diff options
Diffstat (limited to 'src/H5Dchunk.c')
-rw-r--r-- | src/H5Dchunk.c | 208 |
1 files changed, 113 insertions, 95 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index e165569..93b4427 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -313,6 +313,7 @@ const H5D_layout_ops_t H5D_LOPS_CHUNK[1] = {{ H5D__chunk_construct, H5D__chunk_init, H5D__chunk_is_space_alloc, + H5D__chunk_is_data_cached, H5D__chunk_io_init, H5D__chunk_read, H5D__chunk_write, @@ -340,6 +341,7 @@ const H5D_layout_ops_t H5D_LOPS_NONEXISTENT[1] = {{ NULL, NULL, NULL, + NULL, #ifdef H5_HAVE_PARALLEL NULL, NULL, @@ -394,10 +396,13 @@ H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset, FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr) + /* Sanity checks */ + HDassert(layout->type == H5D_CHUNKED); + io_info.dset = dset; /* Allocate dataspace and initialize it if it hasn't been. */ - if(!(*layout->ops->is_space_alloc)(&layout->storage)) + if(!H5D__chunk_is_space_alloc(&layout->storage)) /* Allocate storage */ if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") @@ -435,13 +440,17 @@ H5D__chunk_direct_write(const H5D_t *dset, uint32_t filters, hsize_t *offset, if(0 == idx_info.pline->nused && H5F_addr_defined(old_chunk.offset)) /* If there are no filters and we are overwriting the chunk we can just set values */ need_insert = FALSE; - else + else { /* Otherwise, create the chunk it if it doesn't exist, or reallocate the chunk * if its size has changed. */ if(H5D__chunk_file_alloc(&idx_info, &old_chunk, &udata.chunk_block, &need_insert, scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") + /* Cache the new chunk information */ + H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, &udata); + } /* end else */ + /* Make sure the address of the chunk is returned. */ if(!H5F_addr_defined(udata.chunk_block.offset)) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk address isn't defined") @@ -506,7 +515,8 @@ H5D__chunk_direct_read(const H5D_t *dset, hsize_t *offset, uint32_t* filters, *filters = 0; /* Allocate dataspace and initialize it if it hasn't been. */ - if(!(*layout->ops->is_space_alloc)(&layout->storage)) + if(!H5D__chunk_is_space_alloc(&layout->storage) + && !H5D__chunk_is_data_cached(dset->shared)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized") /* Calculate the index of this chunk */ @@ -1019,6 +1029,30 @@ H5D__chunk_is_space_alloc(const H5O_storage_t *storage) /*------------------------------------------------------------------------- + * Function: H5D__chunk_is_data_cached + * + * Purpose: Query if raw data is cached for dataset + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Neil Fortner + * Wednessday, March 6, 2016 + * + *------------------------------------------------------------------------- + */ +hbool_t +H5D__chunk_is_data_cached(const H5D_shared_t *shared_dset) +{ + FUNC_ENTER_PACKAGE_NOERR + + /* Sanity checks */ + HDassert(shared_dset); + + FUNC_LEAVE_NOAPI(shared_dset->cache.chunk.nused > 0) +} /* end H5D__chunk_is_data_cached() */ + + +/*------------------------------------------------------------------------- * Function: H5D__chunk_io_init * * Purpose: Performs initialization before any sort of I/O on the raw data @@ -1073,21 +1107,19 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf if((file_space_normalized = H5S_hyper_normalize_offset((H5S_t *)file_space, old_offset)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to normalize selection") - /* Decide the number of chunks in each dimension*/ - for(u = 0; u < f_ndims; u++) { + /* Decide the number of chunks in each dimension */ + 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]; - } /* end for */ #ifdef H5_HAVE_PARALLEL /* Calculate total chunk in file map*/ fm->select_chunk = NULL; if(io_info->using_mpi_vfd) { H5_CHECK_OVERFLOW(fm->layout->u.chunk.nchunks, hsize_t, size_t); - if(fm->layout->u.chunk.nchunks) { + if(fm->layout->u.chunk.nchunks) 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 */ @@ -1129,10 +1161,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf 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) 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); @@ -1147,10 +1178,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf hbool_t sel_hyper_flag; /* Whether file selection is a hyperslab */ /* Initialize skip list for chunk selections */ - if(NULL == dataset->shared->cache.chunk.sel_chunks) { + if(NULL == dataset->shared->cache.chunk.sel_chunks) if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, NULL))) 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); @@ -1245,10 +1275,9 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf fm->mchunk_tmpl = tmp_mspace; /* Create temporary datatypes for selection iteration */ - if(!file_type) { + if(!file_type) if(NULL == (file_type = H5T_copy(dataset->shared->type, H5T_COPY_ALL))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype") - } /* end if */ /* Create selection iterator for memory selection */ if(0 == (elmt_size = H5T_get_size(mem_type))) @@ -1540,7 +1569,7 @@ done: /*------------------------------------------------------------------------- * Function: H5D__create_chunk_file_map_hyper * - * Purpose: Create all chunk selections in file. + * Purpose: Create all chunk selections in file, for a hyperslab selection. * * Return: Non-negative on success/Negative on failure * @@ -1556,8 +1585,8 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t #endif /* H5_HAVE_PARALLEL */ *io_info) { - 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 */ + 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 */ hsize_t sel_points; /* Number of elements in file selection */ hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ @@ -1572,7 +1601,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t FUNC_ENTER_STATIC /* Sanity check */ - HDassert(fm->f_ndims>0); + HDassert(fm->f_ndims > 0); /* Get number of elements selected in file */ sel_points = fm->nelmts; @@ -1596,7 +1625,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Iterate through each chunk in the dataset */ while(sel_points) { - /* Check for intersection of temporary chunk and file selection */ + /* Check for intersection of current chunk and file selection */ /* (Casting away const OK - QAK) */ if(TRUE == H5S_hyper_intersect_block((H5S_t *)fm->file_space, coords, end)) { H5S_t *tmp_fchunk; /* Temporary file dataspace */ @@ -1634,7 +1663,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Add temporary chunk to the list of chunks */ /* Allocate the file & memory chunk information */ - if (NULL==(new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) { + if(NULL == (new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") } /* end if */ @@ -1642,7 +1671,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Initialize the chunk information */ /* Set the chunk index */ - new_chunk_info->index=chunk_index; + new_chunk_info->index = chunk_index; #ifdef H5_HAVE_PARALLEL /* Store chunk selection information, for multi-chunk I/O */ @@ -1655,16 +1684,13 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t new_chunk_info->fspace_shared = FALSE; /* Set the memory chunk dataspace */ - new_chunk_info->mspace=NULL; + new_chunk_info->mspace = NULL; new_chunk_info->mspace_shared = FALSE; /* Copy the chunk's scaled coordinates */ - HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); + H5MM_memcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); new_chunk_info->scaled[fm->f_ndims] = 0; - /* Copy the chunk's scaled coordinates */ - HDmemcpy(new_chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); - /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->sel_chunks, new_chunk_info, &new_chunk_info->index) < 0) { H5D__free_chunk_info(new_chunk_info, NULL, NULL); @@ -1688,12 +1714,11 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t chunk_index++; /* Set current increment dimension */ - curr_dim=(int)fm->f_ndims-1; + curr_dim = (int)fm->f_ndims - 1; /* Increment chunk location in fastest changing dimension */ - H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t); - coords[curr_dim]+=fm->chunk_dim[curr_dim]; - end[curr_dim]+=fm->chunk_dim[curr_dim]; + coords[curr_dim] += fm->chunk_dim[curr_dim]; + end[curr_dim] += fm->chunk_dim[curr_dim]; scaled[curr_dim]++; /* Bring chunk location back into bounds, if necessary */ @@ -1707,11 +1732,14 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Decrement current dimension */ curr_dim--; - /* Increment chunk location in current dimension */ - scaled[curr_dim]++; - coords[curr_dim] += fm->chunk_dim[curr_dim]; - end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; - } while(coords[curr_dim] > sel_end[curr_dim]); + /* Check for valid current dim */ + if(curr_dim >= 0) { + /* Increment chunk location in current dimension */ + scaled[curr_dim]++; + coords[curr_dim] += fm->chunk_dim[curr_dim]; + end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1; + } /* end if */ + } while(curr_dim >= 0 && (coords[curr_dim] > sel_end[curr_dim])); /* Re-calculate the index of this chunk */ chunk_index = H5VM_array_offset_pre(fm->f_ndims, fm->layout->u.chunk.down_chunks, scaled); @@ -1743,12 +1771,12 @@ static herr_t H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) { H5SL_node_t *curr_node; /* Current node in skip list */ - hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ - hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ - hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */ - hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */ + hsize_t file_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t file_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + hsize_t mem_sel_start[H5S_MAX_RANK]; /* Offset of low bound of file selection */ + hsize_t mem_sel_end[H5S_MAX_RANK]; /* Offset of high bound of file selection */ + hssize_t adjust[H5S_MAX_RANK]; /* Adjustment to make to all file chunks */ + hssize_t chunk_adjust[H5S_MAX_RANK]; /* Adjustment to make to a particular chunk */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ @@ -1762,7 +1790,7 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ /* Get the node */ - curr_node=H5SL_first(fm->sel_chunks); + curr_node = H5SL_first(fm->sel_chunks); /* Get pointer to chunk's information */ chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node); @@ -1785,15 +1813,15 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") /* Calculate the adjustment for memory selection from file selection */ - HDassert(fm->m_ndims==fm->f_ndims); - for(u=0; u<fm->f_ndims; u++) { - H5_CHECK_OVERFLOW(file_sel_start[u],hsize_t,hssize_t); - H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t); - adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u]; + HDassert(fm->m_ndims == fm->f_ndims); + for(u = 0; u < fm->f_ndims; u++) { + H5_CHECK_OVERFLOW(file_sel_start[u], hsize_t, hssize_t); + H5_CHECK_OVERFLOW(mem_sel_start[u], hsize_t, hssize_t); + adjust[u] = (hssize_t)file_sel_start[u] - (hssize_t)mem_sel_start[u]; } /* end for */ /* Iterate over each chunk in the chunk list */ - curr_node=H5SL_first(fm->sel_chunks); + curr_node = H5SL_first(fm->sel_chunks); while(curr_node) { H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ @@ -1832,7 +1860,7 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to adjust selection") /* Get the next chunk node in the skip list */ - curr_node=H5SL_next(curr_node); + curr_node = H5SL_next(curr_node); } /* end while */ } /* end else */ @@ -1920,9 +1948,9 @@ H5D__chunk_file_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, chunk_info->chunk_points = 0; /* Set the chunk's scaled coordinates */ - HDmemcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); + H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); chunk_info->scaled[fm->f_ndims] = 0; - HDmemcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); + H5MM_memcpy(chunk_info->scaled, scaled, sizeof(hsize_t) * fm->f_ndims); /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->sel_chunks,chunk_info,&chunk_info->index) < 0) { @@ -1976,7 +2004,7 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u { H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */ H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ - hsize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ + hsize_t coords_in_mem[H5S_MAX_RANK]; /* Coordinates of element in memory */ hsize_t chunk_index; /* Chunk index */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2001,11 +2029,10 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, H5_ITER_ERROR, "can't locate chunk in skip list") /* Check if the chunk already has a memory space */ - if(NULL == chunk_info->mspace) { + if(NULL == chunk_info->mspace) /* Copy the template memory chunk dataspace */ if(NULL == (chunk_info->mspace = H5S_copy(fm->mchunk_tmpl, FALSE, FALSE))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, H5_ITER_ERROR, "unable to copy file space") - } /* end else */ /* Update the "last chunk seen" information */ fm->last_index = chunk_index; @@ -2164,11 +2191,11 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, HDassert(fm); /* Set up "nonexistent" I/O info object */ - HDmemcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info)); + H5MM_memcpy(&nonexistent_io_info, io_info, sizeof(nonexistent_io_info)); nonexistent_io_info.layout_ops = *H5D_LOPS_NONEXISTENT; /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); + H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; @@ -2176,7 +2203,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t); /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); + H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); cpt_io_info.store = &cpt_store; cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; @@ -2314,7 +2341,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, HDassert(fm); /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); + H5MM_memcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; @@ -2322,7 +2349,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5_CHECKED_ASSIGN(ctg_store.contig.dset_size, hsize_t, io_info->dset->shared->layout.u.chunk.size, uint32_t); /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); + H5MM_memcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); cpt_io_info.store = &cpt_store; cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; @@ -2677,7 +2704,7 @@ H5D__chunk_cinfo_cache_update(H5D_chunk_cached_t *last, const H5D_chunk_ud_t *ud HDassert(udata->common.scaled); /* Stored the information to cache */ - HDmemcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims); + H5MM_memcpy(last->scaled, udata->common.scaled, sizeof(hsize_t) * udata->common.layout->ndims); last->addr = udata->chunk_block.offset; H5_CHECKED_ASSIGN(last->nbytes, uint32_t, udata->chunk_block.length, hsize_t); last->chunk_idx = udata->chunk_idx; @@ -2914,9 +2941,6 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, /* Check for cached information */ if(!H5D__chunk_cinfo_cache_found(&dset->shared->cache.chunk.last, udata)) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ -#ifdef H5_HAVE_PARALLEL - H5P_coll_md_read_flag_t temp_cmr; /* Temp value to hold the coll metadata read setting */ -#endif /* H5_HAVE_PARALLEL */ /* Compose chunked index info struct */ idx_info.f = dset->oloc.file; @@ -2925,25 +2949,18 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled, idx_info.storage = &dset->shared->layout.storage.u.chunk; #ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) { - /* disable collective metadata read for chunk indexes - as it is highly unlikely that users would read the - same chunks from all processes. MSC - might turn on - for root node? */ - temp_cmr = H5F_COLL_MD_READ(idx_info.f); - H5F_set_coll_md_read(idx_info.f, H5P_FORCE_FALSE); - } /* end if */ + /* Disable collective metadata read for chunk indexes as it is + * highly unlikely that users would read the same chunks from all + * processes. + */ + if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) + H5CX_set_coll_metadata_read(FALSE); #endif /* H5_HAVE_PARALLEL */ /* Go get the chunk information */ if((dset->shared->layout.storage.u.chunk.ops->get_addr)(&idx_info, udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address") -#ifdef H5_HAVE_PARALLEL - if(H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI)) - H5F_set_coll_md_read(idx_info.f, temp_cmr); -#endif /* H5_HAVE_PARALLEL */ - /* * Cache the information retrieved. * @@ -3056,7 +3073,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset) */ if(NULL == (buf = H5MM_malloc(alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for pipeline") - HDmemcpy(buf, ent->chunk, alloc); + H5MM_memcpy(buf, ent->chunk, alloc); } /* end if */ else { /* @@ -3469,7 +3486,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, */ if(NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") - HDmemcpy(chunk, ent->chunk, chunk_size); + H5MM_memcpy(chunk, ent->chunk, chunk_size); ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline); ent->chunk = (uint8_t *)chunk; chunk = NULL; @@ -3495,7 +3512,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, */ if(NULL == (chunk = H5D__chunk_mem_alloc(chunk_size, pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") - HDmemcpy(chunk, ent->chunk, chunk_size); + H5MM_memcpy(chunk, ent->chunk, chunk_size); ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk, old_pline); ent->chunk = (uint8_t *)chunk; @@ -3624,7 +3641,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, (void)H5D__chunk_mem_xfree(tmp_chunk, old_pline); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for raw data chunk") } /* end if */ - HDmemcpy(chunk, tmp_chunk, chunk_size); + H5MM_memcpy(chunk, tmp_chunk, chunk_size); (void)H5D__chunk_mem_xfree(tmp_chunk, old_pline); } /* end if */ } /* end if */ @@ -3705,7 +3722,7 @@ H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, ent->chunk_block.offset = chunk_addr; ent->chunk_block.length = chunk_alloc; ent->chunk_idx = udata->chunk_idx; - HDmemcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); + H5MM_memcpy(ent->scaled, udata->common.scaled, sizeof(hsize_t) * 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); ent->chunk = (uint8_t *)chunk; @@ -3833,7 +3850,7 @@ H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, fake_ent.edge_chunk_state = H5D_RDCC_DISABLE_FILTERS; if(udata->new_unfilt_chunk) fake_ent.edge_chunk_state |= H5D_RDCC_NEWLY_DISABLED_FILTERS; - HDmemcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); + H5MM_memcpy(fake_ent.scaled, udata->common.scaled, sizeof(hsize_t) * layout->u.chunk.ndims); HDassert(layout->u.chunk.size > 0); fake_ent.chunk_idx = udata->chunk_idx; fake_ent.chunk_block.offset = udata->chunk_block.offset; @@ -4120,7 +4137,7 @@ H5D__chunk_allocate(const H5D_io_info_t *io_info, hbool_t full_overwrite, hsize_ if(has_unfilt_edge_chunks) { if(NULL == (unfilt_fill_buf = H5D__chunk_mem_alloc(orig_chunk_size, &def_pline))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for raw data chunk") - HDmemcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size); + H5MM_memcpy(unfilt_fill_buf, fb_info.fill_buf, orig_chunk_size); } /* end if */ /* Retrieve filter settings from API context */ @@ -5654,7 +5671,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) if(udata->chunk_in_cache && udata->chunk) { HDassert(!H5F_addr_defined(chunk_rec->chunk_addr)); - HDmemcpy(buf, udata->chunk, nbytes); + H5MM_memcpy(buf, udata->chunk, nbytes); udata->chunk = NULL; } else { @@ -5688,7 +5705,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) HDassert(H5F_addr_defined(ent->chunk_block.offset)); H5_CHECKED_ASSIGN(nbytes, size_t, shared_fo->layout.u.chunk.size, uint32_t); - HDmemcpy(buf, ent->chunk, nbytes); + H5MM_memcpy(buf, ent->chunk, nbytes); } else { /* read chunk data from the source file */ @@ -5722,7 +5739,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, H5_ITER_ERROR, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ - HDmemcpy(reclaim_buf, buf, reclaim_buf_size); + H5MM_memcpy(reclaim_buf, buf, reclaim_buf_size); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); @@ -5753,7 +5770,7 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata) } /* end if */ /* After fix ref, copy the new reference elements to the buffer to write out */ - HDmemcpy(buf, bkg, buf_size); + H5MM_memcpy(buf, bkg, buf_size); } /* end if */ /* Set up destination chunk callback information for insertion */ @@ -6053,7 +6070,7 @@ H5D__chunk_copy(H5F_t *f_src, H5O_storage_chunk_t *storage_src, for(ent = shared_fo->cache.chunk.head; ent; ent = next) { if(!H5F_addr_defined(ent->chunk_block.offset)) { - HDmemcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled)); + H5MM_memcpy(chunk_rec.scaled, ent->scaled, sizeof(chunk_rec.scaled)); udata.chunk = ent->chunk; udata.chunk_in_cache = TRUE; if(H5D__chunk_copy_cb(&chunk_rec, &udata) < 0) @@ -6303,15 +6320,16 @@ H5D__chunk_stats(const H5D_t *dset, hbool_t headers) HGOTO_DONE(SUCCEED) if (headers) { - fprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); - fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", + HDfprintf(H5DEBUG(AC), "H5D: raw data cache statistics\n"); + HDfprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s+%-8s\n", "Layer", "Hits", "Misses", "MissRate", "Inits", "Flushes"); - fprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", + HDfprintf(H5DEBUG(AC), " %-18s %8s %8s %8s %8s-%-8s\n", "-----", "----", "------", "--------", "-----", "-------"); } #ifdef H5AC_DEBUG - if (H5DEBUG(AC)) headers = TRUE; + if (H5DEBUG(AC)) + headers = TRUE; #endif if (headers) { @@ -6322,12 +6340,12 @@ H5D__chunk_stats(const H5D_t *dset, hbool_t headers) miss_rate = 0.0; } if (miss_rate > 100) { - sprintf(ascii, "%7d%%", (int) (miss_rate + 0.5)); + HDsprintf(ascii, "%7d%%", (int) (miss_rate + 0.5)); } else { - sprintf(ascii, "%7.2f%%", miss_rate); + HDsprintf(ascii, "%7.2f%%", miss_rate); } - fprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", + HDfprintf(H5DEBUG(AC), " %-18s %8u %8u %7s %8d+%-9ld\n", "raw data chunks", rdcc->stats.nhits, rdcc->stats.nmisses, ascii, rdcc->stats.ninits, (long)(rdcc->stats.nflushes)-(long)(rdcc->stats.ninits)); } |