diff options
| -rw-r--r-- | src/H5Dchunk.c | 355 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 30 |
2 files changed, 199 insertions, 186 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 1a5dbee..b5814fa 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -1118,23 +1118,22 @@ H5D__chunk_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo) } } - { /* Set up info for processing chunk cache with selection I/O improvement */ - /* Skip filter for now */ - + { /* Set up info for processing chunk cache with selection I/O improvement */ + /* Skip filter for now */ + if (io_info->use_select_io == H5D_SELECTION_IO_MODE_ON && - (size_t)dinfo->dset->shared->layout.u.chunk.size <= dinfo->dset->shared->cache.chunk.nbytes_max - && + (size_t)dinfo->dset->shared->layout.u.chunk.size <= dinfo->dset->shared->cache.chunk.nbytes_max && !dinfo->dset->shared->dcpl_cache.pline.nused) { H5SL_node_t *chunk_node; /* Current node in chunk skip list */ - dinfo->num_sel_cache_chks = 0; + dinfo->num_sel_cache_chks = 0; dinfo->num_unsel_cache_chks = 0; - dinfo->num_chks_to_load = 0; - dinfo->num_ents_to_evict = 0; - dinfo->free_cache_slots = 0; - dinfo->max_cache_chunks = 0; - dinfo->chunks_to_load = NULL; - dinfo->entries_to_evict = NULL; + dinfo->num_chks_to_load = 0; + dinfo->num_ents_to_evict = 0; + dinfo->free_cache_slots = 0; + dinfo->max_cache_chunks = 0; + dinfo->chunks_to_load = NULL; + dinfo->entries_to_evict = NULL; /* Iterate through nodes in chunk skip list */ chunk_node = H5D_CHUNK_GET_FIRST_NODE(dinfo); @@ -1156,7 +1155,7 @@ H5D__chunk_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo) chunk_info->chunk_block.offset = udata.chunk_block.offset; chunk_info->chunk_block.length = udata.chunk_block.length; - chunk_info->chunk_idx = udata.chunk_idx; + chunk_info->chunk_idx = udata.chunk_idx; if (udata.idx_hint == UINT_MAX) { chunk_info->in_cache = false; @@ -1165,59 +1164,66 @@ H5D__chunk_io_init(H5D_io_info_t *io_info, H5D_dset_io_info_t *dinfo) /* Create skip list for chunks_to_load */ if (!dinfo->chunks_to_load) { if (NULL == (dinfo->chunks_to_load = H5SL_create(H5SL_TYPE_HSIZE, NULL))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for chunk_to_load"); + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, + "can't create skip list for chunk_to_load"); } /* Insert chunk info into chunks_to__load skip list */ if (H5SL_insert(dinfo->chunks_to_load, chunk_info, &chunk_info->index) < 0) { H5D__free_piece_info(chunk_info, NULL, NULL); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list"); - } - } else { + } + } + else { chunk_info->in_cache = true; chunk_info->idx_hint = udata.idx_hint; dinfo->num_sel_cache_chks++; H5D__set_chunk_cache_ent_lock(dataset, chunk_info->idx_hint, true); } - + /* Advance to next chunk in list */ chunk_node = H5D_CHUNK_GET_NEXT_NODE(dinfo, chunk_node); } /* end while */ - dinfo->max_cache_chunks = MIN(dataset->shared->cache.chunk.nbytes_max / dinfo->layout->u.chunk.size, - dataset->shared->cache.chunk.nslots); + dinfo->max_cache_chunks = + MIN(dataset->shared->cache.chunk.nbytes_max / dinfo->layout->u.chunk.size, + dataset->shared->cache.chunk.nslots); - dinfo->num_unsel_cache_chks = (size_t)dataset->shared->cache.chunk.nused - dinfo->num_sel_cache_chks; + dinfo->num_unsel_cache_chks = + (size_t)dataset->shared->cache.chunk.nused - dinfo->num_sel_cache_chks; dinfo->free_cache_slots = dinfo->max_cache_chunks - (size_t)dataset->shared->cache.chunk.nused; - dinfo->num_ents_to_evict = MIN(dinfo->num_unsel_cache_chks, - dinfo->num_chks_to_load > dinfo->free_cache_slots ? - dinfo->num_chks_to_load - dinfo->free_cache_slots : 0); + dinfo->num_ents_to_evict = + MIN(dinfo->num_unsel_cache_chks, dinfo->num_chks_to_load > dinfo->free_cache_slots + ? dinfo->num_chks_to_load - dinfo->free_cache_slots + : 0); - if(dinfo->num_ents_to_evict) { - unsigned ctr = 0; - H5D_rdcc_t *rdcc; /*raw data chunk cache*/ - H5D_rdcc_ent_t *ent; /*cache entry */ - H5D_rdcc_ent_t *next; /*cache entry */ + if (dinfo->num_ents_to_evict) { + unsigned ctr = 0; + H5D_rdcc_t *rdcc; /*raw data chunk cache*/ + H5D_rdcc_ent_t *ent; /*cache entry */ + H5D_rdcc_ent_t *next; /*cache entry */ - rdcc = &(dinfo->dset->shared->cache.chunk); + rdcc = &(dinfo->dset->shared->cache.chunk); /* Create skip list for ents_to_evict: idx index in hash table */ if (NULL == (dinfo->entries_to_evict = H5SL_create(H5SL_TYPE_UNSIGNED, NULL))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "can't create skip list for ents_to_evict"); + HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, + "can't create skip list for ents_to_evict"); for (ent = rdcc->tail; ent && ctr < dinfo->num_ents_to_evict; ent = next) { next = ent->prev; if (!ent->locked) { /* Insert ent info into ents_to_evict skip list */ if (H5SL_insert(dinfo->entries_to_evict, ent, &ent->idx) < 0) { H5D__free_piece_info(ent, NULL, NULL); - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert ent into skip list"); - } + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, + "can't insert ent into skip list"); + } ctr++; } } /* end for */ - } /* end if */ - } + } /* end if */ + } } /* end block */ #ifdef H5_HAVE_PARALLEL @@ -1708,10 +1714,10 @@ H5D__create_piece_map_single(H5D_dset_io_info_t *di, H5D_io_info_t *io_info) /* make connection to related dset info from this piece_info */ piece_info->dset_info = di; - piece_info->in_cache = false; + piece_info->in_cache = false; piece_info->entire_chunk = false; - piece_info->idx_hint = UINT_MAX; - piece_info->buf = NULL; + piece_info->idx_hint = UINT_MAX; + piece_info->buf = NULL; /* Add piece to global piece_count */ io_info->piece_count++; @@ -1846,10 +1852,10 @@ H5D__create_piece_file_map_all(H5D_dset_io_info_t *di, H5D_io_info_t *io_info) new_piece_info->filtered_dset = filtered_dataset; - new_piece_info->in_cache = false; + new_piece_info->in_cache = false; new_piece_info->entire_chunk = false; - new_piece_info->idx_hint = UINT_MAX; - new_piece_info->buf = NULL; + new_piece_info->idx_hint = UINT_MAX; + new_piece_info->buf = NULL; /* Insert the new chunk into the skip list */ if (H5SL_insert(fm->dset_sel_pieces, new_piece_info, &new_piece_info->index) < 0) { @@ -2056,10 +2062,10 @@ H5D__create_piece_file_map_hyper(H5D_dset_io_info_t *dinfo, H5D_io_info_t *io_in new_piece_info->filtered_dset = filtered_dataset; - new_piece_info->in_cache = false; + new_piece_info->in_cache = false; new_piece_info->entire_chunk = false; - new_piece_info->idx_hint = UINT_MAX; - new_piece_info->buf = NULL; + new_piece_info->idx_hint = UINT_MAX; + new_piece_info->buf = NULL; /* Add piece to global piece_count */ io_info->piece_count++; @@ -2753,13 +2759,13 @@ H5D__chunk_may_use_select_io(H5D_io_info_t *io_info, const H5D_dset_io_info_t *d /* Check if the chunk is too large to keep in the cache */ H5_CHECK_OVERFLOW(dataset->shared->layout.u.chunk.size, uint32_t, size_t); /* If a chunk is too big for the cache, just handle everything as before. */ - /* If chunk size is smaller than nbytes_max, the new case will be handled + /* If chunk size is smaller than nbytes_max, the new case will be handled * in H5D__sel_io_chunk_cache() in H5D__chunk_write/read() */ - /* + /* * Remove the code for chunk size less than nbytes_max - * if ((size_t)dataset->shared->layout.u.chunk.size <= dataset->shared->cache.chunk.nbytes_max) { - * io_info->use_select_io = H5D_SELECTION_IO_MODE_OFF; - * io_info->no_selection_io_cause |= H5D_SEL_IO_CHUNK_CACHE; + * if ((size_t)dataset->shared->layout.u.chunk.size <= + * dataset->shared->cache.chunk.nbytes_max) { io_info->use_select_io = + * H5D_SELECTION_IO_MODE_OFF; io_info->no_selection_io_cause |= H5D_SEL_IO_CHUNK_CACHE; * } * } */ @@ -2777,7 +2783,7 @@ done: static herr_t H5D__set_chunk_cache_ent_lock(const H5D_t *dataset, unsigned idx_hint, bool lock) { - H5D_rdcc_ent_t *ent = NULL; /* Cache entry */ + H5D_rdcc_ent_t *ent = NULL; /* Cache entry */ FUNC_ENTER_PACKAGE_NOERR @@ -2798,7 +2804,7 @@ H5D__set_chunk_cache_ent_lock(const H5D_t *dataset, unsigned idx_hint, bool lock * More work needs to be done to this routine: * Put handling of the following steps in separate routines: * --steps #3-4 (io_info->num_ents_to_evict) - * --step $5 (io_info->full_io_chks_to_mds) -- IN PROGRESS + * --step $5 (io_info->full_io_chks_to_mds) -- IN PROGRESS * --step #6 (NOT tackled yet) * --reset lock and in_cache (io_info->num_sel_cache_chks) * --steps #7-10 (io_info->chunks_to_load) @@ -2809,8 +2815,8 @@ H5D__set_chunk_cache_ent_lock(const H5D_t *dataset, unsigned idx_hint, bool lock static herr_t H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) { - H5SL_node_t *chunk_node; /* Current node in chunk skip list */ - herr_t ret_value = SUCCEED; /* Return value */ + H5SL_node_t *chunk_node; /* Current node in chunk skip list */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -2821,15 +2827,15 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Process num_ents_to_evict */ if (dset_info->num_ents_to_evict) { - H5D_chk_idx_info_t idx_info; /* Chunked index info */ - H5D_chunk_ud_t udata; /* Index pass-through */ - struct H5D_rdcc_ent_t *ent; - size_t num_ents_to_evict = dset_info->num_ents_to_evict; - size_t num_ents_vec_evict = 0; - haddr_t *addrs = NULL; - size_t *sizes = NULL; - const void **bufs = NULL; - H5FD_mem_t types[2]; + H5D_chk_idx_info_t idx_info; /* Chunked index info */ + H5D_chunk_ud_t udata; /* Index pass-through */ + struct H5D_rdcc_ent_t *ent; + size_t num_ents_to_evict = dset_info->num_ents_to_evict; + size_t num_ents_vec_evict = 0; + haddr_t *addrs = NULL; + size_t *sizes = NULL; + const void **bufs = NULL; + H5FD_mem_t types[2]; assert(dset_info->dset->shared->layout.u.chunk.size > 0); @@ -2865,13 +2871,12 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) if (ent->dirty) { if (!H5_addr_defined(ent->chunk_block.offset)) { - bool need_insert = false; /* Whether the chunk needs to be inserted into the index */ - + bool need_insert = false; /* Whether the chunk needs to be inserted into the index */ /* Set up the size of chunk for user data */ udata.chunk_block.offset = HADDR_UNDEF; udata.chunk_block.length = dset_info->dset->shared->layout.u.chunk.size; - udata.common.scaled = ent->scaled; + udata.common.scaled = ent->scaled; udata.idx_hint = ent->idx; udata.chunk_idx = ent->chunk_idx; @@ -2895,8 +2900,8 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) addrs[num_ents_vec_evict] = udata.chunk_block.offset; sizes[num_ents_vec_evict] = udata.chunk_block.length; - bufs[num_ents_vec_evict] = ent->chunk; - num_ents_vec_evict++; + bufs[num_ents_vec_evict] = ent->chunk; + num_ents_vec_evict++; } /* Advance to next chunk in list */ @@ -2904,8 +2909,9 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) } if (num_ents_vec_evict) { - if (H5F_shared_vector_write(H5F_SHARED(dset_info->dset->oloc.file), (uint32_t)num_ents_vec_evict, types, addrs, sizes, bufs) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "vector write call failed"); + if (H5F_shared_vector_write(H5F_SHARED(dset_info->dset->oloc.file), (uint32_t)num_ents_vec_evict, + types, addrs, sizes, bufs) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "vector write call failed"); } chunk_node = H5SL_first(dset_info->entries_to_evict); @@ -2938,7 +2944,7 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) chunk_node = H5D_CHUNK_GET_FIRST_NODE(dset_info); while (chunk_node) { - H5D_piece_info_t *chunk_info; /* Chunk information */ + H5D_piece_info_t *chunk_info; /* Chunk information */ /* Get the actual chunk information from the skip list node */ chunk_info = H5D_CHUNK_GET_NODE_INFO(dset_info, chunk_node); @@ -2956,17 +2962,16 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) assert(ctr == dset_info->num_sel_cache_chks); } - /* Process chunks_to_load */ if (dset_info->num_chks_to_load) { - - haddr_t *addrs = NULL; - size_t *sizes = NULL; - void **bufs = NULL; - H5FD_mem_t types[2]; - size_t num_chks_to_load = dset_info->num_chks_to_load; - size_t chunk_size; - size_t num_chks_vec_load = 0; + + haddr_t *addrs = NULL; + size_t *sizes = NULL; + void **bufs = NULL; + H5FD_mem_t types[2]; + size_t num_chks_to_load = dset_info->num_chks_to_load; + size_t chunk_size; + size_t num_chks_vec_load = 0; /* Allocate types, addrs, sizes, wbufs for num_chks_to_load */ types[0] = H5FD_MEM_DRAW; @@ -2985,20 +2990,21 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) if (NULL == (bufs = H5MM_malloc((size_t)(num_chks_to_load) * sizeof(*bufs)))) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate space for I/O buffers vector"); - + /* Iterate through nodes in chunks_to_load skip list */ assert(dset_info->chunks_to_load); chunk_node = H5SL_first(dset_info->chunks_to_load); while (chunk_node) { - H5D_piece_info_t *chunk_info; /* Chunk information */ - H5D_fill_value_t fill_status; - const H5O_fill_t *fill; /* Fill value info */ - H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ - bool fb_info_init = false; /* Whether the fill value buffer has been initialized */ - H5O_pline_t *pline; /* I/O pipeline info - always equal to the pline passed to H5D__chunk_mem_alloc */ + H5D_piece_info_t *chunk_info; /* Chunk information */ + H5D_fill_value_t fill_status; + const H5O_fill_t *fill; /* Fill value info */ + H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ + bool fb_info_init = false; /* Whether the fill value buffer has been initialized */ + H5O_pline_t + *pline; /* I/O pipeline info - always equal to the pline passed to H5D__chunk_mem_alloc */ - fill = &(dset_info->dset->shared->dcpl_cache.fill); - pline = &(dset_info->dset->shared->dcpl_cache.pline); + fill = &(dset_info->dset->shared->dcpl_cache.fill); + pline = &(dset_info->dset->shared->dcpl_cache.pline); /* Get the actual chunk information from the skip list node */ chunk_info = (H5D_piece_info_t *)H5SL_item(chunk_node); @@ -3006,17 +3012,19 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Chunk size on disk isn't [likely] the same size as the final chunk * size in memory, so allocate memory big enough. */ if (NULL == (chunk_info->buf = H5D__chunk_mem_alloc(chunk_size, pline))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate space for I/O sizes vector"); + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "couldn't allocate space for I/O sizes vector"); - if(chunk_info->entire_chunk && io_info->op_type == H5D_IO_OP_WRITE) + if (chunk_info->entire_chunk && io_info->op_type == H5D_IO_OP_WRITE) memset(chunk_info->buf, 0, chunk_size); else if (H5_addr_defined(chunk_info->chunk_block.offset)) { addrs[num_chks_vec_load] = chunk_info->chunk_block.offset; sizes[num_chks_vec_load] = chunk_size; - bufs[num_chks_vec_load] = chunk_info->buf; - num_chks_vec_load++; - } else { + bufs[num_chks_vec_load] = chunk_info->buf; + num_chks_vec_load++; + } + else { /* Sanity check */ assert(fill->alloc_time != H5D_ALLOC_TIME_EARLY); @@ -3026,7 +3034,7 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) if (fill->fill_time == H5D_FILL_TIME_ALLOC || (fill->fill_time == H5D_FILL_TIME_IFSET && - (fill_status == H5D_FILL_VALUE_USER_DEFINED || fill_status == H5D_FILL_VALUE_DEFAULT))) { + (fill_status == H5D_FILL_VALUE_USER_DEFINED || fill_status == H5D_FILL_VALUE_DEFAULT))) { /* * The chunk doesn't exist in the file. Replicate the fill * value throughout the chunk, if the fill value is defined. @@ -3035,8 +3043,9 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Initialize the fill value buffer */ /* (use the compact dataset storage buffer as the fill value buffer) */ if (H5D__fill_init(&fb_info, chunk_info->buf, NULL, NULL, NULL, NULL, - &dset_info->dset->shared->dcpl_cache.fill, dset_info->dset->shared->type, - dset_info->dset->shared->type_id, (size_t)0, chunk_size) < 0) + &dset_info->dset->shared->dcpl_cache.fill, + dset_info->dset->shared->type, dset_info->dset->shared->type_id, + (size_t)0, chunk_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info"); fb_info_init = true; @@ -3061,26 +3070,27 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Vector load of chunks in chunks_to_load */ if (num_chks_vec_load) { - if (H5F_shared_vector_read(H5F_SHARED(dset_info->dset->oloc.file), (uint32_t)num_chks_vec_load, types, addrs, sizes, bufs) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "vector write call failed"); + if (H5F_shared_vector_read(H5F_SHARED(dset_info->dset->oloc.file), (uint32_t)num_chks_vec_load, + types, addrs, sizes, bufs) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "vector write call failed"); } addrs = H5MM_xfree(addrs); sizes = H5MM_xfree(sizes); - bufs = H5MM_xfree(bufs); + bufs = H5MM_xfree(bufs); /* Insert chunks in chunks_to_load to cache */ - { /* begin block */ - H5D_rdcc_t *rdcc; /*raw data chunk cache*/ + { /* begin block */ + H5D_rdcc_t *rdcc; /*raw data chunk cache*/ - rdcc = &(dset_info->dset->shared->cache.chunk); + rdcc = &(dset_info->dset->shared->cache.chunk); chunk_node = H5SL_first(dset_info->chunks_to_load); - + while (chunk_node) { H5D_piece_info_t *chunk_info; /* Chunk information */ - H5D_rdcc_ent_t *ent; - bool disable_filters = false; + H5D_rdcc_ent_t *ent; + bool disable_filters = false; assert(rdcc->nslots > 0); assert(chunk_size <= rdcc->nbytes_max); @@ -3109,7 +3119,8 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) ent->chunk_block.length = chunk_info->chunk_block.length; ent->chunk_idx = chunk_info->chunk_idx; - H5MM_memcpy(ent->scaled, chunk_info->scaled, sizeof(hsize_t) * dset_info->dset->shared->layout.u.chunk.ndims); + H5MM_memcpy(ent->scaled, chunk_info->scaled, + sizeof(hsize_t) * dset_info->dset->shared->layout.u.chunk.ndims); H5_CHECKED_ASSIGN(ent->rd_count, uint32_t, chunk_size, size_t); H5_CHECKED_ASSIGN(ent->wr_count, uint32_t, chunk_size, size_t); @@ -3120,13 +3131,13 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Add it to the cache */ assert(NULL == rdcc->slot[chunk_info->idx_hint]); rdcc->slot[chunk_info->idx_hint] = ent; - ent->idx = chunk_info->idx_hint; + ent->idx = chunk_info->idx_hint; /* ?? Do assert here on nbytes_used < ... */ rdcc->nbytes_used += chunk_size; rdcc->nused++; /* Add it to the linked list */ - /* NOTE: Based on Neil's instruction, should I use head instead: + /* NOTE: Based on Neil's instruction, should I use head instead: (so the last chunk in the list will be at the head of the LRU) */ if (rdcc->tail) { rdcc->tail->next = ent; @@ -3143,7 +3154,7 @@ H5D__sel_io_chunk_cache(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) chunk_node = H5SL_next(chunk_node); } /* end while */ - + } /* end block */ /* Close the skip list for chunks_to_load */ @@ -3237,8 +3248,8 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Handle chunk cache with selection I/O improvement */ /* Skip filter for now */ - if (((size_t)dset_info->dset->shared->layout.u.chunk.size <= dset_info->dset->shared->cache.chunk.nbytes_max) - && + if (((size_t)dset_info->dset->shared->layout.u.chunk.size <= + dset_info->dset->shared->cache.chunk.nbytes_max) && (!dset_info->dset->shared->dcpl_cache.pline.nused)) { if (H5D__sel_io_chunk_cache(io_info, dset_info) < 0) @@ -3302,10 +3313,11 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Check for non-existent chunk & skip it if appropriate */ if (H5_addr_defined(udata.chunk_block.offset) || UINT_MAX != udata.idx_hint || !skip_missing_chunks) { - void *chunk = NULL; /* Pointer to locked chunk buffer */ + void *chunk = NULL; /* Pointer to locked chunk buffer */ /* Determine if we should use the chunk cache */ - if ((cacheable = H5D__chunk_cacheable(io_info, dset_info, udata.chunk_block.offset, false)) < 0) + if ((cacheable = H5D__chunk_cacheable(io_info, dset_info, udata.chunk_block.offset, false)) < + 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable"); if (cacheable) { @@ -3322,7 +3334,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); /* Set up the storage buffer information for this chunk */ - cpt_store.compact.buf = chunk; + cpt_store.compact.buf = chunk; cpt_dset_info.layout_io_info.contig_piece_info = chunk_info; cpt_dset_info.file_space = chunk_info->fspace; cpt_dset_info.mem_space = chunk_info->mspace; @@ -3331,57 +3343,57 @@ H5D__chunk_read(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) cpt_dset_info.type_info.request_nelmts = cpt_dset_info.nelmts; if ((dset_info->io_ops.single_read)(&cpt_io_info, &cpt_dset_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed"); - - } else - /* Check for non-existent chunk & skip it if appropriate */ - if (H5_addr_defined(udata.chunk_block.offset)) { - /* Add chunk to list for selection I/O, if not performing multi dataset I/O */ - if (H5D_LAYOUT_CB_PERFORM_IO(io_info)) { - chunk_mem_spaces[num_chunks] = chunk_info->mspace; - chunk_file_spaces[num_chunks] = chunk_info->fspace; - chunk_addrs[num_chunks] = udata.chunk_block.offset; - num_chunks++; + } + else + /* Check for non-existent chunk & skip it if appropriate */ + if (H5_addr_defined(udata.chunk_block.offset)) { + /* Add chunk to list for selection I/O, if not performing multi dataset I/O */ + if (H5D_LAYOUT_CB_PERFORM_IO(io_info)) { + chunk_mem_spaces[num_chunks] = chunk_info->mspace; + chunk_file_spaces[num_chunks] = chunk_info->fspace; + chunk_addrs[num_chunks] = udata.chunk_block.offset; + num_chunks++; + } /* end if */ + else { + /* Add to mdset selection I/O arrays */ + assert(io_info->mem_spaces); + assert(io_info->file_spaces); + assert(io_info->addrs); + assert(io_info->element_sizes); + assert(io_info->rbufs); + assert(io_info->pieces_added < io_info->piece_count); + + io_info->mem_spaces[io_info->pieces_added] = chunk_info->mspace; + io_info->file_spaces[io_info->pieces_added] = chunk_info->fspace; + io_info->addrs[io_info->pieces_added] = udata.chunk_block.offset; + io_info->element_sizes[io_info->pieces_added] = element_sizes[0]; + io_info->rbufs[io_info->pieces_added] = bufs[0]; + if (io_info->sel_pieces) + io_info->sel_pieces[io_info->pieces_added] = chunk_info; + io_info->pieces_added++; + + if (io_info->sel_pieces && chunk_info->filtered_dset) + io_info->filtered_pieces_added++; + } } /* end if */ else { - /* Add to mdset selection I/O arrays */ - assert(io_info->mem_spaces); - assert(io_info->file_spaces); - assert(io_info->addrs); - assert(io_info->element_sizes); - assert(io_info->rbufs); - assert(io_info->pieces_added < io_info->piece_count); - - io_info->mem_spaces[io_info->pieces_added] = chunk_info->mspace; - io_info->file_spaces[io_info->pieces_added] = chunk_info->fspace; - io_info->addrs[io_info->pieces_added] = udata.chunk_block.offset; - io_info->element_sizes[io_info->pieces_added] = element_sizes[0]; - io_info->rbufs[io_info->pieces_added] = bufs[0]; - if (io_info->sel_pieces) - io_info->sel_pieces[io_info->pieces_added] = chunk_info; - io_info->pieces_added++; - - if (io_info->sel_pieces && chunk_info->filtered_dset) - io_info->filtered_pieces_added++; + /* Set up nonexistent dataset info for (fill value) read from nonexistent chunk */ + nonexistent_dset_info.layout_io_info.contig_piece_info = chunk_info; + nonexistent_dset_info.file_space = chunk_info->fspace; + nonexistent_dset_info.mem_space = chunk_info->mspace; + nonexistent_dset_info.nelmts = chunk_info->piece_points; + + /* Set request_nelmts. This is not normally set by the upper layers because selection + * I/O usually does not use strip mining (H5D__scatgath_write), and instead allocates + * buffers large enough for the entire I/O. Set request_nelmts to be large enough for + * all selected elements in this chunk because it must be at least that large */ + nonexistent_dset_info.type_info.request_nelmts = nonexistent_dset_info.nelmts; + + /* Perform the actual read operation from the nonexistent chunk + */ + if ((dset_info->io_ops.single_read)(&nonexistent_io_info, &nonexistent_dset_info) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed"); } - } /* end if */ - else { - /* Set up nonexistent dataset info for (fill value) read from nonexistent chunk */ - nonexistent_dset_info.layout_io_info.contig_piece_info = chunk_info; - nonexistent_dset_info.file_space = chunk_info->fspace; - nonexistent_dset_info.mem_space = chunk_info->mspace; - nonexistent_dset_info.nelmts = chunk_info->piece_points; - - /* Set request_nelmts. This is not normally set by the upper layers because selection I/O - * usually does not use strip mining (H5D__scatgath_write), and instead allocates buffers - * large enough for the entire I/O. Set request_nelmts to be large enough for all selected - * elements in this chunk because it must be at least that large */ - nonexistent_dset_info.type_info.request_nelmts = nonexistent_dset_info.nelmts; - - /* Perform the actual read operation from the nonexistent chunk - */ - if ((dset_info->io_ops.single_read)(&nonexistent_io_info, &nonexistent_dset_info) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "chunked read failed"); - } /* Release the cache lock on the chunk. */ if (chunk && @@ -3615,7 +3627,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Calculate entire_chunk for each chunk in chunk_info */ chunk_node = H5D_CHUNK_GET_FIRST_NODE(dset_info); while (chunk_node) { - H5D_piece_info_t *chunk_info; /* Chunk information */ + H5D_piece_info_t *chunk_info; /* Chunk information */ /* Get the actual chunk information from the skip list node */ chunk_info = H5D_CHUNK_GET_NODE_INFO(dset_info, chunk_node); @@ -3628,15 +3640,14 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Determine if we will access all the data in the chunk */ if (dst_accessed_bytes != ctg_store.contig.dset_size || - (chunk_info->piece_points * dset_info->type_info.src_type_size) != - ctg_store.contig.dset_size || + (chunk_info->piece_points * dset_info->type_info.src_type_size) != ctg_store.contig.dset_size || dset_info->layout_io_info.chunk_map->fsel_type == H5S_SEL_POINTS) chunk_info->entire_chunk = false; else chunk_info->entire_chunk = true; - /* Advance to next chunk in list */ - chunk_node = H5D_CHUNK_GET_NEXT_NODE(dset_info, chunk_node); + /* Advance to next chunk in list */ + chunk_node = H5D_CHUNK_GET_NEXT_NODE(dset_info, chunk_node); } /* end while */ /* Different blocks depending on whether we're using selection I/O */ @@ -3647,8 +3658,8 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) /* Handle chunk cache with selection I/O improvement */ /* Skip filter for now */ - if (((size_t)dset_info->dset->shared->layout.u.chunk.size <= dset_info->dset->shared->cache.chunk.nbytes_max) - && + if (((size_t)dset_info->dset->shared->layout.u.chunk.size <= + dset_info->dset->shared->cache.chunk.nbytes_max) && (!dset_info->dset->shared->dcpl_cache.pline.nused)) { if (H5D__sel_io_chunk_cache(io_info, dset_info) < 0) @@ -3717,10 +3728,11 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) if (cacheable) { /* Load the chunk into cache. But if the whole chunk is written, * simply allocate space instead of load the chunk. */ - void *chunk; /* Pointer to locked chunk buffer */ + void *chunk; /* Pointer to locked chunk buffer */ /* Lock the chunk into the cache */ - if (NULL == (chunk = H5D__chunk_lock(io_info, dset_info, &udata, chunk_info->entire_chunk, false))) + if (NULL == + (chunk = H5D__chunk_lock(io_info, dset_info, &udata, chunk_info->entire_chunk, false))) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); /* Set up the storage buffer information for this chunk */ @@ -3875,7 +3887,8 @@ H5D__chunk_write(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info) * simply allocate space instead of load the chunk. */ /* Lock the chunk into the cache */ - if (NULL == (chunk = H5D__chunk_lock(io_info, dset_info, &udata, chunk_info->entire_chunk, false))) + if (NULL == + (chunk = H5D__chunk_lock(io_info, dset_info, &udata, chunk_info->entire_chunk, false))) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk"); /* Set up the storage buffer information for this chunk */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 8ef6ade..dc60ff8 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -255,13 +255,13 @@ typedef struct H5D_piece_info_t { bool in_place_tconv; /* Whether to perform type conversion in-place */ size_t buf_off; /* Buffer offset for in-place type conversion */ bool filtered_dset; /* Whether the dataset this chunk is in has filters applied */ - struct H5D_dset_io_info_t *dset_info; /* Pointer to dset_info */ - bool entire_chunk; /* Whether whole chunk is selected */ - bool in_cache; - void *buf; - unsigned idx_hint; /* Index of chunk in cache, if present */ - H5F_block_t chunk_block; /* Offset/length of chunk in file */ - hsize_t chunk_idx; /* Chunk index for EA, FA indexing */ + struct H5D_dset_io_info_t *dset_info; /* Pointer to dset_info */ + bool entire_chunk; /* Whether whole chunk is selected */ + bool in_cache; + void *buf; + unsigned idx_hint; /* Index of chunk in cache, if present */ + H5F_block_t chunk_block; /* Offset/length of chunk in file */ + hsize_t chunk_idx; /* Chunk index for EA, FA indexing */ } H5D_piece_info_t; /* I/O info for a single dataset */ @@ -279,14 +279,14 @@ typedef struct H5D_dset_io_info_t { H5S_t *file_space; /* Pointer to the file dataspace */ H5S_t *mem_space; /* Pointer to the memory dataspace */ - size_t num_sel_cache_chks; /* Number of pieces found in cache */ - size_t num_unsel_cache_chks; /* Number of pieces NOT found in cache */ - size_t num_chks_to_load; /* # of chunks not found in cache that needs to be loaded */ - size_t num_ents_to_evict; /* # of non selected cache entries to be evicted */ - size_t free_cache_slots; /* # of free slots in the cache */ - size_t max_cache_chunks; /* max # of chunks in the cache */ - H5SL_t *chunks_to_load; /* Skip list containing information for chunks to load to cache */ - H5SL_t *entries_to_evict; /* Skip list containing information for entries to evict from cache */ + size_t num_sel_cache_chks; /* Number of pieces found in cache */ + size_t num_unsel_cache_chks; /* Number of pieces NOT found in cache */ + size_t num_chks_to_load; /* # of chunks not found in cache that needs to be loaded */ + size_t num_ents_to_evict; /* # of non selected cache entries to be evicted */ + size_t free_cache_slots; /* # of free slots in the cache */ + size_t max_cache_chunks; /* max # of chunks in the cache */ + H5SL_t *chunks_to_load; /* Skip list containing information for chunks to load to cache */ + H5SL_t *entries_to_evict; /* Skip list containing information for entries to evict from cache */ union { struct H5D_chunk_map_t *chunk_map; /* Chunk specific I/O info */ |