diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 117 |
1 files changed, 48 insertions, 69 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 1833452..227d0d7 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -42,6 +42,7 @@ /* Structure holding information about a chunk's selection for mapping */ typedef struct H5D_chunk_info_t { hsize_t index; /* "Index" of chunk in dataset (must be first for TBBT routines) */ + hsize_t chunk_points; /* Number of elements selected in chunk */ H5S_t *fspace; /* Dataspace describing chunk & selection in it */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */ H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */ @@ -52,11 +53,11 @@ typedef struct H5D_chunk_info_t { typedef struct fm_map { H5TB_TREE *fsel; /* TBBT containing file dataspaces for all chunks */ hsize_t last_index; /* Index of last chunk operated on */ + H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */ const H5S_t *file_space; /* Pointer to the file dataspace */ const H5S_t *mem_space; /* Pointer to the memory dataspace */ unsigned mem_space_copy; /* Flag to indicate that the memory dataspace must be copied */ hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */ - H5S_t *last_chunk; /* Pointer to last memory chunk's dataspace */ H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */ unsigned f_ndims; /* Number of dimensions for file dataspace */ H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ @@ -1075,8 +1076,9 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || H5S_NULL == H5S_get_simple_extent_type(file_space) || dataset->layout.type==H5D_COMPACT); + H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); status = (sconv->read)(dataset->ent.file, &(dataset->layout), - &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type), + &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), (size_t)nelmts, H5T_get_size(dataset->type), file_space, mem_space, dxpl_cache, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].read_timer), &timer); @@ -1299,8 +1301,9 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5 #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif + H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); status = (sconv->write)(dataset->ent.file, &(dataset->layout), - &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type), + &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), (size_t)nelmts, H5T_get_size(dataset->type), file_space, mem_space, dxpl_cache, dxpl_id, buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); @@ -1508,8 +1511,6 @@ UNUSED size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ - hssize_t schunk_nelmts; /* Number of elements selected in current chunk */ - hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ @@ -1552,20 +1553,12 @@ UNUSED /* Get the actual chunk information from the tree node */ chunk_info=chunk_node->data; -#ifdef H5S_DEBUG - /* Get the number of elements selected in this chunk */ - if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection") - H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t); - assert(chunk_nelmts<=nelmts); -#endif /* H5S_DEBUG */ - /* Pass in chunk's coordinates in a union. */ store.chunk_coords = chunk_info->coords; /* Perform the actual read operation */ status = (sconv->read)(dataset->ent.file, &(dataset->layout), - &dataset->dcpl_cache, &store, H5T_get_size(dataset->type), + &dataset->dcpl_cache, &store, chunk_info->chunk_points, H5T_get_size(dataset->type), chunk_info->fspace, chunk_info->mspace, dxpl_cache, dxpl_id, buf); /* Check return value from optimized read */ @@ -1648,12 +1641,6 @@ UNUSED /* Get the actual chunk information from the tree nodes */ chunk_info=chunk_node->data; - /* Get the number of elements selected in this chunk */ - if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection") - H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t); - assert(chunk_nelmts<=nelmts); - /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information") @@ -1668,10 +1655,10 @@ UNUSED /* Pass in chunk's coordinates in a union*/ store.chunk_coords = chunk_info->coords; - for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { + for (smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ - assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); - smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); + assert(H5S_select_iter_nelmts(&file_iter)==(chunk_info->chunk_points-smine_start)); + smine_nelmts = MIN(request_nelmts, (chunk_info->chunk_points-smine_start)); /* * Gather the data from disk into the data type conversion @@ -1821,8 +1808,6 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ - hssize_t schunk_nelmts; /* Number of elements selected in current chunk */ - hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ @@ -1888,20 +1873,12 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* Get the actual chunk information from the tree node */ chunk_info=chunk_node->data; -#ifdef H5S_DEBUG - /* Get the number of elements selected in this chunk */ - if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection") - H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t); - assert(chunk_nelmts<=nelmts); -#endif /* H5S_DEBUG */ - /* Pass in chunk's coordinates in a union. */ store.chunk_coords = chunk_info->coords; /* Perform the actual write operation */ status = (sconv->write)(dataset->ent.file, &(dataset->layout), - &dataset->dcpl_cache, &store, H5T_get_size(dataset->type), + &dataset->dcpl_cache, &store, chunk_info->chunk_points, H5T_get_size(dataset->type), chunk_info->fspace, chunk_info->mspace, dxpl_cache, dxpl_id, buf); /* Check return value from optimized write */ @@ -2004,12 +1981,6 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /* Get the actual chunk information from the tree node */ chunk_info=chunk_node->data; - /* Get the number of elements selected in this chunk */ - if((schunk_nelmts=H5S_get_select_npoints(chunk_info->fspace))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "bad # of elements in selection") - H5_ASSIGN_OVERFLOW(chunk_nelmts,schunk_nelmts,hssize_t,hsize_t); - assert(chunk_nelmts<=nelmts); - /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information") @@ -2024,10 +1995,10 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, /*pass in chunk's coordinates in a union*/ store.chunk_coords = chunk_info->coords; - for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { + for (smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ - assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); - smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); + assert(H5S_select_iter_nelmts(&file_iter)==(chunk_info->chunk_points-smine_start)); + smine_nelmts = MIN(request_nelmts, (chunk_info->chunk_points-smine_start)); /* * Gather the data from disk into the data type conversion @@ -2345,7 +2316,7 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp /* Initialize "last chunk" information */ fm->last_index=(hsize_t)-1; - fm->last_chunk=NULL; + fm->last_chunk_info=NULL; /* Point at the dataspaces */ fm->file_space=file_space; @@ -2370,7 +2341,7 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp /* Reset "last chunk" info */ fm->last_index=(hsize_t)-1; - fm->last_chunk=NULL; + fm->last_chunk_info=NULL; } /* end if */ else { #ifdef QAK @@ -2662,8 +2633,8 @@ H5D_create_chunk_file_map_hyper(const fm_map *fm) /* Check for intersection of temporary chunk and file selection */ if(H5S_hyper_intersect_block(fm->file_space,coords,end)==TRUE) { H5S_t *tmp_fchunk; /* Temporary file dataspace */ - H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */ - hssize_t chunk_points; /* Number of elements in chunk selection */ + H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */ + hssize_t schunk_points; /* Number of elements in chunk selection */ /* Create "temporary" chunk for selection operations (copy file space) */ if((tmp_fchunk = H5S_copy(fm->file_space))==NULL) @@ -2726,11 +2697,12 @@ H5D_create_chunk_file_map_hyper(const fm_map *fm) } /* end if */ /* Get number of elements selected in chunk */ - if((chunk_points=H5S_get_select_npoints(tmp_fchunk))<0) + if((schunk_points=H5S_get_select_npoints(tmp_fchunk))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements") + H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,hsize_t); /* Decrement # of points left in file selection */ - sel_points-=chunk_points; + sel_points-=schunk_points; /* Leave if we are done */ if(sel_points==0) @@ -2977,7 +2949,7 @@ static herr_t H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ - H5S_t *fspace; /* Memory chunk's dataspace */ + H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hsize_t chunk_index; /* Chunk index */ unsigned u; /* Local index variable */ @@ -2992,9 +2964,9 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize /* Find correct chunk in file & memory TBBTs */ if(chunk_index==fm->last_index) { /* If the chunk index is the same as the last chunk index we used, - * get the cached spaces to operate on. + * get the cached info to operate on. */ - fspace=fm->last_chunk; + chunk_info=fm->last_chunk_info; } /* end if */ else { H5TB_NODE *chunk_node; /* TBBT node holding chunk information */ @@ -3004,7 +2976,8 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize */ /* Get the chunk node from the TBBT */ if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))==NULL) { - H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into tree */ + H5D_chunk_info_t *new_chunk_info; /* Chunk information to insert into tree */ + H5S_t *fspace; /* Memory chunk's dataspace */ /* Allocate the file & memory chunk information */ if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) @@ -3035,6 +3008,9 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize new_chunk_info->mspace=NULL; new_chunk_info->mspace_shared=0; + /* Set the number of selected elements in chunk to zero */ + new_chunk_info->chunk_points=0; + /* Compute the chunk's coordinates */ for(u=0; u<fm->f_ndims; u++) { H5_CHECK_OVERFLOW(fm->layout->dim[u],hsize_t,hssize_t); @@ -3047,14 +3023,17 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize H5D_free_chunk_info(new_chunk_info); HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into TBBT") } /* end if */ + + /* Save the chunk info pointer */ + chunk_info=new_chunk_info; } /* end if */ else - /* Get the memory space information from the node */ - fspace=((H5D_chunk_info_t *)(chunk_node->data))->fspace; + /* Get the information from the node */ + chunk_info=(H5D_chunk_info_t *)(chunk_node->data); /* Update the "last chunk seen" information */ fm->last_index=chunk_index; - fm->last_chunk=fspace; + fm->last_chunk_info=chunk_info; } /* end else */ /* Get the coordinates of the element in the chunk */ @@ -3062,9 +3041,12 @@ H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize coords_in_chunk[u]=coords[u]%fm->layout->dim[u]; /* Add point to file selection for chunk */ - if(H5S_select_elements(fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0) + if(H5S_select_elements(chunk_info->fspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_chunk)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") + /* Increment the number of elemented selected in chunk */ + chunk_info->chunk_points++; + done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_file_cb() */ @@ -3092,7 +3074,7 @@ static herr_t H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ - H5S_t *mspace; /* Memory chunk's dataspace */ + H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ hsize_t chunk_index; /* Chunk index */ herr_t ret_value = SUCCEED; /* Return value */ @@ -3108,7 +3090,7 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_ /* If the chunk index is the same as the last chunk index we used, * get the cached spaces to operate on. */ - mspace=fm->last_chunk; + chunk_info=fm->last_chunk_info; } /* end if */ else { H5TB_NODE *chunk_node; /* TBBT node holding chunk information */ @@ -3120,22 +3102,19 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_ if((chunk_node=H5TB_dfind(fm->fsel,&chunk_index,NULL))==NULL) HGOTO_ERROR(H5E_DATASPACE,H5E_NOTFOUND,FAIL,"can't locate chunk in TBBT") - /* Get the memory space information from the node */ - mspace=((H5D_chunk_info_t *)(chunk_node->data))->mspace; + /* Get the chunk info pointer */ + chunk_info=(H5D_chunk_info_t *)(chunk_node->data); /* Check if the chunk already has a memory space */ - if(mspace==NULL) { + if(chunk_info->mspace==NULL) { /* Copy the template memory chunk dataspace */ - if((mspace = H5S_copy(fm->mchunk_tmpl))==NULL) + if((chunk_info->mspace = H5S_copy(fm->mchunk_tmpl))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space") - - /* Set the chunk's memory dataspace for later use */ - ((H5D_chunk_info_t *)(chunk_node->data))->mspace=mspace; } /* end else */ /* Update the "last chunk seen" information */ fm->last_index=chunk_index; - fm->last_chunk=mspace; + fm->last_chunk_info=chunk_info; } /* end else */ /* Get coordinates of selection iterator for memory */ @@ -3144,11 +3123,11 @@ H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_ /* Add point to memory selection for chunk */ if(fm->msel_type==H5S_SEL_POINTS) { - if(H5S_select_elements(mspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_mem)<0) + if(H5S_select_elements(chunk_info->mspace,H5S_SELECT_APPEND,1,(const hssize_t **)coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") } /* end if */ else { - if(H5S_hyper_add_span_element(mspace, fm->m_ndims, coords_in_mem)<0) + if(H5S_hyper_add_span_element(chunk_info->mspace, fm->m_ndims, coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") } /* end else */ |