src/H5.c

@@ -36,11 +36,11 @@
   \defgroup h5_c_api_general
 */
 
-
 #include <stdarg.h>
 #include <hdf5.h>
 #include "h5_core/h5_core.h"
 #include "h5_core/h5_core_private.h"
+#include "H5.h"
 
 /******	General routines *****************************************************/
 
@@ -52,9 +52,6 @@
 
   \return File handle.
   \return NULL on error.
-
-  \note
-  File is always opened in read/writer mode!
 */
 h5_file_t *
 H5OpenFile (

src/H5.h

@@ -16,15 +16,18 @@
 #ifndef __H5_H
 #define __H5_H
 
+#include "H5_inquiry.h"
+
 h5_file_t *
 H5OpenFile (
 	const char * filename,
+	const h5_int32_t oflag,
 	const MPI_Comm comm
 	);
 
 h5_err_t
 H5CloseFile (
-	h5_file_t * fh
+	h5_file_t * f
 	);
 
 h5_err_t

src/H5Block.c

@@ -107,11 +107,12 @@ _normalize_partition (
   \return	H5_SUCCESS or error code
 */
 #ifdef PARALLEL_IO
+jfsdjk fjksdhf jkdsfjksdhfjkds kjf
 static h5_err_t
 _allgather (
-	const h5_file *f		/*!< IN: file handle */
+	h5_file_t * const f		/*!< IN: file handle */
 	) {
-	struct h5b_partition *partition = &f->block->user_layout[f->myproc];
+	struct h5b_partition *partition = &f->b->user_layout[f->myproc];
 	struct h5b_partition *layout = f->b->user_layout;
 
 	MPI_Datatype    partition_m;
@@ -122,6 +123,7 @@ _allgather (
         mpi_err = MPI_Type_commit ( &partition_m );
 	if ( mpi_err != MPI_SUCCESS ) return H5_ERR_MPI;
 	TRY ( _h5_mpi_allgather (
+		      f,
 		      partition,
 		      1,
 		      partition_m,

src/H5Fed.h

@@ -55,11 +55,6 @@ H5FedGetLevel (
 	h5_file_t * f
 	);
 
-h5_size_t
-H5GetNumNodes (
-	h5_file_t * f
-	);
-
 h5_size_t
 H5FedGetNumVertices (
 	h5_file_t * f

src/H5Fed_store.c

@@ -57,24 +57,14 @@ H5FedAddLevel (
 }
 
 h5_err_t
-H5FedAddNumVertices (
-	h5_file_t * f,
+H5FedBeginStoreVertices (
+	h5_file_t * const f,
 	const h5_size_t num
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_add_num_vertices ( f, num );
+	return h5t_begin_store_vertices ( f, num );
 }
 
-h5_err_t
-H5FedAddNumElements (
-	h5_file_t * f,
-	const h5_size_t num
-	) {
-	SET_FNAME ( f, __func__ );
-	return h5t_add_num_elems ( f, num );
-}
-
-
 /*!
   \ingroup h5fed_c_api
 
@@ -101,6 +91,22 @@ H5FedStoreVertex (
 	return h5t_store_vertex ( f, vertex_id, P );
 }
 
+h5_err_t
+H5FedEndStoreVertices (
+	h5_file_t * const f
+	) {
+	return h5t_end_store_vertices ( f );
+}
+
+h5_err_t
+H5FedBeginStoreElements (
+	h5_file_t * f,
+	const h5_size_t num
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_begin_store_elems ( f, num );
+}
+
 /*!
   \ingroup h5fed_c_api
 
@@ -131,12 +137,20 @@ H5FedStoreElement (
 }
 
 h5_err_t
-H5FedRefineNumElements (
+H5FedEndStoreElements (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return h5t_end_store_elems ( f );
+}
+
+h5_err_t
+H5FedBeginRefineElements (
 	h5_file_t * const f,
 	const h5_size_t num
 	) {
 	SET_FNAME ( f, __func__ );
-	return h5t_refine_num_elems ( f, num );
+	return h5t_begin_refine_elems ( f, num );
 }
 
 h5_id_t
@@ -147,3 +161,11 @@ H5FedRefineElement (
 	SET_FNAME ( f, __func__ );
 	return h5t_refine_elem ( f, local_eid );
 }
+
+h5_err_t
+H5FedEndRefineElements (
+	h5_file_t * const f
+	) {
+	SET_FNAME ( f, __func__ );
+	return H5_SUCCESS;
+}

src/H5Fed_store.h

@@ -27,37 +27,48 @@ H5FedAddMesh (
 
 h5_id_t
 H5FedAddLevel (
-	h5_file_t * f
+	h5_file_t * const f
 	);
 
 h5_err_t
-H5FedAddNumVertices (
-	h5_file_t * f,
-	const h5_size_t num
-	);
-
-h5_err_t
-H5FedAddNumElements (
-	h5_file_t * f,
+H5FedBeginStoreVertices (
+	h5_file_t * const f,
 	const h5_size_t num
 	);
 
 h5_id_t
 H5FedStoreVertex (
-	h5_file_t * f,
+	h5_file_t * const f,
 	const h5_id_t id,
 	const h5_float64_t P[3]
 	);
 
+h5_err_t
+H5FedEndStoreVertices (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedBeginStoreElements (
+	h5_file_t * const f,
+	const h5_size_t num
+	);
+
+
 h5_id_t
 H5FedStoreElement (
-	h5_file_t * f,
+	h5_file_t * const f,
 	const h5_id_t local_vids[]
 	);
 
 h5_err_t
-H5FedRefineNumElements (
-	h5_file_t * f,
+H5FedEndStoreElements (
+	h5_file_t * const f
+	);
+
+h5_err_t
+H5FedBeginRefineElements (
+	h5_file_t * const f,
 	const h5_size_t num
 	);
 
@@ -67,4 +78,9 @@ H5FedRefineElement (
 	const h5_id_t local_eid
 	);
 
+h5_err_t
+H5FedEndRefineElements (
+	h5_file_t * const f
+	);
+
 #endif

src/H5Part.c

@@ -613,59 +613,6 @@ H5PartSetStep (
 
 /********************** query file structure *********************************/
 
-
-/*!
-  \ingroup h5part_c_api_read
-
-  Query whether a particular step already exists in the file
-  \c f.
-
-  It works for both reading and writing of files
-
-  \return      true or false
-*/
-h5_int64_t
-H5PartHasStep (
-	h5_file_t *f,		/*!< [in]  Handle to open file */
-	h5_int64_t step	/*!< [in]  Step number to query */
-	) {
-  
-	SET_FNAME ( f, __func__ );
-
-	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
-		return h5_get_errno ( f );
-
-	return h5_has_step( f, step );
-}
-
-/*!
-  \ingroup h5part_c_api_read
-
-  Get the number of time-steps that are currently stored in the file
-  \c f.
-
-  It works for both reading and writing of files, but is probably
-  only typically used when you are reading.
-
-  \return	number of time-steps or error code
-*/
-h5_int64_t
-H5PartGetNumSteps (
-	h5_file_t *f			/*!< [in]  Handle to open file */
-	) {
-
-	SET_FNAME ( f, __func__ );
-
-	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
-		return h5_get_errno ( f );
-
-	return hdf5_get_num_objects_matching_pattern (
-		f->file,
-		"/",
-		H5G_UNKNOWN,
-		f->prefix_step_name );
-}
-
 /*!
   \ingroup h5part_c_api_read
 
@@ -680,9 +627,7 @@ H5PartGetNumDatasets (
 	) {
 
 	SET_FNAME ( f, __func__ );
-
-	if ( h5_check_filehandle ( f ) != H5_SUCCESS )
-		return h5_get_errno ( f );
+	CHECK_FILEHANDLE ( f );
 
 	return hdf5_get_num_objects ( f->file, f->step_name, H5G_DATASET );
 }
@@ -960,7 +905,6 @@ H5PartReadDataInt64 (
 	) {
 
 	SET_FNAME ( f, __func__ );
-
 	CHECK_FILEHANDLE( f );
 
 	return h5u_read_elems ( f, name, array, H5T_NATIVE_INT64 );

src/H5Part.h

@@ -19,16 +19,17 @@
 #define __H5Part_H
 
 #include <hdf5.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 #include "h5_core/h5_core.h"
 #include "H5.h"
 #ifdef PARALLEL_IO
 #include <mpi.h>
 #endif
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 // #define H5PART_SUCCESS		H5_SUCCESS
 #define H5PART_ERR_NOMEM	H5_ERR_NOMEM
 #define H5PART_ERR_INVAL	H5_ERR_INVAL
@@ -108,17 +109,6 @@ H5PartSetStep (
 	const h5_int64_t step
 	);
 
-h5_int64_t
-H5PartHasStep (
-	h5_file_t *f,
-	const h5_int64_t step
-	);
-
-h5_int64_t
-H5PartGetNumSteps (
-	h5_file_t *f
-	);
-
 h5_int64_t
 H5PartGetNumDatasets (
 	h5_file_t *f

src/H5_inquiry.c

@@ -19,39 +19,55 @@
 
 #include <stdarg.h>
 #include <hdf5.h>
-#include "h5/h5.h"
-#include "h5/h5_private.h"
-#include "H5Fed.h"
+#include "h5_core/h5_core.h"
+#include "h5_core/h5_core_private.h"
+#include "H5.h"
 
 /*!
   \ingroup h5_inquiry
 
   Get the number of compute nodes.
 
+  \param[in]	f	File handle.
+
   \return Number of compute notes.
   \return \c -1 on error.
  */
 h5_size_t
 H5GetNumNodes (
-	h5_file_t * f			/*!< file handle		*/
+	h5_file_t * const f
 	) {
-	SET_FNAME ( __func__ );
-	return (h5_size_t)fh->nprocs;
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
+	return (h5_size_t)f->nprocs;
 }
 
-/*`
-  \ingroup h5_inquiry
+/*!
+  \ingroup h5part_c_api_read
 
-  Get the number of steps that are currently stored in the file.
+  Get the number of time-steps that are currently stored in the file
+  \c f.
 
-  \return	number of steps or error code
+  It works for both reading and writing of files, but is probably
+  only typically used when you are reading.
+
+  \param[in]	f	File handle.
+
+  \return	number of time-steps or error code
 */
-h5_id_t
+h5_size_t
 H5GetNumSteps (
-	h5_file_t * fh			/*!< file handle		*/
+	h5_file_t * const f
 	) {
-	SET_FNAME ( __func__ );
-	return h5_get_num_steps( fh );
+
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
+
+	return hdf5_get_num_objects_matching_pattern (
+		f->file,
+		"/",
+		H5G_UNKNOWN,
+		f->prefix_step_name );
 }
 
 /*!
@@ -59,17 +75,21 @@ H5GetNumSteps (
 
   Query whether a particular step already exists in the file.
 
+  \param[in]	f	File handle.
+  \param[in]	stepno	Step number to query for existence
+
   \return      true or false
 */
 h5_err_t
 H5HasStep (
-	h5_file_t *f,		/*!< [in]  Handle to open file */
-	h5part_int64_t step	/*!< [in]  Step number to query */
+	h5_file_t *f,
+	h5_id_t stepno
 	) {
   
-	SET_FNAME ( __func__ );
+	SET_FNAME ( f, __func__ );
+	CHECK_FILEHANDLE ( f );
 
-	return h5_has_step( f, step );
+	return h5_has_step( f, stepno );
 }
 
 

src/Makefile.am

@@ -43,11 +43,13 @@ EXTRA_LIBRARIES = libH5.a
 
 # Header files that I wish to install in $(prefix)/include
 include_HEADERS = \
-	H5Part.h \
+	H5.h \
 	H5Block.h \
 	H5Fed.h \
 	H5Fed_boundaries.h \
-	H5Fed_map.h
+	H5Fed_map.h \
+	H5Fed_store.h \
+	H5Part.h
 
 # Listing of all possible headers that I may include
 EXTRA_HEADERS =
@@ -55,6 +57,7 @@ EXTRA_HEADERS =
 # Listing of sources
 libH5_a_SOURCES = \
 	H5.c \
+	H5_inquiry.c \
 	H5Block.c \
 	H5Fed.c \
 	H5Fed_adjacency.c \