est/H5BlockTestAttributes.c

- adaption to renamed elements in struct h5_file
src/H5PartErrors.h
src/H5BlockTypes.h
src/H5Part.h
src/H5Block.c
- refactoring
src/H5Fed.h
src/H5Fed_statistics.c
src/Makefile.am
src/H5BlockErrors.h
src/h5/h5_types.h
src/h5/attribs.c
src/h5/t_readwrite.c
src/h5/u_readwrite.c
src/h5/t_openclose.c
src/h5/H5.h
src/h5/readwrite.c
src/h5/openclose.c
src/h5/openclose.h
src/H5Fed.c
- H5Fed write vertices and tets

src/H5Block.c

@@ -49,7 +49,6 @@
 
 #include "H5BlockTypes.h"
 #include "H5Block.h"
-#include "H5BlockPrivate.h"
 #include "h5/H5.h"
 #include "H5BlockErrors.h"
 
@@ -442,7 +441,7 @@ _dissolve_ghostzones (
 		 f->nprocs * sizeof (*f->block->user_layout) );
 
 	p_begin = p_max = p_end = (struct list*) malloc ( sizeof ( *p_begin ) );
-	if ( p_begin == NULL ) return HANDLE_H5PART_NOMEM_ERR;
+	if ( p_begin == NULL ) return HANDLE_H5_NOMEM_ERR;
 	
 	memset ( p_begin, 0, sizeof ( *p_begin ) );
 
@@ -456,7 +455,7 @@ _dissolve_ghostzones (
 			if ( _have_ghostzone ( p, q ) ) {
 				p_el = (struct list*) malloc ( sizeof ( *p_el ) );
 				if ( p_el == NULL )
-					return HANDLE_H5PART_NOMEM_ERR;
+					return HANDLE_H5_NOMEM_ERR;
 
 				p_el->p = p;
 				p_el->q = q;
@@ -596,7 +595,7 @@ H5BlockDefine3DFieldLayout(
 	_get_dimension_sizes ( f );
 
 	herr = _dissolve_ghostzones ( f );
-	if ( herr < 0 ) return HANDLE_H5PART_LAYOUT_ERR;
+	if ( herr < 0 ) return HANDLE_H5_LAYOUT_ERR;
 
 	herr = _release_hyperslab ( f );
 	if ( herr < 0 )	return HANDLE_H5S_CLOSE_ERR;
@@ -784,7 +783,7 @@ _open_field_group (
 	if ( h5err < 0 ) return h5err;
 
 	if ( ! _have_object ( b->blockgroup, name ) )
-		return HANDLE_H5PART_NOENT_ERR ( name );
+		return HANDLE_H5_NOENT_ERR ( name );
 
 	herr_t herr = H5Gopen ( b->blockgroup, name );
 	if ( herr < 0 ) return HANDLE_H5G_OPEN_ERR ( name );
@@ -847,14 +846,14 @@ _select_hyperslab_for_reading (
 
 	rank = H5Sget_simple_extent_dims ( b->diskshape, NULL, NULL );
 	if ( rank < 0 )  return HANDLE_H5S_GET_SIMPLE_EXTENT_DIMS_ERR;
-	if ( rank != 3 ) return HANDLE_H5PART_DATASET_RANK_ERR ( rank, 3 );
+	if ( rank != 3 ) return HANDLE_H5_DATASET_RANK_ERR ( rank, 3 );
 
 	rank = H5Sget_simple_extent_dims ( b->diskshape, field_dims, NULL );
 	if ( rank < 0 )  return HANDLE_H5S_GET_SIMPLE_EXTENT_DIMS_ERR;
 	
 	if ( (field_dims[0] < (hsize_t)b->k_max) ||
 	     (field_dims[1] < (hsize_t)b->j_max) ||
-	     (field_dims[2] < (hsize_t)b->i_max) ) return HANDLE_H5PART_LAYOUT_ERR;
+	     (field_dims[2] < (hsize_t)b->i_max) ) return HANDLE_H5_LAYOUT_ERR;
 
 	H5_print_debug (
 		"PROC[%d]: \n"
@@ -1186,7 +1185,7 @@ _create_field_group (
 	if ( h5err < 0 ) return h5err;
 
 	if ( _have_object ( b->blockgroup, name ) )
-		return  HANDLE_H5PART_GROUP_EXISTS_ERR ( name );
+		return  HANDLE_H5_GROUP_EXISTS_ERR ( name );
 
 	herr_t herr = H5Gcreate ( b->blockgroup, name, 0 );
 	if ( herr < 0 ) return HANDLE_H5G_CREATE_ERR ( name );

src/H5BlockErrors.h

@@ -10,26 +10,26 @@
 			H5PART_ERR_LAYOUT, \
 			"No layout defined." )
 
-#define HANDLE_H5PART_LAYOUT_ERR \
+#define HANDLE_H5_LAYOUT_ERR \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
 			H5PART_ERR_LAYOUT, \
 			"Bad layout." );
 
-#define HANDLE_H5PART_NOENT_ERR( name ) \
+#define HANDLE_H5_NOENT_ERR( name ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
 			H5PART_ERR_NOENT, \
 			"Object \"%s\" doesn't exists.", name );
 
-#define HANDLE_H5PART_DATASET_RANK_ERR( m, n ) \
+#define HANDLE_H5_DATASET_RANK_ERR( m, n ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
 			H5PART_ERR_INVAL, \
 			"Wrong rank of dataset: Is %d, but should be %d", \
 			m, n );
 
-#define HANDLE_H5PART_GROUP_EXISTS_ERR( name ) \
+#define HANDLE_H5_GROUP_EXISTS_ERR( name ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
 			H5PART_ERR_INVAL, \

src/H5BlockTypes.h

@@ -1,32 +1,5 @@
 #ifndef __H5BLOCKTYPES_H
 #define __H5BLOCKTYPES_H
 
-struct H5BlockPartition {
-	h5part_int64_t	i_start;
-	h5part_int64_t	i_end;
-	h5part_int64_t	j_start;
-	h5part_int64_t	j_end;
-	h5part_int64_t	k_start;
-	h5part_int64_t	k_end;
-};
-
-struct h5b_fdata {
-	h5part_int64_t step_idx;
-	h5part_int64_t i_max;
-	h5part_int64_t j_max;
-	h5part_int64_t k_max;
-	struct H5BlockPartition *user_layout;
-	struct H5BlockPartition *write_layout;
-	int have_layout;
-
-	hid_t shape;
-	hid_t memshape;
-	hid_t diskshape;
-	hid_t blockgroup;
-	hid_t field_group_id;
-};
-
-#define H5PART_ERR_LAYOUT	-100
-#define H5PART_ERR_NOENT	-101
 
 #endif

src/H5Fed.c

@@ -36,7 +36,7 @@
 */
 
 #include <hdf5.h>
-#include "h5/h5_types.h"
+#include "h5/H5.h"
 #include "H5Fed.h"
 
 

src/H5Fed.h

@@ -54,11 +54,6 @@ h5_int_t H5FedHasBoundaryMesh(
 
 /******	VERTEX statistics routines *******************************************/
 
-h5_size_t H5FedGetNumVertices (
-	h5_file * fh,
-	const h5_id_t level
-	);
-
 h5_size_t H5FedGetNumVerticesTotal(
 	h5_file * fh,
 	const h5_id_t level
@@ -72,17 +67,12 @@ h5_size_t H5FedGetNumVerticesCnode (
 
 /******	EDGE statistics routines ********************************************/
 
-h5_size_t H5FedGetNumEdgesInTetrahedralMesh (
+h5_size_t H5FedGetNumEdgesTotal (
 	h5_file * fh,
 	const h5_id_t level
 	);
 
-h5_size_t H5FedGetNumEdgesInTetrahedralMeshTotal (
-	h5_file * fh,
-	const h5_id_t level
-	);
-
-h5_size_t H5FedGetNumEdgeInTetrahedralMeshCnode (
+h5_size_t H5FedGetNumEdgesCnode (
 	h5_file * fh,
 	const h5_id_t level,
 	const h5_id_t cnode
@@ -90,17 +80,12 @@ h5_size_t H5FedGetNumEdgeInTetrahedralMeshCnode (
 
 /******	TRIANGLE statistics routines *****************************************/
 
-h5_size_t H5FedGetNumTrianglesInTetrahedralMesh (
+h5_size_t H5FedGetNumTrianglesTotal (
 	h5_file * fh,
 	const h5_id_t level
 	);
 
-h5_size_t H5FedGetNumTrianglesInTetrahedralMeshTotal (
-	h5_file * fh,
-	const h5_id_t level
-	);
-
-h5_size_t H5FedGetNumTrianglesInTetrahedralMeshCnode (
+h5_size_t H5FedGetNumTrianglesCnode (
 	h5_file * fh,
 	const h5_id_t level,
 	const h5_id_t cnode
@@ -108,11 +93,6 @@ h5_size_t H5FedGetNumTrianglesInTetrahedralMeshCnode (
 
 /******	TETRAHEDRON statistics routines **************************************/
 
-h5_size_t H5FedGetNumTetrahedra (
-	h5_file * fh,
-	const h5_id_t level
-	);
-
 h5_size_t H5FedGetNumTetrahedraTotal(
 	h5_file * fh,
 	const h5_id_t level
@@ -126,11 +106,6 @@ h5_size_t H5FedGetNumTetrahedraCnode (
 
 /******	BOUNDARY statistics routines ****************************************/
 
-h5_size_t H5FedGetNumBoundaryTriangles (
-	h5_file * fh,
-	const h5_id_t level
-	);
-
 h5_size_t H5FedGetNumBoundaryTrianglesTotal (
 	h5_file * fh,
 	const h5_id_t level
@@ -142,89 +117,145 @@ h5_size_t H5FedGetNumBoundaryTrianglesCnode (
 	const h5_id_t cnode
 	);
 
-/******	RETRIEVAL routines **************************************************/
+/******	STORE / RETRIEVAL routines ********************************************/
 
-h5_vertex * H5FedGetVertexCoordinate (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t vertex_id
+/* vertices */
+h5_size_t
+H5FedSetNumVertices (
+	h5_file * f,
+	const h5_size_t num
 	);
 
-h5_edge * H5FedGetEdge (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t local_id
+h5_size_t
+H5FedGetNumVertices (
+	h5_file * f
 	);
 
-h5_triangle * H5FedGetTriangle (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t local_id
+h5_id_t
+H5FedStoreVertex (
+	h5_file * f,
+	const h5_id_t id,
+	const h5_float64_t P[3]
 	);
 
-h5_tetrahedron * H5FedGetTetrahedron (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t local_id
+h5_id_t
+H5FedGetVertex (
+	h5_file * f,
+	h5_id_t	* const	id,
+	h5_float64_t * const P[3]
 	);
 
-h5_triangle * H5FedGetBoundaryTriangle (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t local_id
+/* edges */
+h5_size_t
+H5FedSetNumEdges (
+	h5_file * f,
+	const h5_size_t num
 	);
 
-/******	STORE routines*****************************************************/
-
-h5_int_t H5FedSetNumVertices (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_size_t num_vertices
+h5_size_t
+H5FedGetNumEdges (
+	h5_file * f
 	);
 
-h5_int_t H5FedSetNumTetrahedra (
+h5_id_t
+H5FedStoreEdge (
+	h5_file * f,
+	const h5_id_t id,
+	const h5_id_t parent_id,
+	const h5_id_t vertex_ids[2]
+	);
+
+h5_id_t
+H5FedGetEdge (
+	h5_file * f,
+	h5_id_t * const id,
+	h5_id_t * const parent_id,
+	h5_id_t * const vertex_ids[2]
+	);
+
+/* triangles */
+h5_size_t
+H5FedSetNumTriangles (
+	h5_file * f,
+	const h5_size_t num
+	);
+
+h5_size_t
+H5FedGetNumTriangles (
+	h5_file * f
+	);
+
+h5_int_t
+H5FedStoreTriangle (
+	h5_file * f,
+	const h5_id_t id,
+	const h5_id_t parent_id,
+	const h5_id_t vertex_ids[3]
+	);
+
+h5_id_t
+H5FedGetTriangle (
+	h5_file * f,
+	h5_id_t * const id,
+	h5_id_t * const parent_id,
+	h5_id_t * const vertex_ids[2]
+	);
+
+/* boundary triangles */
+h5_size_t
+H5FedSetNumBoundaryTriangles (
+	h5_file * f,
+	const h5_size_t num
+	);
+
+h5_size_t
+H5FedGetNumBoundaryTriangles (
+	h5_file * f
+	);
+
+
+h5_id_t
+H5FedStoreBoundaryTriangle (
 	h5_file * fh,
-	const h5_id_t level,
+	const h5_id_t id,
+	const h5_id_t parent_id,
+	const h5_id_t vertex_ids[3]
+	);
+
+h5_id_t
+H5FedGetBoundaryTriangle (
+	h5_file * f,
+	h5_id_t * const id,
+	h5_id_t * const parent_id,
+	h5_id_t * const vertex_ids[3]
+	);
+
+/* tetrahedra */
+h5_size_t
+H5FedSetNumTetrahedra (
+	h5_file * f,
 	const h5_size_t num_tet
 	);
 
-h5_int_t H5FedStoreVertexCoordinate (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t vertex_id,
-	const h5_vertex * const vertex
+h5_size_t
+H5FedGetNumTetrahedra (
+	h5_file * f
 	);
 
-h5_int_t H5FedStoreEdge (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t edge_id,
+h5_id_t
+H5FedStoreTetrahedron (
+	h5_file * f,
+	const h5_id_t id,
 	const h5_id_t parent_id,
-	const h5_edge * const edge
+	const h5_id_t vertex_ids[4]
 	);
 
-h5_int_t H5FedStoreTriangle (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t triangle_id,
-	const h5_id_t parent_id,
-	const h5_triangle * const triangle
-	);
-
-h5_int_t H5FedStoreTetrahedron (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t tet_id,
-	const h5_id_t parent_id,
-	const h5_tetrahedron * const tet/*!< 4-tuple with vertex id's	*/
-	);
-
-h5_int_t H5FedStoreBoundaryTriangle (
-	h5_file * fh,
-	const h5_id_t level,
-	const h5_id_t btriangle_id,
-	const h5_id_t parent_id,
-	const h5_triangle * const btriangle
+h5_id_t
+H5FedGetTetrahedron (
+	h5_file * f,
+	h5_id_t * const id,
+	h5_id_t * parent_id,
+	h5_id_t * const vertex_ids[4]
 	);
 
 /******	UPWARD ADJACENCY routines *********************************************/

src/H5Fed_statistics.c

@@ -18,21 +18,6 @@
 #include "h5/h5_types.h"
 #include "H5Fed.h"
 
-/*!
-  \ingroup h5fed_c_api
-
-  Get the number of vertices used for defining a submesh
-  at level \c level for this compute node in current step.
-
-  \return number of vertices
-  \return \c -1	on error.
-*/
-h5_size_t H5FedGetNumVertices (
-	h5_file * fh,			/*!< file handle		*/
-	const h5_id_t level		/*!< mesh level to query	*/
-	) {
-	return -1;
-}
 
 /*!
   \ingroup h5fed_c_api
@@ -69,31 +54,6 @@ h5_size_t H5FedGetNumVerticesCnode (
 
 /******	EDGE statistics routines ********************************************/
 
-/*!
-  \ingroup h5fed_c_api
-
-  Returns the number of edges present in the mesh at level \c level in 
-  current time step on this compute node.
-
-  \return number of edges
-  \return \c -1	on error.
-
-  \note
-  It is left to the API implementor how to make this information
-  available; in general he can compute it from the definition of
-  the tetrahedral mesh.
-
-  \note
-  After counting the number for the local cnode we call MPI_Gather()
-  to collect the number from the other cnodes and store them into an
-  array.  The inquired number will be provided from this array.
-*/
-h5_size_t H5FedGetNumEdgesInTetrahedralMesh (
-	h5_file * fh,			/*!< file handle		*/
-	const h5_id_t level		/*!< mesh level to query	*/
-	) {
-	return -1;
-}
 
 /*!
   \ingroup h5fed_c_api
@@ -104,7 +64,7 @@ h5_size_t H5FedGetNumEdgesInTetrahedralMesh (
   \return number of edges
   \return \c -1	on error.
 */
-h5_size_t H5FedGetNumEdgesInTetrahedralMeshTotal (
+h5_size_t H5FedGetNumEdgesTotal (
 	h5_file * fh,			/*!< file handle		*/
 	const h5_id_t level		/*!< mesh level to query	*/
 	) {
@@ -120,7 +80,7 @@ h5_size_t H5FedGetNumEdgesInTetrahedralMeshTotal (
   \return number of edges
   \return \c -1 on error.
 */
-h5_size_t H5FedGetNumEdgeInTetrahedralMeshCnode (
+h5_size_t H5FedGetNumEdgesCnode (
 	h5_file * fh,			/*!< file handle		*/
 	const h5_id_t level,		/*!< mesh level to query	*/
 	const h5_id_t cnode		/*!< compute node		*/
@@ -130,27 +90,6 @@ h5_size_t H5FedGetNumEdgeInTetrahedralMeshCnode (
 
 /******	TRIANGLE statistics routines *****************************************/
 
-/*!
-  \ingroup h5fed_c_api
-
-  Get the number of triangles present in the mesh at level \c level in 
-  current time step on this compute note.
-
-  \return Number of triangles
-  \return \c -1 on error.
-
-  \note
-  After counting the number for the local cnode we call MPI_Gather()
-  to collect the number from the other cnodes and store them into an
-  array.  The inquired number will be provided from this array.
-*/
-h5_size_t H5FedGetNumTrianglesInTetrahedralMesh (
-	h5_file * fh,			/*!< file handle		*/
-	const h5_id_t level		/*!< mesh level to query	*/
-	) {
-	return -1;
-}
-
 /*!
   \ingroup h5fed_c_api
 
@@ -160,7 +99,7 @@ h5_size_t H5FedGetNumTrianglesInTetrahedralMesh (
   \return Number of triangles
   \return \c -1 on error.
 */
-h5_size_t H5FedGetNumTrianglesInTetrahedralMeshTotal (
+h5_size_t H5FedGetNumTrianglesTotal (
 	h5_file * fh,			/*!< file handle		*/
 	const h5_id_t level		/*!< mesh level to query	*/
 	) {
@@ -176,7 +115,7 @@ h5_size_t H5FedGetNumTrianglesInTetrahedralMeshTotal (
   \return Number of triangles
   \return \c -1 on error.
 */
-h5_size_t H5FedGetNumTrianglesInTetrahedralMeshCnode (
+h5_size_t H5FedGetNumTrianglesCnode (
 	h5_file * fh,			/*!< file handle		*/
 	const h5_id_t level,		/*!< mesh level to query	*/
 	const h5_id_t cnode		/*!< compute node		*/
@@ -186,27 +125,6 @@ h5_size_t H5FedGetNumTrianglesInTetrahedralMeshCnode (
 
 /******	TETRAHEDRON statistics routines **************************************/
 
-/*!
-  \ingroup h5fed_c_api
-
-  Returns the number of tetrahedral elements present in the mesh at 
-  level \c level in current step on this compute node.
-
-  \return number of tetrahedra
-  \return \c -1 on error.
-
-  \note
-  After counting the number for the local cnode we call MPI_Gather()
-  to collect the number from the other cnodes and store them into an
-  array.  The inquired number will be provided from this array.
-*/
-h5_size_t H5FedGetNumTetrahedra (
-	h5_file * fh,			/*!< file handle		*/
-	const h5_id_t level		/*!< mesh level to query	*/
-	) {
-	return -1;
-}
-
 /*!
   \ingroup h5fed_c_api
 
@@ -242,33 +160,6 @@ h5_size_t H5FedGetNumTetrahedraCnode (
 
 /******	BOUNDARY statistics routines ****************************************/
 
-/*!
-  \ingroup h5fed_c_api
-
-  Get the number of boundary triangles present in the mesh at
-  level \c level in current step on this compute node.
-
-  \return number of tetrahedras
-  \return \c -1 on error.
-
-  \note
-  It is left to the API implementor how to make this information
-  available. In general he can compute it from the definition
-  of the tetrahedral mesh, using the adjacency relations, i.e.
-  the fact that a boundary triangle has only one single adjacent
-  tetrahedron.
-
-  \note
-  After counting the number for the local cnode we call MPI_Gather()
-  to collect the number from the other cnodes and store them into an
-  array.  The inquired number will be provided from this array.
-*/
-h5_size_t H5FedGetNumBoundaryTriangles (
-	h5_file * fh,			/*!< file handle		*/
-	const h5_id_t level		/*!< mesh level to query	*/
-	) {
-	return -1;
-}
 
 /*!
   \ingroup h5fed_c_api

src/H5Part.h

@@ -14,27 +14,21 @@ extern "C" {
 
 #include "H5PartTypes.h"
 
+#define H5PART_SUCCESS		H5_SUCCESS
+#define H5PART_ERR_NOMEM	H5_ERR_NOMEM
+#define H5PART_ERR_INVAL	H5_ERR_INVAL
+#define H5PART_ERR_BADFD	H5_ERR_BADFD
+#define H5PART_ERR_LAYOUT	H5_ERR_LAYOUT
+#define H5PART_ERR_NOENT	H5_ERR_NOENT
+#define H5PART_ERR_INIT         H5_ERR_INIT
+#define H5PART_ERR_NOENTRY	H5_ERR_NOENTRY
 
-#define H5PART_SUCCESS		0
-#define H5PART_ERR_NOMEM	-12
-#define H5PART_ERR_INVAL	-22
-#define H5PART_ERR_BADFD	-77
+#define H5PART_ERR_MPI		H5_ERR_MPI
+#define H5PART_ERR_HDF5		H5_ERR_HDF5
 
-#define H5PART_ERR_INIT         -200
-#define H5PART_ERR_NOENTRY	-201
-
-#define H5PART_ERR_MPI		-201
-#define H5PART_ERR_HDF5		-202
-
-
-#define H5_O_RDONLY		0x01
-#define H5_O_WRONLY		0x02
-#define H5_O_APPEND		0x03
-#define H5_O_RDWR		0x04
-
-#define H5PART_READ		H5_O_RDONLY	# legacy def, will be removed
-#define H5PART_WRITE		H5_O_WRONLY	# legacy def, will be removed
-#define H5PART_APPEND		H5_O_APPEND	# legacy def, will be removed
+#define H5PART_READ		H5_O_RDONLY
+#define H5PART_WRITE		H5_O_WRONLY
+#define H5PART_APPEND		H5_O_APPEND
 
 #define H5PART_INT64		((h5part_int64_t)H5T_NATIVE_INT64)
 #define H5PART_FLOAT64		((h5part_int64_t)H5T_NATIVE_DOUBLE)

src/H5PartErrors.h

@@ -6,85 +6,85 @@
 
 #define CHECK_FILEHANDLE( f ) \
 	if ( H5_check_filehandle ( f ) != H5PART_SUCCESS ) \
-		return HANDLE_H5PART_BADFD_ERR;
+		return HANDLE_H5_BADFD_ERR;
 
 #define CHECK_WRITABLE_MODE( f )  \
 	if ( f->mode==H5PART_READ ) \
 		return (*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_INVAL, \
+			H5_ERR_INVAL, \
 			"Attempting to write to read-only file" );
 
 #define CHECK_READONLY_MODE( f )  \
 	if ( ! f->mode==H5PART_READ ) \
 		return (*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_INVAL, \
+			H5_ERR_INVAL, \
 			"Operation is not allowed on writable files." );
 
 #define CHECK_TIMEGROUP( f ) \
 	if ( f->step_gid <= 0 ) \
 		return (*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_INVAL, \
+			H5_ERR_INVAL, \
 			"Timegroup <= 0.");
 
 /**************** H5Part *********************/
 
-#define HANDLE_H5PART_BADFD_ERR \
+#define HANDLE_H5_BADFD_ERR \
 	(*_err_handler)( \
 		H5_get_funcname(), \
-		H5PART_ERR_BADFD, \
+		H5_ERR_BADFD, \
 		"Called with bad filehandle." );
 
-#define HANDLE_H5PART_INIT_ERR \
+#define HANDLE_H5_INIT_ERR \
         (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_INIT, \
+		H5_ERR_INIT, \
 		"Cannot initialize H5Part." );
 
-#define HANDLE_H5PART_NOMEM_ERR \
+#define HANDLE_H5_NOMEM_ERR \
 	(*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_NOMEM, \
+		H5_ERR_NOMEM, \
 		"Out of memory." );
 
-#define HANDLE_H5PART_SETSTEP_ERR( rc, step ) \
+#define HANDLE_H5_SETSTEP_ERR( rc, step ) \
 	(*_err_handler) ( \
 		H5_get_funcname(), \
 		rc, \
 		"Cannont set time-step to %lld.", (long long)step );
 
-#define HANDLE_H5PART_FILE_ACCESS_TYPE_ERR( flags ) \
+#define HANDLE_H5_FILE_ACCESS_TYPE_ERR( flags ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_INVAL, \
+			H5_ERR_INVAL, \
 			"Invalid file access type \"%d\".", flags);
 
-#define HANDLE_H5PART_STEP_EXISTS_ERR( step ) \
+#define HANDLE_H5_STEP_EXISTS_ERR( step ) \
 	(*_err_handler)( \
 	        H5_get_funcname(), \
-		H5PART_ERR_INVAL, \
+		H5_ERR_INVAL, \
 		"Step #%lld already exists, step cannot be set to an existing" \
 		" step in write and append mode", (long long)step );
 
-#define HANDLE_H5PART_SET_VIEW_ERR( rc, start, end ) \
+#define HANDLE_H5_SET_VIEW_ERR( rc, start, end ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
 			rc, \
 			"Cannot set view to (%lld, %lld).", \
 			(long long)start, (long long)end );
 
-#define HANDLE_H5PART_GET_NUM_PARTICLES_ERR( rc ) \
+#define HANDLE_H5_GET_NUM_PARTICLES_ERR( rc ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
 			rc, \
 			"Cannot get number of particles." );
 
-#define HANDLE_H5PART_NOENTRY_ERR( group_name, type, idx ) \
+#define HANDLE_H5_NOENTRY_ERR( group_name, type, idx ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_NOENTRY, \
+			H5_ERR_NOENTRY, \
 			"No entry with index %lld and type %d in group %s!", \
 			(long long)idx, type, group_name );
 
@@ -93,107 +93,107 @@
 #define HANDLE_H5A_CLOSE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot terminate access to attribute." );
 
 #define HANDLE_H5A_CREATE_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot create attribute \"%s\".", s );
 
 #define HANDLE_H5A_GET_NAME_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot get attribute name." );
 
 #define HANDLE_H5A_GET_NUM_ATTRS_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot get number of attributes." );
 
 #define HANDLE_H5A_GET_SPACE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot get a copy of dataspace for attribute." );
 
 #define HANDLE_H5A_GET_TYPE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot get attribute datatype." );
 
 #define HANDLE_H5A_OPEN_IDX_ERR( n ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot open attribute specified by index \"%lld\".", \
 		(long long)n );
 
 #define HANDLE_H5A_OPEN_NAME_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot open attribute specified by name \"%s\".", s );
 
 #define HANDLE_H5A_READ_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot read attribute" );
 
 #define HANDLE_H5A_WRITE_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot write attribute \"%s\".", s );
 
 /* H5D: Dataset */
 #define HANDLE_H5D_CLOSE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Close of dataset failed." );
 
 #define HANDLE_H5D_CREATE_ERR( s, n ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot create dataset for name \"%s\", step \"%lld\".", \
 		s, (long long) n );
 
 #define HANDLE_H5D_GET_SPACE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot get dataspace identifier.");
 
 #define HANDLE_H5D_GET_TYPE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot determine dataset type.");
 
 #define HANDLE_H5D_OPEN_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot open dataset \"%s\".", s );
 
 #define HANDLE_H5D_READ_ERR( s, n ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Read from dataset \"%s\" failed, step \"%lld\".", \
 		s, (long long) n );
 
 #define HANDLE_H5D_WRITE_ERR( s, n ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Write to dataset \"%s\" failed, step \"%lld\".", \
 		s, (long long)n );
 
@@ -201,13 +201,13 @@
 #define HANDLE_H5F_CLOSE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot terminate access to file." );
 
 #define HANDLE_H5F_OPEN_ERR( filename, flags ) \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_HDF5, \
+			H5_ERR_HDF5, \
 			"Cannot open file \"%s\" with mode \"%d\"", filename, flags );
 
 
@@ -216,25 +216,25 @@
 #define HANDLE_H5G_CLOSE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot terminate access to datagroup." );
 
 #define HANDLE_H5G_CREATE_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot create datagroup \"%s\".", s );
 
 #define HANDLE_H5G_GET_OBJINFO_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot get information about object \"%s\".", s );
 
 #define HANDLE_H5G_OPEN_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot open group \"%s\".", s );
 
 
@@ -242,26 +242,26 @@
 #define HANDLE_H5P_CLOSE_ERR( s ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot terminate access to property list \"%s\".", s );
 
 #define HANDLE_H5P_CREATE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot create property list." );
 
 #define HANDLE_H5P_SET_DXPL_MPIO_ERR \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_HDF5, \
+			H5_ERR_HDF5, \
 			"MPI: Cannot set data transfer mode." );
 
 
 #define HANDLE_H5P_SET_FAPL_MPIO_ERR \
 		(*_err_handler) ( \
 			H5_get_funcname(), \
-			H5PART_ERR_HDF5, \
+			H5_ERR_HDF5, \
 			"Cannot store IO communicator information to the " \
 			"file access property list.");
 
@@ -269,63 +269,63 @@
 #define HANDLE_H5S_CREATE_SIMPLE_ERR( n ) \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot create dataspace with len \"%lld\".", (long long) n );
 
 #define HANDLE_H5S_CLOSE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot terminate access to dataspace." ); 
 
 #define HANDLE_H5S_GET_SELECT_NPOINTS_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot determine the number of elements in dataspace selection." ); 
 
 #define HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot determine number of elements in dataspace." ); 
 
 #define HANDLE_H5S_SELECT_HYPERSLAB_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot set select hyperslap region or add the specified region" );
 
 /* H5T:  type */
 #define HANDLE_H5T_CLOSE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_HDF5, \
+		H5_ERR_HDF5, \
 		"Cannot release datatype." );
 
 /* MPI */
 #define HANDLE_MPI_ALLGATHER_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_MPI, \
+		H5_ERR_MPI, \
 		"Cannot gather data." );
 
 #define HANDLE_MPI_COMM_SIZE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_MPI, \
+		H5_ERR_MPI, \
 		"Cannot get number of processes in my group." );
 
 #define HANDLE_MPI_COMM_RANK_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_MPI, \
+		H5_ERR_MPI, \
 		"Cannot get rank of the calling process in my group." );
 
 #define HANDLE_MPI_UNAVAILABLE_ERR \
 	 (*_err_handler) ( \
 		H5_get_funcname(), \
-		H5PART_ERR_MPI, \
+		H5_ERR_MPI, \
 		"MPI not available" );
 
 #endif

src/Makefile.am

@@ -61,9 +61,8 @@ libH5Part_a_SOURCES = \
 	H5Fed.c \
 	H5Fed_adjacency.c \
 	H5Fed_dof.c \
-	H5Fed_retrieve.c \
 	H5Fed_statistics.c \
-	H5Fed_store.c
+	H5Fed_storeretrieve.c
 
 SUBDIRS = h5 bindings
 
@@ -78,7 +77,10 @@ libH5Part.a: $(libH5Part_a_OBJECTS)
 H5Part.o: H5Part.c H5Part.h H5PartPrivate.h H5PartTypes.h
 H5Block.o: H5Block.c H5Part.h H5PartPrivate.h H5PartTypes.h H5Block.h H5BlockTypes.h
 
-clean:
+clean-recursive:
+	for d in ${SUBDIRS}; do ${MAKE} -C $$d clean; done
+
+clean: clean-recursive
 	rm -f *~ *.o *.a *.so
 
 distclean: clean

src/h5/H5.h

@@ -2,11 +2,13 @@
 #define __H5_H
 
 #include "h5_types.h"
+#include "h5_private.h"
 
 #include "attribs.h"
 #include "errorhandling.h"
 #include "openclose.h"
 #include "readwrite.h"
+#include "t_readwrite.h"
 #include "u_readwrite.h"
 
 #endif

src/h5/attribs.c

@@ -11,7 +11,6 @@
 #include "H5Part.h"
 #include "H5Block.h"
 #include "H5PartPrivate.h"
-#include "H5BlockPrivate.h"
 #include "H5PartErrors.h"
 #include "H5BlockErrors.h"
 #include "H5.h"

src/h5/h5_types.h

@@ -8,6 +8,24 @@
 #include <errno.h>
 #include <fcntl.h>
 
+#define H5_SUCCESS		0
+#define H5_ERR_NOMEM		-12
+#define H5_ERR_INVAL		-22
+#define H5_ERR_BADFD		-77
+
+#define H5_ERR_LAYOUT		-100
+#define H5_ERR_NOENT		-101
+
+#define H5_ERR_INIT		-200
+#define H5_ERR_NOENTRY		-201
+
+#define H5_ERR_MPI		-201
+#define H5_ERR_HDF5		-202
+
+#define H5_O_RDONLY		0x01
+#define H5_O_WRONLY		0x02
+#define H5_O_APPEND		0x03
+#define H5_O_RDWR		0x04
 
 #ifdef   WIN32
 typedef __int64			int64_t;
@@ -24,6 +42,8 @@ typedef double			h5_float64_t;
 typedef	h5_float64_t		h5_float_t;
 typedef	h5_float64_t		h5part_float64_t;
 
+typedef h5_err_t		h5_int32_t;
+
 struct h5_complex {
 	h5_float64_t		r,i;
 };
@@ -38,6 +58,8 @@ struct h5_vertex {  /* 32Byte */
 struct h5_edge { /* 16Bytes */
 	h5_id_t		id;
 	h5_id_t		parent_id;
+	h5_id_t		refined_on_evel; /* = 0 if not refined*/
+	h5_id_t		unused;	/* for right alignment */
 	h5_id_t		vertex_ids[2];
 };
 
@@ -45,17 +67,19 @@ struct h5_triangle { /*24Bytes*/
 	h5_id_t		id;
 	h5_id_t		parent_id;
 	h5_id_t		vertex_ids[3];
-	h5_id_t		unused;	/* for alignment */
+	h5_id_t		refined_on_level;
 };
 
 struct h5_tetrahedron { /* 24Bytes */
 	h5_id_t		id;
 	h5_id_t		parent_id;
+	h5_id_t		refined_on_evel;
+	h5_id_t		unused;	/* for right alignment */
 	h5_id_t		vertex_ids[4];
 };
 
 typedef struct h5_vertex	h5_vertex;
-typedef struct h5_edge		h5_edg;
+typedef struct h5_edge		h5_edge;
 typedef struct h5_triangle	h5_triangle;
 typedef struct h5_tetrahedron	h5_tetrahedron;
 
@@ -71,9 +95,85 @@ typedef h5_error_handler	h5part_error_handler;
 typedef unsigned long		MPI_Comm;
 #endif
 
-struct h5u_fdata;			/* unstructured data */ 
-struct h5b_fdata;			/* block structured data */
-struct h5t_fdata;			/* topology data */
+struct h5u_fdata {
+	hsize_t nparticles;		/* -> u.nparticles */
+	
+	h5part_int64_t viewstart; /* -1 if no view is available: A "view" looks */
+	h5part_int64_t viewend;   /* at a subset of the data. */
+  
+	/**
+	   the number of particles in each processor.
+	   With respect to the "VIEW", these numbers
+	   can be regarded as non-overlapping subsections
+	   of the particle array stored in the file.
+	   So they can be used to compute the offset of
+	   the view for each processor
+	*/
+	h5part_int64_t *pnparticles;
+
+	hid_t shape;
+	hid_t diskshape;
+	hid_t memshape;
+};
+
+struct H5BlockPartition {
+	h5part_int64_t	i_start;
+	h5part_int64_t	i_end;
+	h5part_int64_t	j_start;
+	h5part_int64_t	j_end;
+	h5part_int64_t	k_start;
+	h5part_int64_t	k_end;
+};
+
+struct h5b_fdata {
+	h5part_int64_t step_idx;
+	h5part_int64_t i_max;
+	h5part_int64_t j_max;
+	h5part_int64_t k_max;
+	struct H5BlockPartition *user_layout;
+	struct H5BlockPartition *write_layout;
+	int have_layout;
+
+	hid_t shape;
+	hid_t memshape;
+	hid_t diskshape;
+	hid_t blockgroup;
+	hid_t field_group_id;
+};
+
+struct h5t_fdata_level {
+};
+
+struct h5t_fdata {
+	h5_id_t		new_level;	/* idx of the first new level or -1 */
+	h5_id_t		cur_level;
+	h5_size_t	num_levels;
+
+	h5_size_t	*num_vertices;
+	h5_size_t	*num_tets;
+	h5_size_t	*num_tets_on_level;
+
+	h5_id_t		last_stored_vertex_id; 
+	h5_vertex	* vertices;
+
+	h5_id_t		last_stored_tet_id;
+	h5_tetrahedron	* tets;
+
+	/* HDF5 objects */
+
+	hid_t		topo_gid;	/* grp id of mesh in current level */
+	hid_t		coord_gid;
+	hid_t		vmesh_gid;
+
+	/* type ids' for compound types */
+	hid_t		float64_3tuple_tid;
+	hid_t		int32_2tuple_tid;
+	hid_t		int32_3tuple_tid;
+	hid_t		int32_4tuple_tid;
+	hid_t		vertex_tid;
+	hid_t		tet_tid;
+};
+
 
 /**
    \struct h5_file
@@ -109,6 +209,7 @@ struct h5_file {
 	h5_int64_t step_idx;		/* step index			*/
 	hid_t	step_gid;		/* HDF5 grp id of current step	*/
 
+	int	is_new_step;
 
 	/*
 	  BEGIN unstructured stuff,
@@ -143,57 +244,4 @@ struct h5_file {
 
 typedef struct h5_file h5_file;
 
-struct h5u_fdata {
-	hsize_t nparticles;		/* -> u.nparticles */
-	
-	h5part_int64_t viewstart; /* -1 if no view is available: A "view" looks */
-	h5part_int64_t viewend;   /* at a subset of the data. */
-  
-	/**
-	   the number of particles in each processor.
-	   With respect to the "VIEW", these numbers
-	   can be regarded as non-overlapping subsections
-	   of the particle array stored in the file.
-	   So they can be used to compute the offset of
-	   the view for each processor
-	*/
-	h5part_int64_t *pnparticles;
-
-	hid_t shape;
-	hid_t diskshape;
-	hid_t memshape;
-}
-
-struct h5b_fdata {
-	h5part_int64_t step_idx;
-	h5part_int64_t i_max;
-	h5part_int64_t j_max;
-	h5part_int64_t k_max;
-	struct H5BlockPartition *user_layout;
-	struct H5BlockPartition *write_layout;
-	int have_layout;
-
-	hid_t shape;
-	hid_t memshape;
-	hid_t diskshape;
-	hid_t blockgroup;
-	hid_t field_group_id;
-};
-
-struct h5t_fdata_level {
-	int		new_level;
-	h5_id_t		last_stored_vertex; 
-	h5_size_t	num_vertices;
-	h5_vertex	* vertices;
-	h5_id_t		last_stored_tet;
-	h5_size_t	num_tets;
-	h5_tetrahedron	* tets;
-};
-
-struct h5t_fdata {
-	h5_id_t		cur_level;
-	h5_size_t	num_levels;
-	hid_t		mesh_gid;
-	struct h5t_fdata_level levels[];
-};
 #endif

src/h5/openclose.c

@@ -12,7 +12,6 @@
 #include "H5Part.h"
 #include "H5Block.h"
 #include "H5PartPrivate.h"
-#include "H5BlockPrivate.h"
 #include "H5PartErrors.h"
 #include "H5BlockErrors.h"
 #include "H5.h"
@@ -41,11 +40,11 @@ H5_check_filehandle (
 	) {
 
 	if ( f == NULL )
-		return HANDLE_H5PART_BADFD_ERR;
+		return HANDLE_H5_BADFD_ERR;
 	if ( f->file == 0 )
-		return HANDLE_H5PART_BADFD_ERR;
+		return HANDLE_H5_BADFD_ERR;
 	if ( f->block == NULL )
-		return HANDLE_H5PART_BADFD_ERR;
+		return HANDLE_H5_BADFD_ERR;
 	return H5PART_SUCCESS;
 }
 
@@ -96,8 +95,7 @@ _h5u_open_file (
 	f->pnparticles =
 		(h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
 	if (f->pnparticles == NULL) {
-		HANDLE_H5PART_NOMEM_ERR;
-		goto error_cleanup;
+		return HANDLE_H5_NOMEM_ERR;
 	}
 	return H5_SUCCESS;
 }
@@ -121,23 +119,23 @@ _h5b_open_file (
 	herr = H5_check_filehandle ( f );
 	if ( herr == H5_SUCCESS ) return H5_SUCCESS;
 
-	if ( (f == 0) || (f->file == 0) ) return HANDLE_H5PART_BADFD_ERR;
+	if ( (f == 0) || (f->file == 0) ) return HANDLE_H5_BADFD_ERR;
 
 	f->block = (struct h5b_fdata*) malloc( sizeof (*f->block) );
 	if ( f->block == NULL ) {
-		return HANDLE_H5PART_NOMEM_ERR;
+		return HANDLE_H5_NOMEM_ERR;
 	}
 	b = f->block;
 	memset ( b, 0, sizeof (*b) );
 	b->user_layout = (struct H5BlockPartition*) malloc (
 		f->nprocs * sizeof (b->user_layout[0]) );
 	if ( b->user_layout == NULL ) {
-		return HANDLE_H5PART_NOMEM_ERR;
+		return HANDLE_H5_NOMEM_ERR;
 	}
 	b->write_layout = (struct H5BlockPartition*) malloc (
 		f->nprocs * sizeof (b->write_layout[0]) );
 	if ( b->write_layout == NULL ) {
-		return HANDLE_H5PART_NOMEM_ERR;
+		return HANDLE_H5_NOMEM_ERR;
 	}
 	b->step_idx = -1;
 	b->blockgroup = -1;
@@ -161,7 +159,7 @@ H5_open_file (
 	h5part_int64_t rc = H5PART_SUCCESS;
 
 	if ( _init() < 0 ) {
-		HANDLE_H5PART_INIT_ERR;
+		HANDLE_H5_INIT_ERR;
 		return NULL;
 	}
 	_h5part_errno = H5PART_SUCCESS;
@@ -169,14 +167,14 @@ H5_open_file (
 
 	f = (h5_file*) malloc( sizeof (h5_file) );
 	if( f == NULL ) {
-		HANDLE_H5PART_NOMEM_ERR;
+		HANDLE_H5_NOMEM_ERR;
 		goto error_cleanup;
 	}
 	memset (f, 0, sizeof (h5_file));
 
 	f->prefix_step_name = strdup ( H5PART_GROUPNAME_STEP );
 	if( f->prefix_step_name == NULL ) {
-		HANDLE_H5PART_NOMEM_ERR;
+		HANDLE_H5_NOMEM_ERR;
 		goto error_cleanup;
 	}
 	f->width_step_idx = 0;
@@ -245,7 +243,7 @@ H5_open_file (
 				     f->access_prop);
 		f->empty = 1;
 	}
-	else if ( flags == H5_O_APPEND || H5_O_RDWR ) {
+	else if ( flags == H5_O_APPEND || H5_O_RDWR ) {
 		int fd = open (filename, O_RDONLY, 0);
 		if ( (fd == -1) && (errno == ENOENT) ) {
 			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
@@ -259,7 +257,7 @@ H5_open_file (
 		}
 	}
 	else {
-		HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( flags );
+		HANDLE_H5_FILE_ACCESS_TYPE_ERR ( flags );
 		goto error_cleanup;
 	}
 
@@ -327,20 +325,21 @@ static h5part_int64_t
 _h5u_close_file (
 	h5_file *f		/*!< IN: file handle */
 	) {
+	herr_t herr;
 	_h5part_errno = H5_SUCCESS;
 	if( f->shape > 0 ) {
-		r = H5Sclose( f->shape );
-		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
+		herr = H5Sclose( f->shape );
+		if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR;
 		f->shape = 0;
 	}
 	if( f->diskshape != H5S_ALL ) {
-		r = H5Sclose( f->diskshape );
-		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
+		herr = H5Sclose( f->diskshape );
+		if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR;
 		f->diskshape = 0;
 	}
 	if( f->memshape != H5S_ALL ) {
-		r = H5Sclose( f->memshape );
-		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
+		herr = H5Sclose( f->memshape );
+		if ( herr < 0 ) HANDLE_H5S_CLOSE_ERR;
 		f->memshape = 0;
 	}
 	if( f->pnparticles ) {
@@ -393,30 +392,6 @@ _h5b_close_file (
 	return H5PART_SUCCESS;
 }
 
-/*!
-  \ingroup h5_private
-
-  \internal
-
-  De-initialize topological internal structure.  Open HDF5 objects are 
-  closed and allocated memory freed.
-
-  \return	H5_SUCCESS or error code
-*/
-static h5part_int64_t
-_h5t_close_file (
-	h5_file *fh		/*!< IN: file handle */
-	) {
-
-	h5_err_t herr = H5_SUCCESS;
-	struct h5t_fdata *t = fh->t;
-
-	if ( t->levels ) {
-		free ( levels );
-	}
-	return herr;
-}
-
 h5part_int64_t
 H5_close_file (
 	h5_file *f
@@ -477,7 +452,7 @@ H5_define_stepname (
 	) {
 	f->prefix_step_name = strdup ( name );
 	if( f->prefix_step_name == NULL ) {
-		return HANDLE_H5PART_NOMEM_ERR;
+		return HANDLE_H5_NOMEM_ERR;
 	}
 	f->width_step_idx = (int)width;
 	

src/h5/openclose.h

@@ -5,8 +5,7 @@ h5_file*
 H5_open_file (
 	const char *filename,
 	unsigned flags,
-	MPI_Comm comm,
-	int f_parallel
+	MPI_Comm comm
 	);
 
 h5part_int64_t
@@ -14,14 +13,6 @@ H5_check_filehandle (
 	const h5_file *f
 	);
 
-h5_file*
-H5_open_file (
-	const char *filename,
-	unsigned flags,
-	MPI_Comm comm,
-	int f_parallel
-	);
-
 h5part_int64_t
 H5_close_file (
 	h5_file *f

src/h5/readwrite.c

@@ -11,7 +11,6 @@
 #include "H5Part.h"
 #include "H5Block.h"
 #include "H5PartPrivate.h"
-#include "H5BlockPrivate.h"
 #include "H5PartErrors.h"
 #include "H5BlockErrors.h"
 #include "H5.h"
@@ -180,7 +179,7 @@ H5_get_object_name (
 			    &data );
 	if ( herr < 0 ) return (h5part_int64_t)herr;
 
-	if ( herr == 0 ) HANDLE_H5PART_NOENTRY_ERR( group_name,
+	if ( herr == 0 ) HANDLE_H5_NOENTRY_ERR( group_name,
 						    type, idx );
 
 	return H5PART_SUCCESS;
@@ -210,7 +209,7 @@ _open_step (
 	H5_print_info (
 		"Proc[%d]: Open step #%lld for file %lld",
 		f->myproc,
-		(long long)step,
+		(long long)f->step_idx,
 		(long long)(size_t) f );
 	f->is_new_step = 0;
 	f->step_gid = H5Gopen ( f->file, f->step_name ); 
@@ -222,14 +221,16 @@ _open_step (
 
 static h5_err_t
 _init_step (
+	h5_file * f
+	) {
 	h5_err_t h5err = _h5t_init_step ( f );
 	if ( h5err < 0 ) return h5err;
 
 	return H5_SUCCESS;
 }	
 
-static h5_err_t
-_close_step (
+h5_err_t
+_h5_close_step (
 	h5_file * f
 	) {
 
@@ -265,7 +266,7 @@ _set_step (
 		herr = _open_step ( f );
 		if ( herr < 0 ) return herr;
 	} else if ( (f->mode == H5_O_WRONLY)  || (f->mode == H5_O_APPEND) ) {
-		if ( herr > 0 ) return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
+		if ( herr > 0 ) return HANDLE_H5_STEP_EXISTS_ERR ( step_idx );
  		herr = _create_step ( f );
 		if ( herr < 0 ) return herr;
 	} else if ( (f->mode == H5_O_RDWR) && (herr < 0) ) {
@@ -278,20 +279,20 @@ _set_step (
 	return H5_SUCCESS;
 }
 
-h5p_int64_t
+h5_int64_t
 H5_set_step (
 	h5_file *f,			/*!< [in]  Handle to open file */
 	const h5_int64_t step_idx	/*!< [in]  Step to set. */
 	) {
 
-	herr = _close_step ( f );
-	if ( herr < 0 ) return herr;
+	h5_err_t h5err = _h5_close_step ( f );
+	if ( h5err < 0 ) return h5err;
 
-	herr = _set_step ( f );
-	if ( herr < 0 ) return herr;
+	h5err = _set_step ( f, step_idx );
+	if ( h5err < 0 ) return h5err;
 
-	herr = _init_step ( f );
-	if ( herr < 0 ) return herr;
+	h5err = _init_step ( f );
+	if ( h5err < 0 ) return h5err;
 
 	return H5_SUCCESS;
 }

src/h5/t_openclose.c

@@ -12,10 +12,10 @@
 #include "H5Part.h"
 #include "H5Block.h"
 #include "H5PartPrivate.h"
-#include "H5BlockPrivate.h"
 #include "H5PartErrors.h"
 #include "H5BlockErrors.h"
 #include "H5.h"
+#include "h5/h5_types.h"
 
 extern h5part_error_handler	_err_handler;
 extern h5part_int64_t		_h5part_errno;
@@ -26,7 +26,9 @@ static h5_err_t
 _create_array_types (
 	h5_file * f
 	) {
+	struct h5t_fdata *t = &f->t;
 	hsize_t dims[1] = { 3 };
+
 	t->float64_3tuple_tid = H5Tarray_create ( H5T_NATIVE_DOUBLE, 1, dims,NULL);
 	dims[0] = 2;
 	t->int32_2tuple_tid = H5Tarray_create ( H5T_NATIVE_INT32, 1, dims, NULL );
@@ -42,6 +44,8 @@ static h5_err_t
 _create_vertex_type (
 	h5_file * f
 	) {
+	struct h5t_fdata *t = &f->t;
+
 	t->vertex_tid = H5Tcreate ( H5T_COMPOUND, sizeof(struct h5_vertex) );
 	H5Tinsert (
 		t->vertex_tid,
@@ -65,31 +69,35 @@ static h5_err_t
 _create_tet_type (
 	h5_file * f
 	) {
+	struct h5t_fdata *t = &f->t;
+
 	t->tet_tid = H5Tcreate ( H5T_COMPOUND, sizeof(struct h5_tetrahedron) );
 	H5Tinsert (
 		t->tet_tid,
 		"id",
-		HOFFSET(struct h5_tet, id),
+		HOFFSET(struct h5_tetrahedron, id),
 		H5T_NATIVE_INT32 );
 	H5Tinsert (
 		t->tet_tid,
 		"parent_id",
-		HOFFSET(struct h5_tet, parent_id),
+		HOFFSET(struct h5_tetrahedron, parent_id),
 		H5T_NATIVE_INT32 );
 	H5Tinsert (
 		t->tet_tid,
 		"vertex_ids",
-		HOFFSET(struct h5_tet, vertex_ids),
+		HOFFSET(struct h5_tetrahedron, vertex_ids),
 		t->int32_4tuple_tid );
 
 	return H5_SUCCESS;
+}
 
 /*!
   \ingroup h5_private
 
   \internal
 
-  Initialize H5Block internal structure.
+  Initialize topo internal structure. The structure has already be initialized
+  with zero's.
 
   \return	H5_SUCCESS or error code
 */
@@ -98,15 +106,49 @@ _h5t_open_file (
 	h5_file * f			/*!< IN: file handle */
 	) {
 	h5_err_t h5err = H5_SUCCESS;;
-	struct h5t_fdata * t = &fh->t; 
+	struct h5t_fdata * t = &f->t; 
 
 	t->num_levels = -1;
-	levels = NULL;
-
-	if (h5err = _create_array_types ( f )) < 0 ) return herr;
-	if (h5err = _create_vertex_type ( f )) < 0 ) return herr;
-	if (h5err = _create_tet_type ( f )) < 0 ) return herr;
 
+	if (( h5err = _create_array_types ( f )) < 0 ) return h5err;
+	if (( h5err = _create_vertex_type ( f )) < 0 ) return h5err;
+	if (( h5err = _create_tet_type ( f )) < 0 ) return h5err;
 
 	return H5_SUCCESS;
 }
+
+/*!
+  \ingroup h5_private
+
+  \internal
+
+  De-initialize topological internal structure.  Open HDF5 objects are 
+  closed and allocated memory freed.
+
+  \return	H5_SUCCESS or error code
+*/
+static h5part_int64_t
+_h5t_close_file (
+	h5_file *fh		/*!< IN: file handle */
+	) {
+
+	h5_err_t herr = H5_SUCCESS;
+	struct h5t_fdata *t = &fh->t;
+
+	if ( t->num_vertices ) {
+		free ( t->num_vertices );
+	}
+	if ( t->num_tets ) {
+		free ( t->num_tets );
+	}
+	if ( t->num_tets_on_level ) {
+		free ( t->num_tets_on_level );
+	}
+	if ( t->vertices ) {
+		free ( t->vertices );
+	}
+	if ( t->tets ) {
+		free ( t->tets );
+	}
+	return herr;
+}

src/h5/t_readwrite.c

@@ -11,7 +11,6 @@
 #include "H5Part.h"
 #include "H5Block.h"
 #include "H5PartPrivate.h"
-#include "H5BlockPrivate.h"
 #include "H5PartErrors.h"
 #include "H5BlockErrors.h"
 #include "H5.h"
@@ -23,27 +22,105 @@ h5_err_t
 _h5t_init_step (
 	h5_file * f
 	) {
-	memset ( f->t, 0, sizeof(f->t) );
+	memset ( &f->t, 0, sizeof(f->t) );
 
-	f->t.mesh_gid = -1;
+	f->t.topo_gid = -1;
 	f->t.num_levels = f->is_new_step ? 0 : -1;
 	f->t.cur_level = -1;
 
 	return H5_SUCCESS;
 }
 
+static hid_t
+_open_group (
+	h5_file * f,
+	hid_t parent_gid,
+	const char * const grpname
+	) {
+	hid_t gid;
+	herr_t herr = H5Gget_objinfo(
+		parent_gid, grpname, 1, NULL );
+	if ( herr >= 0 ) {
+		gid = H5Gopen ( parent_gid, grpname );
+	} else {
+		gid = H5Gcreate ( parent_gid, grpname, 0 );
+	}
+	if ( gid < 0 ) 
+		return HANDLE_H5G_OPEN_ERR ( H5T_CONTAINER_GRPNAME );
+
+	return H5_SUCCESS;
+}
+
 static h5_err_t
 _open_topo_group (
 	h5_file * f
 	) {
-	herr_t herr = H5Gget_objinfo( f->step_gid, "Topo", 1, NULL );
-	if ( herr => 0 ) {
-		f->t.mesh_gid = H5Gopen ( f->step_gid, "Topo" );
-	} else {
-		f->t.mesh_gid = H5Gcreate ( f->step_gid, "Topo", 0 );
+	return _open_group ( f, f->step_gid, H5T_CONTAINER_GRPNAME );
+}
+
+static h5_err_t
+_open_coord_group (
+	h5_file * f
+	) {
+	if ( f->t.topo_gid < 0 ) {
+		h5_err_t h5err = _open_topo_group ( f );
+		if ( h5err < 0 ) return h5err;
 	}
-	if ( f->t.mesh_gid < 0 ) 
-		return HANDLE_H5G_OPEN_ERR ( "Topo" );
+	return _open_group ( f, f->t.topo_gid, H5T_COORD_GRPNAME );
+}
+
+static h5_err_t
+_open_vmesh_group (
+	h5_file * f
+	) {
+	if ( f->t.topo_gid < 0 ) {
+		h5_err_t h5err = _open_topo_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+	return _open_group ( f, f->t.topo_gid, H5T_VMESH_GRPNAME );
+}
+
+static h5_err_t
+_write_obj (
+	const hid_t	gid,
+	const hsize_t  current_dims,
+	const hsize_t  max_dims,
+	const hid_t    tid,
+	const void * const object,
+	const char * const dsname
+	) {
+	hsize_t dims[1] = { current_dims };
+	hsize_t maxdims[1] = { max_dims };
+
+	hid_t sid = H5Screate_simple (
+		1,
+		dims,
+		maxdims
+		);
+	if ( sid < 0 ) return -1;
+
+	hid_t did = H5Dcreate (
+		gid,
+		dsname,
+		tid,
+		sid,
+		H5P_DEFAULT);
+	if ( did < 0 ) return -1;
+
+	herr_t herr = H5Dwrite (
+		did,
+		tid,
+		H5S_ALL, H5S_ALL, H5P_DEFAULT,
+		object );
+	if ( herr < 0 ) return -1;
+	
+	herr = H5Dclose ( did );
+	if ( herr < 0 ) return -1;
+
+	herr = H5Sclose ( sid );
+	if ( herr < 0 ) return -1;
+
+	return H5_SUCCESS;
 }
 
 /*
@@ -54,41 +131,23 @@ static h5_err_t
 _write_vertices (
 	h5_file * f
 	) {
-	h5t_fdata t &f->t;
-	herr_t herr;
+	struct h5t_fdata *t = &f->t;
+	h5_err_t h5err;
 
-	if ( t->coord3d_gid < 0 ) {
-		h5err = _open_coord3d_group ( f );
+	if ( t->coord_gid < 0 ) {
+		h5err = _open_coord_group ( f );
 		if ( h5err < 0 ) return h5err;
 	}
 
-	if ( t->num_levels == 0 ) return 0;
-	if ( t->num_levels < 0 ) return -1; 
-
-	hsize_t current_dims[1];
-	current_dims[0] = t->levels[t->num_levels-1].num_vertices;
-
-	t->coord3d_sid = H5Screate_simple (
-		1,
-		current_dims,
-		 H5S_UNLIMITED
+	hsize_t maxdim = H5S_UNLIMITED;
+	h5err = _write_obj (
+		t->coord_gid,
+		t->vertex_tid,
+		t->num_vertices[t->num_levels-1],
+		maxdim,
+		(void*)t->vertices,
+		H5T_COORD3D_DSNAME
 		);
-	if ( t->coord3d_sid < 0 ) return -1;
-
-	t->coord3d_did = H5Dcreate (
-		coord3d_gid,
-		"COORD3D",
-		t->vertex_tid,
-		t->coord3d_sid,
-		H5P_DEFAULT);
-	if ( t->coord3d_did < 0 ) return -1;
-
-	herr = H5Dwrite (
-		coord3d,
-		t->vertex_tid,
-		H5S_ALL, H5S_ALL, H5P_DEFAULT,
-		t->vertices );
-	if ( herr < 0 ) return -1;
 
 	return H5_SUCCESS;
 }
@@ -97,9 +156,26 @@ static h5_err_t
 _write_tets (
 	h5_file * f
 	) {
-	return -1;
-}
+	struct h5t_fdata *t = &f->t;
+	h5_err_t h5err;
 
+	if ( t->vmesh_gid < 0 ) {
+		h5err = _open_vmesh_group ( f );
+		if ( h5err < 0 ) return h5err;
+	}
+
+	hsize_t maxdim = H5S_UNLIMITED;
+	herr_t herr = _write_obj (
+		t->vmesh_gid,
+		t->tet_tid,
+		t->num_tets[t->num_levels-1],
+		maxdim,
+		(void*)t->tets,
+		H5T_TETMESH_DSNAME
+		);
+
+	return H5_SUCCESS;
+}
 
 /*
   determine new levels
@@ -114,6 +190,10 @@ _write_data (
 	) {
 	struct h5t_fdata *t = &f->t;
 	h5_err_t h5err;
+
+	if ( t->num_levels == 0 ) return 0;
+	if ( t->num_levels < 0 ) return -1; 
+
 	if ( t->topo_gid < 0 ) {
 		h5err = _open_topo_group ( f );
 		if ( h5err < 0 ) return h5err;
@@ -156,10 +236,10 @@ _h5t_close_step (
 	h5_err_t h5err = _write_data ( f );
 	if ( h5err < 0 ) return h5err;
 
-	h5_err_t h5err = _close_hdf5_objs ( f );
+	h5err = _close_hdf5_objs ( f );
 	if ( h5err < 0 ) return h5err;
 
-	h5_err_t h5err = _release_memory ( f );
+	h5err = _release_memory ( f );
 	if ( h5err < 0 ) return h5err;
 
 	return H5_SUCCESS;

src/h5/u_readwrite.c

@@ -403,7 +403,7 @@ H5U_set_view (
 	  end==-1 to mean end of file
 	*/
 	total = (hsize_t) H5U_get_num_elems ( f );
-	if ( total < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total );
+	if ( total < 0 ) return HANDLE_H5_GET_NUM_PARTICLES_ERR ( total );
 
 	if ( start == -1 ) start = 0;
 	if ( end == -1 )   end = total;
@@ -471,7 +471,7 @@ H5U_get_view (
 	else {
 		viewend = H5U_get_num_elems ( f );
 		if ( viewend < 0 )
-			return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( viewend );
+			return HANDLE_H5_GET_NUM_PARTICLES_ERR ( viewend );
 	}
 
 	if ( start ) *start = viewstart;
@@ -485,7 +485,7 @@ H5U_set_canonical_view (
 	h5_file *f
 	) {
 	h5part_int64_t herr = H5U_reset_view ( f );
-	if ( herr < 0 ) return HANDLE_H5PART_SET_VIEW_ERR( herr, -1, -1 );
+	if ( herr < 0 ) return HANDLE_H5_SET_VIEW_ERR( herr, -1, -1 );
 
 #ifdef PARALLEL_IO
 	h5part_int64_t start = 0;
@@ -494,7 +494,7 @@ H5U_set_canonical_view (
 	int i = 0;
 	
 	n = H5U_get_num_elems ( f );
-	if ( n < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( n );
+	if ( n < 0 ) return HANDLE_H5_GET_NUM_PARTICLES_ERR ( n );
 	/* 
 	   now lets query the attributes for this group to see if there
 	   is a 'pnparticles' group that contains the offsets for the
@@ -518,7 +518,7 @@ H5U_set_canonical_view (
 	}
 	end = start + f->pnparticles[f->myproc] - 1;
 	herr = H5U_set_view ( f, start, end );
-	if ( herr < 0 ) return HANDLE_H5PART_SET_VIEW_ERR ( herr, start, end );
+	if ( herr < 0 ) return HANDLE_H5_SET_VIEW_ERR ( herr, start, end );
 
 #endif
 

test/H5BlockTestAttributes.c

@@ -31,7 +31,7 @@ _write_data (
 	h5part_int64_t j_dims = layout->j_end - layout->j_start + 1;
 	h5part_int64_t k_dims = layout->k_end - layout->k_start + 1;
 
-	printf ( "Writing Step #%lld\n", (long long)f->timestep );
+	printf ( "Writing Step #%lld\n", (long long)f->step_idx );
 
 	data = malloc ( i_dims * j_dims * k_dims * sizeof ( *data ) );
 	for ( i = 0; i < i_dims; i++ ) {
@@ -168,7 +168,7 @@ _read_data (
 	h5part_int64_t j_dims = layout->j_end - layout->j_start + 1;
 	h5part_int64_t k_dims = layout->k_end - layout->k_start + 1;
 
-	printf ( "Reading Step #%lld\n", (long long)f->timestep );
+	printf ( "Reading Step #%lld\n", (long long)f->step_idx );
 
 	data = malloc ( i_dims * j_dims * k_dims * sizeof ( *data ) );