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authorAllen Byrne <byrn@hdfgroup.org>2019-12-04 17:36:07 (GMT)
committerAllen Byrne <byrn@hdfgroup.org>2019-12-04 17:36:07 (GMT)
commite994c9cb4aa2e304a161145e26e03fcad6be0c2b (patch)
tree0cb0079b8f220f4adf0cf4cdeadf4ac76babebd0
parent915184104b56183174f2ce3a1505dfcf5dcf229d (diff)
parentaa0b54e27e5d6f0b7c23fe5662d5c8f30898d7f4 (diff)
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Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'aa0b54e27e5d6f0b7c23fe5662d5c8f30898d7f4': Fixed missing blob callbacks in test VOL connectors. Add support for scalar dataspaces to H5Sproject_intersection. Add checking for ank validity. Fix issues with using H5Pget_fill_value() with file datatypes retrieved from H5VLget_file_type().
-rw-r--r--src/H5Pdcpl.c8
-rw-r--r--src/H5Shyper.c2
-rw-r--r--src/H5Sselect.c215
-rw-r--r--test/null_vol_connector.c6
-rw-r--r--test/vol.c6
5 files changed, 146 insertions, 91 deletions
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index 721ba89..b83e2cf 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -3324,19 +3324,19 @@ H5P_get_fill_value(H5P_genplist_t *plist, const H5T_t *type, void *value/*out*/)
*/
if(H5T_get_size(type) >= H5T_get_size(fill.type)) {
buf = value;
- if(H5T_path_bkg(tpath) && NULL == (bkg = H5MM_malloc(H5T_get_size(type))))
+ if(H5T_path_bkg(tpath) && NULL == (bkg = H5MM_calloc(H5T_get_size(type))))
HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for type conversion")
} /* end if */
else {
- if(NULL == (buf = H5MM_malloc(H5T_get_size(fill.type))))
+ if(NULL == (buf = H5MM_calloc(H5T_get_size(fill.type))))
HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for type conversion")
- if(H5T_path_bkg(tpath) && NULL == (bkg = H5MM_malloc(H5T_get_size(fill.type))))
+ if(H5T_path_bkg(tpath) && NULL == (bkg = H5MM_calloc(H5T_get_size(fill.type))))
HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for type conversion")
} /* end else */
H5MM_memcpy(buf, fill.buf, H5T_get_size(fill.type));
/* Do the conversion */
- if((dst_id = H5I_register(H5I_DATATYPE, H5T_copy(type, H5T_COPY_TRANSIENT), FALSE)) < 0)
+ if((dst_id = H5I_register(H5I_DATATYPE, H5T_copy(type, H5T_COPY_ALL), FALSE)) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "unable to copy/register datatype")
if(H5T_convert(tpath, src_id, dst_id, (size_t)1, (size_t)0, (size_t)0, buf, bkg) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "datatype conversion failed")
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index ab06eff..acb8b87 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -11503,7 +11503,7 @@ H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space,
HDassert(src_intersect_space);
HDassert(proj_space);
- /* Assert that src_space and src_intersect_space have same extent and there
+ /* Assert that src_space and src_intersect_space have same rank and there
* are no point selections */
HDassert(H5S_GET_EXTENT_NDIMS(src_space) == H5S_GET_EXTENT_NDIMS(src_intersect_space));
HDassert(H5S_GET_SELECT_NPOINTS(src_space) == H5S_GET_SELECT_NPOINTS(dst_space));
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 664f4b5..6c8b898 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -2615,6 +2615,7 @@ H5S_select_project_intersection(const H5S_t *src_space, const H5S_t *dst_space,
HDassert(src_intersect_space);
HDassert(new_space_ptr);
HDassert(H5S_GET_SELECT_NPOINTS(src_space) == H5S_GET_SELECT_NPOINTS(dst_space));
+ HDassert(H5S_GET_EXTENT_NDIMS(src_space) == H5S_GET_EXTENT_NDIMS(src_intersect_space));
/* Create new space, using dst extent. Start with "all" selection. */
if(NULL == (new_space = H5S_create(H5S_SIMPLE)))
@@ -2639,97 +2640,134 @@ H5S_select_project_intersection(const H5S_t *src_space, const H5S_t *dst_space,
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't change selection")
} /* end if */
else {
- /* If the source intersect space is a point selection, convert it to a
- * hyperslab (discarding ordering). We can get away with this because
- * the order does not matter for the source intersect space */
- /* Maybe we should just leave it as a point selection for the point by
- * point algorithm? The search through the selection in
- * H5S_SELECT_INTERSECT_BLOCK will likely be O(N) either way. -NAF */
- if(H5S_GET_SELECT_TYPE(src_intersect_space) == H5S_SEL_POINTS) {
- H5S_pnt_node_t *curr_pnt = src_intersect_space->select.sel_info.pnt_lst->head;
-
- /* Create dataspace and copy extent */
- if(NULL == (tmp_src_intersect_space = H5S_create(H5S_SIMPLE)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create temporary source intersect dataspace")
- if(H5S__extent_copy_real(&tmp_src_intersect_space->extent, &src_intersect_space->extent, FALSE) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy source intersect space extent")
-
- /* Iterate over points */
- for(curr_pnt = src_intersect_space->select.sel_info.pnt_lst->head; curr_pnt; curr_pnt = curr_pnt->next)
- /* Add point to hyperslab selection */
- if(H5S_hyper_add_span_element(tmp_src_intersect_space, src_intersect_space->extent.rank, curr_pnt->pnt) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't add point to temporary dataspace selection")
-
- /* Redirect local src_intersect_space pointer (will not affect
- * calling function) */
- src_intersect_space = tmp_src_intersect_space;
- } /* end for */
-
- /* By this point, src_intersect_space must be a hyperslab selection */
- HDassert(H5S_GET_SELECT_TYPE(src_intersect_space) == H5S_SEL_HYPERSLABS);
-
- /* If either the source space or the destination space is a point
- * selection, iterate element by element */
- if((H5S_GET_SELECT_TYPE(src_space) == H5S_SEL_POINTS)
- || (H5S_GET_SELECT_TYPE(dst_space) == H5S_SEL_POINTS)) {
- hsize_t coords[H5S_MAX_RANK];
+ /* Handle scalar dataspaces. It should not be possible for the source
+ * intersect space or the source space to be scalar since scalar spaces
+ * only support all or none selections, and both of those cases are
+ * covered above, and the source intersect space must have the same
+ * rank, so it also cannot be scalar, as scalar dataspaces have a rank
+ * of 0. */
+ HDassert(H5S_GET_EXTENT_TYPE(src_space) != H5S_SCALAR);
+ HDassert(H5S_GET_EXTENT_TYPE(src_intersect_space) != H5S_SCALAR);
+
+ /* Check for scalar dst_space. In this case we simply check if the
+ * (single) point selected in src_space intersects src_intersect_space,
+ * if so select all in new_space, otherwise select none. */
+ if(H5S_GET_EXTENT_TYPE(dst_space) == H5S_SCALAR) {
+ hsize_t coords_start[H5S_MAX_RANK];
+ hsize_t coords_end[H5S_MAX_RANK];
htri_t intersect;
- /* Start with "none" selection */
- if(H5S_select_none(new_space) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't change selection")
+ /* Get source space bounds. Should be a single point. */
+ if(H5S_SELECT_BOUNDS(src_space, coords_start, coords_end) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get source space bounds")
+ HDassert(0 == HDmemcmp(coords_start, coords_end, H5S_GET_EXTENT_NDIMS(src_space) * sizeof(coords_start[0])));
- /* Initialize iterators */
- if(H5S_select_iter_init(&ss_iter, src_space, 1, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "can't initialize source space selection iterator")
- ss_iter_init = TRUE;
- if(H5S_select_iter_init(&ds_iter, dst_space, 1, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "can't initialize destination space selection iterator")
- ds_iter_init = TRUE;
-
- /* Iterate over points */
- do {
- HDassert(ss_iter.elmt_left > 0);
- HDassert(ss_iter.elmt_left > 0);
-
- /* Get SS coords */
- if(H5S_SELECT_ITER_COORDS(&ss_iter, coords) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get source selection coordinates")
-
- /* Check for intersection */
- if((intersect = H5S_SELECT_INTERSECT_BLOCK(src_intersect_space, coords, coords)) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOMPARE, FAIL, "can't check for intersection")
-
- /* Add point if it intersects */
- if(intersect) {
- /* Get DS coords */
- if(H5S_SELECT_ITER_COORDS(&ds_iter, coords) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get destination selection coordinates")
-
- /* Add point to new_space */
- if(H5S_select_elements(new_space, H5S_SELECT_APPEND, 1, coords) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't add point to new selection")
- } /* end if */
+ /* Check for intersection */
+ if((intersect = H5S_SELECT_INTERSECT_BLOCK(src_intersect_space, coords_start, coords_end)) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOMPARE, FAIL, "can't check for intersection")
- /* Advance iterators */
- if(H5S_SELECT_ITER_NEXT(&ss_iter, 1) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "can't advacne source selection iterator")
- ss_iter.elmt_left--;
- if(H5S_SELECT_ITER_NEXT(&ds_iter, 1) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "can't advacne destination selection iterator")
- ds_iter.elmt_left--;
- } while(ss_iter.elmt_left > 0);
- HDassert(H5S_SELECT_ITER_NELMTS(&ds_iter) == 0);
+ /* Select all or none as appropriate */
+ if(intersect) {
+ if(H5S_select_all(new_space, TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "can't select all")
+ } /* end if */
+ else
+ if(H5S_select_none(new_space) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't change selection")
} /* end if */
else {
- HDassert(H5S_GET_SELECT_TYPE(src_space) != H5S_SEL_NONE);
- HDassert(H5S_GET_SELECT_TYPE(dst_space) != H5S_SEL_NONE);
-
- /* Source and destination selections are all or hyperslab,
- * intersecting selection is hyperslab. Call the hyperslab routine
- * to project to another hyperslab selection. */
- if(H5S__hyper_project_intersection(src_space, dst_space, src_intersect_space, new_space, share_selection) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, FAIL, "can't project hyperslab onto destination selection")
+ /* If the source intersect space is a point selection, convert it to a
+ * hyperslab (discarding ordering). We can get away with this because
+ * the order does not matter for the source intersect space */
+ /* Maybe we should just leave it as a point selection for the point by
+ * point algorithm? The search through the selection in
+ * H5S_SELECT_INTERSECT_BLOCK will likely be O(N) either way. -NAF */
+ if(H5S_GET_SELECT_TYPE(src_intersect_space) == H5S_SEL_POINTS) {
+ H5S_pnt_node_t *curr_pnt = src_intersect_space->select.sel_info.pnt_lst->head;
+
+ /* Create dataspace and copy extent */
+ if(NULL == (tmp_src_intersect_space = H5S_create(H5S_SIMPLE)))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create temporary source intersect dataspace")
+ if(H5S__extent_copy_real(&tmp_src_intersect_space->extent, &src_intersect_space->extent, FALSE) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy source intersect space extent")
+
+ /* Iterate over points */
+ for(curr_pnt = src_intersect_space->select.sel_info.pnt_lst->head; curr_pnt; curr_pnt = curr_pnt->next)
+ /* Add point to hyperslab selection */
+ if(H5S_hyper_add_span_element(tmp_src_intersect_space, src_intersect_space->extent.rank, curr_pnt->pnt) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't add point to temporary dataspace selection")
+
+ /* Redirect local src_intersect_space pointer (will not affect
+ * calling function) */
+ src_intersect_space = tmp_src_intersect_space;
+ } /* end for */
+
+ /* By this point, src_intersect_space must be a hyperslab selection */
+ HDassert(H5S_GET_SELECT_TYPE(src_intersect_space) == H5S_SEL_HYPERSLABS);
+
+ /* If either the source space or the destination space is a point
+ * selection, iterate element by element */
+ if((H5S_GET_SELECT_TYPE(src_space) == H5S_SEL_POINTS)
+ || (H5S_GET_SELECT_TYPE(dst_space) == H5S_SEL_POINTS)) {
+ hsize_t coords[H5S_MAX_RANK];
+ htri_t intersect;
+
+ /* Start with "none" selection */
+ if(H5S_select_none(new_space) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't change selection")
+
+ /* Initialize iterators */
+ if(H5S_select_iter_init(&ss_iter, src_space, 1, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "can't initialize source space selection iterator")
+ ss_iter_init = TRUE;
+ if(H5S_select_iter_init(&ds_iter, dst_space, 1, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "can't initialize destination space selection iterator")
+ ds_iter_init = TRUE;
+
+ /* Iterate over points */
+ do {
+ HDassert(ss_iter.elmt_left > 0);
+ HDassert(ss_iter.elmt_left > 0);
+
+ /* Get SS coords */
+ if(H5S_SELECT_ITER_COORDS(&ss_iter, coords) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get source selection coordinates")
+
+ /* Check for intersection */
+ if((intersect = H5S_SELECT_INTERSECT_BLOCK(src_intersect_space, coords, coords)) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOMPARE, FAIL, "can't check for intersection")
+
+ /* Add point if it intersects */
+ if(intersect) {
+ /* Get DS coords */
+ if(H5S_SELECT_ITER_COORDS(&ds_iter, coords) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get destination selection coordinates")
+
+ /* Add point to new_space */
+ if(H5S_select_elements(new_space, H5S_SELECT_APPEND, 1, coords) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't add point to new selection")
+ } /* end if */
+
+ /* Advance iterators */
+ if(H5S_SELECT_ITER_NEXT(&ss_iter, 1) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "can't advacne source selection iterator")
+ ss_iter.elmt_left--;
+ if(H5S_SELECT_ITER_NEXT(&ds_iter, 1) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTNEXT, FAIL, "can't advacne destination selection iterator")
+ ds_iter.elmt_left--;
+ } while(ss_iter.elmt_left > 0);
+ HDassert(H5S_SELECT_ITER_NELMTS(&ds_iter) == 0);
+ } /* end if */
+ else {
+ HDassert(H5S_GET_SELECT_TYPE(src_space) != H5S_SEL_NONE);
+ HDassert(H5S_GET_SELECT_TYPE(dst_space) != H5S_SEL_NONE);
+
+ /* Source and destination selections are all or hyperslab,
+ * intersecting selection is hyperslab. Call the hyperslab routine
+ * to project to another hyperslab selection. */
+ if(H5S__hyper_project_intersection(src_space, dst_space, src_intersect_space, new_space, share_selection) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCLIP, FAIL, "can't project hyperslab onto destination selection")
+ } /* end else */
} /* end else */
} /* end else */
@@ -2804,10 +2842,15 @@ H5Sselect_project_intersection(hid_t src_space_id, hid_t dst_space_id,
if(NULL == (src_intersect_space = (H5S_t *)H5I_object_verify(src_intersect_space_id, H5I_DATASPACE)))
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "not a dataspace")
- /* Check numbbers of points selected matches in source and destination */
+ /* Check numbers of points selected matches in source and destination */
if(H5S_GET_SELECT_NPOINTS(src_space) != H5S_GET_SELECT_NPOINTS(dst_space))
HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "number of points selected in source space does not match that in destination space")
+ /* Check numbers of dimensions matches in source and source intersect spaces
+ */
+ if(H5S_GET_EXTENT_NDIMS(src_space) != H5S_GET_EXTENT_NDIMS(src_intersect_space))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "rank of source space does not match rank of source intersect space")
+
/* Perform operation */
if(H5S_select_project_intersection(src_space, dst_space,
src_intersect_space, &proj_space, FALSE) < 0)
diff --git a/test/null_vol_connector.c b/test/null_vol_connector.c
index 5ed8545..14e1a38 100644
--- a/test/null_vol_connector.c
+++ b/test/null_vol_connector.c
@@ -116,6 +116,12 @@ static const H5VL_class_t null_vol_g = {
NULL, /* optional */
NULL /* free */
},
+ { /* blob_cls */
+ NULL, /* put */
+ NULL, /* get */
+ NULL, /* specific */
+ NULL /* optional */
+ },
NULL /* optional */
};
diff --git a/test/vol.c b/test/vol.c
index 5ff0af0..da42a1e 100644
--- a/test/vol.c
+++ b/test/vol.c
@@ -131,6 +131,12 @@ static const H5VL_class_t fake_vol_g = {
NULL, /* optional */
NULL /* free */
},
+ { /* blob_cls */
+ NULL, /* put */
+ NULL, /* get */
+ NULL, /* specific */
+ NULL /* optional */
+ },
NULL /* optional */
};