < 0) - HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes") - /* Fill the DXPL cache values for later use */ if(H5D_get_dxpl_cache(dxpl_id, &dxpl_cache) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") @@ -3971,7 +4016,7 @@ H5D_chunk_update_cache(H5D_t *dset, hid_t dxpl_id) next = ent->next; /* Calculate the index of this chunk */ - if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, down_chunks, &idx) < 0) + if(H5V_chunk_index(rank, ent->offset, dset->shared->layout.u.chunk.dim, dset->shared->layout.u.chunk.down_chunks, &idx) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Compute the index for the chunk entry */ |