diff options
Diffstat (limited to 'src/H5Dchunk.c')
| -rw-r--r-- | src/H5Dchunk.c | 89 |
1 files changed, 41 insertions, 48 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index af8ff91..6d1067b 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -1073,21 +1073,19 @@ 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 +1127,9 @@ 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 +1144,9 @@ 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 +1241,9 @@ 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 +1535,7 @@ 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 +1551,8 @@ 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 +1567,7 @@ 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 +1591,7 @@ 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 +1629,7 @@ 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 +1637,7 @@ 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 +1650,13 @@ 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); 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 +1680,11 @@ 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 +1698,14 @@ 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 +1737,12 @@ 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 +1756,7 @@ 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 +1779,15 @@ 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 +1826,7 @@ 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 */ @@ -1976,7 +1970,7 @@ 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 +1995,10 @@ 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; |