src/h5/openclose.c

* adaption to renamed members in "struct h5_file"
* several changes and additions for H5Fed

src/h5/openclose.c

@@ -76,23 +76,50 @@ _init ( void ) {
 }
 
 /*!
-  \ingroup h5block_private
+  \ingroup h5_private
+
+  \internal
+
+  Initialize unstructured data internal data structure.
+
+  \return	H5_SUCCESS or error code
+*/
+static h5part_int64_t
+_h5u_open_file (
+	h5_file *f			/*!< IN: file handle */
+	) {
+ 	f->shape = 0;
+	f->diskshape = H5S_ALL;
+	f->memshape = H5S_ALL;
+	f->viewstart = -1;
+	f->viewend = -1;
+	f->pnparticles =
+		(h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
+	if (f->pnparticles == NULL) {
+		HANDLE_H5PART_NOMEM_ERR;
+		goto error_cleanup;
+	}
+	return H5_SUCCESS;
+}
+
+/*!
+  \ingroup h5_private
 
   \internal
 
   Initialize H5Block internal structure.
 
-  \return	H5PART_SUCCESS or error code
+  \return	H5_SUCCESS or error code
 */
 static h5part_int64_t
-_init_block (
+_h5b_open_file (
 	h5_file *f			/*!< IN: file handle */
 	) {
 	h5part_int64_t herr;
 	struct h5b_fdata *b; 
 
 	herr = H5_check_filehandle ( f );
-	if ( herr == H5PART_SUCCESS ) return H5PART_SUCCESS;
+	if ( herr == H5_SUCCESS ) return H5_SUCCESS;
 
 	if ( (f == 0) || (f->file == 0) ) return HANDLE_H5PART_BADFD_ERR;
 
@@ -112,7 +139,7 @@ _init_block (
 	if ( b->write_layout == NULL ) {
 		return HANDLE_H5PART_NOMEM_ERR;
 	}
-	b->timestep = -1;
+	b->step_idx = -1;
 	b->blockgroup = -1;
 	b->shape = -1;
 	b->diskshape = -1;
@@ -120,11 +147,208 @@ _init_block (
 	b->field_group_id = -1;
 	b->have_layout = 0;
 
-	f->close_block = _close_block;
-
 	return H5PART_SUCCESS;
 }
 
+ 
+h5_file*
+H5_open_file (
+	const char *filename,	/*!< [in] The name of the data file to open. */
+	unsigned flags,		/*!< [in] The access mode for the file. */
+	MPI_Comm comm		/*!< [in] MPI communicator */
+	) {
+
+	h5part_int64_t rc = H5PART_SUCCESS;
+
+	if ( _init() < 0 ) {
+		HANDLE_H5PART_INIT_ERR;
+		return NULL;
+	}
+	_h5part_errno = H5PART_SUCCESS;
+	h5_file *f = NULL;
+
+	f = (h5_file*) malloc( sizeof (h5_file) );
+	if( f == NULL ) {
+		HANDLE_H5PART_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;
+		goto error_cleanup;
+	}
+	f->width_step_idx = 0;
+
+	f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
+
+	f->comm = 0;		/* init values for serial case */
+	f->nprocs = 1;
+	f->myproc = 0;
+
+#ifdef PARALLEL_IO
+		f->comm = comm;
+		if (MPI_Comm_size (comm, &f->nprocs) != MPI_SUCCESS) {
+			HANDLE_MPI_COMM_SIZE_ERR;
+			goto error_cleanup;
+		}
+		if (MPI_Comm_rank (comm, &f->myproc) != MPI_SUCCESS) {
+			HANDLE_MPI_COMM_RANK_ERR;
+			goto error_cleanup;
+		}
+
+
+		/* for the SP2... perhaps different for linux */
+		MPI_Info info = MPI_INFO_NULL;
+
+		/* ks: IBM_large_block_io */
+		MPI_Info_create(&info);
+		MPI_Info_set(info, "IBM_largeblock_io", "true" );
+		if (H5Pset_fapl_mpio (f->access_prop, comm, info) < 0) {
+			HANDLE_H5P_SET_FAPL_MPIO_ERR;
+			goto error_cleanup;
+		}
+		MPI_Info_free(&info);
+
+		f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
+		if (f->access_prop < 0) {
+			HANDLE_H5P_CREATE_ERR;
+			goto error_cleanup;
+		}
+
+		/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
+		f->create_prop = H5P_DEFAULT;
+
+		/* xfer_prop:  also used for parallel I/O, during actual writes
+		   rather than the access_prop which is for file creation. */
+		f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
+		if (f->xfer_prop < 0) {
+			HANDLE_H5P_CREATE_ERR;
+			goto error_cleanup;
+		}
+
+#ifdef COLLECTIVE_IO
+		if (H5Pset_dxpl_mpio (f->xfer_prop,H5FD_MPIO_COLLECTIVE) < 0) {
+			HANDLE_H5P_SET_DXPL_MPIO_ERR;
+			goto error_cleanup;
+		}
+#endif /* COLLECTIVE_IO */
+
+#endif /* PARALLEL_IO */
+
+	if ( flags == H5_O_RDONLY ) {
+		f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
+	}
+	else if ( flags == H5_O_WRONLY ){
+		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
+				     f->access_prop);
+		f->empty = 1;
+	}
+	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,
+					    f->create_prop, f->access_prop);
+			f->empty = 1;
+		}
+		else if (fd != -1) {
+			close (fd);
+			f->file = H5Fopen (filename, H5F_ACC_RDWR,
+					   f->access_prop);
+		}
+	}
+	else {
+		HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( flags );
+		goto error_cleanup;
+	}
+
+	if (f->file < 0) {
+		HANDLE_H5F_OPEN_ERR ( filename, flags );
+		goto error_cleanup;
+	}
+	f->root_gid = H5Gopen( f->file, "/" );
+	if ( f->root_gid < 0 ) {
+		HANDLE_H5G_OPEN_ERR ( "/" );
+		goto error_cleanup;
+	}
+	f->mode = flags;
+	f->step_gid = -1;
+
+	sprintf (
+		f->step_name,
+		"%s#%0*lld",
+		f->prefix_step_name, f->width_step_idx, (long long) f->step_idx );
+
+	if ( _h5u_open_file ( f ) < 0 ) {
+		goto error_cleanup;
+	}
+
+	if ( _h5b_open_file ( f ) < 0 ) {
+		goto error_cleanup;
+	}
+
+	if ( _h5t_open_file ( f ) < 0 ) {
+		goto error_cleanup;
+	}
+
+	H5_print_debug (
+		"Proc[%d]: Opened file \"%s\" val=%lld",
+		f->myproc,
+		filename,
+		(long long)(size_t)f );
+
+	return f;
+
+ error_cleanup:
+	if (f != NULL ) {
+		if (f->prefix_step_name) {
+			free (f->prefix_step_name);
+		}
+		if (f->pnparticles != NULL) {
+			free (f->pnparticles);
+		}
+		free (f);
+	}
+	return NULL;
+}
+
+/*!
+  \ingroup h5_private
+
+  \internal
+
+  De-initialize H5Block internal structure.  Open HDF5 objects are 
+  closed and allocated memory freed.
+
+  \return	H5PART_SUCCESS or error code
+*/
+static h5part_int64_t
+_h5u_close_file (
+	h5_file *f		/*!< IN: file handle */
+	) {
+	_h5part_errno = H5_SUCCESS;
+	if( f->shape > 0 ) {
+		r = H5Sclose( f->shape );
+		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
+		f->shape = 0;
+	}
+	if( f->diskshape != H5S_ALL ) {
+		r = H5Sclose( f->diskshape );
+		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
+		f->diskshape = 0;
+	}
+	if( f->memshape != H5S_ALL ) {
+		r = H5Sclose( f->memshape );
+		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
+		f->memshape = 0;
+	}
+	if( f->pnparticles ) {
+		free( f->pnparticles );
+	}
+	return _h5part_errno;
+}
+
 /*!
   \ingroup h5block_private
 
@@ -136,7 +360,7 @@ _init_block (
   \return	H5PART_SUCCESS or error code
 */
 static h5part_int64_t
-_close_block (
+_h5b_close_file (
 	h5_file *f		/*!< IN: file handle */
 	) {
 
@@ -165,196 +389,34 @@ _close_block (
 	}
 	free ( f->block );
 	f->block = NULL;
-	f->close_block = NULL;
 
 	return H5PART_SUCCESS;
 }
 
+/*!
+  \ingroup h5_private
 
-h5_file*
-H5_open_file (
-	const char *filename,	/*!< [in] The name of the data file to open. */
-	unsigned flags,		/*!< [in] The access mode for the file. */
-	MPI_Comm comm,		/*!< [in] MPI communicator */
-	int f_parallel		/*!< [in] 0 for serial io otherwise parallel */
+  \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 */
 	) {
 
-	h5part_int64_t rc = H5PART_SUCCESS;
+	h5_err_t herr = H5_SUCCESS;
+	struct h5t_fdata *t = fh->t;
 
-	if ( _init() < 0 ) {
-		HANDLE_H5PART_INIT_ERR;
-		return NULL;
+	if ( t->levels ) {
+		free ( levels );
 	}
-	_h5part_errno = H5PART_SUCCESS;
-	h5_file *f = NULL;
-
-	f = (h5_file*) malloc( sizeof (h5_file) );
-	if( f == NULL ) {
-		HANDLE_H5PART_NOMEM_ERR;
-		goto error_cleanup;
-	}
-	memset (f, 0, sizeof (h5_file));
-
-	f->groupname_step = strdup ( H5PART_GROUPNAME_STEP );
-	if( f->groupname_step == NULL ) {
-		HANDLE_H5PART_NOMEM_ERR;
-		goto error_cleanup;
-	}
-	f->stepno_width = 0;
-
-	f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
-
-	if ( f_parallel ) {
-#ifdef PARALLEL_IO
-		/* for the SP2... perhaps different for linux */
-		MPI_Info info = MPI_INFO_NULL;
-
-		/* ks: IBM_large_block_io */
-		MPI_Info_create(&info);
-		MPI_Info_set(info, "IBM_largeblock_io", "true" );
-
-		if (MPI_Comm_size (comm, &f->nprocs) != MPI_SUCCESS) {
-			HANDLE_MPI_COMM_SIZE_ERR;
-			goto error_cleanup;
-		}
-		if (MPI_Comm_rank (comm, &f->myproc) != MPI_SUCCESS) {
-			HANDLE_MPI_COMM_RANK_ERR;
-			goto error_cleanup;
-		}
-
-		f->pnparticles =
-		  (h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
-		if (f->pnparticles == NULL) {
-			HANDLE_H5PART_NOMEM_ERR;
-			goto error_cleanup;
-		}
-		
-		f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
-		if (f->access_prop < 0) {
-			HANDLE_H5P_CREATE_ERR;
-			goto error_cleanup;
-		}
-
-		if (H5Pset_fapl_mpio (f->access_prop, comm, info) < 0) {
-			HANDLE_H5P_SET_FAPL_MPIO_ERR;
-			goto error_cleanup;
-		}
-		
-		/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
-		f->create_prop = H5P_DEFAULT;
-
-		/* xfer_prop:  also used for parallel I/O, during actual writes
-		   rather than the access_prop which is for file creation. */
-		f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
-		if (f->xfer_prop < 0) {
-			HANDLE_H5P_CREATE_ERR;
-			goto error_cleanup;
-		}
-
-#ifdef COLLECTIVE_IO
-		if (H5Pset_dxpl_mpio (f->xfer_prop,H5FD_MPIO_COLLECTIVE) < 0) {
-			HANDLE_H5P_SET_DXPL_MPIO_ERR;
-			goto error_cleanup;
-		}
-#endif
-		f->comm = comm;
-
-		MPI_Info_free(&info);
-#else
-		/* f_parallel is true, but compilation is for serial I/O */
-		HANDLE_MPI_UNAVAILABLE_ERR;
-		goto error_cleanup;
-
-#endif /* PARALLEL_IO */
-	} else {
-		f->comm = 0;
-		f->nprocs = 1;
-		f->myproc = 0;
-		f->pnparticles = 
-			(h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
-	}
-	if ( flags == H5PART_READ ) {
-		f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
-	}
-	else if ( flags == H5PART_WRITE ){
-		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
-				     f->access_prop);
-		f->empty = 1;
-	}
-	else if ( flags == H5PART_APPEND ) {
-		int fd = open (filename, O_RDONLY, 0);
-		if ( (fd == -1) && (errno == ENOENT) ) {
-			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
-					    f->create_prop, f->access_prop);
-			f->empty = 1;
-		}
-		else if (fd != -1) {
-			close (fd);
-			f->file = H5Fopen (filename, H5F_ACC_RDWR,
-					   f->access_prop);
-			/*
-			  The following function call returns an error,
-			  if f->file < 0. But we can safely ignore this.
-			*/
-			f->timestep = H5_get_num_objects_matching_pattern(
-				f->file, "/", H5G_GROUP, f->groupname_step );
-			if ( f->timestep < 0 ) goto error_cleanup;
-		}
-	}
-	else {
-		HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( flags );
-		goto error_cleanup;
-	}
-
-	if (f->file < 0) {
-		HANDLE_H5F_OPEN_ERR ( filename, flags );
-		goto error_cleanup;
-	}
-	f->root_id = H5Gopen( f->file, "/" );
-	if ( f->root_id < 0 ) {
-		HANDLE_H5G_OPEN_ERR ( "/" );
-		goto error_cleanup;
-	}
-	f->mode = flags;
-	f->timegroup = -1;
-	f->shape = 0;
-	f->diskshape = H5S_ALL;
-	f->memshape = H5S_ALL;
-	f->viewstart = -1;
-	f->viewend = -1;
-
-	sprintf (
-		f->index_name,
-		"%s#%0*lld",
-		f->groupname_step, f->stepno_width, (long long) f->timestep );
-
-	rc = _init_block ( f );
-	if ( rc != H5PART_SUCCESS ) {
-		goto error_cleanup;
-	}
-
-	H5_print_debug (
-		"Proc[%d]: Opened file \"%s\" val=%lld",
-		f->myproc,
-		filename,
-		(long long)(size_t)f );
-
-	return f;
-
- error_cleanup:
-	if (f != NULL ) {
-		if (f->groupname_step) {
-			free (f->groupname_step);
-		}
-		if (f->pnparticles != NULL) {
-			free (f->pnparticles);
-		}
-		free (f);
-	}
-	return NULL;
+	return herr;
 }
 
-
 h5part_int64_t
 H5_close_file (
 	h5_file *f
@@ -364,26 +426,15 @@ H5_close_file (
 
 	CHECK_FILEHANDLE ( f );
 
-	if ( f->block && f->close_block ) {
-		(*f->close_block) ( f );
-		f->block = NULL;
-		f->close_block = NULL;
-	}
+	_h5_close_step ( f );
+	_h5u_close_file ( f );
+	_h5b_close_file ( f );
+	_h5t_close_file ( f );
 
-	if( f->shape > 0 ) {
-		r = H5Sclose( f->shape );
-		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
-		f->shape = 0;
-	}
-	if( f->timegroup >= 0 ) {
-		r = H5Gclose( f->timegroup );
+	if( f->step_gid >= 0 ) {
+		r = H5Gclose( f->step_gid );
 		if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
-		f->timegroup = -1;
-	}
-	if( f->diskshape != H5S_ALL ) {
-		r = H5Sclose( f->diskshape );
-		if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
-		f->diskshape = 0;
+		f->step_gid = -1;
 	}
 	if( f->xfer_prop != H5P_DEFAULT ) {
 		r = H5Pclose( f->xfer_prop );
@@ -400,21 +451,18 @@ H5_close_file (
 		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->create_prop" );
 		f->create_prop = H5P_DEFAULT;
 	}
-	if ( f->root_id >= 0 ) {
-		r = H5Gclose ( f->root_id );
+	if ( f->root_gid >= 0 ) {
+		r = H5Gclose ( f->root_gid );
 		if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
-		f->root_id = 0;
+		f->root_gid = 0;
 	}
 	if ( f->file ) {
 		r = H5Fclose( f->file );
 		if ( r < 0 ) HANDLE_H5F_CLOSE_ERR;
 		f->file = 0;
 	}
-	if (f->groupname_step) {
-		free (f->groupname_step);
-	}
-	if( f->pnparticles ) {
-		free( f->pnparticles );
+	if (f->prefix_step_name) {
+		free (f->prefix_step_name);
 	}
 	free( f );
 
@@ -427,11 +475,11 @@ H5_define_stepname (
 	const char *name,
 	const h5part_int64_t width
 	) {
-	f->groupname_step = strdup ( name );
-	if( f->groupname_step == NULL ) {
+	f->prefix_step_name = strdup ( name );
+	if( f->prefix_step_name == NULL ) {
 		return HANDLE_H5PART_NOMEM_ERR;
 	}
-	f->stepno_width = (int)width;
+	f->width_step_idx = (int)width;
 	
 	return H5PART_SUCCESS;
 }