ID-list structure changed

src/C/H5Fed_inquiry.c

@@ -50,7 +50,7 @@ H5FedGetNumLevels (
 	h5_file_t* const f
 	) {
 	H5_API_ENTER;
-	h5_ssize_t num = h5t_get_num_levels (f);
+	h5_ssize_t num = h5t_get_num_leaf_levels (f);
 	H5_API_RETURN (num);
 }
 

src/h5core/h5_maps.c

@@ -4,33 +4,12 @@
 #include "h5core/h5_core.h"
 #include "h5_core_private.h"
 
-static inline h5_err_t
-alloc_idlist_items (
-	h5_file_t* const f,
-	h5_idlist_t* list,
-	const h5_size_t	size	// new size of list
-	) {
-	int new = (list->items == NULL);
-	size_t size_in_bytes = size * sizeof (list->items[0]);
-	TRY( list->items = h5_alloc (f, list->items, size_in_bytes) );
-	list->size = size;
-	if (new) list->num_items = 0;
-	return H5_SUCCESS;
-}
 
-h5_err_t
-h5priv_free_idlist_items (
-	h5_file_t* const f,
-	h5_idlist_t* list
-	) {
-	UNUSED_ARGUMENT (f);
-	if (list->items != NULL) free (list->items);
-	list->items = NULL;
-	list->size = 0;
-	list->num_items = 0;
-	return H5_SUCCESS;
-}
+/*
+  Functions for ID-list handling.
 
+  ID-lists are data blobs to store ID or indices.
+ */
 /*
   Allocate new/empty id-list
  */
@@ -40,9 +19,7 @@ h5priv_alloc_idlist (
 	h5_idlist_t** list,
 	const h5_size_t	size
 	) {
-	TRY( (*list = h5_calloc (f, 1, sizeof (**list))) );
-	size_t size_in_bytes = size * sizeof ((*list)->items[0]);
-	TRY( (*list)->items = h5_alloc (f, (*list)->items, size_in_bytes) );
+	TRY( *list = h5_calloc (f, 1, sizeof (**list)+size*sizeof ((*list)->items[0])) );
 	(*list)->size = size;
 	return H5_SUCCESS;
 }
@@ -53,70 +30,55 @@ h5priv_free_idlist (
 	h5_idlist_t** list
 	) {
 	if (*list == NULL) return H5_SUCCESS;
-	TRY( h5priv_free_idlist_items (f, *list) );
 	TRY( h5_free( f, *list) );
 	*list = NULL;
 	return H5_SUCCESS;
 }
 
-h5_err_t
-h5priv_append_to_idlist (
+static inline h5_err_t
+grow_idlist (
 	h5_file_t* const f,
-	h5_idlist_t* list,
-	h5_loc_id_t id
+	h5_idlist_t** list,
+	size_t num_items
 	) {
-	if (list->num_items == list->size) {
-		h5_size_t size = list->size;
+	size_t size = sizeof (**list) + (num_items-1)*sizeof((*list)->items[0]);
+	TRY( *list = h5_alloc (f, *list, size) );
+	return H5_SUCCESS;
+}
+
+/*
+  Add item to list at position given by \c idx.
+*/
+h5_loc_idx_t
+h5priv_insert_idlist (
+	h5_file_t* const f,
+	h5_idlist_t** list,
+	h5_loc_id_t id,
+	h5_loc_idx_t idx
+	) {
+	if (*list == NULL) {
+		TRY( h5priv_alloc_idlist (f, list, 2) );
+	} else if ((*list)->num_items == (*list)->size) {
+		h5_size_t size = (*list)->size;
 		if (size == 0) {
-			size = 2;
+			size = 16;
 		} else {
 			size *= 2;
 		}
-		TRY( alloc_idlist_items (f, list, size) );
+		TRY( grow_idlist (f, list, size) );
 	}
-	list->items[list->num_items++] = id;
-	return H5_SUCCESS;
-}
-
-int
-h5priv_cmp_ids_by_eid (
-	const void* _id1,
-	const void* _id2
-	) {
-	h5_loc_id_t	id1 = h5tpriv_get_elem_idx (*(h5_loc_id_t*)_id1); 
-	h5_loc_id_t	id2 = h5tpriv_get_elem_idx (*(h5_loc_id_t*)_id2); 
-	
-	if (id1 < id2) return -1;
-	if (id1 > id2) return 1;
-	return 0;
-}
-
-int
-h5priv_cmp_ids (
-	const void* _id1,
-	const void* _id2
-	) {
-	h5_loc_id_t	*id1 = (h5_loc_id_t*)_id1;
-	h5_loc_id_t	*id2 = (h5_loc_id_t*)_id2;
-	
-	if (*id1 < *id2) return -1;
-	if (*id1 > *id2) return 1;
-	return 0;
-}
-
-h5_err_t
-h5priv_sort_idlist_by_eid (
-	h5_file_t* const f,
-	h5_idlist_t* list
-	) {
-	UNUSED_ARGUMENT (f);
-	qsort (
-		list->items,
-		list->num_items,
-		sizeof (list->items[0]),
-		h5priv_cmp_ids_by_eid);
-	
-	return H5_SUCCESS;
+	h5_idlist_t* l = *list;
+	if (idx == -1) {
+		idx = l->num_items;
+	} else {
+		memmove ( 
+			&l->items[idx+1],
+			&l->items[idx],
+			(l->num_items - idx) * sizeof (l->items[0]));
+	}
+	l->items[idx] = id;
+	l->num_items++;
+	return idx;
 }
 
 /*
@@ -129,6 +91,9 @@ h5priv_find_idlist (
 	h5_loc_id_t item
 	) {
 	UNUSED_ARGUMENT (f);
+	if (!list) {
+		return -1;
+	}
 	register h5_loc_idx_t low = 0;
 	register h5_loc_idx_t high = list->num_items - 1;
 	while (low <= high) {
@@ -144,33 +109,6 @@ h5priv_find_idlist (
        	return -(low+1);  // not found
 }
 
-/*
-  Add item to list at position given by \c idx.
-*/
-h5_loc_idx_t
-h5priv_insert_idlist (
-	h5_file_t* const f,
-	h5_idlist_t* list,
-	h5_loc_id_t item,
-	h5_loc_idx_t idx
-	) {
-	if (list->num_items == list->size) {
-		h5_size_t size = list->size;
-		if (size == 0) {
-			size = 16;
-		} else {
-			size *= 2;
-		}
-		TRY( alloc_idlist_items (f, list, size) );
-	}
-	memmove ( 
-		&list->items[idx+1],
-		&list->items[idx],
-		(list->num_items - idx) * sizeof (list->items[0]));
-	list->items[idx] = item;
-	list->num_items++;
-	return idx;
-}
 
 /*
   Search in sorted list. If item is not in list, add it.
@@ -178,10 +116,10 @@ h5priv_insert_idlist (
 h5_loc_idx_t
 h5priv_search_idlist (
 	h5_file_t* const f,
-	h5_idlist_t* list,
+	h5_idlist_t** list,
 	h5_loc_id_t item
 	) {
-	h5_loc_idx_t idx = h5priv_find_idlist (f, list, item);
+	h5_loc_idx_t idx = h5priv_find_idlist (f, *list, item);
 	if (idx < 0) {
 		idx = -(idx+1);
 		idx = h5priv_insert_idlist (f, list, item, idx);

src/h5core/h5_maps_private.h

@@ -14,48 +14,17 @@ h5priv_free_idlist (
 	h5_idlist_t **list
 	);
 
-h5_err_t
-h5priv_free_idlist_items (
-	h5_file_t * const f,
-	h5_idlist_t *list
-	);
-
-h5_err_t
-h5priv_append_to_idlist (
-	h5_file_t * const f,
-	h5_idlist_t *list,
-	h5_loc_id_t id
-	);
-
-int
-h5priv_cmp_ids_by_eid (
-	const void *_id1,
-	const void *_id2
-	);
-
-int
-h5priv_cmp_ids (
-	const void *_id1,
-	const void *_id2
-	);
-
-h5_err_t
-h5priv_sort_idlist_by_eid (
-	h5_file_t * const f,
-	h5_idlist_t *list
-	);
-
 h5_loc_id_t
 h5priv_find_idlist (
 	h5_file_t * const f,
-	h5_idlist_t *list,
+	h5_idlist_t* list,
 	h5_loc_id_t item
 	);
 
 h5_loc_idx_t
 h5priv_insert_idlist (
 	h5_file_t * const f,
-	h5_idlist_t *list,
+	h5_idlist_t** list,
 	h5_loc_id_t	item,
 	h5_loc_idx_t idx
 	);
@@ -63,10 +32,11 @@ h5priv_insert_idlist (
 h5_loc_idx_t
 h5priv_search_idlist (
 	h5_file_t * const f,
-	h5_idlist_t *list,
+	h5_idlist_t** list,
 	h5_loc_id_t item
 	);
 
+
 h5_err_t
 h5priv_alloc_idxmap (
 	h5_file_t * const f,

src/h5core/h5t_adjacencies_tetm.c

@@ -43,7 +43,7 @@ release_tv (
 	h5_loc_idx_t idx = 0;
 	h5_loc_idx_t last = t->num_vertices[t->num_leaf_levels-1];
 	for (; idx < last; idx++) {
-		TRY( h5priv_free_idlist_items (f, &adj->tv.v[idx]) );
+		TRY( h5priv_free_idlist (f, &adj->tv.v[idx]) );
 	}
 	TRY( h5_free (f, adj->tv.v) );
 	adj->tv.v = NULL;
@@ -71,10 +71,11 @@ compute_elems_of_vertices (
 		int num_faces = h5tpriv_ref_elem_get_num_vertices(t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			h5_loc_idx_t vidx = el->vertex_indices[face_idx];
-			TRY( h5priv_append_to_idlist (
+			TRY( h5priv_insert_idlist (
 				     f,
 				     &t->adjacencies.tv.v[vidx],
-				     h5tpriv_build_vertex_id (face_idx, idx)) );
+				     h5tpriv_build_vertex_id (face_idx, idx),
+				     -1) );
 		}
 	}
 	return H5_SUCCESS;
@@ -94,7 +95,6 @@ static inline h5_err_t
 release_te (
 	h5_file_t* const f
 	) {
-	UNUSED_ARGUMENT (f);
 	TRY( h5priv_hwalk (f, &f->t->adjacencies.te_hash, free_idlist) ); 
 	return H5_SUCCESS;
 }
@@ -127,8 +127,7 @@ static inline h5_err_t
 release_td (
 	h5_file_t* const f
 	) {
-	UNUSED_ARGUMENT (f);
-	TRY( h5priv_hwalk (f, &f->t->adjacencies.td_hash, free_idlist) ); 
+	TRY( h5priv_hwalk (f, &f->t->adjacencies.te_hash, free_idlist) ); 
 	return H5_SUCCESS;
 }
 
@@ -175,7 +174,7 @@ compute_children_of_edge (
 		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx (*edge);
 		h5_loc_tet_t* tet = &t->loc_elems.tets[elem_idx];
 		if (h5tpriv_is_leaf_elem (f, (h5_generic_loc_elem_t*)tet) == H5_OK ) {
-			TRY( h5priv_append_to_idlist (f, children, *edge) );
+			TRY( h5priv_insert_idlist (f, &children, *edge, -1) );
 		} else {
 			h5_loc_id_t kids[2];
 			TRY( h5tpriv_get_direct_children_of_edge (
@@ -227,7 +226,7 @@ compute_sections_of_edge (
 		}
 	}
 	if (! refined) {
-		TRY( h5priv_append_to_idlist (f, children, te->items[0]) );
+		TRY( h5priv_insert_idlist (f, &children, te->items[0], -1) );
 	}
 	return H5_SUCCESS;
 }
@@ -268,7 +267,7 @@ compute_direct_children_of_triangle (
 	h5_file_t* const f,
 	h5_loc_idx_t face_idx,
 	h5_loc_idx_t elem_idx,
-	h5_loc_id_t children[4]
+	h5_loc_id_t* children
 	) {
 	h5_loc_idx_t map[4][4][2] = {
 		{{0,0},{0,1},{0,2},{0,5}},
@@ -313,9 +312,9 @@ compute_children_of_triangle (
 		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx (*tri);
 		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[eid];
 		if (h5tpriv_is_leaf_elem (f, tet) == H5_OK) {
-			TRY( h5priv_append_to_idlist (f, children, *tri) );
+			TRY( h5priv_insert_idlist (f, &children, *tri, -1) );
 		} else {
-			h5_loc_id_t dids[4];
+			h5_loc_id_t dids[4] = {-1,-1,-1,-1};
 			TRY( compute_direct_children_of_triangle (
 				      f,
 				      face_idx,
@@ -352,7 +351,7 @@ compute_sections_of_triangle (
 		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[eid];
 		if (! h5tpriv_is_leaf_elem (f, tet) == H5_OK) {
 			refined = 1;
-			h5_loc_id_t dids[4];
+			h5_loc_id_t dids[4] = {-1,-1,-1,-1};
 			TRY( compute_direct_children_of_triangle (
 				     f,
 				     face_idx,
@@ -365,7 +364,7 @@ compute_sections_of_triangle (
 		}
 	}
 	if (! refined) {
-		TRY( h5priv_append_to_idlist (f, children, td->items[0]) );
+		TRY( h5priv_insert_idlist (f, &children, td->items[0], -1) );
 	}
 	return H5_SUCCESS;
 }
@@ -382,7 +381,7 @@ add_edge (
 	) {
 	h5_idlist_t* te;
 	TRY( h5tpriv_find_te2 (f, face_idx, elem_idx, &te) );
-	TRY( h5priv_search_idlist (f, list, te->items[0]) );
+	TRY( h5priv_search_idlist (f, &list, te->items[0]) );
 	return H5_SUCCESS;
 }
 
@@ -400,11 +399,11 @@ get_edges_uadj_to_vertex (
 	h5t_fdata_t* const t = f->t;
 	h5_loc_idx_t idx;
 	TRY( h5t_get_vertex_index_of_vertex (f, id, &idx) );
-	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
+	h5_idlist_t** tv = &t->adjacencies.tv.v[idx];
 	h5_size_t i;
 
-	h5_loc_id_t* vidp = tv->items;	// ptr to upward adjacent elements
-	for (i = 0; i < tv->num_items; i++, vidp++) {
+	h5_loc_id_t* vidp = (*tv)->items;	// ptr to upward adjacent elements
+	for (i = 0; i < (*tv)->num_items; i++, vidp++) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vidp);
 		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*vidp);
 		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[elem_idx];
@@ -432,7 +431,7 @@ add_triangle (
 	) {
 	h5_idlist_t* td;
 	TRY( h5tpriv_find_td2 (f, face_idx, elem_idx, &td) );
-	TRY( h5priv_search_idlist (f, list, td->items[0]) );
+	TRY( h5priv_search_idlist (f, &list, td->items[0]) );
 
 	return H5_SUCCESS;
 }
@@ -453,11 +452,11 @@ get_triangles_uadj_to_vertex (
 	h5t_fdata_t* t = f->t;
 	h5_loc_idx_t idx;
 	TRY( h5t_get_vertex_index_of_vertex (f, id, &idx) );
-	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
+	h5_idlist_t** tv = &t->adjacencies.tv.v[idx];
 
 	h5_size_t i;
-	h5_loc_id_t* vidp = tv->items;
-	for (i = 0; i < tv->num_items; i++, vidp++) {
+	h5_loc_id_t* vidp = (*tv)->items;
+	for (i = 0; i < (*tv)->num_items; i++, vidp++) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vidp);
 		h5_loc_idx_t face_idx = h5tpriv_get_face_idx (*vidp);
 		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[elem_idx];
@@ -487,11 +486,11 @@ get_tets_uadj_to_vertex (
 	h5t_fdata_t* t = f->t;
 	h5_loc_idx_t idx;
 	TRY( h5t_get_vertex_index_of_vertex (f, id, &idx) );
-	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
+	h5_idlist_t** tv = &t->adjacencies.tv.v[idx];
 	h5_size_t i;
 
-	h5_loc_id_t* vidp = tv->items;
-	for (i = 0; i < tv->num_items; i++, vidp++) {
+	h5_loc_id_t* vidp = (*tv)->items;
+	for (i = 0; i < (*tv)->num_items; i++, vidp++) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*vidp);
 		h5_generic_loc_elem_t* tet = (h5_generic_loc_elem_t*)&t->loc_elems.tets[elem_idx];
 
@@ -499,7 +498,7 @@ get_tets_uadj_to_vertex (
 			continue;
 		}
 		// add to result
-		TRY( h5priv_search_idlist (f, *list, elem_idx) );
+		TRY( h5priv_search_idlist (f, list, elem_idx) );
 	}
 	return H5_SUCCESS;
 }
@@ -542,7 +541,7 @@ get_tets_uadj_to_edge (
 	h5_loc_id_t* kidp = children->items;
 	for (i = 0; i < children->num_items; i++, kidp++) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*kidp);
-		TRY( h5priv_search_idlist (f, *list, elem_idx) );
+		TRY( h5priv_search_idlist (f, list, elem_idx) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -562,7 +561,7 @@ get_tets_uadj_to_triangle (
 	h5_loc_id_t *didp = children->items;
 	for (i = 0; i < children->num_items; i++ , didp++) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx (*didp);
-		TRY( h5priv_search_idlist (f, *list, elem_idx) );
+		TRY( h5priv_search_idlist (f, list, elem_idx) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -583,8 +582,8 @@ get_vertices_dadj_to_edge (
 	for (i = 0; i < children->num_items; i++, kidp++) {
 		h5_loc_idx_t vertex_indices[2];
 		TRY( h5t_get_vertex_indices_of_edge (f, *kidp, vertex_indices) );
-		TRY( h5priv_search_idlist (f, *list, vertex_indices[0]) );
-		TRY( h5priv_search_idlist (f, *list, vertex_indices[1]) );
+		TRY( h5priv_search_idlist (f, list, vertex_indices[0]) );
+		TRY( h5priv_search_idlist (f, list, vertex_indices[1]) );
 	}
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -618,8 +617,8 @@ get_vertices_dadj_to_triangle (
 	for (i = 0; i < children->num_items; i++, kid++) {
 		h5_loc_idx_t vertex_indices[2];
 		TRY( h5t_get_vertex_indices_of_edge (f, *kid, vertex_indices) );
-		TRY( h5priv_search_idlist (f, *list, vertex_indices[0]) );
-		TRY( h5priv_search_idlist (f, *list, vertex_indices[1]) );
+		TRY( h5priv_search_idlist (f, list, vertex_indices[0]) );
+		TRY( h5priv_search_idlist (f, list, vertex_indices[1]) );
 	}
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -650,8 +649,8 @@ get_vertices_dadj_to_tet (
 	for (i = 0; i < children->num_items; i++, kid++) {
 		h5_loc_idx_t vertex_indices[2];
 		TRY( h5t_get_vertex_indices_of_edge (f, *kid, vertex_indices) );
-		TRY( h5priv_search_idlist (f, *list, vertex_indices[0]) );
-		TRY( h5priv_search_idlist (f, *list, vertex_indices[1]) );
+		TRY( h5priv_search_idlist (f, list, vertex_indices[0]) );
+		TRY( h5priv_search_idlist (f, list, vertex_indices[1]) );
 	}
 	TRY( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -680,7 +679,7 @@ get_edges_dadj_to_triangle (
 	TRY( h5priv_alloc_idlist (f, list, 8) );
 	h5_loc_id_t *kid = children->items;
 	for (i = 0; i < children->num_items; i++, kid++) {
-		TRY( h5priv_search_idlist (f, *list, *kid) );
+		TRY( h5priv_search_idlist (f, list, *kid) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -706,7 +705,7 @@ get_edges_dadj_to_tet (
 	TRY( h5priv_alloc_idlist (f, list, 8) );
 	h5_loc_id_t* kid = children->items;
 	for (i = 0; i < children->num_items; i++, kid++) {
-		TRY( h5priv_search_idlist (f, *list, *kid) );
+		TRY( h5priv_search_idlist (f, list, *kid) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -732,7 +731,7 @@ get_triangles_dadj_to_tet (
 	TRY( h5priv_alloc_idlist (f, list, 8) );
 	h5_loc_id_t* did = children->items;
 	for (i = 0; i < children->num_items; i++, did++) {
-		TRY( h5priv_search_idlist (f, *list, *did) );
+		TRY( h5priv_search_idlist (f, list, *did) );
 	}
 	TRY( h5priv_free_idlist (f, &children) );
 	return H5_SUCCESS;
@@ -877,10 +876,11 @@ static h5_err_t
 release_internal_structs (
 	h5_file_t * const f
 	) {
+	h5t_fdata_t* t = f->t;
 	TRY( release_tv (f) );
 	TRY( release_te (f) );
 	TRY( release_td (f) );
-
+	bzero (&t->adjacencies, sizeof (t->adjacencies));
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_adjacencies_trim.c

@@ -42,7 +42,7 @@ release_tv (
 	h5_loc_idx_t idx = 0;
 	h5_loc_idx_t last = t->num_vertices[t->num_leaf_levels-1];
 	for (; idx < last; idx++) {
-		TRY( h5priv_free_idlist_items (f, &adj->tv.v[idx]) );
+		TRY( h5priv_free_idlist (f, &adj->tv.v[idx]) );
 	}
 	TRY( h5_free (f, adj->tv.v) );
 	adj->tv.v = NULL;
@@ -71,11 +71,11 @@ compute_elems_of_vertices (
 		int num_faces = h5tpriv_ref_elem_get_num_vertices (t);
 		for (face_idx = 0; face_idx < num_faces; face_idx++) {
 			h5_loc_idx_t vidx = el->vertex_indices[face_idx];
-			TRY( h5priv_append_to_idlist (
+			TRY( h5priv_insert_idlist (
 				     f,
 				     &t->adjacencies.tv.v[vidx],
 				     h5tpriv_build_vertex_id (
-					     face_idx, idx)) );
+					     face_idx, idx), -1) );
 		}
 	}
 	h5_debug (f, "%s (%lld): done", __func__, (long long)from_lvl);
@@ -96,7 +96,6 @@ static inline h5_err_t
 release_te (
 	h5_file_t* const f
 	) {
-	UNUSED_ARGUMENT (f);
 	TRY( h5priv_hwalk (f, &f->t->adjacencies.te_hash, free_idlist) ); 
 	return H5_SUCCESS;
 }
@@ -149,9 +148,7 @@ compute_children_of_edge (
 		h5_loc_idx_t face_idx =  h5tpriv_get_face_idx ( *edge );
 		h5_generic_loc_elem_t *el = (h5_generic_loc_elem_t*)&t->loc_elems.tris[elem_idx];
 		if ( h5tpriv_is_leaf_elem ( f, el ) == H5_OK ) {
-			TRY ( h5priv_append_to_idlist (
-				      f, children, *edge )
-				);
+			TRY( h5priv_insert_idlist (f, &children, *edge, -1) );
 		} else {
 			h5_loc_id_t kids[2];
 			TRY ( h5tpriv_get_direct_children_of_edge (
@@ -208,7 +205,7 @@ compute_sections_of_edge (
 		}
 	}
 	if ( ! refined ) {
-		TRY ( h5priv_append_to_idlist ( f, children, te->items[0] ) );
+		TRY( h5priv_insert_idlist (f, &children, te->items[0], -1) );
 	}
 	return H5_SUCCESS;
 }
@@ -227,7 +224,7 @@ add_edge (
 	) {
 	h5_idlist_t *te;
 	TRY ( h5tpriv_find_te2 ( f, face_idx, elem_idx, &te ) );
-	TRY ( h5priv_search_idlist ( f, list, te->items[0] ) );
+	TRY ( h5priv_search_idlist ( f, &list, te->items[0] ) );
 	return H5_SUCCESS;
 }
 
@@ -243,7 +240,7 @@ get_edges_uadj_to_vertex (
 	h5t_fdata_t* t = f->t;
 	h5_loc_idx_t idx;
 	TRY( h5t_get_vertex_index_of_vertex (f, entity_id, &idx) );
-	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
+	h5_idlist_t* tv = t->adjacencies.tv.v[idx];
 
 	h5_size_t i;
 	h5_loc_id_t* vertex_idp = tv->items;
@@ -275,7 +272,7 @@ get_triangles_uadj_to_vertex (
 	h5t_fdata_t *t = f->t;
 	h5_loc_idx_t idx;
 	TRY( h5t_get_vertex_index_of_vertex (f, entity_id, &idx) );
-	h5_idlist_t* tv = &t->adjacencies.tv.v[idx];
+	h5_idlist_t* tv = t->adjacencies.tv.v[idx];
 
 	h5_size_t i;
 	h5_loc_id_t *vertex_idp = tv->items;
@@ -286,7 +283,7 @@ get_triangles_uadj_to_vertex (
 		if ( h5tpriv_is_leaf_elem ( f, el ) == H5_NOK ) {
 			continue;
 		}
-		TRY( h5priv_search_idlist (f, *list,
+		TRY( h5priv_search_idlist (f, list,
 					   h5tpriv_build_entity_id (
 						   H5T_TYPE_TRIANGLE, 0, elem_idx)) );
 	}
@@ -307,7 +304,7 @@ get_triangles_uadj_to_edge (
 	h5_loc_id_t *end = children->items+children->num_items;
 	for ( ; edge_id < end; edge_id++ ) {
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx ( *edge_id );
-		TRY( h5priv_search_idlist (f, *list,
+		TRY( h5priv_search_idlist (f, list,
 					   h5tpriv_build_entity_id(
 						   H5T_TYPE_TRIANGLE, 0, elem_idx)) );
 	}
@@ -334,7 +331,7 @@ get_edges_adj_to_edge (
 		h5_loc_idx_t face_idx = h5tpriv_get_face_idx(*edge_id);
 		h5_loc_idx_t elem_idx = h5tpriv_get_elem_idx(*edge_id);
 		TRY( h5tpriv_find_te2 (f, face_idx, elem_idx, &te) );
-		TRY( h5priv_search_idlist (f, *list, te->items[0]) );
+		TRY( h5priv_search_idlist (f, list, te->items[0]) );
 	}
 	
 	TRY( h5priv_free_idlist(f, &children) );
@@ -356,8 +353,8 @@ get_vertices_dadj_to_edge (
 	for ( i = 0; i < children->num_items; i++, edge_id++ ) {
 		h5_loc_idx_t vertex_indices[2];
 		TRY ( h5t_get_vertex_indices_of_edge ( f, *edge_id, vertex_indices ) );
-		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[0] ) );
-		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[1] ) );
+		TRY ( h5priv_search_idlist ( f, list, vertex_indices[0] ) );
+		TRY ( h5priv_search_idlist ( f, list, vertex_indices[1] ) );
 	}
 	TRY ( h5priv_free_idlist( f, &children ) );
 	return H5_SUCCESS;
@@ -391,8 +388,8 @@ get_vertices_dadj_to_triangle (
 	for ( i = 0; i < children->num_items; i++, edge_idp++ ) {
 		h5_loc_idx_t vertex_indices[2];
 		TRY ( h5t_get_vertex_indices_of_edge ( f, *edge_idp, vertex_indices ) );
-		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[0] ) );
-		TRY ( h5priv_search_idlist ( f, *list, vertex_indices[1] ) );
+		TRY ( h5priv_search_idlist ( f, list, vertex_indices[0] ) );
+		TRY ( h5priv_search_idlist ( f, list, vertex_indices[1] ) );
 	}
 	TRY ( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -421,7 +418,7 @@ get_edges_dadj_to_triangle (
 	h5_loc_id_t *edge_idp = children->items;
 	int i;
 	for (i = 0; i < children->num_items; i++, edge_idp++) {
-		TRY ( h5priv_search_idlist (f, *list, *edge_idp) );
+		TRY ( h5priv_search_idlist (f, list, *edge_idp) );
 	}
 	TRY ( h5priv_free_idlist(f, &children) );
 	return H5_SUCCESS;
@@ -536,9 +533,10 @@ static inline h5_err_t
 release_internal_structs (
 	h5_file_t* const f
 	) {
+	h5t_fdata_t *t = f->t;
 	TRY( release_tv (f) );
 	TRY( release_te (f) );
-
+	bzero (&t->adjacencies, sizeof (t->adjacencies));
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_hsearch.c

@@ -63,7 +63,7 @@ h5tpriv_search_te2 (
 	h5_file_t* const f,
 	h5_loc_idx_t face_idx,
 	h5_loc_idx_t elem_idx,
-	h5_idlist_t** retval
+	h5_idlist_t** idlist
 	) {
 	h5t_fdata_t* t = f->t;
 	h5t_adjacencies_t* a = &t->adjacencies;
@@ -104,11 +104,13 @@ h5tpriv_search_te2 (
 		     f,
 		     &te_entry->value,
 		     h5tpriv_build_edge_id (face_idx, elem_idx)) );
-	if (entry->value.num_items > 1) {
-		/* search returned an existing entry */
+	if (te_entry->value->num_items > 1) {
+		/* search returned existing entry */
 		TRY( h5_free (f, entry) );
 	}
-	*retval = &te_entry->value;
+	if (idlist) {
+		*idlist = te_entry->value;
+	}
 	return H5_SUCCESS;
 }
 
@@ -120,8 +122,8 @@ h5tpriv_search_te2 (
 h5_err_t
 h5tpriv_find_te (
 	h5_file_t* const f,
-	h5t_te_entry_t* item,
-	h5_idlist_t** retval
+	h5t_te_entry_t* item,	// in: item to find
+	h5_idlist_t** idlist	// out: 
 	) {
 	void* __entry;
 	TRY( h5priv_hsearch (
@@ -132,10 +134,11 @@ h5tpriv_find_te (
 		     &f->t->adjacencies.te_hash) );
 	h5t_te_entry_t* entry = (h5t_te_entry_t*)__entry;
 	if (entry ==NULL) {
-		// not found
-		return H5_NOK;
+		return H5_NOK;	// not found
+	}
+	if (idlist) {
+		*idlist = entry->value;
 	}
-	*retval = &entry->value;
 	return H5_SUCCESS;
 }
 
@@ -147,9 +150,9 @@ h5tpriv_find_te (
 h5_err_t
 h5tpriv_find_te2 (
 	h5_file_t* const f,
-	h5_loc_idx_t face_idx,
-	h5_loc_idx_t elem_idx,
-	h5_idlist_t** retval
+	h5_loc_idx_t face_idx,	// in
+	h5_loc_idx_t elem_idx,	// in 
+	h5_idlist_t** idlist	// out
 	) {
 	h5t_te_entry_t item;
 	TRY( h5t_get_vertex_indices_of_edge2 (
@@ -157,7 +160,7 @@ h5tpriv_find_te2 (
 		     face_idx,
 		     elem_idx,
 		     item.key.vids) );
-	return h5tpriv_find_te (f, &item, retval);
+	return h5tpriv_find_te (f, &item, idlist);
 }
 
 static int
@@ -220,7 +223,7 @@ h5tpriv_search_td2 (
 	h5_file_t* const f,
 	h5_loc_idx_t face_idx,
 	h5_loc_idx_t elem_idx,
-	h5_idlist_t** retval
+	h5_idlist_t** idlist	// out
 	) {
 	h5t_fdata_t* t = f->t;
 	h5t_adjacencies_t* a = &f->t->adjacencies;
@@ -255,11 +258,12 @@ h5tpriv_search_td2 (
 		     f,
 		     &td_entry->value,
 		     h5tpriv_build_triangle_id (face_idx, elem_idx)) );
-	if (td_entry->value.num_items > 1) {
+	if (td_entry->value->num_items > 1) {
 		TRY( h5_free (f, entry) );
 	}
-	*retval = &td_entry->value;
-
+	if (idlist) {
+		*idlist = td_entry->value;
+	}
 	return H5_SUCCESS;
 }
 
@@ -267,7 +271,7 @@ h5_err_t
 h5tpriv_find_td (
 	h5_file_t* const f,
 	h5t_td_entry_t* item,
-	h5_idlist_t** retval
+	h5_idlist_t** idlist	// out
 	) {
 	void* __entry;
 	h5priv_hsearch (
@@ -280,7 +284,7 @@ h5tpriv_find_td (
 		return h5tpriv_error_local_triangle_nexist (f, item->key.vids);
 	}
 	h5t_td_entry_t* entry = (h5t_td_entry_t*)__entry;
-	*retval = &entry->value;
+	*idlist = entry->value;
 	return H5_SUCCESS;
 }
 
@@ -289,7 +293,7 @@ h5tpriv_find_td2 (
 	h5_file_t* const f,
 	h5_loc_idx_t face_idx,
 	h5_loc_idx_t elem_idx,
-	h5_idlist_t** retval
+	h5_idlist_t** idlist
 	) {
 	h5t_td_entry_t item;
 	TRY( h5t_get_vertex_indices_of_triangle2 (
@@ -297,7 +301,7 @@ h5tpriv_find_td2 (
 		     face_idx,
 		     elem_idx,
 		     item.key.vids) );
-	return h5tpriv_find_td (f, &item, retval);
+	return h5tpriv_find_td (f, &item, idlist);
 }
 
 /*
@@ -308,14 +312,11 @@ h5tpriv_find_tv2 (
 	h5_file_t* const f,
 	h5_loc_idx_t face_idx,
 	h5_loc_idx_t elem_idx,
-	h5_idlist_t** retval
+	h5_idlist_t** idlist
 	) {
-
-	h5_loc_idx_t idx = h5tpriv_get_loc_elem_vertex_idx (
-		f, elem_idx, face_idx);
-	*retval = &f->t->adjacencies.tv.v[idx];
+	h5_loc_idx_t idx;
+	TRY( idx = h5tpriv_get_loc_elem_vertex_idx (f, elem_idx, face_idx) );
+	*idlist = f->t->adjacencies.tv.v[idx];
 
 	return H5_SUCCESS;
 }
-
-

src/h5core/h5t_hsearch_private.h

@@ -18,17 +18,17 @@ typedef struct h5t_idlisthash_key {
   The face is specified by its local vertex IDs.
  */
 typedef struct h5_te_entry {
-	h5_idlist_t value;
+	h5_idlist_t* value;
 	h5t_te_entry_key_t key;
 } h5t_te_entry_t;
 
 typedef struct h5_td_entry {
-	h5_idlist_t value;
+	h5_idlist_t* value;
 	h5t_td_entry_key_t key;
 } h5t_td_entry_t;
 
 typedef struct h5t_idlisthash_entry {
-	h5_idlist_t value;
+	h5_idlist_t* value;
 	h5t_idlisthash_key_t key;
 } h5t_idlisthash_entry_t;
 

src/h5core/h5t_openclose.c

@@ -221,8 +221,12 @@ init_fdata (
 	h5t_fdata_t* t = f->t;
 
 	memset (t->mesh_name, 0, sizeof (t->mesh_name));
-	t->num_meshes = -1;
+	memset (t->mesh_label, 0, sizeof (t->mesh_label));
+	t->mesh_type = 0;
+	t->ref_elem = NULL;
 	t->cur_mesh = -1;
+	t->mesh_changed = 0;
+	t->num_meshes = -1;
 	t->num_leaf_levels = -1;
 	t->leaf_level = -1;
 	t->last_stored_vid = -1;
@@ -497,10 +501,15 @@ release_elems (
 	) {
 	h5t_fdata_t* t = f->t;
 	TRY( h5_free (f, t->glb_elems.data) );
+	t->glb_elems.data = NULL;
 	TRY( h5_free (f, t->loc_elems.data) );
+	t->loc_elems.data = NULL;
 	TRY( h5_free (f, t->num_elems) );
+	t->num_elems = NULL;
 	TRY( h5_free (f, t->num_elems_on_leaf_level) );
+	t->num_elems_on_leaf_level = NULL;
 	TRY( h5_free (f, t->map_elem_g2l.items) );
+	t->map_elem_g2l.items = NULL;
 
 	return H5_SUCCESS;
 }
@@ -511,8 +520,11 @@ release_vertices (
 	) {
 	h5t_fdata_t* t = f->t;
 	TRY( h5_free (f, t->vertices) );
+	t->vertices = NULL;
 	TRY( h5_free (f, t->num_vertices) );
+	t->num_vertices = NULL;
 	TRY( h5_free (f, t->map_vertex_g2l.items) );
+	t->map_vertex_g2l.items = NULL;
 
 	return H5_SUCCESS;
 }
@@ -525,7 +537,6 @@ release_memory (
 	TRY( h5tpriv_release_adjacency_structs (f) );
 	TRY( release_elems (f) );
 	TRY( release_vertices (f) );
-
 	return H5_SUCCESS;
 }
 

src/h5core/h5t_store.c

@@ -304,14 +304,9 @@ h5t_store_elem (
 	/* add edges to map  edges -> elements */
 	h5_loc_idx_t face_idx;
 	int num_faces = h5tpriv_ref_elem_get_num_edges (t);
-	h5_idlist_t* retval;
 	for (face_idx = 0; face_idx < num_faces; face_idx++) {
 		// add edges to neighbour struct
-		TRY( h5tpriv_search_te2 (
-			      f,
-			      face_idx,
-			      elem_idx,
-			      &retval) );
+		TRY( h5tpriv_search_te2 (f, face_idx, elem_idx, NULL) );
 	}
 	return elem_idx;
 }
@@ -350,7 +345,7 @@ h5t_mark_entity (
 	const h5_loc_id_t entity_id
 	) {
 	h5t_fdata_t* const t = f->t;
-	return h5priv_append_to_idlist (f, t->marked_entities, entity_id);
+	return h5priv_insert_idlist (f, &t->marked_entities, entity_id, -1);
 }
 
 /*

src/h5core/h5t_types_private.h

@@ -98,7 +98,7 @@ typedef struct h5_dtypes {
 typedef struct h5t_adjacencies {
 	struct {
 		// h5_size_t size;
-		h5_idlist_t* v;
+		h5_idlist_t** v;
 	} tv;
 	h5_hashtable_t te_hash;
 	h5_hashtable_t td_hash;

src/include/h5core/h5_types.h

@@ -78,7 +78,7 @@ typedef unsigned long		MPI_Datatype;
 typedef struct h5_idlist {
 	int32_t		size;		/* allocated space in number of items */
 	int32_t		num_items;	/* stored items	*/
-	h5_id_t		*items;
+	h5_id_t		items[1];
 } h5_idlist_t;
 
 struct h5_idxmap;

src/include/h5core/h5t_inquiry.h

@@ -8,7 +8,7 @@ h5t_get_num_meshes (
 	);
 
 h5_size_t
-h5t_get_num_levels (
+h5t_get_num_leaf_levels (
 	h5_file_t * const f
 	);