Merge branch '21-hdf5-1-12-and-newer-support' into 'master'

Resolve "hdf5 1.12 and newer support"

Closes #21

See merge request H5hut/src!6

ChangeLog

@@ -0,0 +1,15 @@
+2018-09-14  Gsell Achim  <achi.gsell@psi.ch>
+
+	* C-API
+	- H5PartSetNumPoints() renamed to H5PartSetNumItems()
+	- H5PartGetNumPoints() renamed to H5PartGetNumItems()
+	- Dataset names longer then 64 bytes are handled as error.
+	- Same for step/iteration names.
+	* core API
+	- we use the term 'iteration' instead of 'step'
+	- we use the term 'item' instead of 'point'
+	- re-factor function and variable names
+	- in printing messages/debug output fixed
+	- do not flush (sync to disk) after writing a dataset by default,
+	  can be controlled by a property
+

configure.ac

@@ -1,15 +1,16 @@
 #
-#  Copyright (c) 2006-2017, The Regents of the University of California,
+#  Copyright (c) 2006-2018, The Regents of the University of California,
 #  through Lawrence Berkeley National Laboratory (subject to receipt of any
 #  required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
 #  Institut (Switzerland).  All rights reserved.
 #
 #  License: see file COPYING in top level of source distribution.
 #
-AC_INIT([H5hut], [2.0.0rc4], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5hut], [2.0.0rc7], [h5part@lists.psi.ch], H5hut)
 AC_PREREQ(2.60)
 AC_CONFIG_HEADERS(config.h)
 AC_CONFIG_MACRO_DIR([m4])
+LT_INIT
 AM_INIT_AUTOMAKE
 
 ENABLE_DEBUG='no'
@@ -138,7 +139,6 @@ fi
 AC_PROG_CC($c_compilers)
 if test "x$ac_cv_prog_cc_c89" = "xno"; then
 	AC_MSG_ERROR([C compiler not found!])
-	exit 1
 fi
 
 AC_PROG_CXX($cxx_compilers)
@@ -147,7 +147,6 @@ if test "X$ENABLE_FORTRAN" = "Xyes"; then
    	AC_PROG_FC($fc_compiler)
 	if test "x$FC" = "x"; then
 	   	AC_MSG_ERROR([Fortran compiler not found!])
-		exit 1
 	fi
 fi
 
@@ -159,7 +158,6 @@ AX_CXX_COMPILE_STDCXX_11
 AC_PROG_CC_C99
 if test "x$ac_cv_prog_cc_c99" = "xno"; then
 	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
-	exit 1
 fi
 
 
@@ -281,8 +279,7 @@ if test -n "${HDF5_PREFIX}"; then
 fi
 AC_CHECK_LIB([hdf5], [H5open])
 AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes], 
-        [AC_MSG_ERROR([Cannot compile and link a HDF5 program]); 
-        exit 1])
+        [AC_MSG_ERROR([Cannot compile and link a HDF5 program])])
 AC_MSG_CHECKING([checking whether hdf5 lib supports parallel IO])
 AC_COMPILE_IFELSE([AC_LANG_SOURCE([[
 #include "hdf5.h"
@@ -429,12 +426,10 @@ if test "X$ENABLE_PARALLEL" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 
 	AS_IF([test "x$H5_HAVE_PARALLEL" = "xno"],
-	        [AC_MSG_ERROR([hdf5 does not support parallel IO!]);
-        	exit 1])
+	        [AC_MSG_ERROR([hdf5 does not support parallel IO!])])
 
 	if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	   	AC_MSG_ERROR([VTK to H5hut grid converter cannot be compiled parallel!])
-		exit 1
 	fi
 	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
@@ -453,14 +448,12 @@ if test "X$ENABLE_PARALLEL" = "Xyes"; then
 
 	        if test "X$r" = "Xno"; then
 		        AC_MSG_ERROR([ParMETIS])
-		        exit 1
 	        fi
         fi
 else  # --enable-parallel=no
 	AC_MSG_RESULT([no])
 	AS_IF([test "x$H5_HAVE_PARALLEL" = "xyes"],
-	        [AC_MSG_ERROR([hdf5 with support for parallel IO cannot be used for non-parallel H5hut!]);
-        	exit 1])
+	        [AC_MSG_ERROR([hdf5 with support for parallel IO cannot be used for non-parallel H5hut!])])
 fi
 
 ###############################################################################
@@ -481,7 +474,6 @@ if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	if test "X$?" != "X0"; then
 		AC_MSG_RESULT([no])
 	        AC_MSG_ERROR([Cannot compile VTK to H5hut converter])
-        	exit 1
 	else
 		AC_MSG_RESULT([yes])
 	fi
@@ -490,7 +482,6 @@ if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	if test "X$?" != "X0"; then
 		AC_MSG_RESULT([no])
 	        AC_MSG_ERROR([Cannot compile VTK to H5hut converter]); 
-        	exit 1
 	else
 		AC_MSG_RESULT([yes])
 	fi

examples/H5/openclose.c

@@ -19,8 +19,8 @@
   Use H5_DEBUG_ALL to get full debug output
 */
 #if !defined(DEBUGMASK)
-#define DEBUGMASK	H5_DEBUG_NONE
-//#define DEBUGMASK	H5_DEBUG_ALL
+//#define DEBUGMASK	H5_DEBUG_NONE
+#define DEBUGMASK	H5_DEBUG_ALL
 #endif
 
 int

examples/H5Part/write_setview.c

@@ -7,6 +7,8 @@
   License: see file COPYING in top level of source distribution.
 */
 
+#include <stdlib.h>
+
 #include "H5hut.h"
 #include "examples.h"
 
@@ -15,16 +17,51 @@ const char* fname = "example_setview.h5";
 
 // H5hut verbosity level
 const h5_int64_t h5_verbosity = H5_VERBOSE_DEFAULT;
+const h5_int64_t h5_debug_mask = 0;
 
 // we are going to write multiple consecutive blocks
-const h5_int64_t num_blocks = 4;
-const h5_int64_t num_particles_per_block = 32;
+//const h5_int64_t num_blocks = 32;
+//const h5_int64_t num_particles_per_block = 1048576*8;
 
 int
 main (
 	int argc,
 	char* argv[]
         ){
+	if (argc < 3) {
+		fprintf (stderr, "Usage: %s <number_of_blocks> <sizeof_block>\n", argv[0]);
+		exit (1);
+	}
+
+	char* endptr = NULL;
+	long long n = strtoll (argv[1], &endptr, 10);
+	if (*endptr != 0) {
+		fprintf (stderr, "first argument (number of blocks) is not a unsigned integer!\n");
+		exit (1);
+	}
+	if (n < 1) {
+		fprintf (stderr, "first argument (number of block) must be >= 1!\n");
+		exit (1);
+	}
+	if (n == LLONG_MAX) {
+		fprintf (stderr, "first argument (number of block) to large!\n");
+		exit (1);
+	}
+	h5_int64_t num_blocks = (h5_int64_t)n;
+	n = strtoll (argv[2], &endptr, 10);
+	if (*endptr != 0) {
+		fprintf (stderr, "second argument (sizeof blocks) is not a unsigned integer!\n");
+		exit (1);
+	}
+	if (n < 1024) {
+		fprintf (stderr, "second argument (sizeof block) must be >= 1024!\n");
+		exit (1);
+	}
+	if (n == LLONG_MAX) {
+		fprintf (stderr, "second argument (sizeof block) to large!\n");
+		exit (1);
+	}
+	h5_int64_t num_particles_per_block = (h5_int64_t)n;
 
         // initialize MPI & H5hut
         MPI_Init (&argc, &argv);
@@ -33,9 +70,16 @@ main (
         MPI_Comm_rank (comm, &comm_rank);
         H5AbortOnError ();
         H5SetVerbosityLevel (h5_verbosity);
+        H5SetDebugMask (h5_debug_mask);
+
+	h5_prop_t prop = H5CreateFileProp ();
+	H5SetPropFileAlign (prop, 1048576*8);
+	H5SetPropFileMPIOIndependent (prop, &comm);
+	//H5SetPropFileMPIOCollective (prop, &comm);
 
         // open file and create first step
-        h5_file_t file = H5OpenFile (fname, H5_O_WRONLY, H5_PROP_DEFAULT);
+        h5_file_t file = H5OpenFile (fname, H5_O_WRONLY, prop);
+	//H5PartSetChunkSize (file, 1048576*1);
         H5SetStep (file, 0);
 
 	/*
@@ -52,7 +96,9 @@ main (
         // write multiple consecutive blocks
         for (int i = 0; i < num_blocks; i++) {
 		// create fake data
-		h5_int32_t data[num_particles_per_block];
+		//h5_int32_t data[num_particles_per_block];
+		h5_int64_t *data;
+		data = calloc (num_particles_per_block, sizeof(*data));
 		for (int j = 0; j < num_particles_per_block; j++) {
 			data[j] = j + i*num_particles_per_block + offset;
 		}
@@ -63,7 +109,7 @@ main (
                         offset + i*num_particles_per_block,
                         offset + (i+1)*num_particles_per_block - 1);
                 // write data
-                H5PartWriteDataInt32 (file, "data", data);
+                H5PartWriteDataInt64 (file, "data", data);
         }
 
         // done

examples/H5Part/write_setview2.c

@@ -0,0 +1,120 @@
+/*
+  Copyright (c) 2006-2015, The Regents of the University of California,
+  through Lawrence Berkeley National Laboratory (subject to receipt of any
+  required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
+  Institut (Switzerland).  All rights reserved.
+
+  License: see file COPYING in top level of source distribution.
+*/
+
+#include <stdlib.h>
+#include <mpi.h>
+
+#include "H5hut.h"
+#include "examples.h"
+
+// name of output file
+const char* fname = "example_setview.h5";
+
+// H5hut verbosity level
+const h5_int64_t h5_verbosity = H5_VERBOSE_DEFAULT;
+const h5_int64_t h5_debug_mask = 0;
+
+// we are going to write multiple consecutive blocks
+//const h5_int64_t num_blocks = 32;
+//const h5_int64_t num_particles_per_block = 1048576*8;
+
+int
+main (
+	int argc,
+	char* argv[]
+        ){
+	if (argc < 3) {
+		fprintf (stderr, "Usage: %s <number_of_blocks> <sizeof_block>\n", argv[0]);
+		exit (1);
+	}
+
+	char* endptr = NULL;
+	long long n = strtoll (argv[1], &endptr, 10);
+	if (*endptr != 0) {
+		fprintf (stderr, "first argument (number of blocks) is not a unsigned integer!\n");
+		exit (1);
+	}
+	if (n < 1) {
+		fprintf (stderr, "first argument (number of block) must be >= 1!\n");
+		exit (1);
+	}
+	if (n == LLONG_MAX) {
+		fprintf (stderr, "first argument (number of block) to large!\n");
+		exit (1);
+	}
+	h5_int64_t num_blocks = (h5_int64_t)n;
+	n = strtoll (argv[2], &endptr, 10);
+	if (*endptr != 0) {
+		fprintf (stderr, "second argument (sizeof blocks) is not a unsigned integer!\n");
+		exit (1);
+	}
+	if (n < 1024) {
+		fprintf (stderr, "second argument (sizeof block) must be >= 1024!\n");
+		exit (1);
+	}
+	if (n == LLONG_MAX) {
+		fprintf (stderr, "second argument (sizeof block) to large!\n");
+		exit (1);
+	}
+	h5_int64_t num_particles_per_block = (h5_int64_t)n;
+
+        // initialize MPI & H5hut
+        MPI_Init (&argc, &argv);
+        MPI_Comm comm = MPI_COMM_WORLD;
+        int comm_rank = 0;
+        MPI_Comm_rank (comm, &comm_rank);
+        H5AbortOnError ();
+        H5SetVerbosityLevel (h5_verbosity);
+        H5SetDebugMask (h5_debug_mask);
+
+	h5_prop_t prop = H5CreateFileProp ();
+	H5SetPropFileAlign (prop, 1048576*8);
+	H5SetPropFileMPIOIndependent (prop, &comm);
+	//H5SetPropFileMPIOCollective (prop, &comm);
+
+        // open file and create first step
+        h5_file_t file = H5OpenFile (fname, H5_O_WRONLY, prop);
+	//H5PartSetChunkSize (file, 1048576*1);
+        H5SetStep (file, 0);
+
+	/*
+	  If we want to write consecutive blocks, the 'view' can be defined
+	  with H5PartSetview(). Otherwise we have to define the total number
+	  of particles with H5PartSetNumParticles().
+	 */
+        const h5_int64_t offset = comm_rank * num_blocks * num_particles_per_block;
+	H5PartSetView (
+		file,
+		offset,
+		offset + num_blocks*num_particles_per_block -1);
+	dataset_id = H5PartCreateDataSet (file, "data");
+        // write multiple consecutive blocks
+        for (int i = 0; i < num_blocks; i++) {
+		// create fake data
+		//h5_int32_t data[num_particles_per_block];
+		h5_int64_t *data;
+		data = calloc (num_particles_per_block, sizeof(*data));
+		for (int j = 0; j < num_particles_per_block; j++) {
+			data[j] = j + i*num_particles_per_block + offset;
+		}
+		
+                // set the "view" to select a subset of the dataset
+                H5PartSetViewOnDataset (
+                        file,
+                        offset + i*num_particles_per_block,
+                        offset + (i+1)*num_particles_per_block - 1);
+                // write data
+                H5PartWriteDatasetInt64 (dataset_id, data);
+        }
+	H5CloseDataset (dataset_id);
+        // done
+        H5CloseFile(file);
+	MPI_Finalize();
+        return 0;
+}

src/Fortran/H5.c

@@ -165,10 +165,9 @@ h5_openfile (
         h5_int64_t* _props,
 	const int _len_fname
         ) {
-        int len_fname = strlenf (_fname, _len_fname);
         H5_API_ENTER (h5_int64_t,
                       "fname = %*s, mode=%lld, props=%lld",
-                      len_fname, _fname, (long long int)*_mode, (long long int)*_props);
+                      _len_fname, _fname, (long long int)*_mode, (long long int)*_props);
         char* fname = h5_strdupfor2c (_fname, _len_fname);
         h5_int64_t mode = *_mode;
         h5_prop_t props = (h5_prop_t)*_props;
@@ -222,7 +221,7 @@ h5_flushstep (
 	) {
 	h5_file_t fh = h5_filehandlefor2c(f);
 	H5_API_ENTER (h5_int64_t, "f=%p", (h5_file_p)fh);
-	H5_API_RETURN (h5_flush_step (fh));
+	H5_API_RETURN (h5_flush_iteration (fh));
 }
 
 #define h5_finalize FC_MANGLING(		   \

src/Fortran/H5Block_model.c

@@ -69,7 +69,8 @@ h5bl_3d_setview (
 		f,
 		*i_start-1, *i_end-1,
 		*j_start-1, *j_end-1,
-		*k_start-1, *k_end-1 ));
+		*k_start-1, *k_end-1,
+                0));
 }
 
 #define h5bl_3d_getview FC_MANGLING (					\

src/Fortran/H5Part_io.c

@@ -28,7 +28,7 @@ h5pt_writedata_r8 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_write_data (
+	h5_int64_t herr = h5u_write_dataset (
 		f, name2, (void*)data, H5_FLOAT64_T );
 	free ( name2 );
 	H5_API_RETURN(herr);
@@ -49,7 +49,7 @@ h5pt_writedata_r4 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_write_data (
+	h5_int64_t herr = h5u_write_dataset (
 		f, name2, (void*)data, H5_FLOAT32_T );
 	free ( name2 );
 	H5_API_RETURN(herr);
@@ -70,7 +70,7 @@ h5pt_writedata_i8 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_write_data (
+	h5_int64_t herr = h5u_write_dataset (
 		f, name2, (void*)data, H5_INT64_T );
 	free ( name2 );
 	H5_API_RETURN(herr);
@@ -91,7 +91,7 @@ h5pt_writedata_i4 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_write_data (
+	h5_int64_t herr = h5u_write_dataset (
 		f, name2, (void*)data, H5_INT32_T );
 	free ( name2 );
 	H5_API_RETURN(herr);
@@ -114,7 +114,7 @@ h5pt_readdata_r8 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_read_data (
+	h5_int64_t herr = h5u_read_dataset (
 		f, name2, data, H5_FLOAT64_T );
 	free ( name2 );
 	H5_API_RETURN(herr);
@@ -135,7 +135,7 @@ h5pt_readdata_r4 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_read_data (
+	h5_int64_t herr = h5u_read_dataset (
 		f, name2, data, H5_FLOAT32_T );
 	free ( name2 );
 	H5_API_RETURN(herr);
@@ -156,7 +156,7 @@ h5pt_readdata_i8 (
                       "fh=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_read_data (
+	h5_int64_t herr = h5u_read_dataset (
 		f, name2, data, H5_INT64_T );
 
 	free ( name2 );
@@ -178,7 +178,7 @@ h5pt_readdata_i4 (
                       "hf=%p, name='%s', data=%p, l_name=%d",
                       (h5_file_p)f, name, data, l_name);
 	char *name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5u_read_data (
+	h5_int64_t herr = h5u_read_dataset (
 		f, name2, data, H5_INT32_T );
 	free ( name2 );
 	H5_API_RETURN(herr);

src/Fortran/H5Part_model.c

@@ -22,13 +22,13 @@
 h5_int64_t
 h5pt_setnpoints (
 	const h5_int64_t* const fh,
-	const h5_int64_t* const npoints
+	const h5_int64_t* const num_items
 	) {
 	h5_file_t f = h5_filehandlefor2c (fh);
 	H5_API_ENTER (h5_int64_t,
                       "fh=%p, npoints=%lld",
-                      (h5_file_p)f, (long long)*npoints);
-	H5_API_RETURN (h5u_set_num_points (f, *npoints, 1));
+                      (h5_file_p)f, (long long)*num_items);
+	H5_API_RETURN (h5u_set_num_items (f, *num_items, 1));
 }
                 
 #define h5pt_setnpoints_strided FC_MANGLING (				\
@@ -37,14 +37,14 @@ h5pt_setnpoints (
 h5_int64_t
 h5pt_setnpoints_strided (
 	const h5_int64_t* const fh,
-	const h5_int64_t* const npoints,
+	const h5_int64_t* const num_items,
         const h5_int64_t* const stride
 	) {
 	h5_file_t f = h5_filehandlefor2c (fh);
 	H5_API_ENTER (h5_int64_t,
                       "fh=%p, npoints=%lld, stride=%lld",
-                      (h5_file_p)f, (long long)*npoints, (long long)*stride);
-	H5_API_RETURN (h5u_set_num_points (f, *npoints, *stride));
+                      (h5_file_p)f, (long long)*num_items, (long long)*stride);
+	H5_API_RETURN (h5u_set_num_items (f, *num_items, *stride));
 }
 
 
@@ -172,7 +172,7 @@ h5pt_getnpoints (
 	) {
 	h5_file_t f = h5_filehandlefor2c (fh);
 	H5_API_ENTER (h5_int64_t, "fh=%p", (h5_file_p)f);
-	H5_API_RETURN (h5u_get_num_points (f));
+	H5_API_RETURN (h5u_get_num_items (f));
 }
 
 #define h5pt_getdatasetname FC_MANGLING (				\

src/Fortran/H5_attribs.c

@@ -380,7 +380,7 @@ h5_getnstepattribs (
 	H5_API_ENTER (h5_int64_t,
                       "fh=%p",
                       (h5_file_p)f);
-        H5_API_RETURN (h5_get_num_step_attribs (f));
+        H5_API_RETURN (h5_get_num_iteration_attribs (f));
 }
 
 #define h5_getstepattribinfo FC_MANGLING(	 \
@@ -405,7 +405,7 @@ h5_getstepattribinfo (
 		      (h5_file_p)f,
 		      (long long)*attrib_idx,
 		      attrib_name, attrib_type, attrib_nelem);
-        h5_int64_t h5err = h5_get_step_attrib_info_by_idx (
+        h5_int64_t h5err = h5_get_iteration_attrib_info_by_idx (
                 f,
                 *attrib_idx - 1,
                 attrib_name, l_attrib_name,
@@ -435,7 +435,7 @@ h5_getstepattribinfo_by_name (
 		      (h5_file_p)fh,
 		      l_name, _name, _type, _nelem);
 	char* name = h5_strdupfor2c (_name, l_name);
-        h5_int64_t h5err = h5_get_step_attrib_info_by_name (
+        h5_int64_t h5err = h5_get_iteration_attrib_info_by_name (
                 f,
                 name,
                 _type,
@@ -459,7 +459,7 @@ h5_getstepattribinfo_by_name (
 */
 
 static inline h5_int64_t
-write_step_attrib (
+write_iteration_attrib (
         const h5_file_t fh,
 	const char* name,
 	const int l_name,
@@ -468,13 +468,14 @@ write_step_attrib (
 	const hsize_t l_buffer
         ) {
 	char *name2 = h5_strdupfor2c (name, l_name);
-	h5_int64_t herr = h5_write_step_attrib (fh, name2, type, buffer, l_buffer );
+	h5_int64_t herr = h5_write_iteration_attrib (
+		fh, name2, type, buffer, l_buffer );
 	free (name2);
         return herr;
 }
 
 static inline h5_int64_t
-read_step_attrib (
+read_iteration_attrib (
 	const h5_file_t fh,
 	const char* name,
 	const int l_name,
@@ -482,7 +483,7 @@ read_step_attrib (
 	void* const buffer
 	) {
 	char* name2 = h5_strdupfor2c ( name, l_name );
-	h5_int64_t herr = h5_read_step_attrib (fh, name2, type, buffer);
+	h5_int64_t herr = h5_read_iteration_attrib (fh, name2, type, buffer);
 	free (name2);
 	return herr;
 }
@@ -503,7 +504,7 @@ h5_writestepattrib_string (
 		      "f=%p, name='%.*s', buffer='%.*s'",
 		      (h5_file_p)f, l_name, name, l_buffer, buffer);
 	char *buffer2 = h5_strdupfor2c (buffer, l_buffer);
-	h5_int64_t herr = write_step_attrib (
+	h5_int64_t herr = write_iteration_attrib (
 		f, name, l_name, H5_STRING_T, buffer2, strlen(buffer2)+1 );
 	free (buffer2);
 	H5_API_RETURN (herr);
@@ -524,7 +525,8 @@ h5_readstepattrib_string (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer='%.*s'",
 		      (h5_file_p)f, l_name, name, l_buffer, buffer);
-	h5_int64_t herr = read_step_attrib (f, name, l_name, H5_STRING_T, buffer);
+	h5_int64_t herr = read_iteration_attrib (
+		f, name, l_name, H5_STRING_T, buffer);
 	h5_strc2for (buffer, l_buffer);
 	H5_API_RETURN (herr);
 }
@@ -544,7 +546,7 @@ h5_writestepattrib_r8 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p, nelem=%lld",
 		      (h5_file_p)f, l_name, name, buffer, (long long)*nelem);
-        H5_API_RETURN (write_step_attrib(
+        H5_API_RETURN (write_iteration_attrib(
                                f,
                                name, l_name,
                                H5_FLOAT64_T,
@@ -565,7 +567,7 @@ h5_readstepattrib_r8 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p",
 		      (h5_file_p)f, l_name, name, buffer);
-        H5_API_RETURN (read_step_attrib(
+        H5_API_RETURN (read_iteration_attrib(
 		f,
                 name, l_name, 
                 H5_FLOAT64_T,
@@ -587,7 +589,7 @@ h5_writestepattrib_r4 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p, nelem=%lld",
 		      (h5_file_p)f, l_name, name, buffer, (long long)*nelem);
-        H5_API_RETURN (write_step_attrib(
+        H5_API_RETURN (write_iteration_attrib(
                                f,
                                name, l_name,
                                H5_FLOAT32_T,
@@ -608,7 +610,7 @@ h5_readstepattrib_r4 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p",
 		      (h5_file_p)f, l_name, name, buffer);
-        H5_API_RETURN (read_step_attrib(
+        H5_API_RETURN (read_iteration_attrib(
 		f,
                 name, l_name, 
                 H5_FLOAT32_T,
@@ -630,7 +632,7 @@ h5_writestepattrib_i8 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p, nelem=%lld",
 		      (h5_file_p)f, l_name, name, buffer, (long long)*nelem);
-        H5_API_RETURN (write_step_attrib(
+        H5_API_RETURN (write_iteration_attrib(
                                f,
                                name, l_name,
                                H5_INT64_T,
@@ -651,7 +653,7 @@ h5_readstepattrib_i8 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p",
 		      (h5_file_p)f, l_name, name, buffer);
-        H5_API_RETURN (read_step_attrib(
+        H5_API_RETURN (read_iteration_attrib(
 		f,
                 name, l_name, 
                 H5_INT64_T,
@@ -673,7 +675,7 @@ h5_writestepattrib_i4 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p, nelem=%lld",
 		      (h5_file_p)f, l_name, name, buffer, (long long)*nelem);
-        H5_API_RETURN (write_step_attrib(
+        H5_API_RETURN (write_iteration_attrib(
                                f,
                                name, l_name,
                                H5_INT32_T,
@@ -694,7 +696,7 @@ h5_readstepattrib_i4 (
 	H5_API_ENTER (h5_int64_t,
 		      "f=%p, name='%.*s', buffer=%p",
 		      (h5_file_p)f, l_name, name, buffer);
-        H5_API_RETURN (read_step_attrib(
+        H5_API_RETURN (read_iteration_attrib(
 		f,
                 name, l_name, 
                 H5_INT32_T,

src/Fortran/H5_model.c

@@ -28,7 +28,7 @@ h5_hasstep (
                 int,
                 "f=%p, stepno=%lld",
                 (h5_file_p)fh, (long long int)step);
-	H5_API_RETURN (h5_has_step (fh, (*step)-1));
+	H5_API_RETURN (h5_has_iteration (fh, (*step)-1));
 }
 
 #define h5_setstep FC_MANGLING(			\
@@ -41,7 +41,7 @@ h5_setstep (
 
 	h5_file_t fh = h5_filehandlefor2c(f);
 	H5_API_ENTER (h5_int64_t, "f=%p, step=%lld", (h5_file_p)fh, (long long)*step);
-	H5_API_RETURN (h5_set_step (fh, (*step)-1));
+	H5_API_RETURN (h5_set_iteration (fh, (*step)-1));
 }
 
 #define h5_getstep FC_MANGLING(			\
@@ -54,7 +54,7 @@ h5_getstep (
 
 	h5_file_t fh = h5_filehandlefor2c(f);
 	H5_API_ENTER (h5_int64_t, "f=%p", (h5_file_p)fh);
-	H5_API_RETURN (h5_get_step (fh) + 1);
+	H5_API_RETURN (h5_get_iteration (fh) + 1);
 }
 
 #define h5_getnsteps FC_MANGLING(		\
@@ -67,5 +67,5 @@ h5_getnsteps (
 
 	h5_file_t fh = h5_filehandlefor2c(f);
 	H5_API_ENTER (h5_int64_t, "f=%p", (h5_file_p)fh);
-	H5_API_RETURN (h5_get_num_steps (fh));
+	H5_API_RETURN (h5_get_num_iterations (fh));
 }

src/Python/Makefile.am

@@ -28,6 +28,8 @@ H5hut_wrap.c : $(SWIG_SOURCES)
 
 endif
 
+else
+$(info Python is disabled)
 endif
 
 clean: clean-am

src/h5core/Makefile.am

@@ -60,7 +60,7 @@ libH5hut_la_SOURCES =				\
         h5b_model.c				\
         h5b_attribs.c				\
 	private/h5_hdf5.c			\
-	private/h5_init.c			\
+	h5_init.c			\
 	private/h5_hsearch.c			\
 	private/h5_maps.c			\
 	private/h5_fcmp.c			\

src/h5core/h5_attribs.c

@@ -31,7 +31,7 @@ h5_has_file_attrib (
 }
 	
 h5_err_t
-h5_has_step_attrib (
+h5_has_iteration_attrib (
 	const h5_file_t f_,
 	const char* const attrib_name
 	) {
@@ -41,9 +41,8 @@ h5_has_step_attrib (
 			   "attrib_name='%s'",
 			   f,
 			   attrib_name);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	TRY (ret_value = hdf5_attribute_exists (f->step_gid, attrib_name));
+	check_iteration_handle_is_valid (f);
+	TRY (ret_value = hdf5_attribute_exists (f->iteration_gid, attrib_name));
 	H5_RETURN (ret_value);
 }
 
@@ -59,14 +58,13 @@ h5_get_num_file_attribs (
 }
 
 h5_ssize_t
-h5_get_num_step_attribs (
+h5_get_num_iteration_attribs (
 	const h5_file_t f_                     	/*!< handle to open file */
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	TRY (ret_value = hdf5_get_num_attribute (f->step_gid));
+	check_iteration_handle_is_valid (f);
+	TRY (ret_value = hdf5_get_num_attribute (f->iteration_gid));
 	H5_RETURN (ret_value);
 }
 
@@ -122,7 +120,7 @@ h5_get_file_attrib_info_by_name (
 }
 
 h5_err_t
-h5_get_step_attrib_info_by_idx (
+h5_get_iteration_attrib_info_by_idx (
 	const h5_file_t f_,			/*!< handle to open file */
 	const h5_size_t attrib_idx,		/*!< index of attribute */
 	char* attrib_name,			/*!< OUT: name of attribute */
@@ -140,10 +138,9 @@ h5_get_step_attrib_info_by_idx (
 			   (long long unsigned)attrib_idx,
 			   attrib_name, (long long unsigned)len_attrib_name,
 			   attrib_type, attrib_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	TRY (ret_value = h5priv_get_attrib_info_by_idx (
-		     f->step_gid,
+		     f->iteration_gid,
 		     attrib_idx,
 		     attrib_name, len_attrib_name,
 		     attrib_type, attrib_nelem));
@@ -151,7 +148,7 @@ h5_get_step_attrib_info_by_idx (
 }
 
 h5_err_t
-h5_get_step_attrib_info_by_name (
+h5_get_iteration_attrib_info_by_name (
 	const h5_file_t f_,			/*!< handle to open file */
 	const char* const attrib_name,		/*!< OUT: name of attribute */
 	h5_int64_t* const attrib_type,		/*!< OUT: H5 type of attribute */
@@ -165,10 +162,9 @@ h5_get_step_attrib_info_by_name (
 			   f,
 			   attrib_name,
 			   attrib_type, attrib_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	TRY (ret_value = h5priv_get_attrib_info_by_name (
-		     f->step_gid,
+		     f->iteration_gid,
 		     attrib_name,
 		     attrib_type, attrib_nelem));
 	H5_RETURN (ret_value);
@@ -199,7 +195,7 @@ h5_read_file_attrib (
 }
 
 h5_err_t
-h5_read_step_attrib (
+h5_read_iteration_attrib (
 	const h5_file_t f_,
 	const char* const attrib_name,
 	const h5_types_t attrib_type,
@@ -213,12 +209,10 @@ h5_read_step_attrib (
 			   attrib_name,
 			   (long long int)attrib_type,
 			   attrib_value);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	CHECK_READABLE_MODE (f);
+	check_iteration_is_readable (f);
 	
 	TRY (ret_value = h5priv_read_attrib (
-		     f->step_gid,
+		     f->iteration_gid,
 		     attrib_name,
 		     attrib_type,
 		     attrib_value));
@@ -263,7 +257,7 @@ h5_write_file_attrib (
 }
 
 h5_err_t
-h5_write_step_attrib (
+h5_write_iteration_attrib (
 	const h5_file_t f_,
 	const char* const attrib_name,
 	const h5_types_t attrib_type,
@@ -279,19 +273,17 @@ h5_write_step_attrib (
 			   (long long int)attrib_type,
 			   attrib_value,
 			   (long long)attrib_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	CHECK_WRITABLE_MODE (f);
+	check_iteration_is_writable (f);
 	if (is_appendonly (f)) {
 		TRY (h5priv_append_attrib (
-			     f->step_gid,
+			     f->iteration_gid,
 			     attrib_name,
 			     attrib_type,
 			     attrib_value,
 			     attrib_nelem));
 	} else {
 		TRY (h5priv_write_attrib (
-			     f->step_gid,
+			     f->iteration_gid,
 			     attrib_name,
 			     attrib_type,
 			     attrib_value,

src/h5core/h5_err.c

@@ -9,7 +9,9 @@
 
 #include "h5core/h5_log.h"
 #include "h5core/h5_err.h"
-#include "private/h5_init.h"
+
+extern int h5_myproc;
+
 
 #include <stdlib.h>
 
@@ -101,7 +103,7 @@ h5_verror (
         const char* const fmt,
         va_list ap
         ) {
-	if (h5_log_level == 0) return;
+	if (__h5_log_level == 0) return;
 	char fmt2[2048];
 	snprintf (fmt2,
 		  sizeof(fmt2), "[proc %d] E: %s: %s\n",
@@ -125,7 +127,7 @@ h5_report_errorhandler (
         const char* const fmt,
         va_list ap
         ) {
-	if (h5_log_level > 0) {
+	if (__h5_log_level > 0) {
 		h5_verror (fmt, ap);
 	}
 	return h5_errno;
@@ -142,7 +144,7 @@ h5_abort_errorhandler (
         const char* const fmt,
         va_list ap
         ) {
-	if (h5_log_level > 0) {
+	if (__h5_log_level > 0) {
 		h5_verror (fmt, ap);
 	}
 #ifdef H5_HAVE_PARALLEL

src/h5core/h5_file.c

@@ -42,12 +42,7 @@ h5_check_filehandle (
 	const h5_file_t f_               /*!< filehandle  to check validity of */
 	) {
         h5_file_p f = (h5_file_p)f_;
-	if (f == NULL || f_ == H5_FAILURE || f->file < 0 || f->u == NULL || f->b == NULL) {
-		return h5_error (
-			H5_ERR_BADF,
-			"Called with bad filehandle.");
-	}
-	return H5_SUCCESS;
+	return is_valid_file_handle (f) ? H5_SUCCESS : H5_ERR;
 }
 
 hid_t
@@ -56,7 +51,7 @@ h5_get_hdf5_file(
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (hid_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
+	check_file_handle_is_valid (f);
 	H5_RETURN (f->file);
 }
 
@@ -69,7 +64,7 @@ hdf5_error_handler (
 	void*  __f
 	) {
 	UNUSED_ARGUMENT (__f);
-	if (h5_get_loglevel() >= 5) {
+	if (h5_get_loglevel() >= 4) {
 		H5Eprint (estack_id, stderr);
 	}
 	return 0;
@@ -97,7 +92,7 @@ mpi_init (
 		TRY (hdf5_set_fapl_mpiposix_property (f->props->access_prop,
                                                      f->props->comm, use_gpfs));
 
-        } else if ((f->props->flags & H5_VFD_CORE)) {
+        } else if ((f->props->flags & H5_VFD_CORE_IO)) {
 		h5_info("Selecting CORE VFD");
                 TRY (hdf5_set_fapl_core (f->props->access_prop,
                                          f->props->align, 1));
@@ -117,7 +112,7 @@ mpi_init (
 	}
 #else
 	// VFD_MPIO_POSIX has been removed in HDF5 1.8.13
-        if ((f->props->flags & H5_VFD_CORE)) {
+        if ((f->props->flags & H5_VFD_CORE_IO)) {
 		h5_info("Selecting CORE VFD");
                 TRY (hdf5_set_fapl_core (f->props->access_prop,
                                          f->props->align, 1));
@@ -175,12 +170,12 @@ set_default_file_props (
         h5_prop_file_t* props = (h5_prop_file_t*)_props;
         bzero (props, sizeof (*props));
         props->class = H5_PROP_FILE;
-        TRY (props->prefix_step_name = h5_calloc (1, H5_STEPNAME_LEN));
+        TRY (props->prefix_iteration_name = h5_calloc (1, H5_ITERATION_NAME_LEN));
         strncpy (
-                props->prefix_step_name,
-                H5_STEPNAME,
-                H5_STEPNAME_LEN - 1);
-        props->width_step_idx = H5_STEPWIDTH;
+                props->prefix_iteration_name,
+                H5_ITERATION_NAME,
+                H5_ITERATION_NAME_LEN - 1);
+        props->width_iteration_idx = H5_ITERATION_NUM_WIDTH;
 #ifdef H5_HAVE_PARALLEL
         props->comm = MPI_COMM_WORLD;
 #endif
@@ -202,7 +197,7 @@ h5_set_prop_file_mpio_collective (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_POSIX | H5_VFD_MPIO_INDEPENDENT | H5_VFD_CORE);
+        props->flags &= ~(H5_VFD_MPIO_POSIX | H5_VFD_MPIO_INDEPENDENT | H5_VFD_CORE_IO);
         props->flags |= H5_VFD_MPIO_COLLECTIVE;
         props->comm = *comm;
 	if (props->throttle > 0) {
@@ -230,7 +225,7 @@ h5_set_prop_file_mpio_independent (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE);
+        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE_IO);
         props->flags |= H5_VFD_MPIO_INDEPENDENT;
         props->comm = *comm;
 #else
@@ -255,7 +250,7 @@ h5_set_prop_file_mpio_posix (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE);
+        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE_IO);
         props->flags |= H5_VFD_MPIO_INDEPENDENT;
         props->comm = *comm;
 #else
@@ -271,7 +266,8 @@ h5_set_prop_file_core_vfd (
 	const h5_int64_t increment
         ) {
         h5_prop_file_t* props = (h5_prop_file_t*)_props;
-        H5_CORE_API_ENTER (h5_err_t, "props=%p, increment=%lld", props, (long long int)increment);
+        H5_CORE_API_ENTER (h5_err_t, "props=%p, increment=%lld",
+			   props, (long long int)increment);
         
         if (props->class != H5_PROP_FILE) {
                 H5_RETURN_ERROR (
@@ -280,7 +276,9 @@ h5_set_prop_file_core_vfd (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_INDEPENDENT | H5_VFD_MPIO_POSIX);
+        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE |
+			  H5_VFD_MPIO_INDEPENDENT |
+			  H5_VFD_MPIO_POSIX);
         props->flags |= H5_VFD_MPIO_INDEPENDENT;
         props->comm = MPI_COMM_SELF;
 	props->increment = increment;
@@ -315,26 +313,24 @@ h5_set_prop_file_align (
         H5_RETURN (H5_SUCCESS);
 }
 
-#if 0
 h5_err_t
-h5_set_prop_file_flush_step (
+h5_set_prop_file_flush_after_write (
         h5_prop_t _props
         ) {
         h5_prop_file_t* props = (h5_prop_file_t*)_props;
         H5_CORE_API_ENTER (
 		h5_err_t,
-		"props=%p, align=%lld",
-		props, (long long int)align);
+		"props=%p",
+		props);
         if (props->class != H5_PROP_FILE) {
                 H5_RETURN_ERROR (
 			H5_ERR_INVAL,
 			"Invalid property class: %lld",
 			(long long int)props->class);
         }
-        props-> = align;
+        props->flush = 1;
         H5_RETURN (H5_SUCCESS);
 }
-#endif
 
 h5_err_t
 h5_set_prop_file_throttle (
@@ -411,7 +407,7 @@ h5_close_prop (
         switch (prop->class) {
         case H5_PROP_FILE: {
                 h5_prop_file_t* file_prop = (h5_prop_file_t*)prop;
-                TRY (h5_free (file_prop->prefix_step_name));
+                TRY (h5_free (file_prop->prefix_iteration_name));
                 break;
         }
         default:
@@ -436,14 +432,14 @@ open_file (
 
         f->nprocs = 1; // queried later
         f->myproc = 0; // queried later
-        f->step_gid = -1;
+        f->iteration_gid = -1;
 
-        TRY (f->step_name = h5_calloc (2, H5_STEPNAME_LEN));
+        TRY (f->iteration_name = h5_calloc (2, H5_ITERATION_NAME_LEN));
         sprintf (
-                f->step_name,
+                f->iteration_name,
                 "%s#%0*lld",
-                f->props->prefix_step_name,
-                f->props->width_step_idx, (long long)f->step_idx);
+                f->props->prefix_iteration_name,
+                f->props->width_iteration_idx, (long long)f->iteration_idx);
 
         TRY (hdf5_set_errorhandler (H5E_DEFAULT, hdf5_error_handler, NULL));
         
@@ -526,15 +522,17 @@ h5_open_file2 (
                 f->props->align = props->align;
 
                 strncpy (
-                        f->props->prefix_step_name,
-                        props->prefix_step_name,
-                        H5_STEPNAME_LEN - 1);
-                f->props->width_step_idx = props->width_step_idx;
+                        f->props->prefix_iteration_name,
+                        props->prefix_iteration_name,
+                        H5_ITERATION_NAME_LEN - 1);
+                f->props->width_iteration_idx = props->width_iteration_idx;
         }
 
 	TRY (open_file (f, filename, mode));
 
-        TRY (h5_set_stepname_fmt ((uintptr_t)f, H5_STEPNAME, H5_STEPWIDTH));
+        TRY (h5_set_iteration_name_fmt ((uintptr_t)f,
+					H5_ITERATION_NAME,
+					H5_ITERATION_NUM_WIDTH));
 
 	H5_RETURN ((h5_file_t)f);
 }
@@ -595,9 +593,9 @@ h5_close_file (
 	H5_CORE_API_ENTER (h5_err_t, "f=%p", f);
 	h5_errno = H5_SUCCESS;
 
-	CHECK_FILEHANDLE (f);
+	check_file_handle_is_valid (f);
 
-	TRY (h5priv_close_step (f));
+	TRY (h5priv_close_iteration (f));
 	TRY (h5upriv_close_file (f));
 	TRY (h5bpriv_close_file (f));
 	TRY (hdf5_close_property (f->props->xfer_prop));
@@ -607,7 +605,7 @@ h5_close_file (
         TRY (hdf5_flush (f->file, H5F_SCOPE_GLOBAL));
         TRY (h5_close_prop ((h5_prop_t)f->props));
 	TRY (hdf5_close_file (f->file));
-        TRY (h5_free (f->step_name));
+        TRY (h5_free (f->iteration_name));
  	TRY (h5_free (f));
 	H5_RETURN (H5_SUCCESS);
 }
@@ -617,22 +615,21 @@ h5_close_h5hut (
         void
         ) {
 	H5_CORE_API_ENTER (h5_err_t, "%s", "");
-	TRY (h5priv_finalize ());
+	TRY (h5_finalize ());
 	TRY (hdf5_close ());
 	H5_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
-h5_flush_step (
+h5_flush_iteration (
 	const h5_file_t f_
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (h5_err_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_writable (f);
 	ret_value = H5_SUCCESS;
-	if (f->step_gid >= 0) {
-		TRY (ret_value = hdf5_flush (f->step_gid, H5F_SCOPE_LOCAL));
+	if (f->iteration_gid >= 0) {
+		TRY (ret_value = hdf5_flush (f->iteration_gid, H5F_SCOPE_LOCAL));
 	}
 	H5_RETURN (ret_value);
 }
@@ -643,7 +640,7 @@ h5_flush_file (
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (h5_err_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
+	check_file_is_writable (f);
 	TRY (ret_value = hdf5_flush (f->file, H5F_SCOPE_GLOBAL));
 	H5_RETURN (ret_value);
 }
@@ -652,15 +649,15 @@ h5_flush_file (
 /*!
   \ingroup h5_core_filehandling
 
-  Define format of the step names.
+  Define format of the iteration names.
 
-  Example: ==H5FedDefineStepNameFormat( f, "Step", 6 )== defines step names 
-  like ==Step#000042==.
+  Example: ==h5_set_iteration_name_fmt (f, "Step", 6)==
+  defines iteration names like ==Step#000042==.
 
   \return \c H5_SUCCESS or error code
 */
 h5_err_t
-h5_set_stepname_fmt (
+h5_set_iteration_name_fmt (
 	const h5_file_t f_,
 	const char* name,
 	int width
@@ -669,14 +666,14 @@ h5_set_stepname_fmt (
 	H5_CORE_API_ENTER (h5_err_t,
                            "f=%p, name='%s', width=%d",
                            f, name, width);
-	CHECK_FILEHANDLE (f);
+	check_file_handle_is_valid (f);
 	if (width < 0) width = 0;
-	else if (width > H5_STEPNAME_LEN - 1) width = H5_STEPNAME_LEN - 1;
+	else if (width > H5_ITERATION_NAME_LEN - 1) width = H5_ITERATION_NAME_LEN - 1;
 	strncpy (
-		f->props->prefix_step_name,
+		f->props->prefix_iteration_name,
 		name,
-		H5_STEPNAME_LEN - 1);
-	f->props->width_step_idx = width;
+		H5_ITERATION_NAME_LEN - 1);
+	f->props->width_iteration_idx = width;
 
 	H5_RETURN (H5_SUCCESS);
 }
@@ -684,16 +681,16 @@ h5_set_stepname_fmt (
 /*!
   \ingroup h5_core_filehandling
 
-  Get format of the step names.
+  Get format of the iteration names.
 
   \return \c H5_SUCCESS or error code
 */
 h5_err_t
-h5_get_stepname_fmt (
+h5_get_iteration_name_fmt (
 	const h5_file_t f_,		/*!< Handle to file		*/
-	char* const name,			/*!< OUT: Prefix		*/
-	const int l_name,			/*!< length of buffer name	*/
-	int* const width			/*!< OUT: Width of the number	*/
+	char* const name,		/*!< OUT: Prefix		*/
+	const int l_name,		/*!< length of buffer name	*/
+	int* const width		/*!< OUT: Width of the number	*/
 	) {
         h5_file_p f = (h5_file_p)f_;
 	UNUSED_ARGUMENT (f);
@@ -706,19 +703,18 @@ h5_get_stepname_fmt (
 /*!
   \ingroup h5_core_filehandling
 
-  Get current step number.
+  Get current iteration number.
 
-  \return Current step number or error code
+  \return Current iteration number or error code
 */
 h5_id_t
-h5_get_step (
+h5_get_iteration (
 	const h5_file_t f_		/*!< file handle		*/
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (h5_id_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	H5_RETURN (f->step_idx);
+	check_iteration_is_readable (f);
+	H5_RETURN (f->iteration_idx);
 }
 
 /*!
@@ -734,43 +730,42 @@ h5_get_num_procs (
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (int, "f=%p", f);
-	CHECK_FILEHANDLE (f);
+	check_file_handle_is_valid (f);
 	H5_RETURN (f->nprocs);
 }
 
 /*!
   \ingroup h5_core_filehandling
 
-  Get number of steps.
+  Get number of iterations.
 
-  \return Number of steps or error code
+  \return Number of iterations or error code
 */
 h5_ssize_t
-h5_get_num_steps(
+h5_get_num_iterations (
 	const h5_file_t f_		/*!< file handle		*/
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (int, "f=%p", f);
-	CHECK_FILEHANDLE (f);
+	check_file_handle_is_valid (f);
 	TRY (ret_value = hdf5_get_num_groups_matching_prefix (
 		     f->root_gid,
-		     f->props->prefix_step_name));
+		     f->props->prefix_iteration_name));
 	H5_RETURN (ret_value);
 }
 
 /*!
   \ingroup h5_core_filehandling
 
-  Start traversing steps. 
+  Start traversing iterations.
 
   \return \c H5_SUCCESS or error code 
 */
 h5_err_t
-h5_start_traverse_steps (
+h5_start_traverse_iterations (
 	const h5_file_t f_		/*!< file handle		*/
 	) {
-        h5_file_p f = (h5_file_p)f_;
-	H5_CORE_API_ENTER (int, "f=%p", f);
+	H5_CORE_API_ENTER (int, "f=%p", (void*)f_);
 
 	/*
 	  fast test: Does Step#0 or Step#1 exist?
@@ -784,12 +779,12 @@ h5_start_traverse_steps (
 /*!
   \ingroup h5_core_filehandling
 
-  Go to next step.
+  Go to next iteration.
 
   \return \c H5_SUCCESS or error code 
 */
 h5_err_t
-h5_traverse_steps (
+h5_traverse_iterations (
 	const h5_file_t f_		/*!< file handle		*/
 	) {
         h5_file_p f = (h5_file_p)f_;

src/h5core/h5_init.c

@@ -741,9 +741,10 @@ _h5_exit (int status) {
 }
 
 h5_err_t
-h5priv_initialize (
+h5_initialize (
         void
         ) {
+	if (h5_initialized) return 0;
 	memset (&h5_call_stack, 0, sizeof (h5_call_stack));
 	// must be set here, otherwise next statement will fail!
 	h5_initialized = 1;
@@ -785,7 +786,7 @@ h5priv_initialize (
 }
 
 h5_err_t
-h5priv_finalize (
+h5_finalize (
 	void
 	) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "%s", "void");

src/h5core/h5_log.c

@@ -9,9 +9,13 @@
 
 #include "h5core/h5_log.h"
 #include "h5core/h5_err.h"
-#include "private/h5_init.h"
 
-h5_int32_t			h5_log_level = H5_VERBOSE_ERROR;
+extern int h5_myproc;
+
+
+h5_int64_t			__h5_log_level = H5_VERBOSE_ERROR;
+h5_int64_t			__h5_debug_mask = 0;
+
 struct call_stack		h5_call_stack;
 
 char *h5_rfmts[] = {
@@ -20,7 +24,10 @@ char *h5_rfmts[] = {
 	[e_char_p]		= "%s",
 	[e_void_p]		= "%p",
 	[e_h5_err_t]		= "%lld",
+	[e_h5_int32_t]		= "%ld",
+	[e_h5_uint32_t]		= "%lu",
 	[e_h5_int64_t]		= "%lld",
+	[e_h5_uint64_t]		= "%llu",
 	[e_h5_id_t]		= "%lld",
 	[e_h5_ssize_t]		= "%lld",
 	[e_h5_errorhandler_t]	= "%p",
@@ -56,12 +63,17 @@ char *h5_rfmts[] = {
  */
 h5_err_t
 h5_set_loglevel (
-        const h5_id_t level     /*!< debug level */
+        const h5_int64_t level     /*!< log level */
         ) {
-	if (level < 0)
-		h5_log_level = ((1 << 20) - 1) & ~0x7;
-	else
-		h5_log_level = level;
+	__h5_log_level = level & 0x7;
+	return H5_SUCCESS;
+}
+
+h5_err_t
+h5_set_debug_mask (
+        const h5_int64_t mask     /*!< debug level */
+        ) {
+	__h5_debug_mask = mask;
 	return H5_SUCCESS;
 }
 
@@ -72,11 +84,11 @@ h5_set_loglevel (
 
    \return current debug level
  */
-h5_err_t
+h5_int64_t
 h5_get_loglevel (
         void
         ) {
-	return h5_log_level;
+	return __h5_log_level;
 }
 
 void
@@ -98,7 +110,7 @@ h5_warn (
         const char* fmt,
         ...
         ) {
-	if (h5_log_level >= 2) {
+	if (__h5_log_level >= 2) {
 		va_list ap;
 		va_start (ap, fmt);
 		h5priv_vprintf (stderr, "W", h5_get_funcname(), fmt, ap);
@@ -112,7 +124,7 @@ h5_info (
         const char* fmt,
         ...
         ) {
-	if (h5_log_level >= 3) {
+	if (__h5_log_level >= 3) {
 		va_list ap;
 		va_start (ap, fmt);
 		h5priv_vprintf (stdout, "I", h5_get_funcname(), fmt, ap);
@@ -125,7 +137,7 @@ h5_debug (
         const char* const fmt,
         ...
         ) {
-	if (h5_log_level >= 4) {
+	if (__h5_log_level >= 4) {
 		char prefix[1024];
 		snprintf (prefix, sizeof(prefix), "%*s %s",
 		          h5_call_stack_get_level(), "",

src/h5core/h5_model.c

@@ -15,94 +15,94 @@
 #include "private/h5_model.h"
 
 h5_err_t
-h5priv_close_step (
+h5priv_close_iteration (
 	const h5_file_p f
 	) {
 	H5_PRIV_API_ENTER (h5_err_t, "f=%p", f);
-	if (f->step_gid <= 0)
+	if (f->iteration_gid <= 0)
 		H5_LEAVE (H5_SUCCESS);
-	TRY (hdf5_close_group (f->step_gid));
+	TRY (hdf5_close_group (f->iteration_gid));
 
-	f->step_gid = -1;
+	f->iteration_gid = -1;
 
 	H5_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
-h5_set_step (
+h5_set_iteration (
 	const h5_file_t f_,		/*!< [in]  Handle to open file */
-	const h5_id_t step_idx		/*!< [in]  Step to set. */
+	const h5_id_t iteration_idx	/*!< [in]  Iteration to set. */
 	) {
         h5_file_p f = (h5_file_p)f_;
 	H5_CORE_API_ENTER (h5_err_t,
-                           "f=%p, step_idx=%lld",
-                           f, (long long)step_idx);
+                           "f=%p, iteration_idx=%lld",
+                           f, (long long)iteration_idx);
 	CHECK_FILEHANDLE (f);
-	TRY (h5priv_close_step (f));
-	f->step_idx = step_idx;
+	TRY (h5priv_close_iteration (f));
+	f->iteration_idx = iteration_idx;
 
 	sprintf (
-		f->step_name,
+		f->iteration_name,
 		"%s#%0*lld",
-		f->props->prefix_step_name, f->props->width_step_idx,
-                (long long) f->step_idx);
+		f->props->prefix_iteration_name, f->props->width_iteration_idx,
+                (long long) f->iteration_idx);
 	h5_info (
-		"Open step #%lld for file %lld",
-		(long long)f->step_idx,
+		"Open iteration #%lld in file %lld",
+		(long long)f->iteration_idx,
 		(long long)(size_t) f);
 
 	h5_err_t exists;
-	TRY (exists = hdf5_link_exists (f->file, f->step_name));
+	TRY (exists = hdf5_link_exists (f->file, f->iteration_name));
 	if (exists) {
-		TRY (f->step_gid = h5priv_open_group (
+		TRY (f->iteration_gid = h5priv_open_group (
 			     f->file,
-			     f->step_name));
+			     f->iteration_name));
 	} else if (is_writable (f)) {
-		TRY (f->step_gid = h5priv_create_group (
+		TRY (f->iteration_gid = h5priv_create_group (
 			     f->file,
-			     f->step_name));
+			     f->iteration_name));
 	}
 	H5_RETURN (H5_SUCCESS);
 }
 
 /*
   returns:
-  TRUE (value > 0): if step exists
-  FALSE (i.e. 0): if step does not exist
+  TRUE (value > 0): if iteration exists
+  FALSE (i.e. 0):   if iteration does not exist
   H5_FAILURE: on error
  */
 h5_err_t
-h5_has_step (
+h5_has_iteration (
 	const h5_file_t f_,		/*!< [in]  Handle to open file */
-	const h5_id_t step_idx		/*!< [in]  Step number to query */
+	const h5_id_t iteration_idx	/*!< [in]  Step number to query */
 	) {
         h5_file_p f = (h5_file_p)f_;
-	H5_CORE_API_ENTER (h5_err_t, "f=%p, step_idx=%lld", f, (long long)step_idx);
+	H5_CORE_API_ENTER (h5_err_t,
+			   "f=%p, iteration_idx=%lld",
+			   f, (long long)iteration_idx);
 	CHECK_FILEHANDLE (f);
-	char name[2*H5_STEPNAME_LEN];
+	char name[2*H5_ITERATION_NAME_LEN];
 	sprintf (name,
 		"%s#%0*lld",
-		f->props->prefix_step_name, f->props->width_step_idx,
-		 (long long)step_idx);
+		f->props->prefix_iteration_name, f->props->width_iteration_idx,
+		 (long long)iteration_idx);
         TRY (ret_value = hdf5_link_exists (f->file, name));
 	H5_RETURN (ret_value);
 }
 
 h5_err_t
 h5priv_normalize_dataset_name (
-	const char *name,
-	char *name2
+	char* const name
 	) {
-	H5_CORE_API_ENTER (h5_err_t, "name='%s', name2='%p'", name, name2);
-	if ( strlen(name) > H5_DATANAME_LEN-1 ) {
-		strncpy ( name2, name, H5_DATANAME_LEN-1 );
-		name2[H5_DATANAME_LEN-1] = '\0';
-		h5_warn ("Truncated name '%s' to '%s'.", name, name2);
-	} else {
-		strcpy (name2, name);
+	H5_CORE_API_ENTER (h5_err_t, "name='%s'", name);
+	if (strlen(name) > H5_DATANAME_LEN-1) {
+		H5_RETURN_ERROR (
+			H5_ERR_INVAL,
+			"Dataset name '%s' to long! "
+			"Must be less then %d characters.",
+			 name, H5_DATANAME_LEN);
 	}
-
-	if ( strcmp( name2, H5BLOCK_GROUPNAME_BLOCK ) == 0 ) {
+	if (strcmp (name, H5BLOCK_GROUPNAME_BLOCK) == 0) {
 		H5_RETURN_ERROR (
 			H5_ERR_INVAL,
 			"Can't create dataset or field with name '%s'"

src/h5core/h5b_attribs.c

@@ -33,9 +33,7 @@ h5b_write_field_attrib (
 	                   (long long int)attrib_type,
 	                   attrib_value,
 	                   (long long)attrib_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_WRITABLE_MODE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_writable (f);
 
 	TRY( h5bpriv_create_field_group(f, field_name) );
 	if (is_appendonly (f)) {
@@ -74,8 +72,7 @@ h5b_read_field_attrib (
 	                   attrib_name,
 	                   (long long)attrib_type,
 	                   buffer);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_readable (f);
 
 	TRY (h5bpriv_open_field_group(f, field_name));
 
@@ -102,8 +99,7 @@ h5b_has_field_attrib (
 	                   f,
 	                   field_name,
 	                   attrib_name);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	TRY (h5bpriv_open_field_group(f, field_name));
 
@@ -120,8 +116,7 @@ h5b_get_num_field_attribs (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t, "f=%p field_name='%s'", f, field_name);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	TRY (h5bpriv_open_field_group(f, field_name));
 
@@ -151,8 +146,7 @@ h5b_get_field_attrib_info_by_idx (
 	                   (long long unsigned)attrib_idx,
 	                   attrib_name, (long long unsigned)len_attrib_name,
 	                   attrib_type, attrib_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	TRY (h5bpriv_open_field_group(f, field_name));
 	TRY (ret_value = h5priv_get_attrib_info_by_idx (
 		     f->b->field_gid,
@@ -180,8 +174,7 @@ h5b_get_field_attrib_info_by_name (
 	                   field_name,
 	                   attrib_name,
 	                   attrib_type, attrib_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	TRY (h5bpriv_open_field_group(f, field_name));
 	TRY (ret_value = h5priv_get_attrib_info_by_name (
 		     f->b->field_gid,
@@ -248,8 +241,7 @@ h5b_set_3d_field_coords (
 			   field_name,
                            attrib_name,
 			   coords, (long long unsigned)n_coords);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_writable (f);
 
         TRY (check_coords (f, rank, n_coords));
 	TRY (h5b_write_field_attrib (
@@ -284,8 +276,8 @@ h5b_get_3d_field_coords (
 			   field_name,
                            attrib_name,
 			   coords, (long long unsigned)n_coords);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+
+	check_iteration_is_readable (f);
 
         TRY (check_coords (f, rank, n_coords));
 	TRY (h5b_read_field_attrib (

src/h5core/h5b_io.c

@@ -256,9 +256,7 @@ h5b_write_scalar_data (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, field_name='%s', data=%p, type=%lld",
 	                   f, field_name, data, (long long int)type);
-	CHECK_FILEHANDLE (f);
-	CHECK_WRITABLE_MODE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_writable (f);
 	CHECK_LAYOUT (f);
 
 	TRY (h5bpriv_create_field_group (f, field_name));
@@ -285,9 +283,7 @@ h5b_write_vector3d_data (
 	                   "zdata=%p, "
 	                   "type=%lld",
 	                   f, field_name, xdata, ydata, zdata, (long long int)type);
-	CHECK_FILEHANDLE (f);
-	CHECK_WRITABLE_MODE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_writable (f);
 	CHECK_LAYOUT (f);
 
 	TRY (h5bpriv_create_field_group(f, field_name));
@@ -430,8 +426,7 @@ h5b_read_scalar_data (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, field_name='%s', data=%p, type=%lld",
 	                   f, field_name, data, (long long int)type);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_readable (f);
 	CHECK_LAYOUT (f);
 
 	TRY (h5bpriv_open_field_group(f, field_name));
@@ -457,8 +452,7 @@ h5b_read_vector3d_data (
 	                   "zdata=%p, "
 	                   "type=%lld",
 	                   f, field_name, xdata, ydata, zdata, (long long int)type);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_readable (f);
 	CHECK_LAYOUT (f);
 
 	TRY (h5bpriv_open_field_group(f, field_name));

src/h5core/h5b_model.c

@@ -41,9 +41,8 @@ h5b_has_field_data (
         ) {
         h5_file_p f = (h5_file_p)fh;
         H5_CORE_API_ENTER (h5_err_t, "f=%p", f);
-        CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-        TRY (ret_value = hdf5_link_exists (f->step_gid, H5BLOCK_GROUPNAME_BLOCK));
+	check_iteration_handle_is_valid (f);
+        TRY (ret_value = hdf5_link_exists (f->iteration_gid, H5BLOCK_GROUPNAME_BLOCK));
         H5_RETURN (ret_value);
 }
 
@@ -418,7 +417,6 @@ _dissolve_ghostzones (
 				p_el = p_save;
 			}
 		}
-
 	}
 	h5_free (p_begin);
 	H5_RETURN (H5_SUCCESS);
@@ -453,12 +451,12 @@ h5bpriv_open_block_group (
 	h5b_fdata_t *b = f->b;
 
 	TRY (hdf5_close_group (b->block_gid));
-	b->block_gid = hdf5_open_group (f->step_gid, H5BLOCK_GROUPNAME_BLOCK);
+	b->block_gid = hdf5_open_group (f->iteration_gid, H5BLOCK_GROUPNAME_BLOCK);
 	if (f->b->block_gid < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_INVAL,
 			"%s",
-			"Time step does not contain H5Block data!");
+			"step/iteration does not contain H5Block data!");
 
 	H5_RETURN (H5_SUCCESS);
 }
@@ -469,14 +467,14 @@ _create_block_group (
 	) {
 	H5_PRIV_FUNC_ENTER (h5_err_t, "f=%p", f);
 	h5_err_t exists;
-	TRY (exists = hdf5_link_exists (f->step_gid, H5BLOCK_GROUPNAME_BLOCK));
+	TRY (exists = hdf5_link_exists (f->iteration_gid, H5BLOCK_GROUPNAME_BLOCK));
 
 	if (exists > 0) {
 		TRY (h5bpriv_open_block_group(f));
 	} else {
 		TRY (hdf5_close_group(f->b->block_gid) );
 		TRY (f->b->block_gid = hdf5_create_group(
-			     f->step_gid, H5BLOCK_GROUPNAME_BLOCK) );
+			     f->iteration_gid, H5BLOCK_GROUPNAME_BLOCK) );
 	}
 	H5_RETURN (H5_SUCCESS);
 }
@@ -484,19 +482,18 @@ _create_block_group (
 h5_err_t
 h5bpriv_open_field_group (
 	const h5_file_p f,			/*!< IN: file handle */
-	const char *name
+	char* const name
 	) {
 	H5_PRIV_API_ENTER (h5_err_t, "f=%p, name='%s'", f, name);
-	char name2[H5_DATANAME_LEN];
-	h5priv_normalize_dataset_name (name, name2);
+	h5priv_normalize_dataset_name (name);
 
 	TRY (hdf5_close_group (f->b->field_gid));
 	TRY (h5bpriv_open_block_group (f));
-	f->b->field_gid = hdf5_open_group (f->b->block_gid, name2);
+	f->b->field_gid = hdf5_open_group (f->b->block_gid, name);
 	if (f->b->field_gid < 0)
 		return h5_error(
 		               H5_ERR_INVAL,
-		               "Field '%s' does not exist!", name2);
+		               "Field '%s' does not exist!", name);
 
 	H5_RETURN (H5_SUCCESS);
 }
@@ -504,24 +501,23 @@ h5bpriv_open_field_group (
 h5_err_t
 h5bpriv_create_field_group (
 	const h5_file_p f,		/*!< IN: file handle */
-	const char *name		/*!< IN: name of field group to create */
+	char* const name		/*!< IN: name of field group to create */
 	) {
 	H5_PRIV_API_ENTER (h5_err_t, "f=%p, name='%s'", f, name);
 	h5b_fdata_t *b = f->b;
 
 	TRY( _create_block_group(f) );
 
-	char name2[H5_DATANAME_LEN];
-	h5priv_normalize_dataset_name (name, name2);
+	h5priv_normalize_dataset_name (name);
 
 	h5_err_t exists;
-	TRY (exists = hdf5_link_exists ( b->block_gid, name2));
+	TRY (exists = hdf5_link_exists ( b->block_gid, name));
 
 	if (exists > 0) {
-		TRY (h5bpriv_open_field_group (f, name2));
+		TRY (h5bpriv_open_field_group (f, name));
 	} else {
 		TRY (hdf5_close_group (f->b->field_gid) );
-		TRY (b->field_gid = hdf5_create_group (b->block_gid, name2));
+		TRY (b->field_gid = hdf5_create_group (b->block_gid, name));
 	}
 
 	H5_RETURN (H5_SUCCESS);
@@ -535,8 +531,7 @@ h5b_3d_has_view (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, ",
 	                   f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	H5_RETURN (((h5_file_p)fh)->b->have_layout > 0);
 }
 
@@ -548,7 +543,8 @@ h5b_3d_set_view (
 	const h5_size_t j_start,	/*!< IN: start index of \c j	*/ 
 	const h5_size_t j_end,		/*!< IN: end index of \c j	*/ 
 	const h5_size_t k_start,	/*!< IN: start index of \c k	*/ 
-	const h5_size_t k_end		/*!< IN: end index of \c k	*/
+	const h5_size_t k_end,		/*!< IN: end index of \c k	*/
+        const h5_int64_t dissolve_ghostzones /*!< IN: bool: dissolve ghost-zones */ 
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t,
@@ -560,8 +556,7 @@ h5b_3d_set_view (
 	                   (long long unsigned)i_start, (long long unsigned)i_end,
 	                   (long long unsigned)j_start, (long long unsigned)j_end,
 	                   (long long unsigned)k_start, (long long unsigned)k_end);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5b_fdata_t *b = f->b;
 	b->user_layout[0].i_start = i_start;
 	b->user_layout[0].i_end =   i_end;
@@ -576,7 +571,6 @@ h5b_3d_set_view (
 	h5b_partition_t *write_layout;
 
 	TRY (user_layout =  h5_calloc (f->nprocs, sizeof (*user_layout)));
-	TRY (write_layout = h5_calloc (f->nprocs, sizeof (*write_layout)));
 
         user_layout[f->myproc] = b->user_layout[0];
 
@@ -585,11 +579,7 @@ h5b_3d_set_view (
                      user_layout, 1, f->b->partition_mpi_t, f->props->comm));
 
 	_get_max_dimensions(f, user_layout);
-
-	TRY (_dissolve_ghostzones (f, user_layout, write_layout));
-	b->user_layout[0] = user_layout[f->myproc];
-	b->write_layout[0] = write_layout[f->myproc];
-
+	//b->user_layout[0] = user_layout[f->myproc];
 	h5_debug (
 		"User layout: %lld:%lld, %lld:%lld, %lld:%lld",
 		(long long)b->user_layout[0].i_start,
@@ -599,17 +589,25 @@ h5b_3d_set_view (
 		(long long)b->user_layout[0].k_start,
                 (long long)b->user_layout[0].k_end );
 
-	h5_debug (
-		"Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld",
-		(long long)b->write_layout[0].i_start,
-                (long long)b->write_layout[0].i_end,
-		(long long)b->write_layout[0].j_start,
-                (long long)b->write_layout[0].j_end,
-		(long long)b->write_layout[0].k_start,
-                (long long)b->write_layout[0].k_end );
+        if (dissolve_ghostzones) {
+                TRY (write_layout = h5_calloc (f->nprocs, sizeof (*write_layout)));
+                TRY (_dissolve_ghostzones (f, user_layout, write_layout));
+                b->write_layout[0] = write_layout[f->myproc];
+
+                h5_debug (
+                        "Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld",
+                        (long long)b->write_layout[0].i_start,
+                        (long long)b->write_layout[0].i_end,
+                        (long long)b->write_layout[0].j_start,
+                        (long long)b->write_layout[0].j_end,
+                        (long long)b->write_layout[0].k_start,
+                        (long long)b->write_layout[0].k_end );
+                h5_free(write_layout);
+        } else {
+                b->write_layout[0] = b->user_layout[0];
+        }
 
 	h5_free(user_layout);
-	h5_free(write_layout);
 #else
 	b->write_layout[0] = b->user_layout[0];
 	b->i_max = b->user_layout->i_end;
@@ -642,8 +640,7 @@ h5b_3d_get_view (
 	                   i_start, i_end,
 	                   j_start, j_end,
 	                   k_start, k_end);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5b_partition_t *p = f->b->user_layout;
 
 	*i_start = p->i_start;
@@ -676,8 +673,7 @@ h5b_3d_get_reduced_view (
 	                   i_start, i_end,
 	                   j_start, j_end,
 	                   k_start, k_end);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5b_partition_t *p = f->b->write_layout;
 
 	*i_start = p->i_start;
@@ -704,8 +700,7 @@ h5b_3d_set_chunk (
 	                   (long long unsigned)i,
 	                   (long long unsigned)j,
 	                   (long long unsigned)k);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	if ( i == 0 || j == 0 || k == 0 )
 	{
 		h5_info ("Disabling chunking" );
@@ -724,21 +719,20 @@ h5b_3d_set_chunk (
 h5_err_t
 h5b_3d_get_chunk (
 	const h5_file_t fh,		/*!< IN: File handle */
-	const char *field_name, 	/*!< IN: name of dataset */
-	h5_size_t *const i,		/*!< OUT: size of \c i */ 
-	h5_size_t *const j,		/*!< OUT: size of \c j */  
-	h5_size_t *const k		/*!< OUT: size of \c k */ 
+	char* const field_name, 	/*!< IN: name of dataset */
+	h5_size_t* const i,		/*!< OUT: size of \c i */ 
+	h5_size_t* const j,		/*!< OUT: size of \c j */  
+	h5_size_t* const k		/*!< OUT: size of \c k */ 
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, i=%p, j=%p, k=%p",
 	                   f, i, j, k);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	h5b_fdata_t *b = f->b;
 
-	TRY( h5bpriv_open_field_group ( f, field_name ) );
+	TRY (h5bpriv_open_field_group (f, field_name));
 
 	hid_t dataset_id;
 	hid_t plist_id;
@@ -776,8 +770,7 @@ h5b_3d_set_grid (
 	                   (long long unsigned)i,
 	                   (long long unsigned)j,
 	                   (long long unsigned)k);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	if (i*j*k != f->nprocs) {
 		H5_RETURN_ERROR (
 		        H5_ERR_INVAL,
@@ -793,9 +786,9 @@ h5b_3d_set_grid (
 	f->b->j_grid = j;
 	f->b->i_grid = k;
 
+#ifdef H5_HAVE_PARALLEL
 	int dims[3] = { k, j, i };
 	int period[3] = { 0, 0, 0 };
-#ifdef H5_HAVE_PARALLEL
 	TRY( h5priv_mpi_cart_create(
 	             f->props->comm, 3, dims, period, 0, &f->b->cart_comm) );
 #else
@@ -817,8 +810,7 @@ h5b_3d_get_grid_coords (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, proc=%d, i=%p, j=%p, k=%p",
 	                   f, proc, i, j, k);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	if ( !f->b->have_grid )
 		H5_RETURN_ERROR (
 		        H5_ERR_INVAL,
@@ -852,8 +844,7 @@ h5b_3d_set_dims (
 	                   (long long unsigned)i,
 	                   (long long unsigned)j,
 	                   (long long unsigned)k);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	if ( !f->b->have_grid )
 		H5_RETURN_ERROR (
 		        H5_ERR_INVAL,
@@ -924,8 +915,7 @@ h5b_3d_set_halo (
 	                   (long long unsigned)j,
 	                   (long long unsigned)k);
 
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	if ( !f->b->have_grid ) {
 		H5_RETURN_ERROR (
 		        H5_ERR_INVAL,
@@ -955,8 +945,7 @@ h5b_get_num_fields (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	TRY (h5bpriv_open_block_group(f));
 	TRY (ret_value = hdf5_get_num_objs_in_group (f->b->block_gid));
@@ -972,35 +961,33 @@ h5b_has_field (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, name='%s'",
 	                   f, name);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	const char* path[] = { H5BLOCK_GROUPNAME_BLOCK, name };
-	TRY (ret_value = h5priv_link_exists_(f->step_gid, path, 2));
+	TRY (ret_value = h5priv_link_exists_(f->iteration_gid, path, 2));
 	H5_RETURN (ret_value);
 }
 
 h5_err_t
 h5b_get_field_info_by_name (
 	const h5_file_t fh,			/*!< IN:  file handle */
-	const char *name,			/*!< IN:  field name */
-	h5_size_t *field_rank,			/*!< OUT: field rank */
-	h5_size_t *field_dims,			/*!< OUT: field dimensions */
-	h5_size_t *elem_rank,			/*!< OUT: element rank */
-	h5_int64_t *type			/*!< OUT: datatype */
+	char* const name,			/*!< IN:  field name */
+	h5_size_t* field_rank,			/*!< OUT: field rank */
+	h5_size_t* field_dims,			/*!< OUT: field dimensions */
+	h5_size_t* elem_rank,			/*!< OUT: element rank */
+	h5_int64_t* type			/*!< OUT: datatype */
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, name='%s', "
 	                   "field_rank=%p, field_dims=%p, elem_rank=%p, type=%p",
 	                   f, name, field_rank, field_dims, elem_rank, type);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	/* give it plenty of space even though we don't expect rank > 3 */
 	hsize_t dims[16];
 
-	TRY( h5bpriv_open_field_group(f, name) );
+	TRY (h5bpriv_open_field_group (f, name));
 
 	hid_t dataset_id;
 	hid_t dataspace_id;
@@ -1054,8 +1041,7 @@ h5b_get_field_info (
 	                   (long long unsigned)idx,
 	                   name, (long long unsigned)len_name,
 	                   field_rank, field_dims, elem_rank, type);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 
 	TRY (h5bpriv_open_block_group(f));
 	TRY (hdf5_get_objname_by_idx(

src/h5core/h5t_io.c

@@ -2002,7 +2002,7 @@ distribute_octree_parmetis (
 	TRY (vtxdist = h5_calloc (m->f->nprocs+1, sizeof (*vtxdist)));
 	vtxdist[0] = 0;
 #if !defined(NDEBUG)
-	if (h5_log_level & (1<<5) ) {
+	if (__h5_debug_mask & (1<<5) ) {
 		h5_debug ("vtxdist[%d]: %d", 0, 0);
 	}
 #endif
@@ -2014,7 +2014,7 @@ distribute_octree_parmetis (
 			vtxdist[i] = vtxdist[i-1] + n;
 		}
 #if !defined(NDEBUG)
-		if (h5_log_level & (1<<5) ) {
+		if (__h5_debug_mask & (1<<5) ) {
 			h5_debug ("vtxdist[%d]: %d", i, vtxdist[i]);
 		}
 #endif
@@ -2060,7 +2060,7 @@ distribute_octree_parmetis (
 			}
 			xadj[i+1] = xadj[i] + num_neigh;
 #if !defined(NDEBUG)
-			if (h5_log_level & (1<<5) ) {
+			if (__h5_debug_mask & (1<<5) ) {
 				h5_debug ("xadj[%d]: %d", i+1, xadj[i+1]);
 			}
 #endif
@@ -2070,7 +2070,7 @@ distribute_octree_parmetis (
 					if (new_numbering[j] == neighbors[k]) {
 						adjncy[counter] = j;
 #if !defined(NDEBUG)
-						if (h5_log_level & (1<<5) ) {
+						if (__h5_debug_mask & (1<<5) ) {
 							h5_debug ("adjncy[%d]: %d", counter, adjncy[counter]);
 						}
 #endif
@@ -2139,7 +2139,7 @@ distribute_octree_parmetis (
 		TRY (h5_free (ubvec));
 
 #if !defined(NDEBUG)
-		if (h5_log_level & (1<<5) ) {
+		if (__h5_debug_mask & (1<<5) ) {
 			for (i = 0; i < num_interior_oct; i++) {
 				h5_debug ("part[%d]: %llu", i, (unsigned long long)part[i]);
 			}
@@ -2498,7 +2498,7 @@ read_chunked_elements (
 
 
 #if NDEBUG == 0
-	if (h5_log_level & (1<<6) ) {
+	if (__h5_debug_mask & (1<<6) ) {
 		sleep (m->f->myproc*2);
 		for (int i = 0; i < num_interior_elems;i++) {
 			h5_debug ("\n"

src/h5core/h5t_model.c

@@ -23,8 +23,6 @@
 #include "private/h5t_io.h"
 #include "private/h5t_tags.h"
 
-#include "private/h5_init.h"
-
 #include "h5core/h5_model.h"
 #include "private/h5t_core.h"
 #include "private/h5t_store.h"

src/h5core/h5t_store.c

@@ -17,7 +17,6 @@
 #include "private/h5t_store.h"
 #include "private/h5t_core.h"
 #include "private/h5t_io.h"
-#include "private/h5_init.h"
 #include "private/h5_file.h"
 #include "private/h5_mpi.h"
 
@@ -687,6 +686,8 @@ rebuild_map_elem_g2l (
 	h5priv_sort_idxmap (map);
 	H5_RETURN (H5_SUCCESS);
 }
+
+#if defined(WITH_PARALLEL_H5GRID)
 /*
    Rebuild mapping of global element indices to their local indices.
  */
@@ -716,6 +717,7 @@ rebuild_map_elem_g2l_partial (
 	h5priv_sort_idxmap (map);
 	H5_RETURN (H5_SUCCESS);
 }
+#endif
 
 h5_err_t
 h5t_end_store_elems (

src/h5core/h5t_tags.c

@@ -21,8 +21,6 @@
 #include "private/h5t_model.h"
 #include "private/h5t_tags.h"
 
-#include "private/h5_init.h"
-
 #include <assert.h>
 
 static h5_err_t

src/h5core/h5u_io.c

@@ -76,9 +76,9 @@ h5upriv_close_file (
 }
 
 h5_err_t
-h5u_read_data (
+h5u_read_dataset (
 	const h5_file_t fh,	/*!< [in] Handle to open file */
-	const char* name,	/*!< [in] Name to associate dataset with */
+	char* const name,	/*!< [in] Name to associate dataset with */
 	void* data,		/*!< [out] Array of data */
 	const h5_types_t type
 	) {
@@ -86,36 +86,30 @@ h5u_read_data (
 	H5_CORE_API_ENTER (h5_err_t,
 			   "f=%p, name='%s', data=%p, type=%lld",
 	                   f, name, data, (long long int)type);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_is_readable (f);
 
+	TRY (h5priv_normalize_dataset_name (name));
 	hid_t hdf5_type;
 	TRY (hdf5_type = h5priv_map_enum_to_normalized_type (type));
-	
-	struct h5u_fdata *u = f->u;
-	hid_t dataset_id;
-	hid_t space_id;
-	hid_t memspace_id;
-	hsize_t ndisk, nread, nmem;
-
-	if ( f->step_gid < 0 ) {
-		TRY (h5_set_step ((h5_file_t)f, f->step_idx));
+	if ( f->iteration_gid < 0 ) {
+		TRY (h5_set_iteration ((h5_file_t)f, f->iteration_idx));
 	}
 
-	char name2[H5_DATANAME_LEN];
-	TRY (h5priv_normalize_dataset_name (name, name2));
-
-	TRY (dataset_id = hdf5_open_dataset_by_name (f->step_gid, name2));
+	hid_t dataset_id;
+	TRY (dataset_id = hdf5_open_dataset_by_name (f->iteration_gid, name));
 
+	
 	/* default spaces, if not using a view selection */
-	memspace_id = H5S_ALL;
+	hid_t memspace_id = H5S_ALL;
+	hid_t space_id;
 	TRY (space_id = hdf5_get_dataset_space (dataset_id));
 
 	/* get the number of elements on disk for the datset */
+	hsize_t ndisk;
 	TRY (ndisk = hdf5_get_npoints_of_dataspace (space_id));
-
-	if (u->diskshape != H5S_ALL) {
-		TRY (nread = hdf5_get_selected_npoints_of_dataspace (u->diskshape));
+	hsize_t nread;
+	if (f->u->diskshape != H5S_ALL) {
+		TRY (nread = hdf5_get_selected_npoints_of_dataspace (f->u->diskshape));
 
 		/* make sure the disk space selected by the view doesn't
 		 * exceed the size of the dataset */
@@ -131,7 +125,7 @@ h5u_read_data (
 			        "Ignoring view: dataset[%s] has fewer "
 			        "elements on disk (%lld) than are selected "
 			        "(%lld).",
-			        name2, (long long)ndisk, (long long)nread );
+			        name, (long long)ndisk, (long long)nread );
 			nread = ndisk;
 		}
 	} else {
@@ -140,8 +134,9 @@ h5u_read_data (
 		nread = ndisk;
 	}
 
-	if (u->memshape != H5S_ALL) {
-		TRY (nmem = hdf5_get_npoints_of_dataspace (u->memshape));
+	if (f->u->memshape != H5S_ALL) {
+		hid_t nmem;
+		TRY (nmem = hdf5_get_npoints_of_dataspace (f->u->memshape));
 
 		/* make sure the memory space selected by the view has
 		 * enough capacity for the read */
@@ -154,7 +149,7 @@ h5u_read_data (
 			        "Ignoring view: dataset[%s] has more "
 			        "elements selected (%lld) than are available "
 			        "in memory (%lld).",
-			        name2, (long long)nread, (long long)nmem );
+			        name, (long long)nread, (long long)nmem );
 			memspace_id = H5S_ALL;
 		}
 	}
@@ -177,63 +172,88 @@ h5u_read_data (
 }
 
 h5_err_t
-h5u_write_data (
+h5u_write (
 	const h5_file_t fh,	/*!< IN: Handle to open file */
-	const char *name,	/*!< IN: Name to associate array with */
-	const void *data,	/*!< IN: Array to commit to disk */
+	hid_t dset_id,
+	hid_t type,
+	const void* data
+	) {
+	h5_file_p f = (h5_file_p)fh;
+	H5_CORE_API_ENTER (h5_err_t,
+			   "f=%p, dset_id=%lld, type=%lld, data=%p",
+	                   f, (long long)dset_id, (long long int)type, data);
+	TRY (h5priv_start_throttle (f));
+	hid_t hdf5_type;
+	TRY (hdf5_type = h5priv_map_enum_to_normalized_type (type));
+	TRY (hdf5_write_dataset (
+	             dset_id,
+	             hdf5_type,
+	             f->u->memshape,
+	             f->u->diskshape,
+	             f->props->xfer_prop,
+	             data));
+	TRY (h5priv_end_throttle (f));
+	f->empty = 0;
+	if (f->props->flush) {
+		TRY (hdf5_flush (f->iteration_gid, H5F_SCOPE_LOCAL));
+	}
+	H5_RETURN (H5_SUCCESS);
+}	
+
+hid_t
+h5u_open_dataset (
+	const h5_file_t fh,	/*!< IN: Handle to open file */
+	char* const name,	/*!< IN: Name to associate array with */
 	const h5_types_t type	/*!< IN: Type of data */
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t,
-			   "f=%p, name='%s', data=%p, type=%lld",
-	                   f, name, data, (long long int)type);
-	CHECK_FILEHANDLE (f);
-	CHECK_WRITABLE_MODE (f);
-	CHECK_TIMEGROUP (f);
+			   "f=%p, name='%s', type=%lld",
+	                   f, name, (long long int)type);
+	check_iteration_handle_is_valid (f);
+
+	TRY (h5priv_normalize_dataset_name (name));
 	hid_t hdf5_type;
 	TRY (hdf5_type = h5priv_map_enum_to_normalized_type (type));
-	
-	struct h5u_fdata *u = f->u;
-	hid_t dset_id;
+	if ( f->iteration_gid < 0 ) {
+		TRY (h5_set_iteration ((h5_file_t)f, f->iteration_idx));
+	}
 
-	char name2[H5_DATANAME_LEN];
-	TRY (h5priv_normalize_dataset_name (name, name2));
-
-	if ( u->shape == H5S_ALL )
+	if (f->u->shape == H5S_ALL )
 		h5_warn("The view is unset or invalid.");
 
-	/* test for existing dataset */
+	hid_t dset_id;
 	H5E_BEGIN_TRY
-	        dset_id = H5Dopen(f->step_gid, name2, H5P_DEFAULT);
+	        dset_id = H5Dopen(f->iteration_gid, name, H5P_DEFAULT);
 	H5E_END_TRY
 
 	if (dset_id > 0) {
 		h5_warn("Dataset %s/%s already exists",
-		        hdf5_get_objname(f->step_gid), name2);
+		        hdf5_get_objname (f->iteration_gid), name);
 	} else {
 		TRY (dset_id = hdf5_create_dataset (
-		             f->step_gid,
-		             name2,
+		             f->iteration_gid,
+		             name,
 		             hdf5_type,
-		             u->shape,
+		             f->u->shape,
 		             H5P_DEFAULT));
 	}
+	H5_RETURN (dset_id);
+}
 
-	TRY (h5priv_start_throttle (f));
-	h5_info ("Writing dataset %s/%s.",
-	         hdf5_get_objname(f->step_gid), name2);
-	TRY (hdf5_write_dataset (
-	             dset_id,
-	             hdf5_type,
-	             u->memshape,
-	             u->diskshape,
-	             f->props->xfer_prop,
-	             data));
-	TRY (h5priv_end_throttle (f));
-	TRY (hdf5_close_dataset (dset_id));
-
-	f->empty = 0;
-	TRY (hdf5_flush (f->step_gid, H5F_SCOPE_LOCAL));
-
+h5_err_t
+h5u_write_dataset (
+	const h5_file_t fh,	/*!< IN: Handle to open file */
+	char* const name,	/*!< IN: Name to associate array with */
+	const void* data,	/*!< IN: Array to commit to disk */
+	const h5_types_t type	/*!< IN: Type of data */
+	) {
+	H5_CORE_API_ENTER (h5_err_t,
+			   "f=%p, name='%s', data=%p, type=%lld",
+	                   (void*)fh, name, data, (long long int)type);
+	hid_t dset_id;
+	TRY (dset_id = h5u_open_dataset (fh, name, type));
+	TRY (h5u_write (fh, dset_id, type, data));
+        TRY (hdf5_close_dataset(dset_id));
 	H5_RETURN (H5_SUCCESS);
 }

src/h5core/h5u_model.c

@@ -22,21 +22,20 @@
 #include <string.h>
 
 h5_ssize_t
-h5u_get_num_points (
+h5u_get_num_items (
 	const h5_file_t fh      /*!< [in]  Handle to open file */
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5_ssize_t nparticles;
 
 	if (h5u_has_view ((h5_file_t)f)) {
                 /* if a view exists, use its size as the number of particles */
-		TRY (nparticles = h5u_get_num_points_in_view (fh));
+		TRY (nparticles = h5u_get_num_items_in_view (fh));
 	} else {
 		/* otherwise, report all particles on disk in the first dataset
-                   for this timestep */
+                   for this iteration */
                 TRY (nparticles = h5u_get_totalnum_particles_by_idx (fh, 0));
 	}
 
@@ -44,13 +43,12 @@ h5u_get_num_points (
 }
 
 h5_ssize_t
-h5u_get_num_points_in_view (
+h5u_get_num_items_in_view (
 	const h5_file_t fh      /*!< [in]  Handle to open file */
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5_ssize_t nparticles;
 
 	if (!h5u_has_view (fh)) {
@@ -73,16 +71,26 @@ h5u_get_totalnum_particles_by_name (
 	H5_CORE_API_ENTER (h5_ssize_t,
 			   "f=%p, dataset_name=%s",
 			   f, dataset_name);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5_ssize_t nparticles;
         TRY (nparticles = hdf5_get_npoints_of_dataset_by_name (
-		     f->step_gid, dataset_name));
+		     f->iteration_gid, dataset_name));
         h5_debug ("Found %lld particles in dataset %s.",
 		  (long long)nparticles, dataset_name);
 	H5_RETURN (nparticles);
 }
 
+/*
+  Query number of items in dataset in current timestep. Dataset is
+  given by index.
+
+  returns:
+    H5_NOK if dataset does not exist
+    H5_ERROR on error
+    else number of items
+
+*/
+
 h5_ssize_t
 h5u_get_totalnum_particles_by_idx (
 	const h5_file_t fh,     ///< [in] Handle to open file
@@ -90,13 +98,12 @@ h5u_get_totalnum_particles_by_idx (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p, idx=%lld", f, (long long)idx);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
         char dataset_name[H5_DATANAME_LEN];
         dataset_name[0] = '\0';
 	h5_err_t h5err;
         TRY (h5err = hdf5_get_name_of_dataset_by_idx (
-                    f->step_gid,
+                    f->iteration_gid,
                     idx,
                     dataset_name,
                     H5_DATANAME_LEN));
@@ -104,14 +111,14 @@ h5u_get_totalnum_particles_by_idx (
 		H5_LEAVE (H5_NOK);
 	h5_ssize_t nparticles;
         TRY (nparticles = hdf5_get_npoints_of_dataset_by_name (
-		     f->step_gid, dataset_name));
+		     f->iteration_gid, dataset_name));
         h5_debug ("Found %lld particles in dataset %s.",
 		  (long long)nparticles, dataset_name);
 	H5_RETURN (nparticles);
 }
 
 h5_err_t
-h5u_set_num_points (
+h5u_set_num_items (
 	const h5_file_t fh,		/*!< [in] Handle to open file */
 	const h5_size_t nparticles,	/*!< [in] Number of particles */
 	const h5_size_t stride		/*!< [in] Stride of particles in memory */
@@ -122,10 +129,9 @@ h5u_set_num_points (
 	                   f, (long long unsigned)nparticles,
 	                   (long long unsigned)stride);
 	CHECK_FILEHANDLE (f);
-	if (f->step_gid < 0) {
-                TRY (h5_set_step (fh, 0));
+	if (f->iteration_gid < 0) {
+                TRY (h5_set_iteration (fh, 0));
         }
-	CHECK_TIMEGROUP (f);
 	struct h5u_fdata *u = f->u;
 	hsize_t start;
 	hsize_t dmax = H5S_UNLIMITED;
@@ -146,6 +152,8 @@ h5u_set_num_points (
 
 	TRY (hdf5_close_dataspace (u->shape));
 	u->shape = H5S_ALL;
+        TRY (hdf5_close_dataspace (u->memshape));
+        u->memshape = H5S_ALL;
 
 	u->nparticles = (hsize_t)nparticles;
 
@@ -206,7 +214,8 @@ h5u_set_num_points (
 	TRY( u->shape = hdf5_create_dataspace(1, &count, NULL) );
 
 	/* declare overall data size  but then will select a subset */
-	TRY( u->diskshape = hdf5_create_dataspace(1, &count, NULL) );
+        TRY (hdf5_close_dataspace (u->diskshape));
+        TRY (u->diskshape = hdf5_create_dataspace(1, &count, NULL));
 
 	count = nparticles;
 	if (count > 0) {
@@ -229,8 +238,7 @@ h5u_has_view (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	H5_RETURN (f->u->viewindexed || f->u->viewstart >= 0);
 }
 
@@ -240,8 +248,7 @@ h5u_reset_view (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	struct h5u_fdata *u = f->u;
 
 	u->viewstart = -1;
@@ -270,10 +277,7 @@ h5u_set_view (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, start=%lld, end=%lld",
 	                   f, (long long)start, (long long)end);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	hsize_t total = 0;
-	hsize_t dmax = H5S_UNLIMITED;
+	check_iteration_handle_is_valid (f);
 	struct h5u_fdata *u = f->u;
 
 	TRY (h5u_reset_view (fh));
@@ -281,72 +285,49 @@ h5u_set_view (
 	if (start == -1 && end == -1)   // we are already done
 		H5_LEAVE (H5_SUCCESS);
 
+	hssize_t total = 0;
 	if (f->u->shape > 0) {
 		TRY (total = hdf5_get_npoints_of_dataspace (f->u->shape) );
         } else {
-                TRY (total = (hsize_t)h5u_get_totalnum_particles_by_idx (fh, 0));
+		// if iteration does not contain a dataset, next function
+		// returns -1
+                TRY (total = h5u_get_totalnum_particles_by_idx (fh, 0));
         }
 	h5_debug ("Total = %lld", (long long) total);
-	if ((long long)total <= 0) {
+	if (total <= 0) {
 		/*
-		  No datasets have been created yet and no views are set.
-		  We have to leave the view empty because we don't know how
-		  many particles there should be!
-
-		  :FIXME: Should 'total == 0' be considered valid or not?
-		  :FIXME: why not gather total size?
+		  iteration does not contain a dataset yet! 
+		*/
+		/*
+		  :FIXME: Should 'total == 0' be considered valid or not?
 		*/
-		if (start < 0) {
-			H5_RETURN_ERROR (
-				H5_ERR_INVAL,
-				"Start of selection '%lld' out of range: "
-				"must be >= 0",
-				(long long)start);
-		}
-		if (end < start) {
-			H5_RETURN_ERROR (
-				H5_ERR_INVAL,
-				"End of selection '%lld' out of range: "
-				"must be >= %lld",
-				(long long)end,
-				(long long)start);
-		}
 #if H5_HAVE_PARALLEL
 		TRY (
 			h5priv_mpi_allreduce_max (
 			     &end, &total, 1, MPI_LONG_LONG, f->props->comm)
 			);
 #else
-		total = end - start;
+		total = end;
 #endif
 		total++;
-		TRY (h5u_reset_view(fh));
-
 		TRY (hdf5_close_dataspace (u->shape));
-		TRY (u->shape = hdf5_create_dataspace(1, &total, NULL) );
+		hsize_t htotal = (hsize_t)total;
+		TRY (u->shape = hdf5_create_dataspace(1, &htotal, NULL) );
 	} else {
 		if (end < 0) {
-			end = total+end;
-		}
-	
-		if (start < 0 || start >= total) {
-			H5_RETURN_ERROR (
-				H5_ERR_INVAL,
-				"Start of selection '%lld' out of range: "
-				"must be in [0..%lld]",
-				(long long)start, (long long)total-1);
-		} else if (end < 0 || end >= total) {
-			H5_RETURN_ERROR (
-				H5_ERR_INVAL,
-				"End of selection '%lld' out of range: "
-				"must be in [0..%lld]",
-				(long long)end, (long long)total-1);
-		} else if (end+1 < start) {
-			H5_RETURN_ERROR (
-				H5_ERR_INVAL,
-				"Invalid selection: start=%lld > end=%lld!\n",
-				(long long)start, (long long)end);
+			end = total + end;
 		}
+	}	
+	if ((start < 0)      ||
+	    (start >= total) ||
+	    (end >= total)   ||
+	    (end+1 < start)) {
+		H5_RETURN_ERROR (
+			H5_ERR_INVAL,
+			"Invalid view: start=%lld, end=%lld, total=%lld!",
+			(long long)start,
+			(long long)end,
+			(long long)total);
 	}
 	
 	/* setting up the new view */
@@ -361,8 +342,9 @@ h5u_set_view (
 	        "This view includes %lld particles.",
 	        (long long)u->nparticles );
 
+	hsize_t htotal = (hsize_t)total;
 	/* declare overall data size  but then will select a subset */
-	TRY (u->diskshape = hdf5_create_dataspace ( 1, &total, NULL ));
+	TRY (u->diskshape = hdf5_create_dataspace (1, &htotal, NULL));
 
 	hsize_t hstart = (hsize_t)start;
 	hsize_t hstride = 1;
@@ -375,6 +357,7 @@ h5u_set_view (
 	             NULL));
 
 	/* declare local memory datasize */
+	hsize_t dmax = H5S_UNLIMITED;
 	TRY (u->memshape = hdf5_create_dataspace (1, &hcount, &dmax));
 	H5_RETURN (H5_SUCCESS);
 }
@@ -389,8 +372,7 @@ h5u_set_view_length (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, start=%lld, length=%lld",
 	                   f, (long long)start, (long long)length);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	struct h5u_fdata *u = f->u;
 
 	TRY (h5u_reset_view (fh));
@@ -460,10 +442,9 @@ h5u_set_view_indices (
 	                   "f=%p, indices=%p, nelems=%llu",
 	                   f, indices, (long long unsigned)nelems);
         CHECK_FILEHANDLE (f);
-        if (f->step_gid < 0) {
-                TRY (h5_set_step (fh, 0));
+        if (f->iteration_gid < 0) {
+                TRY (h5_set_iteration (fh, 0));
         }
-	CHECK_TIMEGROUP (f);
 	hsize_t total = 0;
 	hsize_t dmax = H5S_UNLIMITED;
 	struct h5u_fdata *u = f->u;
@@ -520,8 +501,7 @@ h5u_get_view (
 	H5_CORE_API_ENTER (h5_err_t,
 	                   "f=%p, start=%p, end=%p",
 	                   f, start, end);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	struct h5u_fdata *u = f->u;
 
 	if ( u->viewindexed ) {
@@ -542,7 +522,7 @@ h5u_get_view (
 		viewend = u->viewend;
 	}
 	else {
-		TRY (viewend = h5u_get_num_points (fh));
+		TRY (viewend = h5u_get_num_items (fh));
 	}
 
 	if ( start ) *start = viewstart;
@@ -557,15 +537,14 @@ h5u_set_canonical_view (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_int64_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	h5u_fdata_t* u = f->u;
 	TRY( h5u_reset_view (fh) );
 
 	h5_int64_t start = 0;
 	h5_int64_t total = 0;
 
-	TRY (total = h5u_get_num_points (fh));
+	TRY (total = h5u_get_num_items (fh));
 
 	u->nparticles = total / f->nprocs;
 
@@ -595,9 +574,8 @@ h5u_get_num_datasets (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_ssize_t, "f=%p", f);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-	TRY (ret_value = hdf5_get_num_datasets (f->step_gid));
+	check_iteration_handle_is_valid (f);
+	TRY (ret_value = hdf5_get_num_datasets (f->iteration_gid));
 	H5_RETURN (ret_value);
 }
 
@@ -610,9 +588,8 @@ h5u_has_dataset (
 	H5_CORE_API_ENTER (h5_err_t, 
 			   "f=%p, name='%s'",
 			   f, name);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
-        TRY (ret_value = hdf5_link_exists (f->step_gid, name));
+	check_iteration_handle_is_valid (f);
+        TRY (ret_value = hdf5_link_exists (f->iteration_gid, name));
 	H5_RETURN (ret_value);
 }
 
@@ -693,10 +670,9 @@ h5u_get_dataset_info_by_idx (
 			   dataset_name,
 			   (long long unsigned)len_dataset_name,
 			   dataset_type, dataset_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	TRY (h5priv_get_dataset_info_by_idx (
-	             f->step_gid,
+	             f->iteration_gid,
 	             idx,
 	             dataset_name, len_dataset_name,
 		     dataset_type, dataset_nelem));
@@ -742,10 +718,9 @@ h5u_get_dataset_info_by_name (
 	                   f,
 	                   dataset_name,
 	                   dataset_type, dataset_nelem);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	TRY (h5priv_get_dataset_info_by_name (
-	             f->step_gid,
+	             f->iteration_gid,
 		     dataset_name,
 		     dataset_type, dataset_nelem));
 	H5_RETURN (H5_SUCCESS);
@@ -782,13 +757,12 @@ h5u_get_chunk (
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_int64_t, "f=%p, name='%s', size=%p", f,name,size);
-	CHECK_FILEHANDLE (f);
-	CHECK_TIMEGROUP (f);
+	check_iteration_handle_is_valid (f);
 	hid_t dataset_id;
 	hid_t plist_id;
 	hsize_t hsize;
 
-	TRY (dataset_id = hdf5_open_dataset_by_name (f->step_gid, name) );
+	TRY (dataset_id = hdf5_open_dataset_by_name (f->iteration_gid, name) );
 	TRY (plist_id = hdf5_get_dataset_create_plist (dataset_id) );
 	TRY (hdf5_get_chunk_property (plist_id, 1, &hsize) );
 	TRY (hdf5_close_property ( plist_id) );

src/h5core/private/h5_attribs.h

@@ -99,7 +99,7 @@ h5priv_write_attrib (
 	                   attrib_name,
 	                   (long long int)attrib_type,
 	                   attrib_value,
-	                   attrib_nelem);
+	                   (long long unsigned)attrib_nelem);
 	hid_t space_id;
 	hid_t attrib_id;
 	hid_t hdf5_type;
@@ -147,7 +147,7 @@ h5priv_append_attrib (
 	                   attrib_name,
 	                   (long long int)attrib_type,
 	                   attrib_value,
-	                   attrib_nelem);
+	                   (long long unsigned)attrib_nelem);
 	h5_err_t exists;
 	TRY (exists = hdf5_attribute_exists (id, attrib_name));
 	if (exists) {

src/h5core/private/h5_fcmp.c

@@ -29,11 +29,13 @@ h5priv_fcmp (
 	assert (sizeof (long long) == sizeof (h5_int64_t) );
 
 	// Make [ab]Int lexicographically ordered as a twos-complement int
-	h5_int64_t aInt = *(h5_int64_t*)&A;
+	void* p = (void*)&A;
+	h5_int64_t aInt = *(h5_int64_t*)p;
 	if (aInt < 0)
 		aInt = 0x8000000000000000LL - aInt;
 
-	h5_int64_t bInt = *(h5_int64_t*)&B;
+	p = (void*)&B;
+	h5_int64_t bInt = *(h5_int64_t*)p;
 	if (bInt < 0)
 		bInt = 0x8000000000000000LL - bInt;
 

src/h5core/private/h5_file.h

@@ -9,38 +9,50 @@
 #define H5_VFD_MPIO_POSIX       0x00000010
 #define H5_VFD_MPIO_INDEPENDENT 0x00000020
 #define H5_VFD_MPIO_COLLECTIVE  0x00000040
-#define H5_VFD_CORE		0x00000080
+#define H5_VFD_CORE_IO		0x00000080
 
 #define H5_FLUSH_FILE		0x00001000
-#define H5_FLUSH_STEP		0x00002000
+#define H5_FLUSH_ITERATION	0x00002000
 #define H5_FLUSH_DATASET	0x00004000
 
 #define H5_FS_LUSTRE		0x00010000
 
-static inline h5_err_t
-check_filehandle (
-	const h5_file_p f
-	) {
-	if (f == NULL || f->file < 0 || f->u == NULL || f->b == NULL) {
-		return h5_error (
-			H5_ERR_BADF,
-			"Called with bad filehandle.");
-	}
-	return H5_SUCCESS;
+static inline int
+is_valid_file_handle(h5_file_p f) {
+	return ((f != NULL) &&
+		(f->file > 0) &&
+		(f->u != NULL) &&
+		(f->b != NULL));
 }
 
-#define CHECK_FILEHANDLE(f)   \
-        TRY (check_filehandle (f));
-
-static inline int is_writable(h5_file_p f) {
+static inline int
+is_writable (h5_file_p f) {
 	return (f->props->flags & (H5_O_RDWR | H5_O_WRONLY | H5_O_APPENDONLY));
 }
-#define is_readable(f) (f->props->flags & (H5_O_RDWR | H5_O_RDONLY))
-#define is_readonly(f) (f->props->flags & H5_O_RDONLY)
-#define is_appendonly(f) (f->props->flags & H5_O_APPENDONLY)
+
+static inline int
+is_readable (h5_file_p f) {
+	return (f->props->flags & (H5_O_RDWR | H5_O_RDONLY));
+}
+
+static inline int
+is_readonly (h5_file_p f) {
+	return (f->props->flags & H5_O_RDONLY);
+}
+
+static inline int
+is_appendonly (h5_file_p f) {
+	return (f->props->flags & H5_O_APPENDONLY);
+}
+
+#define CHECK_FILEHANDLE(f)			\
+        TRY (is_valid_file_handle(f) ? H5_SUCCESS : h5_error (	\
+		     H5_ERR_BADF,					\
+		     "Called with bad filehandle."));
+
 
 #define CHECK_WRITABLE_MODE(f)                                          \
-	TRY (is_writable (f) ? H5_SUCCESS : h5_error (                  \
+	TRY (is_writable (f) ? H5_SUCCESS : h5_error (			\
                      H5_ERR_INVAL,                                      \
                      "Attempting to write to read-only file handle"));
 
@@ -50,10 +62,29 @@ static inline int is_writable(h5_file_p f) {
                      "Attempting to read from write-only file handle"));
 
 #define CHECK_TIMEGROUP(f)                                             \
-	TRY ((f->step_gid > 0) ? H5_SUCCESS : h5_error (               \
+	TRY ((f->iteration_gid > 0) ? H5_SUCCESS : h5_error (               \
                      H5_ERR_INVAL,                                     \
-                     "Time step is invalid! Have you set the time step?"));
+                     "Iteration is invalid! Have you set the time step?"));
 
+#define check_file_handle_is_valid(f)		\
+	CHECK_FILEHANDLE(f);			\
 
+#define check_file_is_writable(f)		\
+	CHECK_FILEHANDLE(f);			\
+	CHECK_WRITABLE_MODE(f);
+
+#define check_iteration_handle_is_valid(f)	\
+	CHECK_FILEHANDLE(f);			\
+	CHECK_TIMEGROUP(f);
+	
+#define check_iteration_is_readable(f)		\
+	CHECK_FILEHANDLE(f);			\
+	CHECK_READABLE_MODE(f);			\
+	CHECK_TIMEGROUP(f);
+
+#define check_iteration_is_writable(f)		\
+	CHECK_FILEHANDLE(f);			\
+	CHECK_WRITABLE_MODE(f);			\
+	CHECK_TIMEGROUP(f);
 
 #endif

src/h5core/private/h5_hdf5.c

@@ -110,10 +110,18 @@ iter_op_get_obj_type (
 			        name);
 			return H5O_TYPE_UNKNOWN;
 		}
+#if H5_VERSION_GE(1,12,0)
+		herr = H5Oget_info(obj_id, &objinfo, H5O_INFO_ALL);
+#else
 		herr = H5Oget_info(obj_id, &objinfo);
+#endif
 	}
 	else { // H5L_TYPE_HARD
+#if H5_VERSION_GE(1,12,0)
+	  herr = H5Oget_info_by_name(g_id, name, &objinfo, H5O_INFO_BASIC, H5P_DEFAULT);
+#else
 		herr = H5Oget_info_by_name(g_id, name, &objinfo, H5P_DEFAULT);
+#endif
 	}
 
 	if (herr < 0) {
@@ -245,7 +253,8 @@ hdf5_get_name_of_group_by_idx (
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "loc_id=%lld (%s), idx=%llu, name=%p, len=%llu",
 	                    (long long int)loc_id, hdf5_get_objname (loc_id),
-	                    idx, name, (unsigned long long)len);
+	                    (long long unsigned)idx,
+			    name, (unsigned long long)len);
 	op_data_t op_data;
 	memset (&op_data, 0, sizeof (op_data));
 	op_data.type = H5O_TYPE_GROUP;
@@ -304,7 +313,8 @@ hdf5_get_name_of_dataset_by_idx (
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "loc_id=%lld (%s), idx=%llu, name=%p, len=%llu",
 	                    (long long int)loc_id, hdf5_get_objname (loc_id),
-	                    idx, name, (unsigned long long)len);
+	                    (long long unsigned)idx,
+			    name, (unsigned long long)len);
 	op_data_t op_data;
 	memset (&op_data, 0, sizeof (op_data));
 	op_data.type = H5O_TYPE_DATASET;

src/h5core/private/h5_hdf5.h

@@ -718,7 +718,7 @@ hdf5_set_dataset_extent (
 	                    "dataset_id=%lld (%s), size=%llu",
 	                    (long long int)dataset_id,
 	                    hdf5_get_objname(dataset_id),
-	                    *size);
+	                    (long long unsigned int)*size);
 	if (H5Dset_extent(dataset_id, size) < 0) {
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
@@ -873,7 +873,7 @@ static inline hid_t
 hdf5_create_string_type(
         const hsize_t len
         ) {
-	HDF5_WRAPPER_ENTER (hid_t, "len = %llu", len);
+  HDF5_WRAPPER_ENTER (hid_t, "len = %llu", (long long unsigned)len);
 	hid_t type_id = H5Tcopy (H5T_C_S1);
 	if (type_id < 0)
 		H5_RETURN_ERROR (
@@ -1003,7 +1003,7 @@ hdf5_set_chunk_property (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "plist=%lld, rank=%d, dims[0]=%llu ...",
-	                    (long long int)plist, rank, dims[0]);
+	                    (long long int)plist, rank, (long long unsigned)dims[0]);
 	if (H5Pset_chunk (plist, rank, dims) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
@@ -1146,7 +1146,8 @@ hdf5_set_btree_ik_property (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "fapl_id=%lld, btree_ik=%llu",
-	                    (long long int)fcpl_id, btree_ik);
+	                    (long long int)fcpl_id,
+			    (long long unsigned)btree_ik);
 	if (H5Pset_istore_k (fcpl_id, btree_ik) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
@@ -1164,13 +1165,16 @@ hdf5_set_alignment_property (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "plist=%lld, threshold=%llu, alignment=%llu",
-	                    (long long int)plist, threshold, alignment);
+	                    (long long int)plist, 
+			    (long long unsigned)threshold,
+			    (long long unsigned)alignment);
 	if (H5Pset_alignment (plist, threshold, alignment) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
 			"Cannot set alignment property to %llu "
 			"and threshold %llu",
-			alignment, threshold);
+			(long long unsigned)alignment,
+			(long long unsigned)threshold);
 	H5_RETURN (H5_SUCCESS);
 }
 
@@ -1181,12 +1185,13 @@ hdf5_set_meta_block_size (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "fapl_id=%lld, size=%llu",
-	                    (long long int)fapl_id, size);
+	                    (long long int)fapl_id,
+			    (long long unsigned)size);
 	if (H5Pset_meta_block_size (fapl_id, size) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
 			"Cannot set meta block size property to %llu",
-			size);
+			(long long unsigned)size);
 	H5_RETURN (H5_SUCCESS);
 }
 
@@ -1292,9 +1297,15 @@ hdf5_close_file (
 		for (ssize_t i = 0; i < max_objs; i++) {
 			hid_t object_id = obj_id_list [i];
 			h5_debug ("Open object: %lld", (long long)object_id);
+#if H5_VERSION_GE(1,12,0)
+			H5O_info_t object_info;
+			if (H5Oget_info (object_id, &object_info, H5O_INFO_ALL) < 0)
+				continue;
+#else
 			H5O_info_t object_info;
 			if (H5Oget_info (object_id, &object_info) < 0)
 				continue;
+#endif
 			switch (object_info.type) {
 			case H5O_TYPE_GROUP:
 			case H5O_TYPE_DATASET:

src/h5core/private/h5_init.h

@@ -20,10 +20,10 @@ extern "C" {
 #endif
 
 h5_err_t
-h5priv_initialize (void);
+h5_initialize (void);
 
 h5_err_t
-h5priv_finalize (void);
+h5_finalize (void);
 
 extern int h5_initialized;
 extern h5_dta_types_t h5_dta_types;

src/h5core/private/h5_io.h

@@ -58,8 +58,7 @@ h5priv_read_dataset (
 
 h5_err_t
 h5priv_normalize_dataset_name (
-	const char *name,
-	char *name2
+	char* const name
 	);
 
 #endif

src/h5core/private/h5_log.h

@@ -23,8 +23,8 @@
 
 #define __FUNC_ENTER(type, mask, fmt, ...)				\
 	type ret_value = (type)H5_ERR;					\
-	int __log__ = h5_log_level & mask;				\
-	if (__log__ ) {							\
+	int __log__ = __h5_debug_mask & mask;				\
+	if (__log__) {							\
 		h5_call_stack_push (__func__,e_##type);			\
 		h5_debug ("(" fmt ")", __VA_ARGS__);			\
 	}
@@ -33,7 +33,7 @@
 
 #define H5_CORE_API_ENTER(type, fmt, ...)				\
 	if (!h5_initialized) {						\
-		h5priv_initialize();					\
+		h5_initialize();					\
 	}								\
 	__FUNC_ENTER(type, H5_DEBUG_CORE_API, fmt, __VA_ARGS__)
 
@@ -43,9 +43,15 @@
 #define H5_PRIV_FUNC_ENTER(type, fmt, ...)				\
 	__FUNC_ENTER(type, H5_DEBUG_PRIV_FUNC, fmt, __VA_ARGS__ )
 
+#ifdef NDEBUG
+#define H5_INLINE_FUNC_ENTER(type)			\
+	type ret_value = (type)H5_ERR;
+
+#else
 #define H5_INLINE_FUNC_ENTER(type)			\
 	type ret_value = (type)H5_ERR; int __log__ = 0;
-
+#endif
+	
 #define HDF5_WRAPPER_ENTER(type, fmt, ...)			\
 	__FUNC_ENTER(type, H5_DEBUG_HDF5, fmt, __VA_ARGS__ )
 

src/h5core/private/h5_model.h

@@ -15,9 +15,9 @@
  * file incompatibilities with previous versions. */
 
 #define H5_DATANAME_LEN		H5_MAX_NAME_LEN
-#define H5_STEPNAME_LEN		H5_MAX_NAME_LEN
-#define H5_STEPNAME		"Step"
-#define H5_STEPWIDTH		1
+#define H5_ITERATION_NAME_LEN	H5_MAX_NAME_LEN
+#define H5_ITERATION_NAME	"Step"
+#define H5_ITERATION_NUM_WIDTH	1
 #define H5BLOCK_GROUPNAME_BLOCK	"Block"
 #define H5_BLOCKNAME_X		"0"
 #define H5_BLOCKNAME_Y		"1"
@@ -115,7 +115,7 @@ h5priv_end_throttle (const h5_file_p f) {
 
 
 h5_err_t
-h5priv_close_step (
+h5priv_close_iteration (
 	const h5_file_p f
 	);
 
@@ -123,6 +123,7 @@ h5priv_close_step (
   Map given enumeration type to corresponding HDF5 type. We use this HDF5
   type for reading and writing datasets and attributes.
  */
+
 static inline hid_t
 h5priv_map_enum_to_normalized_type (
 	h5_types_t type

src/h5core/private/h5_types.h

@@ -41,8 +41,9 @@ struct h5_prop_file {                   // file property
 	hid_t	xfer_prop;		// dataset transfer properties
 	hid_t	access_prop;		// file access properties
 	hid_t	create_prop;		// file create properties
-	char*	prefix_step_name;	// Prefix of step name
-	int	width_step_idx;		// pad step index with 0 up to this
+	char*	prefix_iteration_name;	// Prefix of step name
+	int	width_iteration_idx;	// pad iteration index with 0 up to this
+	int     flush;                  // flush iteration after writing dataset
 };
 typedef struct h5_prop_file h5_prop_file_t;
 typedef h5_prop_file_t* h5_prop_file_p;
@@ -66,12 +67,12 @@ struct h5_file {
 
 	/* HDF5 */
 	hid_t           root_gid;	// HDF5 group id of root
-	hid_t           step_gid;	// HDF5 group id of current step
+	hid_t           iteration_gid;	// HDF5 group id of current iteration
 
-	/* step internal data						*/
-	char*           step_name;      // full current step name
-	h5_int64_t      step_idx;	// current step index
-	int             is_new_step;    // :FIXME: ?
+	/* iteration internal data					*/
+	char*           iteration_name; // full current iteration name
+	h5_int64_t      iteration_idx;	// current iteration index
+	int             is_new_iteration;// :FIXME: ?
 
 	struct h5u_fdata *u;            // pointer to unstructured data
 	struct h5b_fdata *b;            // pointer to block data

src/h5core/private/h5b_types.h

@@ -11,7 +11,7 @@ struct h5b_partition {
 };
 
 struct h5b_fdata {
-	h5_id_t step_idx;
+	h5_id_t iteration_idx;
 	h5_size_t i_max;
 	h5_size_t j_max;
 	h5_size_t k_max;

src/h5core/private/h5t_access_tetm.c

@@ -12,7 +12,6 @@
 
 #include "private/h5_file.h"
 #include "private/h5_types.h"
-#include "private/h5_init.h"
 #include "private/h5t_types.h"
 #include "private/h5t_model.h"
 #include "private/h5t_access.h"

src/h5core/private/h5t_access_trim.c

@@ -11,7 +11,6 @@
 #include "h5core/h5_syscall.h"
 
 #include "private/h5_file.h"
-#include "private/h5_init.h"
 #include "private/h5t_types.h"
 #include "private/h5t_model.h"
 #include "private/h5t_access.h"

src/h5core/private/h5t_core_trim.c

@@ -219,7 +219,7 @@ update_internal_structs (
 	// create index sets
 
 
-#if (!defined(NDEBUG) && (h5_log_level & (1<<5)))
+#if (!defined(NDEBUG) && (__h5_debug_mask & (1<<5)))
 	if (!m->is_chunked) {
 	h5t_adjacencies_t* adj = &m->adjacencies;
 	h5_loc_idx_t idx = 0;

src/h5core/private/h5t_model_tetm.c

@@ -21,7 +21,6 @@
 #include "private/h5t_store.h"
 
 #include "private/h5_file.h"
-#include "private/h5_init.h"
 #include "private/h5t_core.h"
 
 static struct h5t_methods tet_funcs = {
@@ -192,9 +191,9 @@ h5t_add_chunked_tetrahedral_mesh (
         const h5_weight_t num_weights,
         h5t_mesh_t** 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);
+	H5_CORE_API_ENTER (h5_err_t, "f=%p, name=%s, mesh=%p", (void*)fh, name, mesh);
 #ifdef WITH_PARALLEL_H5GRID
+        h5_file_p f = (h5_file_p)fh;
 	CHECK_WRITABLE_MODE (f);
 	h5_err_t exists;
 	TRY (exists = h5priv_link_exists (

src/h5core/private/h5t_model_trim.c

@@ -20,7 +20,6 @@
 #include "private/h5t_retrieve.h"
 #include "private/h5t_store.h"
 
-#include "private/h5_init.h"
 #include "private/h5t_core.h"
 
 static struct h5t_methods tri_funcs = {
@@ -210,9 +209,9 @@ h5t_add_chunked_triangle_mesh(
         const h5_weight_t num_weights,
         h5t_mesh_t** 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);
+	H5_CORE_API_ENTER (h5_err_t, "f=%p, name=%s, mesh=%p", (void*)fh, name, mesh);
 #ifdef WITH_PARALLEL_H5GRID
+        h5_file_p f = (h5_file_p)fh;
 	int size = -1;
 	TRY (h5priv_mpi_comm_size (f->props->comm, &size));
 	if (size != 1) {

src/h5core/private/h5t_store_trim.c

@@ -202,7 +202,7 @@ compute_neighbor_of_face (
 			}
 			if (elem_idx < -1) { // this should only happen if we are on the boarder
 				// of a loaded chunk and the parent is on a different chunk
-				if (h5_log_level >= 6) {
+				if (__h5_debug_mask >= 6) {
 					h5_debug ("Elem %d is on different proc than its parent %d \n"
 						"therefore neighborhood idx is not correct resolved", old_elem_idx, elem_idx);
 				}

src/h5core/private/h5t_tags.h

@@ -21,11 +21,11 @@
  * Complex numbers can be stored as array of float64 with even dimension
  * Tags are addressed via a name and the entity id.
  * Tags with the same name are called a "tagset"
- * Tagsets can be used to store time/step-constant data. These tagsets are
+ * Tagsets can be used to store iteration-constant data. These tagsets are
     called "m-tagsets" and are assigned directly to a mesh.
- * Tagsets can be used to store data which may change from step to step.
-    These tagsets are called "s-tagsets" and are assigned to a mesh and a
-    (time-)step.
+ * Tagsets can be used to store data which may change from iteration to
+    iteration. These tagsets are called "s-tagsets" and are assigned to
+    a mesh and a step/iteration.
 
    ToDo
  * Scalar values

src/include/H5Block_attribs.h

@@ -233,7 +233,8 @@ H5Block3dGetFieldOrigin (
 }
 
 /**
-  Set field spacing for field \c field_name in the current step.
+  Set field spacing for field \c field_name in the current
+  step/iteration.
 
   \return \c H5_SUCCESS on success
   \return \c H5_FAILURE on error
@@ -263,7 +264,8 @@ H5Block3dSetFieldSpacing (
 }
 
 /**
-  Get field spacing for field \c field_name in the current time step.
+  Get field spacing for field \c field_name in the current
+  step/iteration.
 
   \return \c H5_SUCCESS on success
   \return \c H5_FAILURE on error
@@ -316,7 +318,7 @@ H5Block3dGetFieldSpacing (
 	)
 
   Set an explicit list of X,Y respective Z coordinates for field \c
-  field_name in the current time step. The coordinates are a 1D array
+  field_name in the current step/iteration. The coordinates are a 1D array
   of floating point values with dimension \c n_coords.
 
   By convention, the \c coords array should have the same length as
@@ -414,8 +416,8 @@ H5Block3dSetFieldZCoords (
 	)
 
   Get the explicit list of X, Y respective Z coordinates for field \c
-  field_name in the current step. The coordinates are read into the 1D
-  array \c coords which has length \c n_coords.
+  field_name in the current step/iteration. The coordinates are read
+  into the 1D array \c coords which has length \c n_coords.
 
   By convention, the \c coords array should have the same length as
   the X, Y respective Z dimension of the field. A warning will be

src/include/H5Block_io.h

@@ -56,9 +56,10 @@ extern "C" {
 	const h5_int32_t* buffer
 	)
 
-  Write a 3-dimensional field with scalar values to the current step
-  using the previously defined field view.  Ensure that the size of
-  the buffer matches the number of elements in the view.
+  Write a 3-dimensional field with scalar values to the current
+  step/iteration using the previously defined field view.  Ensure
+  that the size of the buffer matches the number of elements in
+  the view.
 
   Supported data types are
 
@@ -176,8 +177,8 @@ H5Block3dWriteScalarFieldInt32 (
 	h5_int32_t* buffer
 	)
 
-  Read a 3-dimensional field with scalar values from the current step
-  using the previously defined field layout.
+  Read a 3-dimensional field with scalar values from the current
+  step/iteration using the previously defined field layout.
 
   Ensure that the size of the buffer matches the number of elements in
   the view.
@@ -295,9 +296,9 @@ H5Block3dReadScalarFieldInt32 (
 	)
 
   Write a 3-dimensional field with 3-dimensional vectors as values to
-  the current step using the previously defined field view.  Ensure
-  that the size of the buffer matches the number of elements in the
-  view.
+  the current step/iteration using the previously defined field view.
+  Ensure that the size of the buffer matches the number of elements in
+  the view.
 
   Supported data types are
 
@@ -439,7 +440,7 @@ H5Block3dWriteVector3dFieldInt32 (
 	)
 
   Read a 3-dimensional field with 3-dimensional vectors as values from
-  the current step using the previously defined field layout.
+  the current step/iteration using the previously defined field layout.
 
   Ensure that the size of the buffer matches the number of elements in
   the view.

src/include/H5Block_model.h

@@ -33,10 +33,10 @@ extern "C" {
 */
 
 /**
-  Checks whether the current time-step has field data or not.
+  Checks whether the current step/iteration has field data or not.
 
-  \return      true (value \c >0) if step exists
-  \return      false (\c 0) if step does not exist
+  \return      true (value \c >0) if step/iteration exists
+  \return      false (\c 0) if step/iteration does not exist
   \return      \c H5_FAILURE on error
 */
 static inline h5_err_t
@@ -51,7 +51,7 @@ H5BlockHasFieldData (
 
 
 /**
-  Query number of fields in current time step.
+  Query number of fields in current step/iteration.
 
   \return \c number of fields
   \return H5_FAILURE on error
@@ -74,8 +74,8 @@ H5BlockGetNumFields (
   (e.g. scalar or vector).
 
   This function can be used to retrieve all fields bound to the
-  current time-step by looping from \c 0 to the number of fields
-  minus one.  The number of fields bound to the current time-step
+  current step/iteration by looping from \c 0 to the number of fields
+  minus one.  The number of fields bound to the current step/iteration
   can be queried by calling the function \ref H5BlockGetNumFields.
 
   \return \c H5_SUCCESS on success
@@ -171,8 +171,8 @@ H5BlockGetFieldInfoByName (
   Tests whether a view has been set, either directly with
   \ref H5Block3dSetView or indirectly with \ref H5Block3dSetGrid.
 
-  \return      true (value \c >0) if step exists
-  \return      false (\c 0) if step does not exist
+  \return      true (value \c >0) if step/iteration exists
+  \return      false (\c 0) if step/iteration does not exist
   \return      \c H5_FAILURE on error
 */
 static inline h5_int64_t
@@ -190,9 +190,9 @@ H5Block3dHasView (
   Fortran ordering: the fastest moving index is \c i.
 
   This routine uses an MPI_Allgather, so at large concurrency it should
-  be called as infrequently as possible. For instance, if several timesteps
-  use the same field dimensions, set the layout only once before the
-  first timestep.
+  be called as infrequently as possible. For instance, if several
+  steps/iteration use the same field dimensions, set the layout only
+  once.
 
   \return \c H5_SUCCESS on success
   \return \c H5_FAILURE on error
@@ -220,7 +220,51 @@ H5Block3dSetView (
 		h5b_3d_set_view (f,
 				 i_start, i_end,
 				 j_start, j_end,
-				 k_start, k_end));
+				 k_start, k_end,
+                                 0
+                        ));
+}
+
+/**
+  Defines the partition of the field that this processor owns, using
+  Fortran ordering: the fastest moving index is \c i.
+
+  For writing ghost-zone are dissolved.
+
+  This routine uses an MPI_Allgather, so at large concurrency it should
+  be called as infrequently as possible. For instance, if several
+  steps/iteration use the same field dimensions, set the layout only
+  once.
+
+  \return \c H5_SUCCESS on success
+  \return \c H5_FAILURE on error
+*/
+static inline h5_err_t
+H5Block3dSetViewDissolveGhostZones (
+	const h5_file_t f,		///< [in]  File handle.
+	const h5_int64_t i_start,	///< [in]  start index of \c i
+	const h5_int64_t i_end,         ///< [in]  end index of \c i
+	const h5_int64_t j_start,	///< [in]  start index of \c j
+	const h5_int64_t j_end,	        ///< [in]  end index of \c j
+	const h5_int64_t k_start,	///< [in]  start index of \c k
+	const h5_int64_t k_end	        ///< [in]  end index of \c k
+	) {
+	H5_API_ENTER (h5_err_t,
+		      "f=%p, "
+		      "i_start=%lld, i_end=%lld, "
+		      "j_start=%lld, j_end=%lld, "
+		      "k_start=%lld, k_end=%lld",
+		      (h5_file_p)f,
+		      (long long)i_start, (long long)i_end,
+		      (long long)j_start, (long long)j_end,
+		      (long long)k_start, (long long)k_end);
+	H5_API_RETURN (
+		h5b_3d_set_view (f,
+				 i_start, i_end,
+				 j_start, j_end,
+				 k_start, k_end,
+                                 1
+                        ));
 }
 
 /**

src/include/H5Part_io.h

@@ -56,12 +56,13 @@ extern "C" {
 	const h5_int32_t* data
 	)
 
-  Write a dataset to the current step.
+  Write a dataset to the current step/iteration.
 
-  After the current (time-)step and view, you can start writing datasets
-  into the file. Each dataset has a name associated with it (chosen by the
-  user) in order to facilitate later retrieval. The name of the dataset is
-  specified in the parameter \c name, which must be a null-terminated string.
+  After setting the current (time-)step/iteration and view, you can start
+  writing datasets into the file. Each dataset has a name associated with
+  it (chosen by the user) in order to facilitate later retrieval. The name
+  of the dataset is specified in the parameter \c name, which must be a
+  null-terminated string.
 
   There are no restrictions on naming of datasets, but it is useful to arrive
   at some common naming convention when sharing data with other groups.
@@ -70,9 +71,10 @@ extern "C" {
   the array can be reconstructed properly on other systems with incompatible
   type representations.
 
-  All data that is written after setting the timestep is associated with that
-  timestep. While the number of elements can change for each timestep, you
-  cannot change the number of elements in the middle of a given timestep.
+  All data that is written after setting the (time-)step/iteration is
+  associated with that (time-)step/iteratiion. While the number of
+  elements can change for each timestep, you cannot change the number
+  of elements in the middle of a given (time-)step/iteration.
 
   The data is committed to disk before the routine returns.
   \param f	[in]  file handle.
@@ -97,7 +99,7 @@ H5PartWriteDataFloat64 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_write_data (
+		h5u_write_dataset (
 			f, name, (void*)data,
 			H5_FLOAT64_T));
 }
@@ -112,7 +114,7 @@ H5PartWriteDataFloat32 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_write_data(
+		h5u_write_dataset (
 			f, name, (void*)data,
 			H5_FLOAT32_T));
 }
@@ -127,7 +129,7 @@ H5PartWriteDataInt64 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_write_data (
+		h5u_write_dataset (
 			f, name, (void*)data,
 			H5_INT64_T));
 }
@@ -142,7 +144,7 @@ H5PartWriteDataInt32 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_write_data (
+		h5u_write_dataset (
 			f, name, (void*)data,
 			H5_INT32_T));
 }
@@ -198,7 +200,7 @@ H5PartReadDataFloat64 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_read_data (
+		h5u_read_dataset (
 			f, name, data, H5_FLOAT64_T));
 }
 
@@ -212,7 +214,7 @@ H5PartReadDataFloat32 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_read_data (
+		h5u_read_dataset (
 			f, name, data, H5_FLOAT32_T));
 }
 
@@ -226,7 +228,7 @@ H5PartReadDataInt64 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_read_data (
+		h5u_read_dataset (
 			f, name, data,
 			H5_INT64_T));
 }
@@ -241,7 +243,7 @@ H5PartReadDataInt32 (
                       "f=%p, name='%s', date=%p",
                       (h5_file_p)f, name, data);
 	H5_API_RETURN (
-		h5u_read_data (
+		h5u_read_dataset (
 			f, name, data,
 			H5_INT32_T));
 }

src/include/H5Part_model.h

@@ -33,9 +33,10 @@ extern "C" {
 */
 
 /**
-  Get the number of datasets that are stored at the current step.
+  Get the number of datasets that are stored at the current
+  step/iteration.
 
-  \return   number of datasets in current timestep
+  \return   number of datasets in current step/iteration
   \return   \c H5_FAILURE on error
 */
 static inline h5_ssize_t
@@ -49,7 +50,8 @@ H5PartGetNumDatasets (
 }
 
 /**
-  Query the name of a dataset given by it's index in the current step.
+  Query the name of a dataset given by it's index in the current
+  step/iteration.
 
   If the number of datasets is \c n, the range of \c _index is \c 0 to \c n-1.
 
@@ -80,7 +82,7 @@ H5PartGetDatasetName (
 
 /**
   Gets the name, type and number of elements of a dataset based on its
-  index in the current timestep.
+  index in the current step/iteration.
 
   Type is one of the following values:
 
@@ -121,10 +123,11 @@ H5PartGetDatasetInfo (
 			type, nelems));
 }
 /**
-  Determines whether a dataset with given name exists in current step.
+  Determines whether a dataset with given name exists in current
+  step/iteration.
 
-  \return      true (value \c >0) if step exists
-  \return      false (\c 0) if step does not exist
+  \return      true (value \c >0) if step/iteration exists
+  \return      false (\c 0) if step/iteration does not exist
   \return      \c H5_FAILURE on error
 */
 static inline h5_err_t
@@ -140,7 +143,7 @@ H5PartHasDataset (
 
 /**
   Gets the type and number of elements of a dataset based on its
-  name in the current timestep.
+  name in the current step/iteration.
 
   Type is one of the following values:
 
@@ -177,7 +180,7 @@ H5PartGetDatasetInfoByName (
 }
 
 /**
-  Set the number of points/particles for the current time-step.
+  Set the number of items/particles for the current step/iteration.
   After you call this subroutine, all subsequent 
   operations will assume this number of particles will be written.
 
@@ -203,19 +206,19 @@ H5PartGetDatasetInfoByName (
   \return \c H5_FAILURE on error
  */
 static inline h5_err_t
-H5PartSetNumPoints (
+H5PartSetNumItems (
 	const h5_file_t f,		///< [in]  file handle.
-	h5_size_t npoints               ///< [in]  Number of elements.
+	h5_size_t num_items               ///< [in]  Number of elements.
 	) {
 	H5_API_ENTER (h5_err_t,
-		      "f=%p, npoints=%llu",
-		      (h5_file_p)f, (long long unsigned)npoints);
+		      "f=%p, num_items=%llu",
+		      (h5_file_p)f, (long long unsigned)num_items);
 	h5_size_t stride = 1;
-	H5_API_RETURN (h5u_set_num_points (f, npoints, stride));
+	H5_API_RETURN (h5u_set_num_items (f, num_items, stride));
 }
 
 /**
-  \see H5PartSetNumPoints()
+  \see H5PartSetNumItems()
 */
 static inline h5_err_t
 H5PartSetNumParticles (
@@ -226,7 +229,7 @@ H5PartSetNumParticles (
 		      "f=%p, nparticles=%llu",
 		      (h5_file_p)f, (long long unsigned)nparticles);
 	h5_size_t stride = 1;
-	H5_API_RETURN (h5u_set_num_points (f, nparticles, stride));
+	H5_API_RETURN (h5u_set_num_items (f, nparticles, stride));
 }
 
 /**
@@ -238,28 +241,28 @@ H5PartSetNumParticles (
 
   If you have neither set the number of particles
   nor set a view, then this returns the total number of
-  particles in the first data set of the current time step.
-  Note that H5Part assumes that all data sets within a given time step
+  particles in the first data set of the current step/iteration.
+  Note that H5Part assumes that all data sets within a given step/iteration
   have the same number of particles (although the number particles can
-  vary across time steps).
+  vary across steps/iteration).
   
   If none of these conditions are met, an error is thrown.
 
-  \return	number of elements in datasets in current step.
+  \return	number of elements in datasets in current step/iteration.
   \return       \c H5_FAILURE on error.
  */
 	static inline h5_ssize_t
-H5PartGetNumPoints (
+H5PartGetNumItems (
 	const h5_file_t f		///< [in]  file handle.
 	) {
 	H5_API_ENTER (h5_ssize_t,
                       "f=%p",
                       (h5_file_p)f);
-	H5_API_RETURN (h5u_get_num_points (f));
+	H5_API_RETURN (h5u_get_num_items (f));
 }
 
 /**
-  \see H5PartGetNumPoints()
+  \see H5PartGetNumItems()
 */
 static inline h5_ssize_t
 H5PartGetNumParticles (
@@ -268,12 +271,12 @@ H5PartGetNumParticles (
 	H5_API_ENTER (h5_ssize_t,
                       "f=%p",
                       (h5_file_p)f);
-	H5_API_RETURN (h5u_get_num_points (f));
+	H5_API_RETURN (h5u_get_num_items (f));
 }
 
 
 /**
-  Set the number of particles for the current time-step.
+  Set the number of particles for the current step/iteration.
   After you call this subroutine, all subsequent 
   operations will assume this number of particles will be written.
 
@@ -301,15 +304,15 @@ H5PartGetNumParticles (
 static inline h5_err_t
 H5PartSetNumParticlesStrided (
 	const h5_file_t f,              ///< [in]  file handle.
-	h5_size_t npoints,              ///< [in]  number of elements.
+	h5_size_t num_items,            ///< [in]  number of elements.
 	h5_size_t stride                ///< [in]  stride value (e.g. number
                                         ///<       of fields in the particle array).
 	) {
 	H5_API_ENTER (h5_err_t,
-		      "f=%p, npoints=%llu, stride=%llu",
-		      (h5_file_p)f, (long long unsigned)npoints,
+		      "f=%p, num_items=%llu, stride=%llu",
+		      (h5_file_p)f, (long long unsigned)num_items,
 		      (long long unsigned)stride);
-	H5_API_RETURN (h5u_set_num_points (f, npoints, stride));
+	H5_API_RETURN (h5u_set_num_items (f, num_items, stride));
 }
 
 /**
@@ -361,8 +364,8 @@ H5PartResetView (
   \ref H5PartSetNumParticles() or manually with \ref H5PartSetView
   or \ref H5PartSetViewIndices.
 
-  \return      true (value \c >0) if step exists
-  \return      false (\c 0) if step does not exist
+  \return      true (value \c >0) if step/iteration exists
+  \return      false (\c 0) if step/iteration does not exist
   \return      \c H5_FAILURE on error
 */
 static inline h5_err_t
@@ -384,10 +387,10 @@ H5PartHasView (
   is set, or the number of particles in a dataset changes, or the view is
   "unset" by calling \c H5PartSetView(file,-1,-1);
 
-  Before you set a view, \ref H5PartGetNumPoints will return the
-  total number of particles in the current time-step (even for the parallel
-  reads).  However, after you set a view, it will return the number of
-  particles contained in the view.
+  Before you set a view, \ref H5PartGetNumItems will return the
+  total number of particles in the current step/iteration (even for
+  the parallel reads).  However, after you set a view, it will
+  return the number of particles contained in the view.
 
   The range is \e inclusive: the end value is the last index of the
   data.
@@ -421,10 +424,10 @@ H5PartSetView (
   for all the intermediate values (which will not be touched by the read
   or write).
 
-  Before you set a view, the \c H5PartGetNumPoints() will return the
-  total number of particles in the current time-step (even for the parallel
-  reads).  However, after you set a view, it will return the number of
-  particles contained in the view.
+  Before you set a view, the \c H5PartGetNumItems() will return the
+  total number of particles in the current step/iteration (even for
+  the parallel reads).  However, after you set a view, it will return
+  the number of particles contained in the view.
 
   \return \c H5_SUCCESS on success
   \return \c H5_FAILURE on error

src/include/H5_const.f90

@@ -13,7 +13,8 @@
 
   INTEGER*8, PARAMETER :: H5_VFD_MPIPOSIX =        Z'00000010'
   INTEGER*8, PARAMETER :: H5_VFD_MPIIO_IND =       Z'00000020'
-  INTEGER*8, PARAMETER :: H5_VFD_CORE =            Z'00000040'
+  INTEGER*8, PARAMETER :: H5_VFD_MPIIO_COL =       Z'00000040'
+  INTEGER*8, PARAMETER :: H5_VFD_CORE_IO =         Z'00000080'
 
   INTEGER*8, PARAMETER :: H5_PROP_DEFAULT =        0
 

src/include/H5_file.h

@@ -233,6 +233,26 @@ H5SetPropFileThrottle (
         H5_API_RETURN (h5_set_prop_file_throttle (prop, throttle));
 }
 
+/**
+   Flush data after each write.
+
+  \return \c H5_SUCCESS on success
+  \return \c H5_FAILURE on error
+
+  \note 
+  | Release     | Change                               |
+  | :------     | :-----			       |
+  | \c 2.0.0rc5 | Function introduced in this release. |
+ */
+static inline h5_err_t
+H5SetPropFileFlush (
+        h5_prop_t prop			///< [in,out] identifier for file property list
+	) {
+	H5_API_ENTER (h5_err_t, "prop=%p",
+		      (void*)prop);
+        H5_API_RETURN (h5_set_prop_file_flush_after_write (prop));
+}
+
 /**
   Close file property list.
 
@@ -357,7 +377,7 @@ H5CheckFile (
 }
 
 /**
-  Flush step data to disk.
+  Flush step/iteration data to disk.
 
   \return \c H5_SUCCESS on success
   \return \c H5_FAILURE on error
@@ -369,7 +389,7 @@ H5FlushStep (
 	H5_API_ENTER (h5_err_t, 
                       "f=%p",
                       (h5_file_p)f);
-	H5_API_RETURN (h5_flush_step (f));
+	H5_API_RETURN (h5_flush_iteration (f));
 }
 
 /**

src/include/H5_log.h

@@ -50,7 +50,7 @@ extern "C" {
 */
 static inline h5_err_t
 H5SetVerbosityLevel2 (
-	const h5_id_t level     ///< [in] verbosity level.
+	const h5_int32_t level     ///< [in] verbosity level.
 	) {
 	return h5_set_loglevel (level & 0x03);
 }
@@ -72,7 +72,7 @@ H5SetVerbosityLevel2 (
 */
 static inline h5_err_t
 H5SetVerbosityLevel1 (
-	const h5_id_t level     ///< [in] verbosity level.
+	const h5_int64_t level     ///< [in] verbosity level.
 	) {
 	return h5_set_loglevel (level);
 }
@@ -84,7 +84,7 @@ H5SetVerbosityLevel1 (
 
   \see H5SetVerbosityLevel()
 */
-static inline h5_id_t
+static inline h5_int64_t
 H5GetVerbosityLevel (
 	void
 	) {
@@ -123,9 +123,9 @@ H5GetVerbosityLevel (
 */
 static inline h5_err_t
 H5SetDebugMask (
-	const h5_id_t mask     ///< [in] debug mask
+	const h5_int64_t mask     ///< [in] debug mask
 	) {
-	return h5_set_loglevel (mask & ~0x03);
+	return h5_set_debug_mask (mask);
 }
 
 /**
@@ -140,7 +140,7 @@ H5SetDebugMask (
   | :------    | :-----			  	      |
   | \c 1.99.15 | Function introduced in this release. |
 */
-static inline h5_id_t
+static inline h5_int32_t
 H5GetDebugMask (
 	void
 	) {

src/include/H5_model.h

@@ -23,7 +23,7 @@ extern "C" {
 #endif
 
 /**
-  Define format of the step names.
+  Define format of the step/iteration names.
 
   Example: ==H5SetStepNameFormat( f, "Step", 6 )== defines step names 
   like ==Step#000042==.
@@ -35,16 +35,16 @@ static inline h5_err_t
 H5SetStepNameFormat (
 	const h5_file_t f,	///< [in] file handle
 	const char* name,	///< [in] prefix, defaults to \c Step
-	const h5_int64_t width	///< [in] width of step number
+	const h5_int64_t width	///< [in] width of step/iteration number
 	) {
 	H5_API_ENTER (h5_err_t,
 		      "f=%p, name='%s', width=%lld",
 		      (h5_file_p)f, name, (long long) width);
-	H5_API_RETURN (h5_set_stepname_fmt (f, name, width));
+	H5_API_RETURN (h5_set_iteration_name_fmt (f, name, width));
 }
 
 /**
-  Get format of the step names.
+  Get format of the step/iteration names.
 
   \return   \c H5_SUCCESS on success
   \return   \c H5_FAILURE on error
@@ -54,16 +54,16 @@ H5GetStepNameFormat (
 	const h5_file_t f,	///< [in]  file handle
 	char* name,		///< [out] prefix
 	const h5_size_t l_name,	///< [in]  length of buffer name
-	int* width		///< [out] width of step number
+	int* width		///< [out] width of step/iteration number
 	) {
 	H5_API_ENTER (h5_err_t,
 		      "f=%p, name=%p, l_name=%llu, width=%p",
 		      (h5_file_p)f, name, (unsigned long long)l_name, width);
-	H5_API_RETURN (h5_get_stepname_fmt (f, name, l_name, width));
+	H5_API_RETURN (h5_get_iteration_name_fmt (f, name, l_name, width));
 }
 
 /**
-  Set the current step.
+  Set the current step/iteration.
 
   \return   \c H5_SUCCESS on success
   \return   \c H5_FAILURE on error
@@ -71,18 +71,18 @@ H5GetStepNameFormat (
 static inline h5_err_t
 H5SetStep (
 	const h5_file_t f,	///< [in]  file handle.
-	const h5_id_t step	///< [in]  step to set.
+	const h5_id_t step	///< [in]  step/iteration to set.
 	) {
 	H5_API_ENTER (h5_err_t,
                       "f=%p, step=%lld",
                       (h5_file_p)f, (long long)step);
-	H5_API_RETURN (h5_set_step (f, step));
+	H5_API_RETURN (h5_set_iteration (f, step));
 }
 
 /**
-  Get current step.
+  Get current step/iteration.
 
-  \return   Step number
+  \return   Step/iteration number
   \return   \c H5_FAILURE on error
 */
 static inline h5_id_t
@@ -92,17 +92,17 @@ H5GetStep (
 	H5_API_ENTER (h5_err_t,
                       "f=%p",
                       (h5_file_p)f);
-	H5_API_RETURN (h5_get_step (f));
+	H5_API_RETURN (h5_get_iteration (f));
 }
 
 /**
-  Get the number of time-steps that are currently stored in the file
-  \c f.
+  Get the number of steps/iterations 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
+  \return	Number of steps/iterations
   \return       \c H5_FAILURE on error.
 */
 static inline h5_ssize_t
@@ -112,14 +112,14 @@ H5GetNumSteps (
 	H5_API_ENTER (h5_err_t,
                       "f=%p",
                       (h5_file_p)f);
-	H5_API_RETURN (h5_get_num_steps(f));
+	H5_API_RETURN (h5_get_num_iterations(f));
 }
 
 /**
-  Query whether a particular step already exists in the file.
+  Query whether a particular step/iteration already exists in the file.
 
-  \return      true (value \c >0) if step exists
-  \return      false (\c 0) if step does not exist
+  \return      true (value \c >0) if step/iteration exists
+  \return      false (\c 0) if step/iteration does not exist
   \return      \c H5_FAILURE on error
 */
 static inline h5_err_t
@@ -130,7 +130,7 @@ H5HasStep (
 	H5_API_ENTER (h5_err_t, 
 		      "f=%p, stepno=%lld",
 		      (h5_file_p)f, (long long)stepno);
-	H5_API_RETURN (h5_has_step (f, stepno));
+	H5_API_RETURN (h5_has_iteration (f, stepno));
 }
 
 /**

src/include/H5_step_attribs.h

@@ -29,12 +29,13 @@ extern "C" {
    !
 */
 /**
-   \addtogroup h5_step_attribs
+   \addtogroup h5_iteration_attribs
    @{
 */
 
 /**
-  Query the number of attributes attached to the current step.
+  Query the number of attributes attached to the current
+  step/iteration.
 
   \return   number of attributes
   \return   \c H5_FAILURE on error
@@ -46,17 +47,17 @@ H5GetNumStepAttribs (
 	H5_API_ENTER (h5_int64_t,
                       "f=%p",
                       (h5_file_p)f);
-	H5_API_RETURN (h5_get_num_step_attribs (f));
+	H5_API_RETURN (h5_get_num_iteration_attribs (f));
 }
 
 /**
-  Gets the name, type and number of elements of the step attribute
+  Gets the name, type and number of elements of the iteration attribute
   given by its index.
 
   This function can be used to retrieve all attributes attached to the
-  current step by looping from \c 0 to the number of attribute
+  current step/iteration by looping from \c 0 to the number of attribute
   minus one.  The number of attributes attached to the current
-  step can be queried by calling \ref H5GetNumStepAttribs().
+  step/iteration can be queried by calling \ref H5GetNumStepAttribs().
 
   \return   \c H5_SUCCESS on success
   \return   \c H5_FAILURE on error
@@ -81,7 +82,7 @@ H5GetStepAttribInfo (
                       attrib_type,
                       nelems);
 	H5_API_RETURN (
-		h5_get_step_attrib_info_by_idx (
+		h5_get_iteration_attrib_info_by_idx (
 			f,
 			idx,
 			attrib_name,
@@ -105,7 +106,7 @@ H5GetStepAttribName (
                       attrib_name,
                       (long long unsigned)len_attrib_name);
 	H5_API_RETURN (
-		h5_get_step_attrib_info_by_idx (
+		h5_get_iteration_attrib_info_by_idx (
 			f,
 			idx,
 			attrib_name, len_attrib_name,
@@ -114,7 +115,8 @@ H5GetStepAttribName (
 }
 
 /**
-   Determines whether a step attribute with a given name exists in current step.
+   Determines whether a step attribute with a given name exists in
+   current step/iteration.
 
    \return      true (value \c >0) if atrribute exists
    \return      false (\c 0) if attribute does not exist
@@ -131,13 +133,14 @@ H5HasStepAttrib (
 		      (h5_file_p)f,
 		      attrib_name);
 	H5_API_RETURN (
-		h5_has_step_attrib (
+		h5_has_iteration_attrib (
 			f,
 			attrib_name));
 }
 
 /**
-  Gets the type and number of elements of a given step attribute.
+  Gets the type and number of elements of a given step/iteration
+  attribute.
 
   \return   \c H5_SUCCESS on success
   \return   \c H5_FAILURE on error
@@ -157,7 +160,7 @@ H5GetStepAttribInfoByName (
                       attrib_name,
                       attrib_type, nelems);
 	H5_API_RETURN (
-		h5_get_step_attrib_info_by_name (
+		h5_get_iteration_attrib_info_by_name (
 			f,
 			attrib_name,
 			attrib_type, nelems));
@@ -240,7 +243,7 @@ H5WriteStepAttribString (
                       "f=%p, attrib_name='%s', buffer='%s'",
                       (h5_file_p)f, attrib_name, buffer);
 	H5_API_RETURN (
-		h5_write_step_attrib (
+		h5_write_iteration_attrib (
 			f, 
 			attrib_name,
 			H5_STRING_T,
@@ -259,7 +262,7 @@ H5WriteStepAttribFloat64 (
                       "f=%p, attrib_name='%s', buffer=%p, nelems=%llu",
 		      (h5_file_p)f, attrib_name, buffer, (long long unsigned)nelems);
 	H5_API_RETURN (
-		h5_write_step_attrib (
+		h5_write_iteration_attrib (
 			f,
 			attrib_name,
 			H5_FLOAT64_T,
@@ -278,7 +281,7 @@ H5WriteStepAttribFloat32 (
                       "f=%p, attrib_name='%s', buffer=%p, nelems=%llu",
 		      (h5_file_p)f, attrib_name, buffer, (long long unsigned)nelems);
 	H5_API_RETURN (
-		h5_write_step_attrib (
+		h5_write_iteration_attrib (
 			f,
 			attrib_name,
 			H5_FLOAT32_T,
@@ -297,7 +300,7 @@ H5WriteStepAttribInt64 (
                       "f=%p, attrib_name='%s', buffer=%p, nelems=%llu",
 		      (h5_file_p)f, attrib_name, buffer, (long long unsigned)nelems);
 	H5_API_RETURN (
-		h5_write_step_attrib (
+		h5_write_iteration_attrib (
 			f,
 			attrib_name,
 			H5_INT64_T,
@@ -316,7 +319,7 @@ H5WriteStepAttribInt32 (
                       "f=%p, attrib_name='%s', buffer=%p, nelems=%llu",
 		      (h5_file_p)f, attrib_name, buffer, (long long unsigned)nelems);
 	H5_API_RETURN (
-		h5_write_step_attrib (
+		h5_write_iteration_attrib (
 			f,
 			attrib_name,
 			H5_INT32_T,
@@ -393,7 +396,7 @@ H5ReadStepAttribString (
                       "f=%p, attrib_name='%s', buffer=%p",
 		      (h5_file_p)f, attrib_name, buffer);
 	H5_API_RETURN (
-		h5_read_step_attrib (
+		h5_read_iteration_attrib (
 			f, 
 			attrib_name,
 			H5_STRING_T,
@@ -410,7 +413,7 @@ H5ReadStepAttribFloat64 (
                       "f=%p, attrib_name='%s', buffer=%p",
 		      (h5_file_p)f, attrib_name, buffer);
 	H5_API_RETURN (
-		h5_read_step_attrib (
+		h5_read_iteration_attrib (
 			f,
 			attrib_name,
 			H5_FLOAT64_T,
@@ -427,7 +430,7 @@ H5ReadStepAttribFloat32 (
                       "f=%p, attrib_name='%s', buffer=%p",
 		      (h5_file_p)f, attrib_name, buffer);
 	H5_API_RETURN (
-		h5_read_step_attrib (
+		h5_read_iteration_attrib (
 			f,
 			attrib_name,
 			H5_FLOAT32_T,
@@ -444,7 +447,7 @@ H5ReadStepAttribInt64 (
                       "f=%p, attrib_name='%s', buffer=%p",
 		      (h5_file_p)f, attrib_name, buffer);
 	H5_API_RETURN (
-		h5_read_step_attrib (
+		h5_read_iteration_attrib (
 			f,
 			attrib_name,
 			H5_INT64_T,
@@ -461,7 +464,7 @@ H5ReadStepAttribInt32 (
                       "f=%p, attrib_name='%s', buffer=%p",
 		      (h5_file_p)f, attrib_name, buffer);
 	H5_API_RETURN (
-		h5_read_step_attrib (
+		h5_read_iteration_attrib (
 			f,
 			attrib_name,
 			H5_INT32_T,

src/include/H5hut.h

@@ -29,7 +29,7 @@
   \ingroup h5block_model
 
   \note
-  Different field sizes are allowed in the same time-step.
+  Different field sizes are allowed in the same step/iteration.
 
   \note
   The same layout can be used, if the size of the field matches the

src/include/h5core/h5_file.h

@@ -45,6 +45,10 @@ h5_err_t
 h5_set_prop_file_core_vfd (
         h5_prop_t, h5_int64_t);
 
+h5_err_t
+h5_set_prop_file_flush_after_write (
+        h5_prop_t _props);
+
 h5_err_t
 h5_close_prop (
         h5_prop_t);
@@ -70,7 +74,7 @@ h5_close_h5hut (
 	void);
 
 h5_err_t
-h5_flush_step (
+h5_flush_iteration (
 	const h5_file_t);
 
 h5_err_t

src/include/h5core/h5_log.h

@@ -13,6 +13,7 @@
 #include <stdio.h>
 #include <stddef.h>
 
+
 extern const char* H5_VER_STRING;
 
 #include "h5core/h5_types.h"
@@ -22,6 +23,7 @@ extern const char* H5_VER_STRING;
 #define H5_VERBOSE_ERROR   	(1)
 #define H5_VERBOSE_WARN    	(2)
 #define H5_VERBOSE_INFO    	(3)
+#define H5_VERBOSE_DEBUG    	(4)
 
 #define H5_VERBOSE_DEFAULT      H5_VERBOSE_ERROR
 
@@ -45,7 +47,10 @@ enum h5_rtypes {
 	e_char_p,
 	e_void_p,
 	e_h5_err_t,
+	e_h5_int32_t,
+	e_h5_uint32_t,
 	e_h5_int64_t,
+	e_h5_uint64_t,
 	e_h5_id_t,
 	e_h5_ssize_t,
 	e_h5_errorhandler_t,
@@ -75,13 +80,18 @@ struct call_stack {
 	struct call_stack_entry entry[1024];
 };
 
-extern h5_int32_t h5_log_level;
+extern h5_int64_t __h5_log_level;
+extern h5_int64_t __h5_debug_mask;
 extern struct call_stack h5_call_stack;
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
+// :FIXME: Should go to another header file
+h5_err_t
+h5_initialize (void);
+
 static inline void
 h5_call_stack_push (
         const char* fname,
@@ -182,9 +192,13 @@ __attribute__ ((format (printf, 1, 2)))
 
 h5_err_t
 h5_set_loglevel (
-	const h5_id_t);
+	const h5_int64_t);
 
 h5_err_t
+h5_set_debug_mask (
+	const h5_int64_t);
+
+h5_int64_t
 h5_get_loglevel (
 	void);
 
@@ -196,17 +210,21 @@ h5_get_loglevel (
 // function enter macro
 #if defined(NDEBUG)
 
-#define H5_API_ENTER(type, fmt, ...)		\
-	type ret_value = (type)H5_ERR;
+#define H5_API_ENTER(type, fmt, ...)					\
+	type ret_value = (type)H5_ERR;					\
+	h5_initialize();						\
+	h5_call_stack_reset ();						\
+	h5_call_stack_push (__func__,e_##type);
 
 #else   // NDEBUG not defined
 
 #define H5_API_ENTER(type, fmt, ...)					\
-	h5_call_stack_reset ();						\
 	type ret_value = (type)H5_ERR;					\
-	int __log__ = h5_log_level & H5_DEBUG_API;			\
+	h5_initialize();						\
+	h5_call_stack_reset ();						\
+	h5_call_stack_push (__func__,e_##type);				\
+	int __log__ = __h5_debug_mask & H5_DEBUG_API;			\
 	if (__log__) {							\
-		h5_call_stack_push (__func__,e_##type);			\
 		h5_debug ("(" fmt ")", __VA_ARGS__);			\
 	}
 
@@ -220,7 +238,7 @@ h5_get_loglevel (
 	}
 
 #define H5_RETURN_ERROR(errno, fmt, ...) {				\
-		ret_value = h5_error (errno, "(" fmt ")", __VA_ARGS__);	\
+		ret_value = h5_error (errno, fmt, __VA_ARGS__);		\
 		goto done;						\
 	}
 

src/include/h5core/h5_model.h

@@ -19,29 +19,29 @@ extern "C" {
 #define H5_MAX_NAME_LEN          64
 
 h5_err_t
-h5_set_stepname_fmt (
+h5_set_iteration_name_fmt (
 	const h5_file_t, const char*, const int);
 
 h5_err_t
-h5_get_stepname_fmt (
+h5_get_iteration_name_fmt (
 	const h5_file_t, char* const, const int, int* const);
 
 
 h5_int64_t
-h5_set_step (
+h5_set_iteration (
 	const h5_file_t, const h5_int64_t);
 
 
 h5_int64_t
-h5_get_step (
+h5_get_iteration (
 	const h5_file_t);
 
 h5_ssize_t
-h5_get_num_steps (
+h5_get_num_iterations (
 	const h5_file_t);
 
 h5_int64_t
-h5_has_step (
+h5_has_iteration (
 	const h5_file_t, const h5_int64_t);
 
 int

src/include/h5core/h5_step_attribs.h

@@ -18,30 +18,30 @@ extern "C" {
 #endif
 	
 h5_err_t
-h5_has_step_attrib (
+h5_has_iteration_attrib (
 	const h5_file_t, const char* const);
 
 h5_err_t
-h5_get_step_attrib_info_by_name (
+h5_get_iteration_attrib_info_by_name (
 	const h5_file_t, const char* const,
 	h5_int64_t* const, h5_size_t* const);
 
 h5_ssize_t
-h5_get_num_step_attribs (
+h5_get_num_iteration_attribs (
 	const h5_file_t f);
 
 h5_err_t
-h5_get_step_attrib_info_by_idx (
+h5_get_iteration_attrib_info_by_idx (
 	const h5_file_t, const h5_size_t, char* const, const h5_size_t,
 	h5_int64_t* const, h5_size_t* const);
 
 h5_err_t
-h5_read_step_attrib (
+h5_read_iteration_attrib (
 	const h5_file_t, const char* const, const h5_types_t,
 	void* const);
 
 h5_err_t
-h5_write_step_attrib (
+h5_write_iteration_attrib (
 	const h5_file_t, const char* const, const h5_types_t,
 	const void* const, const h5_size_t);
 

src/include/h5core/h5_types.h

@@ -148,7 +148,7 @@ typedef struct h5_glb_idxlist {
 } h5_glb_idxlist_t;
 
 enum h5_iterators {
-	step_iterator
+	iteration_iterator
 };
 
 struct h5_iterator;

src/include/h5core/h5b_model.h

@@ -51,7 +51,8 @@ h5b_3d_set_view (
         const h5_file_t,
         const h5_size_t, const h5_size_t,
         const h5_size_t, const h5_size_t,
-        const h5_size_t, const h5_size_t);
+        const h5_size_t, const h5_size_t,
+        const h5_int64_t);
 
 h5_err_t
 h5b_3d_get_view (

src/include/h5core/h5u_io.h

@@ -18,12 +18,12 @@ extern "C" {
 #endif
 
 h5_int64_t
-h5u_read_data (
+h5u_read_dataset (
 	const h5_file_t,
 	const char* const, void* const, const h5_types_t);
 
 h5_int64_t
-h5u_write_data (
+h5u_write_dataset (
 	const h5_file_t,
 	const char* const, const void* const, const h5_types_t);
 

src/include/h5core/h5u_model.h

@@ -41,11 +41,11 @@ h5u_get_dataset_info_by_name (
         );
 
 h5_ssize_t
-h5u_get_num_points (
+h5u_get_num_items (
 	const h5_file_t);
 
 h5_ssize_t
-h5u_get_num_points_in_view (
+h5u_get_num_items_in_view (
 	const h5_file_t);
 
 h5_ssize_t
@@ -59,7 +59,7 @@ h5u_get_totalnum_particles_by_idx (
         h5_id_t);
 
 h5_err_t
-h5u_set_num_points (
+h5u_set_num_items (
 	const h5_file_t,
 	const h5_size_t, const h5_size_t);
 

test/h5u_read.c

@@ -360,7 +360,7 @@ test_read_data32(h5_file_t file, int nparticles, int step)
 		status = H5PartReadDataFloat32(file, "pz", pz);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataFloat32");
 
-		status = H5PartReadDataInt32(file, LONGNAME2, id);
+		status = H5PartReadDataInt32(file, "id", id);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataInt32");
 
 		for (i=0; i<nparticles; i++)
@@ -471,25 +471,37 @@ void h5u_test_read2(void)
 	RETURN(status, H5_SUCCESS, "H5CloseFile");
 }
 
-#if H5_VERSION_LE(1,8,12)
 void h5u_test_read3(void)
 {
 	h5_file_t file1;
 	h5_int64_t status;
 
+#if H5_VERSION_LE(1,8,12)
 	TEST("Opening file once, read-only, MPI-POSIX VFD");
+#else
+	TEST("Opening file once, read-only, MPI-IO Independent VFD");
+#endif
+
 	h5_prop_t props = H5CreateFileProp ();
+
 #if defined(H5_HAVE_PARALLEL)
         MPI_Comm comm = MPI_COMM_WORLD;
+
+#if H5_VERSION_LE(1,8,12)
         status = H5SetPropFileMPIOPosix (props, &comm);
 	RETURN(status, H5_SUCCESS, "H5SetPropFileMPIOPosix");
+#else
+        status = H5SetPropFileMPIOIndependent (props, &comm);
+	RETURN(status, H5_SUCCESS, "H5SetPropFileMPIOIndependent");
 #endif
+
+#endif // H5_HAVE_PARALLEL
 	file1 = H5OpenFile(FILENAME, H5_O_RDONLY, props);
 	status = H5CheckFile(file1);
 	RETURN(status, H5_SUCCESS, "H5CheckFile");
 
 	TEST("Redefining step name");
-	status = H5SetStepNameFormat(file1, LONGNAME, 16);
+	status = H5SetStepNameFormat(file1, "data", 16);
 	RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
 
 	test_read_strided_data64(file1, NPARTICLES, 0);
@@ -498,7 +510,6 @@ void h5u_test_read3(void)
 	status = H5CloseFile(file1);
 	RETURN(status, H5_SUCCESS, "H5CloseFile");
 }
-#endif
 
 void h5u_test_read4(void)
 {
@@ -525,10 +536,10 @@ void h5u_test_read4(void)
 	RETURN(status, H5_SUCCESS, "H5CloseProp");
 
 	TEST("Redefining step name");
-	status = H5SetStepNameFormat(file1, LONGNAME, 16);
+	status = H5SetStepNameFormat(file1, "data", 16);
 	RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
 
-	status = H5SetStepNameFormat(file2, LONGNAME, 16);
+	status = H5SetStepNameFormat(file2, "data", 16);
 	RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
 
 	test_read_file_attribs(file1, 1);

test/h5u_write.c

@@ -266,7 +266,7 @@ test_write_data32(h5_file_t file, int nparticles, int step)
 		status = H5PartWriteDataFloat32(file, "pz", pz);
 		RETURN(status, H5_SUCCESS, "H5PartWriteDataFloat32");
 
-		status = H5PartWriteDataInt32(file, LONGNAME2, id);
+		status = H5PartWriteDataInt32(file, "id", id);
 		RETURN(status, H5_SUCCESS, "H5PartWriteDataInt32");
 
 		/* the second write phase... */
@@ -293,7 +293,7 @@ test_write_data32(h5_file_t file, int nparticles, int step)
 		status = H5PartWriteDataFloat32(file, "pz", pz+32);
 		RETURN(status, H5_SUCCESS, "H5PartWriteDataFloat32");
 
-		status = H5PartWriteDataInt32(file, LONGNAME, id+32);
+		status = H5PartWriteDataInt32(file, "id", id+32);
 		RETURN(status, H5_SUCCESS, "H5PartWriteDataInt32");
 	}
 }
@@ -411,21 +411,32 @@ void h5u_test_write2(void)
 	RETURN(status, H5_SUCCESS, "H5CloseFile");
 }
 
-#if H5_VERSION_LE(1,8,12)
 void h5u_test_write3(void)
 {
 	h5_file_t file1;
 	h5_err_t status;
 
+#if H5_VERSION_LE(1,8,12)
 	TEST("Opening file once, write-truncate, MPI-POSIX VFD");
-
+#else
+	TEST("Opening file once, write-truncate, MPI-IO Independent VFD");
+#endif
+	
         h5_prop_t props = H5CreateFileProp ();
 
 #if defined(H5_HAVE_PARALLEL)
         MPI_Comm comm = MPI_COMM_WORLD;
+
+#if H5_VERSION_LE(1,8,12)
         status = H5SetPropFileMPIOPosix (props, &comm);
 	RETURN(status, H5_SUCCESS, "H5SetPropFileMPIOPosix");
+#else
+        status = H5SetPropFileMPIOIndependent (props, &comm);
+	RETURN(status, H5_SUCCESS, "H5SetPropFileMPIOIndependent");
 #endif
+
+#endif // H5_HAVE_PARALLEL
+
 	file1 = H5OpenFile(FILENAME, H5_O_WRONLY, props);
 
 	status = H5CheckFile(file1);
@@ -435,7 +446,7 @@ void h5u_test_write3(void)
 	RETURN(status, H5_SUCCESS, "H5CloseProp");
 
 	TEST("Redefining step name");
-	status = H5SetStepNameFormat(file1, LONGNAME, 16);
+	status = H5SetStepNameFormat(file1, "data", 16);
 	RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
 
 	test_write_strided_data64(file1, NPARTICLES, 0);
@@ -444,7 +455,6 @@ void h5u_test_write3(void)
 	status = H5CloseFile(file1);
 	RETURN(status, H5_SUCCESS, "H5CloseFile");
 }
-#endif
 
 void h5u_test_write4(void)
 {
@@ -474,10 +484,10 @@ void h5u_test_write4(void)
 	RETURN(status, H5_SUCCESS, "H5CloseProp");
 
 	TEST("Redefining step name");
-	status = H5SetStepNameFormat(file1, LONGNAME, 16);
+	status = H5SetStepNameFormat(file1, "data", 16);
 	RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
 
-	status = H5SetStepNameFormat(file2, LONGNAME, 16);
+	status = H5SetStepNameFormat(file2, "data", 16);
 	RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
 
 	status = H5PartSetChunkSize(file1, NPARTICLES);

test/testframe.c

@@ -658,7 +658,11 @@ test_open_objects(h5_file_t file, int max_objects)
 		H5O_info_t info;
 		int i;
 		for (i=0; i<nopen; i++) {
-			H5Oget_info(list[i], &info);
+#if H5_VERSION_GE(1,12,0)
+		  H5Oget_info(list[i], &info, H5O_INFO_BASIC);
+#else
+		  H5Oget_info(list[i], &info);
+#endif
 			switch (info.type) {
 			case H5O_TYPE_GROUP:
 				TestErrPrintf("obj%d has type GROUP\n", i);