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authorQuincey Koziol <koziol@koziol.gov>2019-03-16 01:14:41 (GMT)
committerQuincey Koziol <koziol@koziol.gov>2019-03-16 01:14:41 (GMT)
commit9d86314f8b71f090b71d7edec8014935f5cd3cc7 (patch)
tree26422b8cc0217bf579594dd1a7a8ec011a5cb5c6 /src/H5Dchunk.c
parent07baf44a86de400c170006557e7595ea6ba9c20a (diff)
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Core changes to selection code from the hyperslab_updates branch.
Diffstat (limited to 'src/H5Dchunk.c')
-rw-r--r--src/H5Dchunk.c372
1 files changed, 279 insertions, 93 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index dcd3a8d..e7d1b15 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -276,6 +276,8 @@ static hbool_t H5D__chunk_cinfo_cache_found(const H5D_chunk_cached_t *last,
static herr_t H5D__free_chunk_info(void *item, void *key, void *opdata);
static herr_t H5D__create_chunk_map_single(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
+static herr_t H5D__create_chunk_file_map_all(H5D_chunk_map_t *fm,
+ const H5D_io_info_t *io_info);
static herr_t H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm,
const H5D_io_info_t *io_info);
static herr_t H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm);
@@ -1044,7 +1046,6 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */
unsigned f_ndims; /* The number of dimensions of the file's dataspace */
int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */
- H5SL_node_t *curr_node; /* Current node in skip list */
char bogus; /* "bogus" buffer to pass to selection iterator */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
@@ -1168,25 +1169,17 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
/* Check if file selection is a not a hyperslab selection */
if(sel_hyper_flag) {
/* Build the file selection for each chunk */
- if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
-
- /* Clean file chunks' hyperslab span "scratch" information */
- curr_node = H5SL_first(fm->sel_chunks);
- while(curr_node) {
- H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
-
- /* Get pointer to chunk's information */
- chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
- HDassert(chunk_info);
-
- /* Clean hyperslab span's "scratch" information */
- if(H5S_hyper_reset_scratch(chunk_info->fspace) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
+ if(H5S_SEL_ALL == fm->fsel_type) {
+ if(H5D__create_chunk_file_map_all(fm, io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ } /* end if */
+ else {
+ /* Sanity check */
+ HDassert(fm->fsel_type == H5S_SEL_HYPERSLABS);
- /* Get the next chunk node in the skip list */
- curr_node = H5SL_next(curr_node);
- } /* end while */
+ if(H5D__create_chunk_file_map_hyper(fm, io_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections")
+ } /* end else */
} /* end if */
else {
H5S_sel_iter_op_t iter_op; /* Operator for iteration */
@@ -1248,7 +1241,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
/* Create selection iterator for memory selection */
if(0 == (elmt_size = H5T_get_size(mem_type)))
HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid")
- if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size) < 0)
+ if(H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size, 0) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
iter_init = TRUE; /* Selection iteration info has been initialized */
@@ -1258,26 +1251,6 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
/* Spaces aren't the same shape, iterate over the memory selection directly */
if(H5S_select_iterate(&bogus, file_type, file_space, &iter_op, fm) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections")
-
- /* Clean up hyperslab stuff, if necessary */
- if(fm->msel_type != H5S_SEL_POINTS) {
- /* Clean memory chunks' hyperslab span "scratch" information */
- curr_node = H5SL_first(fm->sel_chunks);
- while(curr_node) {
- H5D_chunk_info_t *chunk_info; /* Pointer chunk information */
-
- /* Get pointer to chunk's information */
- chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
- HDassert(chunk_info);
-
- /* Clean hyperslab span's "scratch" information */
- if(H5S_hyper_reset_scratch(chunk_info->mspace) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info")
-
- /* Get the next chunk node in the skip list */
- curr_node = H5SL_next(curr_node);
- } /* end while */
- } /* end if */
} /* end else */
} /* end else */
@@ -1533,6 +1506,211 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D__create_chunk_file_map_all
+ *
+ * Purpose: Create all chunk selections in file, for an "all" selection.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Quincey Koziol
+ * Monday, January 21, 2019
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__create_chunk_file_map_all(H5D_chunk_map_t *fm, const H5D_io_info_t
+#ifndef H5_HAVE_PARALLEL
+ H5_ATTR_UNUSED
+#endif /* H5_HAVE_PARALLEL */
+ *io_info)
+{
+ H5S_t *tmp_fchunk = NULL; /* Temporary file dataspace */
+ hsize_t file_dims[H5S_MAX_RANK]; /* File dataspace dims */
+ hsize_t sel_points; /* Number of elements in file selection */
+ hsize_t zeros[H5S_MAX_RANK]; /* All zero vector (for start parameter to setting hyperslab on partial chunks) */
+ hsize_t coords[H5S_MAX_RANK]; /* Current coordinates of chunk */
+ hsize_t end[H5S_MAX_RANK]; /* Final coordinates of chunk */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ hsize_t chunk_index; /* "Index" of chunk */
+ hsize_t curr_partial_clip[H5S_MAX_RANK]; /* Current partial dimension sizes to clip against */
+ hsize_t partial_dim_size[H5S_MAX_RANK]; /* Size of a partial dimension */
+ hbool_t is_partial_dim[H5S_MAX_RANK]; /* Whether a dimension is currently a partial chunk */
+ unsigned num_partial_dims; /* Current number of partial dimensions */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC
+
+ /* Sanity check */
+ HDassert(fm->f_ndims > 0);
+
+ /* Get number of elements selected in file */
+ sel_points = fm->nelmts;
+
+ /* Get dataspace dimensions */
+ if(H5S_get_simple_extent_dims(fm->file_space, file_dims, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info")
+
+ /* Set initial chunk location, partial dimensions, etc */
+ num_partial_dims = 0;
+ HDmemset(zeros, 0, sizeof(zeros));
+ for(u = 0; u < fm->f_ndims; u++) {
+ /* Validate this chunk dimension */
+ if(fm->layout->u.chunk.dim[u] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
+
+ /* Set up start / end coordinates for first chunk */
+ scaled[u] = 0;
+ coords[u] = 0;
+ end[u] = fm->chunk_dim[u] - 1;
+
+ /* Iniitialize partial chunk dimension information */
+ partial_dim_size[u] = file_dims[u] % fm->chunk_dim[u];
+ if(file_dims[u] < fm->chunk_dim[u]) {
+ curr_partial_clip[u] = partial_dim_size[u];
+ is_partial_dim[u] = TRUE;
+ num_partial_dims++;
+ } /* end if */
+ else {
+ curr_partial_clip[u] = fm->chunk_dim[u];
+ is_partial_dim[u] = FALSE;
+ } /* end else */
+ } /* end for */
+
+ /* Set the index of this chunk */
+ chunk_index = 0;
+
+ /* Create "temporary" chunk for selection operations (copy file space) */
+ if(NULL == (tmp_fchunk = H5S_create_simple(fm->f_ndims, fm->chunk_dim, NULL)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk")
+
+ /* Iterate through each chunk in the dataset */
+ while(sel_points) {
+ H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */
+ hssize_t schunk_points; /* Number of elements in 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)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk info")
+
+ /* Initialize the chunk information */
+
+ /* Set the chunk index */
+ new_chunk_info->index = chunk_index;
+
+#ifdef H5_HAVE_PARALLEL
+ /* Store chunk selection information, for multi-chunk I/O */
+ if(io_info->using_mpi_vfd)
+ fm->select_chunk[chunk_index] = new_chunk_info;
+#endif /* H5_HAVE_PARALLEL */
+
+ /* Set the file chunk dataspace */
+ if(NULL == (new_chunk_info->fspace = H5S_copy(tmp_fchunk, TRUE, FALSE)))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy chunk dataspace")
+ new_chunk_info->fspace_shared = FALSE;
+
+ /* If there are partial dimensions for this chunk, set the hyperslab for them */
+ if(num_partial_dims > 0)
+ if(H5S_select_hyperslab(new_chunk_info->fspace, H5S_SELECT_SET, zeros, NULL, curr_partial_clip, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk selection")
+
+ /* Set the memory chunk dataspace */
+ 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;
+
+ /* 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);
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINSERT, FAIL, "can't insert chunk into skip list")
+ } /* end if */
+
+ /* Get number of elements selected in chunk */
+ if((schunk_points = H5S_GET_SELECT_NPOINTS(new_chunk_info->fspace)) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
+ H5_CHECKED_ASSIGN(new_chunk_info->chunk_points, uint32_t, schunk_points, hssize_t);
+
+ /* Decrement # of points left in file selection */
+ sel_points -= (hsize_t)schunk_points;
+
+ /* Advance to next chunk if we are not done */
+ if(sel_points > 0) {
+ int curr_dim; /* Current dimension to increment */
+
+ /* Increment chunk index */
+ chunk_index++;
+
+ /* Set current increment dimension */
+ curr_dim = (int)fm->f_ndims - 1;
+
+ /* Increment chunk location in fastest changing dimension */
+ coords[curr_dim] += fm->chunk_dim[curr_dim];
+ scaled[curr_dim]++;
+ end[curr_dim] += fm->chunk_dim[curr_dim];
+
+ /* Bring chunk location back into bounds, if necessary */
+ if(coords[curr_dim] >= file_dims[curr_dim]) {
+ do {
+ /* Reset current dimension's location to 0 */
+ coords[curr_dim] = 0;
+ scaled[curr_dim] = 0;
+ end[curr_dim] = fm->chunk_dim[curr_dim] - 1;
+
+ /* Check for previous partial chunk in this dimension */
+ if(is_partial_dim[curr_dim] && end[curr_dim] < file_dims[curr_dim]) {
+ /* Sanity check */
+ HDassert(num_partial_dims > 0);
+
+ /* Reset partial chunk information for this dimension */
+ curr_partial_clip[curr_dim] = fm->chunk_dim[curr_dim];
+ is_partial_dim[curr_dim] = FALSE;
+ num_partial_dims--;
+ } /* end if */
+
+ /* Decrement current dimension */
+ curr_dim--;
+
+ /* Check for valid current dim */
+ if(curr_dim >= 0) {
+ /* Increment chunk location in current dimension */
+ coords[curr_dim] += fm->chunk_dim[curr_dim];
+ scaled[curr_dim]++;
+ end[curr_dim] = (coords[curr_dim] + fm->chunk_dim[curr_dim]) - 1;
+ } /* end if */
+ } while(curr_dim >= 0 && (coords[curr_dim] >= file_dims[curr_dim]));
+ } /* end if */
+
+ /* Check for valid current dim */
+ if(curr_dim >= 0) {
+ /* Check for partial chunk in this dimension */
+ if(!is_partial_dim[curr_dim] && file_dims[curr_dim] <= end[curr_dim]) {
+ /* Set partial chunk information for this dimension */
+ curr_partial_clip[curr_dim] = partial_dim_size[curr_dim];
+ is_partial_dim[curr_dim] = TRUE;
+ num_partial_dims++;
+
+ /* Sanity check */
+ HDassert(num_partial_dims <= fm->f_ndims);
+ } /* end if */
+ } /* end if */
+ } /* end if */
+ } /* end while */
+
+done:
+ /* Clean up */
+ if(tmp_fchunk && H5S_close(tmp_fchunk) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release temporary dataspace")
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__create_chunk_file_map_all() */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__create_chunk_file_map_hyper
*
* Purpose: Create all chunk selections in file, for a hyperslab selection.
@@ -1551,6 +1729,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
#endif /* H5_HAVE_PARALLEL */
*io_info)
{
+ H5S_t *tmp_fchunk = NULL; /* Temporary file dataspace */
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 */
@@ -1594,45 +1773,28 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* 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 */
H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */
hssize_t schunk_points; /* Number of elements in chunk selection */
- /* Create "temporary" chunk for selection operations (copy file space) */
- if(NULL == (tmp_fchunk = H5S_copy(fm->file_space, TRUE, FALSE)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
-
- /* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */
- if(H5S_hyper_convert(tmp_fchunk) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees")
- } /* end if */
-
- /* "AND" temporary chunk and current chunk */
- if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection")
- } /* end if */
+ /* Create dataspace for chunk, 'AND'ing the overall selection with
+ * the current chunk.
+ */
+ if(H5S_combine_hyperslab(fm->file_space, H5S_SELECT_AND, coords, NULL, fm->chunk_dim, NULL, &tmp_fchunk) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to combine file space selection with chunk block")
/* Resize chunk's dataspace dimensions to size of chunk */
- if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
- } /* end if */
+ if(H5S_set_extent_real(tmp_fchunk, fm->chunk_dim) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions")
/* Move selection back to have correct offset in chunk */
- if(H5S_SELECT_ADJUST_U(tmp_fchunk, coords) < 0) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection")
- }
+ 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))) {
- (void)H5S_close(tmp_fchunk);
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info")
- } /* end if */
+ if(NULL == (new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk info")
/* Initialize the chunk information */
@@ -1648,6 +1810,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
/* Set the file chunk dataspace */
new_chunk_info->fspace = tmp_fchunk;
new_chunk_info->fspace_shared = FALSE;
+ tmp_fchunk = NULL;
/* Set the memory chunk dataspace */
new_chunk_info->mspace = NULL;
@@ -1664,7 +1827,7 @@ 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((schunk_points = H5S_GET_SELECT_NPOINTS(tmp_fchunk)) < 0)
+ if((schunk_points = H5S_GET_SELECT_NPOINTS(new_chunk_info->fspace)) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements")
H5_CHECKED_ASSIGN(new_chunk_info->chunk_points, uint32_t, schunk_points, hssize_t);
@@ -1713,6 +1876,11 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t
} /* end while */
done:
+ /* Clean up on failure */
+ if(ret_value < 0)
+ if(tmp_fchunk && H5S_close(tmp_fchunk) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release temporary dataspace")
+
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__create_chunk_file_map_hyper() */
@@ -1736,13 +1904,13 @@ done:
static herr_t
H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
{
+ H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
H5SL_node_t *curr_node; /* Current node in skip list */
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 */
@@ -1753,8 +1921,6 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
/* Check for all I/O going to a single chunk */
if(H5SL_count(fm->sel_chunks)==1) {
- H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
-
/* Get the node */
curr_node = H5SL_first(fm->sel_chunks);
@@ -1789,41 +1955,61 @@ H5D__create_chunk_mem_map_hyper(const H5D_chunk_map_t *fm)
/* Iterate over each chunk in the chunk list */
curr_node = H5SL_first(fm->sel_chunks);
while(curr_node) {
- H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */
+ hsize_t coords[H5S_MAX_RANK]; /* Current coordinates of chunk */
+ hssize_t chunk_adjust[H5S_MAX_RANK]; /* Adjustment to make to a particular chunk */
+ H5S_sel_type chunk_sel_type; /* Chunk's selection type */
/* Get pointer to chunk's information */
chunk_info = (H5D_chunk_info_t *)H5SL_item(curr_node);
HDassert(chunk_info);
+ /* Compute the chunk coordinates from the scaled coordinates */
+ for(u = 0; u < fm->f_ndims; u++)
+ coords[u] = chunk_info->scaled[u] * fm->layout->u.chunk.dim[u];
+
/* Copy the information */
/* Copy the memory dataspace */
if((chunk_info->mspace = H5S_copy(fm->mem_space, TRUE, FALSE)) == NULL)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space")
- /* Release the current selection */
- if(H5S_SELECT_RELEASE(chunk_info->mspace) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
+ /* Get the chunk's selection type */
+ if((chunk_sel_type = H5S_GET_SELECT_TYPE(chunk_info->fspace)) < H5S_SEL_NONE)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "unable to get type of selection")
- /* Copy the file chunk's selection */
- if(H5S_select_copy(chunk_info->mspace,chunk_info->fspace,FALSE) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection")
+ /* Set memory selection for "all" chunk selections */
+ if(H5S_SEL_ALL == chunk_sel_type) {
+ /* Adjust the chunk coordinates */
+ for(u = 0; u < fm->f_ndims; u++)
+ coords[u] -= adjust[u];
- /* Compute the adjustment for this chunk */
- for(u = 0; u < fm->f_ndims; u++) {
- hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */
+ /* Set to same shape as chunk */
+ if(H5S_select_hyperslab(chunk_info->mspace, H5S_SELECT_SET, coords, NULL, fm->chunk_dim, NULL) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSELECT, FAIL, "can't create chunk memory selection")
+ } /* end if */
+ else {
+ /* Sanity check */
+ HDassert(H5S_SEL_HYPERSLABS == chunk_sel_type);
- /* Compute the chunk coordinates from the scaled coordinates */
- coords[u] = chunk_info->scaled[u] * fm->layout->u.chunk.dim[u];
+ /* Release the current selection */
+ if(H5S_SELECT_RELEASE(chunk_info->mspace) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
- /* Compensate for the chunk offset */
- H5_CHECK_OVERFLOW(coords[u], hsize_t, hssize_t);
- chunk_adjust[u] = adjust[u] - (hssize_t)coords[u]; /*lint !e771 The adjust array will always be initialized */
- } /* end for */
+ /* Copy the file chunk's selection */
+ if(H5S_select_copy(chunk_info->mspace, chunk_info->fspace, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection")
- /* Adjust the selection */
- if(H5S_hyper_adjust_s(chunk_info->mspace, chunk_adjust) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to adjust selection")
+ /* Compute the adjustment for this chunk */
+ for(u = 0; u < fm->f_ndims; u++) {
+ /* Compensate for the chunk offset */
+ H5_CHECK_OVERFLOW(coords[u], hsize_t, hssize_t);
+ chunk_adjust[u] = adjust[u] - (hssize_t)coords[u]; /*lint !e771 The adjust array will always be initialized */
+ } /* end for */
+
+ /* Adjust the selection */
+ if(H5S_hyper_adjust_s(chunk_info->mspace, chunk_adjust) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to adjust selection")
+ } /* end else */
/* Get the next chunk node in the skip list */
curr_node = H5SL_next(curr_node);
@@ -4821,12 +5007,12 @@ H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata, hbool_t new_unfilt_chunk)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk selection iterator")
/* Create a selection iterator for scattering the elements to memory buffer */
- if(H5S_select_iter_init(chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank]) < 0)
+ if(H5S_select_iter_init(chunk_iter, udata->chunk_space, layout->u.chunk.dim[rank], 0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize chunk selection information")
chunk_iter_init = TRUE;
/* Scatter the data into memory */
- if(H5D__scatter_mem(udata->fb_info.fill_buf, udata->chunk_space, chunk_iter, (size_t)sel_nelmts, chunk/*out*/) < 0)
+ if(H5D__scatter_mem(udata->fb_info.fill_buf, chunk_iter, (size_t)sel_nelmts, chunk/*out*/) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed")