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-rw-r--r--src/H5Dchunk.c152
1 files changed, 73 insertions, 79 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 0f7bccf..36c47d0 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -724,15 +724,18 @@ H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims,
/* Compute the # of chunks in dataset dimensions */
for(u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) {
- /* Sanity check */
- HDassert(layout->dim[u] > 0);
-
/* Round up to the next integer # of chunks, to accommodate partial chunks */
layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
if(H5S_UNLIMITED == max_dims[u])
layout->max_chunks[u] = H5S_UNLIMITED;
else
+ {
+ /* Sanity check */
+ if(layout->dim[u] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "dimension size must be > 0, dim = %u ", u)
+
layout->max_chunks[u] = ((max_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
+ }
/* Accumulate the # of chunks */
layout->nchunks *= layout->chunks[u];
@@ -1126,21 +1129,19 @@ 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 */
@@ -1182,10 +1183,9 @@ 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);
@@ -1200,10 +1200,9 @@ 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);
@@ -1272,7 +1271,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
} /* end else */
/* Build the memory selection for each chunk */
- if(sel_hyper_flag && H5S_select_shape_same(file_space, mem_space) == TRUE) {
+ if(sel_hyper_flag && H5S_SELECT_SHAPE_SAME(file_space, mem_space) == TRUE) {
/* Reset chunk template information */
fm->mchunk_tmpl = NULL;
@@ -1298,10 +1297,9 @@ 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)))
@@ -1404,7 +1402,7 @@ H5D__chunk_mem_alloc(size_t size, const H5O_pline_t *pline)
/*-------------------------------------------------------------------------
* Function: H5D__chunk_mem_xfree
*
- * Purpose: Free space for a chunk in memory. This routine allocates
+ * Purpose: Free space for a chunk in memory. This routine releases
* memory space for non-filtered chunks from a block free list
* and uses malloc()/free() for filtered chunks.
*
@@ -1565,7 +1563,8 @@ H5D__create_chunk_map_single(H5D_chunk_map_t *fm, const H5D_io_info_t
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file selection")
/* Move selection back to have correct offset in chunk */
- H5S_SELECT_ADJUST_U(fm->single_space, coords);
+ if(H5S_SELECT_ADJUST_U(fm->single_space, coords) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
#ifdef H5_HAVE_PARALLEL
/* store chunk selection information */
@@ -1626,7 +1625,7 @@ 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;
@@ -1652,7 +1651,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
while(sel_points) {
/* Check for intersection of temporary chunk and file selection */
/* (Casting away const OK - QAK) */
- if(TRUE == H5S_hyper_intersect_block((H5S_t *)fm->file_space, coords, end)) {
+ if(TRUE == H5S_hyper_intersect_block(fm->file_space, coords, end)) {
H5S_t *tmp_fchunk; /* Temporary file dataspace */
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */
hsize_t chunk_points; /* Number of elements in chunk selection */
@@ -1680,12 +1679,13 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
} /* end if */
/* Move selection back to have correct offset in chunk */
- H5S_SELECT_ADJUST_U(tmp_fchunk, coords);
+ if(H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
/* 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 */
@@ -1693,7 +1693,7 @@ 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 */
@@ -1706,16 +1706,13 @@ 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 */
- H5MM_memcpy(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 */
- H5MM_memcpy(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);
@@ -1723,8 +1720,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
} /* end if */
/* Get number of elements selected in chunk */
- if((chunk_points = H5S_GET_SELECT_NPOINTS(tmp_fchunk)) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
+ chunk_points = H5S_GET_SELECT_NPOINTS(tmp_fchunk);
H5_CHECKED_ASSIGN(new_chunk_info->chunk_points, uint32_t, chunk_points, hsize_t);
/* Decrement # of points left in file selection */
@@ -1739,12 +1735,12 @@ 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 */
@@ -1794,12 +1790,12 @@ 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 */
@@ -1813,7 +1809,7 @@ 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);
@@ -1836,15 +1832,15 @@ 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 */
@@ -1879,11 +1875,11 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
} /* end for */
/* Adjust the selection */
- if(H5S_hyper_adjust_s(chunk_info->mspace, chunk_adjust) < 0) /*lint !e772 The chunk_adjust array will always be initialized */
+ if(H5S_hyper_adjust_s(chunk_info->mspace, chunk_adjust) < 0)
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 */
@@ -2052,11 +2048,10 @@ H5D__chunk_mem_cb(void H5_ATTR_UNUSED *elem, const H5T_t H5_ATTR_UNUSED *type, u
HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "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, FAIL, "unable to copy file space")
- } /* end else */
/* Update the "last chunk seen" information */
fm->last_index = chunk_index;
@@ -5236,7 +5231,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, const hsize_t *old_dim)
} /* end if */
else
dims_outside_fill[u] = FALSE;
- } /* end if */
+ } /* end else */
carry = FALSE;
while(!carry) {
@@ -5690,9 +5685,8 @@ H5D__chunk_copy_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
/* Check for an edge chunk that is not filtered */
if(pline && pline->nused) {
must_filter = TRUE;
- if( (udata->common.layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) &&
- (H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim,
- chunk_rec->scaled, udata->dset_dims)) )
+ if((udata->common.layout->flags & H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS) &&
+ H5D__chunk_is_partial_edge_chunk(udata->dset_ndims, udata->common.layout->dim, chunk_rec->scaled, udata->dset_dims))
must_filter = FALSE;
}
@@ -6816,7 +6810,7 @@ H5D__chunk_format_convert(H5D_t *dset, H5D_chk_idx_info_t *idx_info, H5D_chk_idx
udata.dset_ndims = dset->shared->ndims;
udata.dset_dims = dset->shared->curr_dims;
- /* terate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */
+ /* Iterate over the chunks in the current index and insert the chunk addresses into version 1 B-tree index */
if((idx_info->storage->ops->iterate)(idx_info, H5D__chunk_format_convert_cb, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to iterate over chunk index to chunk info")
@@ -6878,8 +6872,8 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
{
H5D_chk_idx_info_t idx_info; /* Chunked index info */
hsize_t num_chunks = 0; /* Number of written chunks */
- H5D_rdcc_ent_t *ent; /* Cache entry */
- const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
+ H5D_rdcc_ent_t *ent; /* Cache entry */
+ const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
@@ -6889,8 +6883,7 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
HDassert(space);
HDassert(nchunks);
- /* Get the raw data chunk cache */
- rdcc = &(dset->shared->cache.chunk);
+ rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
HDassert(rdcc);
/* Search for cached chunks that haven't been written out */
@@ -6906,28 +6899,27 @@ H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_
idx_info.storage = &dset->shared->layout.storage.u.chunk;
/* If the dataset is not written, number of chunks will be 0 */
- if(!H5F_addr_defined(idx_info.storage->idx_addr)) {
+ if(!H5F_addr_defined(idx_info.storage->idx_addr))
*nchunks = 0;
- HGOTO_DONE(SUCCEED);
- }
else {
- /* Iterate over the allocated chunks */
- if((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_num_chunks_cb, &num_chunks) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
- *nchunks = num_chunks;
+ /* Iterate over the allocated chunks */
+ if((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_num_chunks_cb, &num_chunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
+ *nchunks = num_chunks;
}
done:
- FUNC_LEAVE_NOAPI(ret_value)
+ FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5D__get_num_chunks() */
/*-------------------------------------------------------------------------
* Function: H5D__get_chunk_info_cb
*
- * Purpose: Get the chunk info of the desired chunk, given by its index.
+ * Purpose: Get the chunk info of the queried chunk, given by its index.
*
* Return: Success: H5_ITER_CONT or H5_ITER_STOP
+ * H5_ITER_STOP indicates the queried chunk is found
* Failure: Negative (H5_ITER_ERROR)
*
* Programmer: Binh-Minh Ribler
@@ -6939,8 +6931,7 @@ static int
H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
{
H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata;
- hsize_t ii = 0; /* Dimension index */
- int ret_value = H5_ITER_CONT; /* Callback return value */
+ int ret_value = H5_ITER_CONT; /* Callback return value */
FUNC_ENTER_STATIC_NOERR
@@ -6948,19 +6939,22 @@ H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
HDassert(chunk_rec);
HDassert(chunk_info);
- /* If this is the desired chunk, retrieve its info and stop iterating */
- if (chunk_info->curr_idx == chunk_info->chunk_idx) {
+ /* If this is the queried chunk, retrieve its info and stop iterating */
+ if(chunk_info->curr_idx == chunk_info->chunk_idx) {
+ hsize_t ii = 0; /* Dimension index */
+
+ /* Copy info */
chunk_info->filter_mask = chunk_rec->filter_mask;
chunk_info->chunk_addr = chunk_rec->chunk_addr;
chunk_info->nbytes = chunk_rec->nbytes;
- for (ii = 0; ii < chunk_info->ndims; ii++)
+ for(ii = 0; ii < chunk_info->ndims; ii++)
chunk_info->scaled[ii] = chunk_rec->scaled[ii];
chunk_info->found = TRUE;
/* Stop iterating */
ret_value = H5_ITER_STOP;
}
- /* Iterate the next chunk */
+ /* Go to the next chunk */
else
chunk_info->curr_idx++;
@@ -7150,18 +7144,18 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned*
if(H5D__chunk_flush_entry(dset, ent, FALSE) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ /* Set addr & size for when dset is not written or queried chunk is not found */
+ if(addr)
+ *addr = HADDR_UNDEF;
+ if(size)
+ *size = 0;
+
/* Compose chunked index info struct */
idx_info.f = dset->oloc.file;
idx_info.pline = &dset->shared->dcpl_cache.pline;
idx_info.layout = &dset->shared->layout.u.chunk;
idx_info.storage = &dset->shared->layout.storage.u.chunk;
- /* Set addr & size for when dset is not written or queried chunk is not found */
- if (addr)
- *addr = HADDR_UNDEF;
- if (size)
- *size = 0;
-
/* If the dataset is not written, return without errors */
if(!H5F_addr_defined(idx_info.storage->idx_addr)) {
HGOTO_DONE(SUCCEED);
generated by cgit v0.12 at 2025-03-10 05:47:19 (GMT)