src/h5core/h5t_xyz

- get serial mesh working again

src/h5core/h5_init.c

@@ -237,10 +237,12 @@ create_tet_type (
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 
+#if defined(WITH_PARALLEL_H5GRID)
+
 static inline h5_err_t
 create_chunk_type (
-		void
-		) {
+	void
+	) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "%s", "void");
 	TRY(
 	        h5_dta_types.h5_chunk_t = hdf5_create_type (
@@ -339,6 +341,7 @@ create_octree_type (
 
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
+
 static inline h5_err_t
 create_userdata_type (
 		void
@@ -357,7 +360,7 @@ create_userdata_type (
 
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
-#if defined(PARALLEL_IO)
+
 static inline h5_err_t
 create_mpi_type_glb_tet (
         void
@@ -674,11 +677,12 @@ h5_initialize (
 	TRY (create_triangle_type ());
 	TRY (create_tet_type ());
 	TRY (create_tag_types ());
+
+#if defined(WITH_PARALLEL_H5GRID)
 	TRY (create_chunk_type ());
 	TRY (create_octree_type ());
 	TRY (create_userdata_type ());
 
-#if defined(PARALLEL_IO)
 	TRY (create_mpi_type_glb_tri ());
 	TRY (create_mpi_type_glb_tet ());
 	TRY (create_mpi_type_glb_vtx ());

src/h5core/h5b_readwrite.c

@@ -7,6 +7,7 @@
   License: see file COPYING in top level of source distribution.
 */
 
+#include "h5core/h5.h"
 #include "h5_types_private.h"
 #include "h5_hdf5_private.h"
 

src/h5core/h5t_access_private.h

@@ -14,7 +14,7 @@
 #include "h5t_types_private.h"
 
 struct h5t_access_methods {
-#if defined(PARALLEL_IO)
+#if defined(WITH_PARALLEL_H5GRID)
 	MPI_Datatype (*get_mpi_type_of_glb_elem)(
 	        h5t_mesh_t* const m);
 #endif
@@ -75,7 +75,7 @@ struct h5t_access_methods {
 extern struct h5t_access_methods h5tpriv_access_trim_methods;
 extern struct h5t_access_methods h5tpriv_access_tetm_methods;
 
-#if defined(PARALLEL_IO)
+#if defined(WITH_PARALLEL_H5GRID)
 static inline MPI_Datatype
 h5tpriv_get_mpi_type_of_glb_elem (
         h5t_mesh_t* const m

src/h5core/h5t_access_tetm.c

@@ -8,6 +8,7 @@
 */
 
 #include "h5core/h5.h"
+#include "h5_private.h"
 #include "h5_types_private.h"
 #include "h5_init_private.h"
 #include "h5t_types_private.h"
@@ -16,7 +17,7 @@
 
 /*** op's on local elements ***/
 
-#if defined(PARALLEL_IO)
+#if defined(WITH_PARALLEL_H5GRID)
 static MPI_Datatype
 get_mpi_type_of_glb_elem (
         h5t_mesh_t* const m
@@ -685,7 +686,7 @@ get_loc_entity_children (
 }
 
 struct h5t_access_methods h5tpriv_access_tetm_methods = {
-#if defined(PARALLEL_IO)
+#if defined(WITH_PARALLEL_H5GRID)
 	get_mpi_type_of_glb_elem,
 #endif
 	get_loc_elem,

src/h5core/h5t_access_trim.c

@@ -8,12 +8,13 @@
 */
 
 #include "h5core/h5.h"
+#include "h5_private.h"
 #include "h5_init_private.h"
 #include "h5t_types_private.h"
 #include "h5t_model_private.h"
 #include "h5t_access_private.h"
 
-#if defined(PARALLEL_IO)
+#if defined(WITH_PARALLEL_H5GRID)
 static MPI_Datatype
 get_mpi_type_of_glb_elem (
         h5t_mesh_t* const m
@@ -385,7 +386,7 @@ get_loc_entity_children (
 }
 
 struct h5t_access_methods h5tpriv_access_trim_methods = {
-#if defined(PARALLEL_IO)
+#if defined(WITH_PARALLEL_H5GRID)
 	get_mpi_type_of_glb_elem,
 #endif
 	get_loc_elem,

src/h5core/h5t_adjacencies.c

@@ -8,7 +8,7 @@
 */
 
 #include "h5core/h5.h"
-
+#include "h5_private.h"
 #include "h5t_types_private.h"
 #include "h5t_adjacencies_private.h"
 #include "h5t_map_private.h"

src/h5core/h5t_map.c

@@ -456,7 +456,7 @@ h5t_get_loc_vertex_indices_of_tet (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 int
 compare_glb_idx_oct (const void *  p_a,const void*  p_b) {
 	return *(h5_glb_idx_t*) p_a - *(h5_glb_idx_t*) p_b;

src/h5core/h5t_model.c

@@ -8,6 +8,7 @@
 */
 
 #include "h5core/h5.h"
+#include "h5_private.h"
 #include "h5_mpi_private.h"
 #include "h5_errorhandling_private.h"
 
@@ -72,10 +73,12 @@ h5tpriv_init_mesh (
 	m->timing.next_time = 0;
 	m->timing.f = NULL;
 	m->is_chunked = 0;
+#if defined(WITH_PARALLEL_H5GRID)
 
 	/* initialize pointers */
 	m->octree = 					NULL;
 	m->chunks = 					NULL;
+#endif
 	m->loc_elems =                  NULL;
 	m->num_interior_elems =         NULL;
 	m->num_glb_elems =              NULL;
@@ -89,6 +92,7 @@ h5tpriv_init_mesh (
 	m->first_b_vtx = 				NULL;
 //	m->weights = 					NULL;
 
+#if defined(WITH_PARALLEL_H5GRID)
 	/* chunks */
 	strcpy (m->dsinfo_chunks.name, "Chunks");
 	m->dsinfo_chunks.rank = 1;
@@ -133,7 +137,8 @@ h5tpriv_init_mesh (
 	             m->dsinfo_userdata.rank,
 	             m->dsinfo_userdata.chunk_dims) );
 	m->dsinfo_userdata.access_prop = H5P_DEFAULT;
-
+#endif
+	
 	/* vertices */
 	strcpy (m->dsinfo_vertices.name, "Vertices");
 	m->dsinfo_vertices.rank = 1;
@@ -302,7 +307,7 @@ release_memory (
 	TRY (h5tpriv_release_adjacency_structs (m));
 	TRY (release_elems (m));
 	TRY (release_vertices (m));
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	if (m->is_chunked) {
 		TRY (h5tpriv_free_chunks (m));
 		TRY (H5t_free_octree (m->octree));
@@ -374,7 +379,7 @@ h5t_close_mesh (
         h5t_mesh_t* const m
         ) {
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	TRY (h5priv_mpi_barrier (m->f->props->comm));
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 #endif
@@ -389,9 +394,9 @@ h5t_close_mesh (
 		TRY (h5tpriv_write_mesh (m));
 	}
 	TRY (hdf5_close_group (m->mesh_gid));
-
+#ifdef WITH_PARALLEL_H5GRID
 	TRY (write_timing (m));
-
+#endif
 	TRY (release_memory (m));
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }

src/h5core/h5t_model_tetm.c

@@ -85,7 +85,7 @@ h5t_open_tetrahedral_mesh (
 	             &h5t_tet_ref_elem,
 	             &tet_funcs,
 	             0));
-#ifdef PARALLEL_IO  // reason: even if we have a chunked mesh, if h5hut is not parallel
+#ifdef WITH_PARALLEL_H5GRID  // reason: even if we have a chunked mesh, if h5hut is not parallel
 	// it does not support reading chunked meshes
 	TRY (m->is_chunked ? h5tpriv_read_chunked_mesh (m) :h5tpriv_read_mesh (m));
 #else
@@ -199,7 +199,7 @@ h5t_add_chunked_tetrahedral_mesh (
         ) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t, "f=%p, name=%s, mesh=%p", f, name, mesh);
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	CHECK_WRITABLE_MODE (f);
 	h5_err_t exists;
 	TRY (exists = h5priv_link_exists (

src/h5core/h5t_model_trim.c

@@ -67,7 +67,7 @@ h5t_open_triangle_mesh (
                 h5_err_t,
                 "f=%p, name=%s, mesh=%p",
                 f, name, mesh);
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	MPI_Barrier (f->props->comm);
 	double start = MPI_Wtime();
 #endif
@@ -90,7 +90,7 @@ h5t_open_triangle_mesh (
 	             &h5t_tri_ref_elem,
 	             &tri_funcs,
 	             0));
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	MPI_Barrier (m->f->props->comm);
 	m->timing.measure[m->timing.next_time++] = start;
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
@@ -114,7 +114,7 @@ h5t_open_triangle_mesh_part (
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t, "f=%p, name=%s, mesh=%p", f, name, mesh);
 	hid_t mesh_hid;
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	MPI_Barrier (f->props->comm);
 	double start = MPI_Wtime();
 #endif
@@ -136,7 +136,7 @@ h5t_open_triangle_mesh_part (
 	             &h5t_tri_ref_elem,
 	             &tri_funcs,
 	             0));
-#ifdef PARALLEL_IO  // reason: even if we have a chunked mesh, if h5hut is not parallel
+#ifdef WITH_PARALLEL_H5GRID  // reason: even if we have a chunked mesh, if h5hut is not parallel
 	MPI_Barrier (m->f->props->comm);
 	m->timing.measure[m->timing.next_time++] = start;
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
@@ -216,7 +216,7 @@ h5t_add_chunked_triangle_mesh(
         ) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t, "f=%p, name=%s, mesh=%p", f, name, mesh);
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	int size = -1;
 	TRY (h5priv_mpi_comm_size (f->props->comm, &size));
 	if (size != 1) {

src/h5core/h5t_octree.c

@@ -1,7 +1,7 @@
 #include "h5t_octree_private.h"
 #include "h5t_core_private.h"
 
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 
 #include <stdlib.h>
 #include <string.h>

src/h5core/h5t_octree_private.h

@@ -10,14 +10,10 @@
 #ifndef __H5T_OCTREE_PRIVATE_H
 #define __H5T_OCTREE_PRIVATE_H
 
+
 #include "h5core/h5_types.h"
 #include "h5core/h5t_octree.h"
 
-// iterators
-#if defined(PARALLEL_IO)
-#include <mpi.h>
-#endif
-
 #define OCT_MAX_NEIGHBORS 1000
 
 struct h5_oct_point {
@@ -174,7 +170,5 @@ h5_err_t plot_octant_anc (h5t_octree_t* octree, h5_oct_idx_t oct_idx);
 
 h5_err_t plot_leaf_octants (h5t_octree_t* octree);
 void print_array (h5_int32_t* neigh, h5_oct_idx_t nbr_neigh, int rank);
+
 #endif
-
-
-

src/h5core/h5t_readwrite.c

@@ -7,17 +7,15 @@
   License: see file COPYING in top level of source distribution.
 */
 
-#include <unistd.h> // for the use of sleep
-#if defined (PARALLEL_IO)
-//#define WITH_PARALLEL_H5FED
-#endif
+#include "h5core/h5.h"
+#include "h5_types_private.h"
 
-//#if defined (WITH_PARALLEL_H5FED) // WARNING just used for eclipse to index all code...
-#ifdef PARALLEL_IO
+#include <stdlib.h>
+#include <unistd.h> // for the use of sleep
+
+#ifdef WITH_PARALLEL_H5GRID
 #include <parmetis.h>
 #endif
-#include <stdlib.h>
-//#endif
 
 #include "h5_attribs_private.h"
 #include "h5_hdf5_private.h"
@@ -153,7 +151,7 @@ write_vertices (
 	             1));
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 
 h5_err_t
 add_chunk_to_list (
@@ -211,7 +209,7 @@ h5tpriv_get_list_of_chunks_to_write (
 	}
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
-#endif
+
 static h5_err_t
 exchange_g2l_vtx_map (
 		h5t_mesh_t* const m,
@@ -220,7 +218,6 @@ exchange_g2l_vtx_map (
 		h5_glb_idx_t** glb_vtx
 		) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "m=%p map=%p, range=%p, glb_vtx=%p", m, map, range, glb_vtx);
-#ifdef PARALLEL_IO
 	// alloc/get range
 	TRY (*range = h5_calloc (m->f->nprocs + 1, sizeof (**range)));
 	TRY (h5tpriv_get_ranges (m,*range, map->num_items, 0));
@@ -250,9 +247,9 @@ exchange_g2l_vtx_map (
 				recvdisp,
 				MPI_LONG,
 				m->f->props->comm));
-#endif
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
+#endif
 
 int sort_glb_idx(const void *p_a, const void *p_b)
 {
@@ -288,6 +285,8 @@ remove_item_from_idxmap (
 	map->num_items--;
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
+
+#if defined(WITH_PARALLEL_H5GRID)
 /*
  * Check if any proc with lower rank already writes a vtx that this proc has planed to write
  * if so remove it from the map. Only the proc with the lowest rank writes the vertex
@@ -323,6 +322,7 @@ check_multiple_vtx_writes (
 	}
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
+#endif
 
 h5_int32_t
 find_proc_to_write (
@@ -330,7 +330,7 @@ find_proc_to_write (
 		h5_loc_idx_t elem_idx
 		) {
 	H5_PRIV_FUNC_ENTER (int, "m=%p ", m);
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	h5_glb_idx_t glb_idx = h5tpriv_get_loc_elem_glb_idx (m, elem_idx);
 	for (int i = 0; i < m->chunks->num_alloc; i++) {
 		if ( glb_idx >= m->chunks->chunks[i].elem &&
@@ -341,6 +341,8 @@ find_proc_to_write (
 #endif
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
+
+#ifdef WITH_PARALLEL_H5GRID
 /*
  * function returns a map with all the vtx that should be written by this proc
  *
@@ -354,7 +356,6 @@ get_map_vertices_write (
 		h5_idxmap_t* map
 		) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "m=%p, map=%p", m, map);
-#ifdef PARALLEL_IO
 	h5_chk_idx_t* list_of_chunks;
 	int num_chunks = 0;
 	TRY (h5tpriv_get_list_of_chunks_to_write (m, &list_of_chunks, &num_chunks));
@@ -409,7 +410,7 @@ get_map_vertices_write (
 	h5priv_sort_idxmap (map);
 	TRY (h5_free (range));
 	TRY (h5_free (glb_vtx));
-#endif
+
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 
@@ -420,7 +421,6 @@ write_vertices_chk (
         ) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "m=%p", m);
 	assert (m->num_leaf_levels > 0);
-#ifdef PARALLEL_IO
 	hid_t dset_id;
 	TRY (dset_id = hdf5_open_dataset (m->mesh_gid, m->dsinfo_vertices.name));
 	hid_t mspace_id;
@@ -518,10 +518,10 @@ write_vertices_chk (
 	TRY (hdf5_close_dataspace (mspace_id));
 	TRY (hdf5_close_dataset (dset_id));
 	m->f->empty = 0;
-#endif
+
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
-#if defined(WITH_PARALLEL_H5FED)
+
 static h5_err_t
 write_elems (
         h5t_mesh_t* const m
@@ -599,7 +599,7 @@ write_elems (
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 #endif
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 //TODO maybe use ifdef to have name without _chk
 static h5_err_t
 write_elems_chk (
@@ -1042,7 +1042,7 @@ h5tpriv_write_mesh (
 	H5_PRIV_API_ENTER (h5_err_t, "m=%p", m);
 	if (m->mesh_changed) {
 		if (m->is_chunked) {
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 			if (m->num_weights > 0) {
 				TRY (write_weights (m));
 			}
@@ -2847,7 +2847,7 @@ h5tpriv_read_mesh_part (
         h5_glb_idx_t num_elems
         ) {
 	H5_PRIV_API_ENTER (h5_err_t, "m=%p", m);
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	TRY (h5priv_mpi_barrier (m->f->props->comm)); // octree
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 	TRY (h5priv_mpi_barrier (m->f->props->comm)); // chunks
@@ -2857,11 +2857,11 @@ h5tpriv_read_mesh_part (
 	TRY (h5priv_mpi_barrier (m->f->props->comm)); // distribute chunks
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 #endif
-	h5_glb_elem_t* glb_elems;
+	h5_glb_elem_t* glb_elems = NULL;
 	TRY (read_elems_part (m, &glb_elems, elem_indices, num_elems));
 	h5_loc_idx_t num_interior_elems = m->num_interior_elems[0];
 	h5_loc_idx_t num_ghost_elems = m->num_ghost_elems[0] = 0;
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	TRY (h5priv_mpi_barrier (m->f->props->comm)); // read elems
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 #endif
@@ -2904,7 +2904,7 @@ h5tpriv_read_mesh_part (
 	TRY (read_vertices (m, map));
 	TRY (h5tpriv_alloc_loc_elems (m, 0, num_interior_elems+num_ghost_elems));
 	m->num_loaded_levels = 1;
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	TRY (h5priv_mpi_barrier (m->f->props->comm)); // read vtx
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 #endif
@@ -2913,7 +2913,7 @@ h5tpriv_read_mesh_part (
 	TRY (h5tpriv_update_internal_structs (m, 0));
 
 	TRY (h5_free (glb_elems));
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	TRY (h5priv_mpi_barrier (m->f->props->comm)); // init update
 	m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 #endif

src/h5core/h5t_readwrite_tetm.c

@@ -116,7 +116,7 @@ init_elem_flags (
 			// elem is not ghost so it must be interior (for the time
 			// being we have no overlap
 			elem->flags |= H5_INTERIOR_ENTITY;
-			if (elem->neighbor_indices[i] < -1 ||
+			if (elem->neighbor_indices[i] <= -1 ||
 			    (elems[elem->neighbor_indices[i]].flags & H5_GHOST_ENTITY)) {
 				// if neighbor is < -1 we do not have ghost cells and cell
 				// is border cell

src/h5core/h5t_readwrite_trim.c

@@ -196,7 +196,7 @@ init_glb_elems_struct_chk (
         int num_chk
         ) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "m=%p", m);
-
+#if defined(WITH_PARALLEL_H5GRID)
 	h5_chk_idx_t chk_idx = -1;
 	h5_chk_size_t num_elems = -1;
 	h5_size_t counter = 0;
@@ -224,8 +224,10 @@ init_glb_elems_struct_chk (
 				if (loc_elem->neighbor_indices[i] > -1) {
 					glb_elem->neighbor_indices[i] =  ((H5_LOC_ELEM_T*)m->loc_elems)[loc_elem->neighbor_indices[i]].glb_idx;
 				} else {
-					if (loc_elem->neighbor_indices[i] < -1) {// if elem not locally available we store the - (glb_idx + 2)
-						glb_elem->neighbor_indices[i] = -( loc_elem->neighbor_indices[i] + 2); //TODO is there a func or makro that does that?
+					if (loc_elem->neighbor_indices[i] < -1) {
+						// if elem not locally available we store the - (glb_idx + 2)
+						//TODO is there a func or makro that does that?
+						glb_elem->neighbor_indices[i] = -( loc_elem->neighbor_indices[i] + 2);
 					} else {
 					glb_elem->neighbor_indices[i] = loc_elem->neighbor_indices[i]; // geometrical border
 					}
@@ -236,7 +238,7 @@ init_glb_elems_struct_chk (
 		}
 
 	}
-
+#endif
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 

src/h5core/h5t_retrieve.c

@@ -7,6 +7,9 @@
   License: see file COPYING in top level of source distribution.
 */
 
+#include "h5core/h5.h"
+#include "h5_private.h"
+
 #include "h5t_types_private.h"
 #include "h5t_errorhandling_private.h"
 #include "h5t_map_private.h"
@@ -15,7 +18,6 @@
 #include "h5t_tags_private.h"
 #include "h5t_retrieve_private.h"
 
-#include "h5core/h5.h"
 #include "h5core/h5t_map.h"
 
 /*

src/h5core/h5t_store.c

@@ -31,7 +31,7 @@
  */
 int max_num_elems_p_chunk = 120;
 
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 // that probably doesn't belong here... //TODO put in right place + print variables
 h5_edge_list_t*
 h5tpriv_init_edge_list (
@@ -294,7 +294,7 @@ assign_global_vertex_indices (
 	H5_PRIV_FUNC_ENTER 	(h5_err_t, "m=%p", m);
 	h5_loc_idx_t local_idx = (m->leaf_level == 0) ?
 	                         0 : m->num_loc_vertices[m->leaf_level-1];
-
+#if defined(WITH_PARALLEL_H5GRID)
         if (m->is_chunked && m->f->nprocs > 1) {
                 // exchange num vertices and calc range
                 h5_glb_idx_t* range = NULL;
@@ -311,7 +311,9 @@ assign_global_vertex_indices (
                         H5_PRIV_FUNC_LEAVE (H5_ERR_INTERNAL);
                 }
                 TRY (h5_free (range));
-        } else {
+        } else
+#endif
+	{
                 // simple in serial runs: global_id = local_id
                 for (
                         ;
@@ -322,6 +324,8 @@ assign_global_vertex_indices (
         }
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
+
+#if defined(WITH_PARALLEL_H5GRID)
 /*
  * there is a different version needed for after the refinement because
  * not all vertices need to get a glb_idx from this proc
@@ -355,25 +359,6 @@ assign_global_vertex_indices_chk (
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 
-/*!
-   Assign unique global indices to new elements.
- */
-static h5_err_t
-assign_glb_elem_indices (
-        h5t_mesh_t* const m
-        ) {
-	/*
-	   simple in serial runs: global index = local index
-	 */
-	h5_loc_idx_t loc_idx = (m->leaf_level == 0) ? 0 : m->num_interior_elems[m->leaf_level-1];
-
-	for (; loc_idx < m->num_interior_elems[m->leaf_level]; loc_idx++) {
-		h5tpriv_set_loc_elem_glb_idx (m, loc_idx, loc_idx);
-	}
-
-	return H5_SUCCESS;
-}
-
 /*!
    Assign unique global indices to new elements.
  */
@@ -399,6 +384,27 @@ assign_glb_elem_indices_chk ( //TODO use ifdef instead of new func name
 }
 
 
+#endif
+
+/*!
+   Assign unique global indices to new elements.
+ */
+static h5_err_t
+assign_glb_elem_indices (
+        h5t_mesh_t* const m
+        ) {
+	/*
+	   simple in serial runs: global index = local index
+	 */
+	h5_loc_idx_t loc_idx = (m->leaf_level == 0) ? 0 : m->num_interior_elems[m->leaf_level-1];
+
+	for (; loc_idx < m->num_interior_elems[m->leaf_level]; loc_idx++) {
+		h5tpriv_set_loc_elem_glb_idx (m, loc_idx, loc_idx);
+	}
+
+	return H5_SUCCESS;
+}
+
 h5_lvl_idx_t
 h5tpriv_add_level (
         h5t_mesh_t* const m
@@ -714,6 +720,8 @@ h5t_end_store_elems (
 
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
+
+#if defined(WITH_PARALLEL_H5GRID)
 /*
  * linear search trough chunks to find chk_idx which contains element
  */
@@ -824,7 +832,7 @@ h5tpriv_calc_vtx_revpermutation (
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 #endif // CHUNKING_OF_VTX
-
+#endif // WITH_PARALLEL_H5GRID
 // used to chunk vtx
 //static h5_err_t
 //h5tpriv_store_vtx_range_to_chk (
@@ -852,14 +860,13 @@ h5tpriv_calc_vtx_revpermutation (
 //	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 //}
 
-
 h5_err_t
 h5t_end_store_ckd_elems (
         h5t_mesh_t* const m
         ) {
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
 	h5_debug ("end storing elements");
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 	m->num_interior_elems[m->leaf_level] = m->last_stored_eid+1;
 	m->num_glb_elems[m->leaf_level] = m->last_stored_eid+1;// only works for serial case
 	m->num_glb_leaf_elems[m->leaf_level] = m->num_interior_leaf_elems[m->leaf_level];
@@ -1106,7 +1113,7 @@ h5t_end_store_ckd_elems (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 h5_err_t
 h5tpriv_find_oct_proc_of_point (
 		h5t_mesh_t* m,
@@ -1212,7 +1219,7 @@ h5t_pre_refine (
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
 	H5_CORE_API_RETURN (m->methods->store->pre_refine (m));
 }
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 //TODO maybe use ifdef to have name without _chk
 h5_err_t
 h5t_pre_refine_chk (
@@ -1256,7 +1263,7 @@ h5t_refine_marked_elems (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
-#ifdef PARALLEL_IO
+#ifdef WITH_PARALLEL_H5GRID
 /*
  * Calculate the global entity range
  * range[i] = first glb entity of proc i
@@ -1401,6 +1408,7 @@ get_new_vtx_of_edge(
 	}
 	H5_PRIV_FUNC_RETURN (H5_ERR_INTERNAL); //edge that should be refined in not refined
 }
+
 /*
  * Go through elements and find boundary edges that were refined on this proc.
  * we try to find edges that are shared with non-local elements (they could have
@@ -2241,8 +2249,7 @@ h5t_post_refine (
 }
 
 
-#ifdef PARALLEL_IO
-
+#ifdef WITH_PARALLEL_H5GRID
 h5_err_t
 h5t_post_refine_chk (
         h5t_mesh_t* const m,
@@ -2251,7 +2258,8 @@ h5t_post_refine_chk (
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
 	h5_debug("post_refine_chk");
 	// get boundary edges
-	h5_edge_list_t* b_edges = h5tpriv_init_edge_list(h5tpriv_ref_elem_get_num_edges(m) * m->marked_entities->num_items);
+	h5_edge_list_t* b_edges = h5tpriv_init_edge_list (
+		h5tpriv_ref_elem_get_num_edges(m) * m->marked_entities->num_items);
 	TRY (h5tpriv_find_boundary_edges (m, marked_glb_elems, b_edges));
 
 	// exchange boundary edges
@@ -2482,7 +2490,7 @@ h5t_end_refine_elems (
         ) {
 	H5_CORE_API_ENTER (h5_err_t, "m=%p", m);
 	if (m->is_chunked) {
-#ifdef PARALLEL_IO		
+#ifdef WITH_PARALLEL_H5GRID		
 		TRY (h5priv_mpi_barrier (m->f->props->comm));
                 m->timing.measure[m->timing.next_time++] = MPI_Wtime();
 		h5_glb_idxlist_t* glb_list = NULL;
@@ -2510,7 +2518,7 @@ h5t_end_refine_elems (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
-
+#if defined(WITH_PARALLEL_H5GRID)
 h5_err_t
 h5tpriv_init_chunks (
 		h5t_mesh_t* const m
@@ -2639,7 +2647,6 @@ h5tpriv_create_chunk (
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }
 
-#ifdef PARALLEL_IO
 /*
  * exchange newly created chunks
  */

src/h5core/h5t_store_private.h

@@ -57,6 +57,7 @@ h5tpriv_get_num_new_elems (
 	return m->methods->store->get_num_new_elems ();
 }
 
+#if defined(WITH_PARALLEL_H5GRID)
 h5_err_t
 h5tpriv_init_chunks (h5t_mesh_t* const);
 
@@ -86,5 +87,6 @@ h5tpriv_octant_is_full (h5t_octree_t* octree, h5_oct_idx_t oct_idx);
 
 h5_err_t
 h5tpriv_get_ranges (h5t_mesh_t* const m, h5_glb_idx_t* range, h5_glb_idx_t mycount, h5_glb_idx_t glb_start);
+#endif
 
 #endif

src/h5core/h5t_types_private.h

@@ -259,11 +259,13 @@ struct h5t_mesh {
 
 	/*** chunking ***/
 	h5_lvl_idx_t is_chunked;		/* == 1 if mesh is chunked */
+#if defined(WITH_PARALLEL_H5GRID)
 	h5t_octree_t* octree;
 	h5t_chunks_t* chunks;
 	h5_dsinfo_t dsinfo_chunks;
 	h5_dsinfo_t dsinfo_octree;
 	h5_dsinfo_t dsinfo_userdata;
+#endif
 	h5t_timing_t timing;
 
 	h5_strlist_t*   mtagsets;

src/include/h5core/h5t_octree.h

@@ -19,18 +19,18 @@ extern "C" {
 // it is very unlikely that there are more than 2^32 octants needed. since there is no id
 // we dont need that...
 //#if defined(USE_LARGE_INDICES)
-//typedef int64_t h5_oct_idx_t;                   // type for a octant
-//typedef h5_uint64_t	h5_oct_userlev_t;			// type for user defined levels
+//typedef int64_t h5_oct_idx_t;                 // type for a octant
+//typedef h5_uint64_t	h5_oct_userlev_t;	// type for user defined levels
 //#define OCT_USERLEV_LENGTH 64
 //#else
-typedef h5_int32_t h5_oct_idx_t;                   // type for a octant
-typedef h5_uint32_t	h5_oct_userlev_t;			// type for user defined levels
+typedef h5_int32_t h5_oct_idx_t;                // type for a octant
+typedef h5_uint32_t	h5_oct_userlev_t;	// type for user defined levels
 #define OCT_USERLEV_LENGTH 32
 //#endif
 
 typedef h5_int32_t h5_oct_level_t;
-typedef int16_t h5_oct_orient_t;			// orientation of an octant
-typedef int16_t h5_oct_dir_t; 				// direction to look for neighboring octants
+typedef int16_t h5_oct_orient_t;		// orientation of an octant
+typedef int16_t h5_oct_dir_t; 			// direction to look for neighboring octants
 
 
 #define OCT_CHG_INTERNAL  11