1.6.1 tag

.gitattributes

@@ -10,7 +10,6 @@
 /README -text
 /autogen.sh -text
 /config.guess -text
-/config.h.in -text
 /config.sub -text
 /configure-crayxt -text
 /configure.ac -text
@@ -19,7 +18,9 @@ doc/Doxyfile -text
 doc/H5X_File_Format.txt -text
 doc/Makefile.am -text
 doc/doxyfooter -text
+examples/simplef.F90 -text
 examples/stridedf.F90 -text
+examples/write_setview.c -text
 /install-sh -text
 /license.txt -text
 /missing -text

Makefile.am

@@ -7,6 +7,8 @@ SUBDIRS = \
 	test \
 	tools
 
+EXTRA_DIST = configure-crayxt
+
 MAINTAINERCLEANFILES = \
 	config.h \
 	config.log \

NEWS

@@ -1,3 +1,41 @@
+#### H5PART 1.6.1 ############################################################
+
+Chunking in the H5Part API
+--------------------------
+
+There is now an H5Part equivalent H5PartSetChunkSize to the existing
+H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
+mechanism in the underlying HDF5 layer. Chunking is used in combination
+with the aligned open calls to pad datasets to alignment multiples
+on disk.
+
+All Steps Available on Write
+----------------------------
+
+Previously, existing steps in a file were only accessible in read-only mode.
+Now, all steps are available in all modes, including write-truncate and
+write-append. Thus, it is now possible to overwrite existing data in write
+mode. To help alert the user to this possibility, a warning is issued every
+time an existing dataset is written to. Warnings can be printed by setting
+the verbosity to H5PART_VERB_WARN or higher.
+
+New Throttling Routine
+----------------------
+
+Previously, a throttle factor of N meant that for P processors, the total
+number of P writes were divided into N batches of P/N writes.
+
+To better accommodate round-robin lustre striping, the new policy is to
+execute P/N batches of N writes. Thus, matching N to the number of stripes
+results in the desirable 1-1 matching of writers to stripes.
+
+Other Fixes
+-----------
+
+* The configure script should correctly detect PGI compilers now.
+* There was a small memory leak in the Fortran file open calls.
+* There was a compile error with HDF5 1.6.x due to a missing assignment.
+
 #### H5PART 1.6 ##############################################################
 
 Updated Documentation
@@ -122,7 +160,7 @@ calls.
 Previously, a user could overrun internal buffers for dataset names. Now, a
 fixed limit of 64 chars is imposed. Dataset names that are longer than this are
 truncated and a warning is printed. We expect that most users are using
-short canoncical names like x, px, id, etc.
+short canonical names like x, px, id, etc.
 
 Changes to Existing API
 -----------------------

config.h.in

@@ -1,99 +0,0 @@
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* "" */
-#undef MY_BUILD_CPU
-
-/* "" */
-#undef MY_BUILD_OS
-
-/* "" */
-#undef MY_BUILD_VENDOR
-
-/* "" */
-#undef MY_GNUNAME
-
-/* "" */
-#undef MY_UNAME
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* Enable extensions on AIX 3, Interix.  */
-#ifndef _ALL_SOURCE
-# undef _ALL_SOURCE
-#endif
-/* Enable GNU extensions on systems that have them.  */
-#ifndef _GNU_SOURCE
-# undef _GNU_SOURCE
-#endif
-/* Enable threading extensions on Solaris.  */
-#ifndef _POSIX_PTHREAD_SEMANTICS
-# undef _POSIX_PTHREAD_SEMANTICS
-#endif
-/* Enable extensions on HP NonStop.  */
-#ifndef _TANDEM_SOURCE
-# undef _TANDEM_SOURCE
-#endif
-/* Enable general extensions on Solaris.  */
-#ifndef __EXTENSIONS__
-# undef __EXTENSIONS__
-#endif
-
-
-/* Version number of package */
-#undef VERSION
-
-/* Define to 1 if on MINIX. */
-#undef _MINIX
-
-/* Define to 2 if the system does not provide POSIX.1 features except with
-   this defined. */
-#undef _POSIX_1_SOURCE
-
-/* Define to 1 if you need to in order for `stat' and other things to work. */
-#undef _POSIX_SOURCE

configure.ac

@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.6.0], [h5part@lists.psi.ch], H5Part)
+AC_INIT([H5Part], [1.6.1], [h5part@lists.psi.ch], H5Part)
 
 
 # Ensure that a recent enough version of Autoconf is being used. 
@@ -168,7 +168,7 @@ fi
 # If CC is not already set in the environment, check for gcc and cc, then
 # for other C compilers. 
 # Set output variable CC to the name of the compiler found.
-AC_PROG_CC(pathcc icc cc_r gcc cc)
+AC_PROG_CC(pgcc pathcc icc cc_r gcc cc)
 
 # AC_PROG_CC doesn't pick up cc_r in Bassi. The following AC_PATH_PROGS
 # is the fix.
@@ -189,7 +189,7 @@ fi
 # then search for a C++ compiler under the likely names (first g++ and c++
 # then other names). 
 # If none of those checks succeed, then as a last resort set CXX to g++.
-AC_PROG_CXX(pathCC icc cc_r g++ gcc cc)
+AC_PROG_CXX(pgCC pathCC icc cc_r g++ gcc cc)
 
 
 # Set output variable INSTALL to the path of a BSD-compatible install program,
@@ -248,7 +248,8 @@ AC_MSG_CHECKING([if 64-bit compilation is enabled])
 
 
 # If --enable-64 is set in the configure line
-if test "X$USE_64" = "Xyes"; then
+if test "X$USE_64:/f90
+" = "Xyes"; then
     AC_MSG_RESULT([yes])
     if test $uname = "AIX"; then
         CFLAGS="$CFLAGS -q64"
@@ -269,7 +270,7 @@ AC_MSG_CHECKING([if fortran interface enabled])
 if test "X$USE_FORTRAN" = "Xyes"; then
     AC_MSG_RESULT([yes])
 
-    AC_PROG_FC(ifort xlf_r pathf90 g95 g90 ftn gfortran)
+    AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
     if test -z "$FC" ; then
         AC_MSG_ERROR([Cannot find a fortran compiler!!!])
         exit 1

doc/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.6.0
+PROJECT_NUMBER         = 1.6.1
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English

examples/simplef.F90

@@ -0,0 +1,49 @@
+program H5PartTest
+  implicit none
+
+  include 'mpif.h'
+  include 'H5PartF.h'
+
+  integer :: comm, rank, ierr
+  integer*8 :: file_id, status, npoints, i
+  real*8, allocatable :: particles(:)
+  integer*8, allocatable :: id(:)
+
+  comm = MPI_COMM_WORLD
+  call mpi_init(ierr)
+  call mpi_comm_rank(comm, rank, ierr)
+
+  ! open the a file for parallel writing
+  file_id = h5pt_openw_par('test.h5', comm)
+
+  ! in the Fortran API, time steps start at 1
+  status = h5pt_setstep(file_id, 1_8)
+
+  ! write an attribute to the file
+  status = h5pt_writefileattrib_string(file_id, 'desc', 'This is a test.')
+
+  ! create fake data
+  npoints = 99
+  allocate(particles(npoints), id(npoints))
+  do i=1,npoints
+    particles(i) = real(i+npoints*rank)
+    id(i) = i+npoints*rank
+  enddo
+
+  ! set the size of the 1D array
+  status = h5pt_setnpoints(file_id, npoints)
+
+  ! write the particles
+  status = h5pt_writedata_r8(file_id, "x",  particles)
+
+  ! write the ids
+  status = h5pt_writedata_i8(file_id, "id", id)
+
+  ! close the file
+  status = h5pt_close(file_id)
+
+  deallocate(particles, id)
+
+  call mpi_finalize(ierr)
+
+end program H5PartTest

examples/write_setview.c

@@ -0,0 +1,57 @@
+#include <stdlib.h>
+#include <assert.h>
+#include <mpi.h>
+#include <H5Part.h>
+
+#define DATASIZE 32
+#define ITERS 4
+
+int main(int argc, char** argv)
+{
+    int i, rank, nprocs;
+    h5part_int32_t data[ITERS*DATASIZE];
+    h5part_int64_t stat;
+    h5part_int64_t offset;
+    H5PartFile *file;
+
+    // initialize MPI
+    MPI_Init (&argc, &argv);
+    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
+
+    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
+
+    file = H5PartOpenFileParallel("test.h5", H5PART_WRITE, MPI_COMM_WORLD);
+    assert (file != NULL);
+
+    stat = H5PartSetStep(file, 0);
+    assert (stat == H5PART_SUCCESS);
+
+    stat = H5PartSetNumParticles(file, ITERS*DATASIZE);
+    assert (stat == H5PART_SUCCESS);
+
+    // create fake data
+    for (i=0; i<ITERS*DATASIZE; i++) {
+        data[i] = i + rank * ITERS * DATASIZE;
+    }
+
+    offset = rank * ITERS * DATASIZE;
+
+    // iterate over arrays
+    for (i=0; i<ITERS; i++) {
+        // set the "view" to select a subset of the dataset
+        stat = H5PartSetView(file,
+                offset + i*DATASIZE,
+                offset + (i+1)*DATASIZE - 1);
+        assert (stat == H5PART_SUCCESS);
+        // write the data
+        stat = H5PartWriteDataInt32(file, "data", data + i*DATASIZE);
+        assert (stat == H5PART_SUCCESS);
+    }
+
+    H5PartCloseFile(file);
+
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+}
+

src/H5Block.c

@@ -721,8 +721,13 @@ _release_hyperslab (
 /*!
   \ingroup h5block_model
 
-  Define the field layout given the dense index space at the actual
-  time step.
+  Defines the partition of the field that this processor owns, using
+  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.
 
   \return \c H5PART_SUCCESS on success<br>
   \c H5PART_ERR_MPI<br>
@@ -1186,6 +1191,11 @@ _H5Block_read_data (
 	herr = _H5Block_select_hyperslab_for_reading ( f, dataset_id );
 	if ( herr < 0 ) return herr;
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_start_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dread ( 
 		dataset_id,
 		type,
@@ -1195,6 +1205,11 @@ _H5Block_read_data (
 		data );
 	if ( herr < 0 ) return HANDLE_H5D_READ_ERR ( name, f->timestep );
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_end_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dclose ( dataset_id );
 	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
 
@@ -1443,6 +1458,11 @@ _H5Block_write_data (
 		);
 	if ( dataset < 0 ) return HANDLE_H5D_CREATE_ERR ( name, f->timestep );
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_start_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dwrite ( 
 		dataset,
 		type,
@@ -1452,6 +1472,11 @@ _H5Block_write_data (
 		data );
 	if ( herr < 0 ) return HANDLE_H5D_WRITE_ERR ( name, f->timestep );
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_end_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dclose ( dataset );
 	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
 

src/H5MultiBlockReadWrite.c

@@ -10,8 +10,11 @@
 #include "H5MultiBlockErrors.h"
 #include "H5MultiBlockPrivate.h"
 
+#ifdef PARALLEL_IO
+
+
 /*!
-  \ingroup h5multiblock_write
+  \ingroup h5multiblock_data
 
   Write a multiblock field \c name from the buffer starting at \c data
   to the current time-step using the defined block decomposition and dimensions.
@@ -39,7 +42,7 @@ H5MultiBlock3dWriteFieldFloat64 (
 }
 
 /*!
-  \ingroup h5multiblock_read
+  \ingroup h5multiblock_data
 
   Allocate a buffer to hold a block from a multiblock field and place the
   pointer in \c data, then read the block into the buffer. Uses the block
@@ -68,7 +71,7 @@ H5MultiBlock3dReadFieldFloat64 (
 }
 
 /*!
-  \ingroup h5multiblock_write
+  \ingroup h5multiblock_data
 
   Write a multiblock field \c name from the buffer starting at \c data
   to the current time-step using the defined block decomposition and dimensions.
@@ -96,7 +99,7 @@ H5MultiBlock3dWriteFieldFloat32 (
 }
 
 /*!
-  \ingroup h5multiblock_read
+  \ingroup h5multiblock_data
 
   Allocate a buffer to hold a block from a multiblock field and place the
   pointer in \c data, then read the block into the buffer. Uses the block
@@ -125,7 +128,7 @@ H5MultiBlock3dReadFieldFloat32 (
 }
 
 /*!
-  \ingroup h5multiblock_write
+  \ingroup h5multiblock_data
 
   Write a multiblock field \c name from the buffer starting at \c data
   to the current time-step using the defined block decomposition and dimensions.
@@ -153,7 +156,7 @@ H5MultiBlock3dWriteFieldInt64 (
 }
 
 /*!
-  \ingroup h5multiblock_read
+  \ingroup h5multiblock_data
 
   Allocate a buffer to hold a block from a multiblock field and place the
   pointer in \c data, then read the block into the buffer. Uses the block
@@ -182,7 +185,7 @@ H5MultiBlock3dReadFieldInt64 (
 }
 
 /*!
-  \ingroup h5multiblock_write
+  \ingroup h5multiblock_data
 
   Write a multiblock field \c name from the buffer starting at \c data
   to the current time-step using the defined block decomposition and dimensions.
@@ -210,7 +213,7 @@ H5MultiBlock3dWriteFieldInt32 (
 }
 
 /*!
-  \ingroup h5multiblock_read
+  \ingroup h5multiblock_data
 
   Allocate a buffer to hold a block from a multiblock field and place the
   pointer in \c data, then read the block into the buffer. Uses the block
@@ -237,3 +240,5 @@ H5MultiBlock3dReadFieldInt32 (
 
 	return H5PART_SUCCESS;
 }
+
+#endif // PARALLEL_IO

src/H5Part.c

@@ -98,6 +98,7 @@ h5part_error_handler	_err_handler = H5PartReportErrorHandler;
 
 /********* Private Variable Declarations *************/
 
+static unsigned			_is_root_proc = 0;
 static unsigned			_debug = H5PART_VERB_ERROR;
 static h5part_int64_t		_h5part_errno = H5PART_SUCCESS;
 static char *__funcname;
@@ -125,6 +126,14 @@ _h5_error_handler (
 	void *
 	);
 
+static void
+_vprint (
+	FILE* f,
+	const char *prefix,
+	const char *fmt,
+	va_list ap
+	);
+
 /*========== File Opening/Closing ===============*/
 
 static H5PartFile*
@@ -154,7 +163,7 @@ _H5Part_open_file (
 	strncpy ( f->groupname_step, H5PART_GROUPNAME_STEP, H5PART_STEPNAME_LEN );
 	f->stepno_width = 0;
 
-	f->xfer_prop = f->create_prop = H5P_DEFAULT;
+	f->xfer_prop = f->dcreate_prop = f->fcreate_prop = H5P_DEFAULT;
 
 	f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
 	if (f->access_prop < 0) {
@@ -175,6 +184,9 @@ _H5Part_open_file (
 			goto error_cleanup;
 		}
 
+		if ( f-> myproc == 0 ) _is_root_proc = 1;
+		else _is_root_proc = 0;
+
 		f->pnparticles =
 		  (h5part_int64_t*) malloc (f->nprocs * sizeof (h5part_int64_t));
 		if (f->pnparticles == NULL) {
@@ -182,69 +194,38 @@ _H5Part_open_file (
 			goto error_cleanup;
 		}
 
-		/* select the HDF5 VFD */
-		if (flags & H5PART_VFD_MPIPOSIX) {
-			if (f->myproc == 0) {
-				_H5Part_print_info ( "Selecting MPI-POSIX VFD" );
-			}
-			if (H5Pset_fapl_mpiposix ( f->access_prop, comm, 0 ) < 0) {
-				HANDLE_H5P_SET_FAPL_ERR;
-				goto error_cleanup;
-			}
-		}
-		else {
-			if (f->myproc == 0) {
-				_H5Part_print_info ( "Selecting MPI-IO VFD" );
-			}
-			if (H5Pset_fapl_mpio ( f->access_prop, comm, info ) < 0) {
-				HANDLE_H5P_SET_FAPL_ERR;
-				goto error_cleanup;
-			}
-			if (flags & H5PART_VFD_MPIIO_IND) {
-				if (f->myproc == 0) {
-					_H5Part_print_info ( "Using independent mode" );
-				}
-			} else {
-				if (f->myproc == 0) {
-					_H5Part_print_info ( "Using collective mode" );
-				}
-				f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
-				if (f->xfer_prop < 0) {
-					HANDLE_H5P_CREATE_ERR;
-					goto error_cleanup;
-				}
-				if (H5Pset_dxpl_mpio ( f->xfer_prop, H5FD_MPIO_COLLECTIVE ) < 0) {
-					HANDLE_H5P_SET_DXPL_MPIO_ERR;
-					goto error_cleanup;
-				}
-			}
-		}
-
+		/* optional lustre optimizations */
 		if ( flags & H5PART_FS_LUSTRE )
 		{
 			/* extend the btree size so that metadata pieces are
-			 * close to the alignment value */
-			unsigned int btree_ik = (align - 256) / 96;
-			unsigned int btree_bytes = 64 + 96*btree_ik;
-			if ( btree_bytes > align ) {
-				HANDLE_H5PART_INVALID_ERR(
-					"btree_ik", btree_ik );
-				goto error_cleanup;
-			}
+		 	* close to the alignment value */
+			if ( align > 0 )
+			{
+				unsigned int btree_ik = (align - 4096) / 96;
+				unsigned int btree_bytes = 64 + 96*btree_ik;
+				if ( btree_bytes > align ) {
+					HANDLE_H5PART_INVALID_ERR(
+						"btree_ik", btree_ik );
+					goto error_cleanup;
+				}
 
-			if (f->myproc == 0) {
 				_H5Part_print_info (
 					"Setting HDF5 btree parameter to %u",
 					btree_ik );
 				_H5Part_print_info (
-					"Extending HDF5 btree size to %u bytes at rank 3",
-					btree_bytes );
+					"Extending HDF5 btree size to %u "
+					"bytes at rank 3", btree_bytes );
+
+				f->fcreate_prop = H5Pcreate(H5P_FILE_CREATE);
+				if ( f->fcreate_prop < 0 ) {
+					HANDLE_H5P_CREATE_ERR;
+					goto error_cleanup;
+				}
+
+				H5Pset_istore_k (f->fcreate_prop, btree_ik);
 			}
 
-			f->create_prop = H5Pcreate(H5P_FILE_CREATE);
-			H5Pset_istore_k (f->create_prop, H5PART_BTREE_IK);
-
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 			/* defer metadata cache flushing until file close */
 			H5AC_cache_config_t cache_config;
 			cache_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
@@ -257,14 +238,50 @@ _H5Part_open_file (
 			cache_config.decr_mode = H5C_decr__off;
 			H5Pset_mdc_config (f->access_prop, &cache_config);
 #else // H5_USE_16_API
-			_H5Part_print_info (
-					"Unable to defer metadata write: need HDF5 1.8");
+			_H5Part_print_warn (
+				"Unable to defer metadata write: need HDF5 1.8");
 #endif // H5_USE_16_API
 		}
 
+		/* select the HDF5 VFD */
+		if (flags & H5PART_VFD_MPIPOSIX) {
+			_H5Part_print_info ( "Selecting MPI-POSIX VFD" );
+			if (H5Pset_fapl_mpiposix ( f->access_prop, comm, 0 ) < 0) {
+				HANDLE_H5P_SET_FAPL_ERR;
+				goto error_cleanup;
+			}
+		} else if (flags & H5PART_VFD_CORE) {
+			_H5Part_print_info ( "Selecting CORE VFD" );
+			if (H5Pset_fapl_core ( f->access_prop, comm, 0 ) < 0) {
+				HANDLE_H5P_SET_FAPL_ERR;
+				goto error_cleanup;
+			}
+		} else {
+			_H5Part_print_info ( "Selecting MPI-IO VFD" );
+			if (H5Pset_fapl_mpio ( f->access_prop, comm, info ) < 0) {
+				HANDLE_H5P_SET_FAPL_ERR;
+				goto error_cleanup;
+			}
+			if (flags & H5PART_VFD_MPIIO_IND) {
+				_H5Part_print_info ( "Using independent mode" );
+			} else {
+				_H5Part_print_info ( "Using collective mode" );
+				f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
+				if (f->xfer_prop < 0) {
+					HANDLE_H5P_CREATE_ERR;
+					goto error_cleanup;
+				}
+				if (H5Pset_dxpl_mpio ( f->xfer_prop, H5FD_MPIO_COLLECTIVE ) < 0) {
+					HANDLE_H5P_SET_DXPL_MPIO_ERR;
+					goto error_cleanup;
+				}
+			}
+		}
+
 		f->comm = comm;
 #endif // PARALLEL_IO
 	} else {
+		_is_root_proc = 1;
 		f->comm = 0;
 		f->nprocs = 1;
 		f->myproc = 0;
@@ -273,34 +290,27 @@ _H5Part_open_file (
 	}
 
 	if ( align != 0 ) {
-		if (f->myproc == 0) {
-			_H5Part_print_info ( "Setting HDF5 alignment to %ld bytes", align );
-		}
+		_H5Part_print_info (
+			"Setting HDF5 alignment to %ld bytes",
+			align );
 		if (H5Pset_alignment ( f->access_prop, 0, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
 		}
-		if (f->myproc == 0) {
-			_H5Part_print_info ( "Setting HDF5 meta block to %ld bytes", align );
-		}
+		_H5Part_print_info (
+			"Setting HDF5 meta block to %ld bytes",
+			align );
 		if (H5Pset_meta_block_size ( f->access_prop, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
 		}
-		/*if (f->myproc == 0) {
-			_H5Part_print_info ( "Setting HDF5 sieve buffer to %ld bytes", align );
-		}
-		if (H5Pset_sieve_buf_size ( f->access_prop, align ) < 0) {
-			HANDLE_H5P_SET_FAPL_ERR;
-			goto error_cleanup;
-		}*/
 	}
 
 	if ( flags & H5PART_READ ) {
 		f->file = H5Fopen(filename, H5F_ACC_RDONLY, f->access_prop);
 	}
 	else if ( flags & H5PART_WRITE ){
-		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
+		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->fcreate_prop,
 				f->access_prop);
 		f->empty = 1;
 	}
@@ -308,7 +318,7 @@ _H5Part_open_file (
 		int fd = open(filename, O_RDONLY, 0);
 		if ( (fd == -1) && (errno == ENOENT) ) {
 			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
-					f->create_prop, f->access_prop);
+					f->fcreate_prop, f->access_prop);
 			f->empty = 1;
 		}
 		else if (fd != -1) {
@@ -367,13 +377,17 @@ _H5Part_open_file (
 
   Opens file with specified filename. 
 
-  If you open with flag \c H5PART_WRITE, it will truncate any
-  file with the specified filename and start writing to it. If 
-  you open with \c H5PART_APPEND, then you can append new timesteps.
-  If you open with \c H5PART_READ, then it will open the file
-  readonly.
+  Flags are bit values that can be combined with the bit operator \c |
+  and include:
 
-  The typical extension for these files is \c .h5.
+  - \c H5PART_WRITE - truncate file and open for writing
+  - \c H5PART_APPEND - open file for writing without truncating
+  - \c H5PART_READ - open file read-only
+  - \c H5PART_FS_LUSTRE - enable optimizations for the Lustre file system
+  - \c H5PART_VFD_MPIPOSIX - use the HDF5 MPI-POSIX virtual file driver
+  - \c H5PART_VFD_MPIO_IND - use MPI-IO in indepedent mode
+
+  The typical file extension is \c .h5.
   
   H5PartFile should be treated as an essentially opaque
   datastructure.  It acts as the file handle, but internally
@@ -403,6 +417,23 @@ H5PartOpenFileParallel (
   Opens file with specified filename, and also specifices an alignment
   value used for HDF5 tuning parameters.
 
+  Flags are bit values that can be combined with the bit operator \c |
+  and include:
+
+  - \c H5PART_WRITE - truncate file and open for writing
+  - \c H5PART_APPEND - open file for writing without truncating
+  - \c H5PART_READ - open file read-only
+  - \c H5PART_FS_LUSTRE - enable optimizations for the Lustre file system
+  - \c H5PART_VFD_MPIPOSIX - use the HDF5 MPI-POSIX virtual file driver
+  - \c H5PART_VFD_MPIO_IND - use MPI-IO in indepedent mode
+
+  The typical file extension is \c .h5.
+  
+  H5PartFile should be treated as an essentially opaque
+  datastructure.  It acts as the file handle, but internally
+  it maintains several key state variables associated with 
+  the file.
+
   \return	File handle or \c NULL
  */
 H5PartFile*
@@ -426,13 +457,14 @@ H5PartOpenFileParallelAlign (
 
   Opens file with specified filename. 
 
-  If you open with flag \c H5PART_WRITE, it will truncate any
-  file with the specified filename and start writing to it. If 
-  you open with \c H5PART_APPEND, then you can append new timesteps.
-  If you open with \c H5PART_READ, then it will open the file
-  readonly.
+  Flags are bit values that can be combined with the bit operator \c |
+  and include:
 
-  The typical extension for these files is \c .h5.
+  - \c H5PART_WRITE - truncate file and open for writing
+  - \c H5PART_APPEND - open file for writing without truncating
+  - \c H5PART_READ - open file read-only
+
+  The typical file extension is \c .h5.
   
   H5PartFile should be treated as an essentially opaque
   datastructure.  It acts as the file handle, but internally
@@ -462,6 +494,20 @@ H5PartOpenFile (
   Opens file with specified filename, and also specifices an alignment
   value used for HDF5 tuning parameters.
 
+  Flags are bit values that can be combined with the bit operator \c |
+  and include:
+
+  - \c H5PART_WRITE - truncate file and open for writing
+  - \c H5PART_APPEND - open file for writing without truncating
+  - \c H5PART_READ - open file read-only
+
+  The typical file extension is \c .h5.
+  
+  H5PartFile should be treated as an essentially opaque
+  datastructure.  It acts as the file handle, but internally
+  it maintains several key state variables associated with 
+  the file.
+
   \return	File handle or \c NULL
  */
 H5PartFile*
@@ -497,12 +543,23 @@ _H5Part_file_is_valid (
 		return H5PART_ERR_BADFD;
 }
 
+/*!
+  \ingroup h5part_open
+
+  Closes an open file.
+
+  \return	\c H5PART_SUCCESS or error code
+*/
 h5part_int64_t
-_H5Part_close_hdf_ids (
+H5PartCloseFile (
 	H5PartFile *f		/*!< [in] filehandle of the file to close */
 	) {
 
+	SET_FNAME ( "H5PartCloseFile" );
 	herr_t r = 0;
+	_h5part_errno = H5PART_SUCCESS;
+
+	CHECK_FILEHANDLE ( f );
 
 	if ( f->block && f->close_block ) {
 		(*f->close_block) ( f );
@@ -543,46 +600,28 @@ _H5Part_close_hdf_ids (
 		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->xfer_prop" );
 		f->xfer_prop = H5P_DEFAULT;
 	}
-	if( f->access_prop != H5P_DEFAULT ) {
-		r = H5Pclose( f->access_prop );
-		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->access_prop" );
-		f->access_prop = H5P_DEFAULT;
-	}  
-	if( f->create_prop != H5P_DEFAULT ) {
-		r = H5Pclose( f->create_prop );
-		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->create_prop" );
-		f->create_prop = H5P_DEFAULT;
+	if( f->dcreate_prop != H5P_DEFAULT ) {
+		r = H5Pclose( f->dcreate_prop );
+		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->dcreate_prop" );
+		f->dcreate_prop = H5P_DEFAULT;
 	}
 
-	return H5PART_SUCCESS;
-}
-
-/*!
-  \ingroup h5part_open
-
-  Closes an open file.
-
-  \return	\c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5PartCloseFile (
-	H5PartFile *f		/*!< [in] filehandle of the file to close */
-	) {
-
-	SET_FNAME ( "H5PartCloseFile" );
-	herr_t r = 0;
-	_h5part_errno = H5PART_SUCCESS;
-
-	CHECK_FILEHANDLE ( f );
-
-	r = _H5Part_close_hdf_ids ( f );
-	if ( r < 0 ) return r;
 
 	if ( f->file ) {
 		r = H5Fclose( f->file );
 		if ( r < 0 ) HANDLE_H5F_CLOSE_ERR;
 		f->file = 0;
 	}
+	if( f->access_prop != H5P_DEFAULT ) {
+		r = H5Pclose( f->access_prop );
+		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->access_prop" );
+		f->access_prop = H5P_DEFAULT;
+	}  
+	if( f->fcreate_prop != H5P_DEFAULT ) {
+		r = H5Pclose( f->fcreate_prop );
+		if ( r < 0 ) HANDLE_H5P_CLOSE_ERR ( "f->fcreate_prop" );
+		f->fcreate_prop = H5P_DEFAULT;
+	}
 
 	/* free memory from H5PartFile struct */
 	if( f->pnparticles ) {
@@ -763,10 +802,10 @@ _set_num_particles (
 	if ( ret != MPI_SUCCESS) return HANDLE_MPI_ALLGATHER_ERR;
 
 	if ( f->myproc == 0 ) {
-		_H5Part_print_debug ( "Particle offsets:" );
 		for ( i=0; i<f->nprocs; i++ ) 
-			_H5Part_print_debug ( "\t[%d] np=%lld", i,
-					(long long) f->pnparticles[i] );
+			_H5Part_print_debug_detail (
+				"[%d] np=%lld",
+				i, (long long) f->pnparticles[i] );
 	}
 
 	/* compute start offsets */
@@ -896,6 +935,47 @@ H5PartSetNumParticlesStrided (
 	return H5PART_SUCCESS;
 }
 
+/*!
+  \ingroup h5part_model
+
+  Define the chunk \c size and enables chunking in the underlying
+  HDF5 layer. When combined with the \c align value in the
+  \ref H5PartOpenFileAlign or \ref H5PartOpenFileParallelAlign
+  function, this causes each group of \c size particles to be
+  padded on disk out to the nearest multiple of \c align bytes.
+
+  Note that this policy wastes disk space, but can improve write
+  bandwidth on parallel filesystems that are sensitive to alignment
+  to stripe boundaries (e.g. lustre).
+
+  \return	\c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5PartSetChunkSize (
+	H5PartFile *f,
+	const h5part_int64_t size
+	) {
+
+	SET_FNAME ( "H5PartSetChunkSize" );
+	CHECK_FILEHANDLE( f );
+
+	_H5Part_print_info (
+		"Setting chunk size to %lld elements",
+		(long long)size );
+
+	if ( f->dcreate_prop == H5P_DEFAULT ) {
+		f->dcreate_prop = H5Pcreate (H5P_DATASET_CREATE);
+		if ( f->dcreate_prop < 0 ) return HANDLE_H5P_CREATE_ERR;
+	}
+
+	hsize_t hsize = (hsize_t)size;
+
+	herr_t herr = H5Pset_chunk ( f->dcreate_prop, 1, &hsize );
+	if ( herr < 0 ) return HANDLE_H5P_SET_CHUNK_ERR;
+
+	return H5PART_SUCCESS;
+}
+
 static void
 _normalize_dataset_name (
 	const char *name,
@@ -953,23 +1033,19 @@ _write_data (
 			"Dataset[%s] at timestep %lld "
 			"already exists", name2, (long long)f->timestep );
 	} else {
-#ifndef H5_USE_16_API
-		dataset_id = H5Dcreate2 ( 
-			f->timegroup,
-			name2,
-			type,
-			f->shape,
-			H5P_DEFAULT,
-			H5P_DEFAULT,
-			H5P_DEFAULT );
-#else
 		dataset_id = H5Dcreate ( 
 			f->timegroup,
 			name2,
 			type,
 			f->shape,
-			H5P_DEFAULT );
+#ifndef H5_USE_16_API
+			H5P_DEFAULT,
+			f->dcreate_prop,
+			H5P_DEFAULT
+#else
+			f->dcreate_prop
 #endif
+                );
 		if ( dataset_id < 0 )
 			return HANDLE_H5D_CREATE_ERR ( name2, f->timestep );
 	}
@@ -1259,7 +1335,7 @@ _H5Part_read_attrib (
 	hid_t space_id;
 	hid_t type_id;
 
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 	if (! H5Aexists ( id, attrib_name )) {
 		_H5Part_print_warn ( "Attribute '%s' does not exist!", attrib_name );
 	}
@@ -1851,9 +1927,11 @@ _H5Part_set_step (
 	char stepname[H5PART_STEPNAME_LEN];
 	_H5Part_get_step_name(f, step, stepname);
 
+#if H5PART_SET_STEP_READ_ONLY
 	if ( (!(f->flags & H5PART_READ)) && _H5Part_have_group ( f->file, stepname ) ) {
 		return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
 	}
+#endif
 
 	if ( f->timegroup >= 0 ) {
 		herr_t herr = H5Gclose ( f->timegroup );
@@ -1862,6 +1940,9 @@ _H5Part_set_step (
 	f->timegroup = -1;
 	f->timestep = step;
 
+#if H5PART_SET_STEP_READ_ONLY
+	// in this mode, existing steps can be selecting only
+	// for a READ file handle
 	if ( f->flags & H5PART_READ ) {
 		_H5Part_print_debug (
 			"Proc[%d]: Set step to #%lld for file %lld",
@@ -1893,6 +1974,33 @@ _H5Part_set_step (
 			return HANDLE_H5G_CREATE_ERR ( stepname );
 	}
 
+#else // H5PART_SET_STEP_READ_ONLY
+
+	// in this mode, existing steps can be selected for all file
+	// handles: first try to open the step, and create it if it
+	// doesn't exist
+	H5E_BEGIN_TRY
+	f->timegroup = H5Gopen ( f->file, stepname
+#ifndef H5_USE_16_API
+					  , H5P_DEFAULT
+#endif
+					  );
+	H5E_END_TRY
+
+	
+	if ( f->timegroup < 0 )
+	{
+		f->timegroup = H5Gcreate( f->file, stepname, 0
+#ifndef H5_USE_16_API
+					  , H5P_DEFAULT, H5P_DEFAULT
+#endif
+					  );
+		if ( f->timegroup < 0 )
+			return HANDLE_H5G_CREATE_ERR ( stepname );
+	}
+
+#endif // H5PART_SET_STEP_READ_ONLY
+
 	return H5PART_SUCCESS;
 }
 
@@ -1937,11 +2045,12 @@ _H5Part_have_group (
 	const hid_t id,
 	const char *name
 	) {
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 	return (H5Lexists( id, name, H5P_DEFAULT ) ? 1 : 0);
 #else
+	herr_t exists = 0;
 	H5E_BEGIN_TRY
-	herr_t exists = H5Gget_objinfo( id, name, 1, NULL );
+	exists = H5Gget_objinfo( id, name, 1, NULL );
 	H5E_END_TRY
 	return (exists >= 0 ? 1 : 0);
 #endif
@@ -1955,7 +2064,7 @@ _H5Part_have_group (
 
   Iterator for \c H5Giterate().
 */
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 herr_t
 _H5Part_iteration_operator2 (
 	hid_t group_id,			/*!< [in] parent object id */
@@ -2079,7 +2188,7 @@ _H5Part_iteration_operator (
 
 	if ( data->type != H5G_UNKNOWN )
 	{
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF6_18
 		H5O_info_t objinfo;
 
 		hid_t obj_id = H5Oopen(group_id, member_name, H5P_DEFAULT);
@@ -2159,7 +2268,7 @@ _H5Part_get_num_objects_matching_pattern (
 	data.type = type;
 	data.pattern = pattern;
 
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 	hid_t child_id = H5Gopen( group_id, group_name, H5P_DEFAULT );
 	if ( child_id < 0 ) return child_id;
  	herr = H5Literate( child_id, H5_INDEX_NAME, H5_ITER_INC, 0,
@@ -2170,7 +2279,7 @@ _H5Part_get_num_objects_matching_pattern (
 #endif
 	if ( herr < 0 ) return herr;
 
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 	herr = H5Gclose ( child_id );
 	if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;
 #endif
@@ -2204,7 +2313,7 @@ _H5Part_get_object_name (
 	data.name = obj_name;
 	data.len = (size_t)len_obj_name;
 
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 	hid_t child_id = H5Gopen ( group_id, group_name, H5P_DEFAULT );
 	if ( child_id < 0 ) return child_id;
  	herr = H5Literate ( child_id, H5_INDEX_NAME, H5_ITER_INC, 0,
@@ -2217,7 +2326,7 @@ _H5Part_get_object_name (
 		return HANDLE_H5L_ITERATE_ERR;
 	}
 
-#ifndef H5_USE_16_API
+#ifdef H5PART_HAVE_HDF5_18
 	herr_t herr2 = H5Gclose ( child_id );
 	if ( herr2 < 0 ) return HANDLE_H5G_CLOSE_ERR;
 #endif
@@ -2873,6 +2982,34 @@ H5PartSetViewIndices (
 	return _set_view_indices ( f, indices, nelems );
 }
 
+/*!
+  \ingroup h5part_model
+
+  In MPI-IO collective mode, all MPI tasks must participate in I/O
+  operations. \c H5PartSetViewEmpty() allows a task to participate
+  but with an empty view of the file, so that it contributes no data
+  to the I/O operation.
+
+  \return	\c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5PartSetViewEmpty (
+	H5PartFile *f			/*!< [in]  Handle to open file */
+	) {
+
+	SET_FNAME ( "H5PartSetViewEmpty" );
+
+	CHECK_FILEHANDLE( f );
+
+	if ( f->timegroup < 0 ) {
+		h5part_int64_t herr = _H5Part_set_step ( f, 0 );
+		if ( herr < 0 ) return herr;
+	}
+
+        /* using a null indices list will set an empty view */
+	return _set_view_indices ( f, NULL, 0 );
+}
+
 /*!
   \ingroup h5part_model
 
@@ -3343,7 +3480,7 @@ H5PartSetThrottle (
 	if ( f->flags & H5PART_VFD_MPIIO_IND || f->flags & H5PART_VFD_MPIPOSIX ) {
 		f->throttle = factor;
 		_H5Part_print_info (
-			"Throttling set with factor '%d'", f->throttle );
+			"Throttling set with factor = %d", f->throttle );
 	} else {
 		_H5Part_print_warn (
 			"Throttling is only permitted with the MPI-POSIX "
@@ -3361,25 +3498,26 @@ _H5Part_start_throttle (
 	if (f->throttle > 0) {
 		int ret;
 		int token = 1;
-		if (f->myproc == 0) {
-			_H5Part_print_info ("Throttling with factor = %d",
-				f->throttle);
-		}
-		if (f->myproc % f->throttle > 0) {
+		_H5Part_print_info (
+			"Throttling with factor = %d",
+			f->throttle);
+		if (f->myproc / f->throttle > 0) {
 			_H5Part_print_debug_detail (
 				"[%d] throttle: waiting on token from %d",
-				f->myproc, f->myproc - 1);
+				f->myproc, f->myproc - f->throttle);
 			// wait to receive token before continuing with read
 			ret = MPI_Recv(
 				&token, 1, MPI_INT,
-				f->myproc - 1, // receive from previous proc
+				f->myproc - f->throttle, // receive from previous proc
 				f->myproc, // use this proc id as message tag
 				f->comm,
 				MPI_STATUS_IGNORE
 				);
 			if ( ret != MPI_SUCCESS ) return HANDLE_MPI_SENDRECV_ERR;
 		}
-		_H5Part_print_debug_detail ("[%d] throttle: received token", f->myproc);
+		_H5Part_print_debug_detail (
+			"[%d] throttle: received token",
+			f->myproc);
 	}
 	return H5PART_SUCCESS;
 }
@@ -3392,19 +3530,17 @@ _H5Part_end_throttle (
 	if (f->throttle > 0) {
 		int ret;
 		int token;
-		if (f->myproc % f->throttle < f->throttle - 1) {
+		if (f->myproc + f->throttle < f->nprocs) {
 			// pass token to next proc 
-			if (f->myproc + 1 < f->nprocs) {
-				_H5Part_print_debug_detail (
-					"[%d] throttle: passing token to %d",
-					f->myproc, f->myproc + 1);
-				ret = MPI_Send(
-					&token, 1, MPI_INT,
-					f->myproc + 1, // send to next proc
-					f->myproc + 1, // use the id of the target as tag
-					f->comm
-					);
-			}
+			_H5Part_print_debug_detail (
+				"[%d] throttle: passing token to %d",
+				f->myproc, f->myproc + f->throttle);
+			ret = MPI_Send(
+				&token, 1, MPI_INT,
+				f->myproc + f->throttle, // send to next proc
+				f->myproc + f->throttle, // use the id of the target as tag
+				f->comm
+				);
 			if ( ret != MPI_SUCCESS ) return HANDLE_MPI_SENDRECV_ERR;
 		}
 	}
@@ -3488,10 +3624,10 @@ H5PartReportErrorHandler (
 	) {
 
 	_h5part_errno = eno;
-	if ( _debug > 0 ) {
+	if ( _debug > 0 && _is_root_proc ) {
 		va_list ap;
 		va_start ( ap, fmt );
-		_H5Part_vprint_error ( fmt, ap );
+		_vprint ( stderr, "E", fmt, ap );
 		va_end ( ap );
 	}
 	return _h5part_errno;
@@ -3512,7 +3648,7 @@ H5PartAbortErrorHandler (
 	) {
 
 	_h5part_errno = eno;
-	if ( _debug > 0 ) {
+	if ( _debug > 0 && _is_root_proc ) {
 		va_list ap;
 		va_start ( ap, fmt );
 		fprintf ( stderr, "%s: ", funcname );
@@ -3575,113 +3711,68 @@ _vprint (
 	free ( fmt2 );
 }
 
-void
-_H5Part_vprint_error (
-	const char *fmt,
-	va_list ap
-	) {
-
-	if ( _debug < 1 ) return;
-	_vprint ( stderr, "E", fmt, ap );
-}
-
 void
 _H5Part_print_error (
 	const char *fmt,
 	...
 	) {
 
+	if ( _debug < 1 || !_is_root_proc) return;
 	va_list ap;
 	va_start ( ap, fmt );
-	_H5Part_vprint_error ( fmt, ap );
+	_vprint ( stderr, "E", fmt, ap );
 	va_end ( ap );
 }
 
-void
-_H5Part_vprint_warn (
-	const char *fmt,
-	va_list ap
-	) {
-
-	if ( _debug < 2 ) return;
-	_vprint ( stderr, "W", fmt, ap );
-}
-
 void
 _H5Part_print_warn (
 	const char *fmt,
 	...
 	) {
 
+	if ( _debug < 2 || !_is_root_proc ) return;
 	va_list ap;
 	va_start ( ap, fmt );
-	_H5Part_vprint_warn ( fmt, ap );
+	_vprint ( stderr, "W", fmt, ap );
 	va_end ( ap );
 }
 
-void
-_H5Part_vprint_info (
-	const char *fmt,
-	va_list ap
-	) {
-
-	if ( _debug < 3 ) return;
-	_vprint ( stdout, "I", fmt, ap );
-}
-
 void
 _H5Part_print_info (
 	const char *fmt,
 	...
 	) {
 
+	if ( _debug < 3 || !_is_root_proc ) return;
 	va_list ap;
 	va_start ( ap, fmt );
-	_H5Part_vprint_info ( fmt, ap );
+	_vprint ( stdout, "I", fmt, ap );
 	va_end ( ap );
 }
 
-void
-_H5Part_vprint_debug (
-	const char *fmt,
-	va_list ap
-	) {
-
-	if ( _debug < 4 ) return;
-	_vprint ( stdout, "D", fmt, ap );
-}
-
 void
 _H5Part_print_debug (
 	const char *fmt,
 	...
 	) {
 
+	if ( _debug < 4 || !_is_root_proc ) return;
 	va_list ap;
 	va_start ( ap, fmt );
-	_H5Part_vprint_debug ( fmt, ap );
+	_vprint ( stdout, "D", fmt, ap );
 	va_end ( ap );
 }
 
-void
-_H5Part_vprint_debug_detail (
-	const char *fmt,
-	va_list ap
-	) {
-
-	if ( _debug < 5 ) return;
-	_vprint ( stdout, "DD", fmt, ap );
-}
-
 void
 _H5Part_print_debug_detail (
 	const char *fmt,
 	...
 	) {
 
+	if ( _debug < 5 ) return;
 	va_list ap;
 	va_start ( ap, fmt );
-	_H5Part_vprint_debug_detail ( fmt, ap );
+	_vprint ( stdout, "DD", fmt, ap );
 	va_end ( ap );
 }
 
@@ -3690,6 +3781,7 @@ _H5Part_set_funcname (
 	char *fname
 	) {
 	__funcname = fname;
+	_H5Part_print_debug ("(entered function)");
 }
 
 char*

src/H5Part.f90

@@ -108,17 +108,32 @@ END FUNCTION
 !> \ingroup h5partf_open
 !! Opens a parallel file for reading and specifies an HDF5 alignment.
 !! See \ref H5PartOpenFileParallelAlign
+!!
+!! Flags are specified as a comma separated string that can include:
+!!
+!! - \c fs_lustre - enable optimizations for the Lustre file system
+!! - \c vfd_mpiposix - use the HDF5 MPI-POSIX virtual file driver
+!! - \c vfd_mpio_ind - use MPI-IO in indepedent mode
+!!
 !! \return 0 on success or error code
 !<
 INTEGER*8 FUNCTION h5pt_openr_par_align ( filename, mpi_communicator, align )
     CHARACTER(LEN=*), INTENT(IN) :: filename    !< the filename to open for reading
     INTEGER, INTENT(IN) :: mpi_communicator     !< the MPI_Communicator used by the program
     INTEGER*8, INTENT(IN) :: align              !< alignment value in bytes
+    CHARACTER(LEN=*), INTENT(IN) :: flags       !< additional flags
 END FUNCTION
 
 !> \ingroup h5partf_open
 !! Opens a parallel file for writing in truncate mode and specifies
 !! an HDF5 alignment.
+!!
+!! Flags are specified as a comma separated string that can include:
+!!
+!! - \c fs_lustre - enable optimizations for the Lustre file system
+!! - \c vfd_mpiposix - use the HDF5 MPI-POSIX virtual file driver
+!! - \c vfd_mpio_ind - use MPI-IO in indepedent mode
+!!
 !! See \ref H5PartOpenFileParallelAlign
 !! \return 0 on success or error code
 !<
@@ -132,6 +147,13 @@ END FUNCTION
 !> \ingroup h5partf_open
 !! Opens a parallel file for writing in append mode and specifies
 !! an HDF5 alignment.
+!!
+!! Flags are specified as a comma separated string that can include:
+!!
+!! - \c fs_lustre - enable optimizations for the Lustre file system
+!! - \c vfd_mpiposix - use the HDF5 MPI-POSIX virtual file driver
+!! - \c vfd_mpio_ind - use MPI-IO in indepedent mode
+!!
 !! See \ref H5PartOpenFileParallelAlign
 !! \return 0 on success or error code
 !<
@@ -243,6 +265,14 @@ INTEGER*8 FUNCTION h5pt_setview_indices (filehandle,indices,nelem)
     INTEGER*8, INTENT(IN) :: nelem      !< number of particles in the list
 END FUNCTION
 
+!> \ingroup h5partf_model
+!! See \ref H5PartSetViewEmpty
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5pt_setview_empty (filehandle)
+    INTEGER*8, INTENT(IN) :: filehandle !< the handle returned during file open
+END FUNCTION
+
 !> \ingroup h5partf_model
 !! See \ref H5PartResetView
 !! \return 0 on success or error code

src/H5Part.h

@@ -16,10 +16,10 @@ extern "C" {
 #include "H5MultiBlock.h"
 #endif
 
-#define H5PART_VER_STRING	"1.6.0"
+#define H5PART_VER_STRING	"1.6.2"
 #define H5PART_VER_MAJOR	1
 #define H5PART_VER_MINOR	6
-#define H5PART_VER_RELEASE	0
+#define H5PART_VER_RELEASE	2
 
 /* error values */
 #define H5PART_SUCCESS		0
@@ -42,6 +42,7 @@ extern "C" {
 #define H5PART_VFD_MPIPOSIX	0x08
 #define H5PART_FS_LUSTRE	0x10
 #define H5PART_VFD_MPIIO_IND	0x20
+#define H5PART_VFD_CORE		0x40
 
 /* verbosity level flags */
 #define H5PART_VERB_NONE	0
@@ -99,6 +100,10 @@ H5PartCloseFile (
 	H5PartFile *f
 	);
 
+h5part_int64_t
+H5PartFileIsValid (
+	H5PartFile *f
+	);
 
 /*============== File Writing Functions ==================== */
 h5part_int64_t
@@ -121,6 +126,12 @@ H5PartSetNumParticlesStrided (
 	const h5part_int64_t stride		/*!< [in] Stride (e.g. number of fields in the particle array) */
 	);
 
+h5part_int64_t
+H5PartSetChunkSize (
+	H5PartFile *f,
+	const h5part_int64_t size
+	);
+
 h5part_int64_t
 H5PartWriteDataFloat64 (
 	H5PartFile *f,
@@ -209,6 +220,11 @@ H5PartSetViewIndices (
 	h5part_int64_t nelems		/*!< [in]  Size of list */
 	);
 
+h5part_int64_t
+H5PartSetViewEmpty (
+	H5PartFile *f
+	);
+
 h5part_int64_t
 H5PartGetView (
 	H5PartFile *f,

src/H5PartF.c

@@ -100,6 +100,9 @@
 #define h5pt_setview_indices F77NAME (					\
 					h5pt_setview_indices_,		\
 					H5PT_SETVIEW_INDICES )
+#define h5pt_setview_empty F77NAME (					\
+					h5pt_setview_empty_,		\
+					H5PT_SETVIEW_EMPTY )
 #define h5pt_resetview F77NAME (					\
 					h5pt_resetview_,		\
 					H5PT_RESETVIEW )
@@ -197,6 +200,10 @@ _H5Part_flagsfor2c (
 	while ( flags != NULL ) {
 		if ( strcmp ( flags, "vfd_mpiposix" ) == 0 )
 				fbits |= H5PART_VFD_MPIPOSIX;
+		else if ( strcmp ( flags, "vfd_core" ) == 0 )
+				fbits |= H5PART_VFD_CORE;
+		else if ( strcmp ( flags, "vfd_mpio_ind" ) == 0 )
+				fbits |= H5PART_VFD_MPIIO_IND;
 		else if ( strcmp ( flags, "fs_lustre" ) == 0 )
 		    		fbits |= H5PART_FS_LUSTRE;
 		flags = strtok ( NULL, "," );
@@ -351,16 +358,22 @@ h5pt_openr_par_align (
 	const char *file_name,
 	MPI_Fint *fcomm,
 	const h5part_int64_t *align,
-	const int l_file_name
+	const char *flags,
+	const int l_file_name,
+	const int l_flags
 	) {
 
 	MPI_Comm ccomm = MPI_Comm_f2c (*fcomm);
 	char *file_name2 = _H5Part_strdupfor2c ( file_name, l_file_name );
+	char *flags2 = _H5Part_strdupfor2c ( flags, l_flags );
+
+	char fbits = H5PART_READ | _H5Part_flagsfor2c ( flags2 );
 
 	H5PartFile* f = H5PartOpenFileParallelAlign (
-		file_name2, H5PART_READ, ccomm, *align );
+		file_name2, fbits, ccomm, *align );
 
 	free ( file_name2 );
+	free ( flags2 );
 	return (h5part_int64_t)(size_t)f; 
 }
 
@@ -384,6 +397,7 @@ h5pt_openw_par_align (
 		file_name2, fbits, ccomm, *align );
 
 	free ( file_name2 );
+	free ( flags2 );
 	return (h5part_int64_t)(size_t)f; 
 }
 
@@ -407,6 +421,7 @@ h5pt_opena_par_align (
 		file_name2, fbits, ccomm, *align );
 
 	free ( file_name2 );
+	free ( flags2 );
 	return (h5part_int64_t)(size_t)f;
 }
 #endif
@@ -626,6 +641,16 @@ h5pt_setview_indices (
 	return H5PartSetViewIndices ( filehandle, indices, *nelem );
 }
 
+h5part_int64_t
+h5pt_setview_empty (
+	const h5part_int64_t *f
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5PartSetViewEmpty ( filehandle );
+}
+
 h5part_int64_t
 h5pt_resetview (
 	const h5part_int64_t *f

src/H5PartPrivate.h

@@ -2,12 +2,17 @@
 #define __H5PART_PRIVATE_H
 
 #if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 6
+#define H5PART_USE_HDF5_16
 #define H5_USE_16_API
 #endif
 
+#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR >= 8
+#define H5PART_HAVE_HDF5_18
+#endif
+
 #define H5PART_GROUPNAME_STEP	"Step"
 
-#define H5PART_BTREE_IK 10000
+#define H5PART_SET_STEP_READ_ONLY 0
 
 h5part_int64_t
 _H5Part_file_is_valid (
@@ -167,12 +172,6 @@ _H5Part_get_err_handle (
 	void
 	);
 
-void
-_H5Part_vprint_error (
-	const char *fmt,
-	va_list ap
-	);
-
 void
 _H5Part_print_error (
 	const char *fmt,
@@ -182,12 +181,6 @@ __attribute__ ((format (printf, 1, 2)))
 #endif
 ;
 
-void
-_H5Part_vprint_warn (
-	const char *fmt,
-	va_list ap
-	);
-
 void
 _H5Part_print_warn (
 	const char *fmt,
@@ -198,12 +191,6 @@ __attribute__ ((format (printf, 1, 2)))
 #endif
 ;
 
-void
-_H5Part_vprint_info (
-	const char *fmt,
-	va_list ap
-	);
-
 void
 _H5Part_print_info (
 	const char *fmt,
@@ -214,12 +201,6 @@ __attribute__ ((format (printf, 1, 2)))
 #endif
 ;
 
-void
-_H5Part_vprint_debug (
-	const char *fmt,
-	va_list ap
-	);
-
 void
 _H5Part_print_debug (
 	const char *fmt,
@@ -230,12 +211,6 @@ __attribute__ ((format (printf, 1, 2)))
 #endif
 ;
 
-void
-_H5Part_vprint_debug_detail (
-	const char *fmt,
-	va_list ap
-	);
-
 void
 _H5Part_print_debug_detail (
 	const char *fmt,

src/H5PartTypes.h

@@ -20,8 +20,10 @@ __attribute__ ((format (printf, 3, 4)))
  ;
 
 #ifndef MPI_INCLUDED
+#ifndef OPEN_MPI
 typedef unsigned long		MPI_Comm;
 #endif
+#endif
 
 #define H5PART_STEPNAME_LEN	64
 #define H5PART_DATANAME_LEN	64
@@ -50,8 +52,9 @@ struct H5PartFile {
 	hid_t timegroup;
 	hid_t shape;
 	hid_t xfer_prop;
-	hid_t create_prop;
 	hid_t access_prop;
+	hid_t dcreate_prop;
+	hid_t fcreate_prop;
 
 	/* the dataspace on disk for the current view */
 	hid_t diskshape;

src/generate-h5multi-readwrite.py

@@ -11,6 +11,13 @@ c_head = """
 
 #include "H5MultiBlockErrors.h"
 #include "H5MultiBlockPrivate.h"
+
+#ifdef PARALLEL_IO
+
+"""
+
+c_tail = """
+#endif // PARALLEL_IO
 """
 
 h_head = """
@@ -237,6 +244,7 @@ def write_calls():
 #	fcfile.write(create_call(read_fc,type,dim));
 #	fifile.write(create_call(write_fi,type,dim));
 #	fifile.write(create_call(read_fi,type,dim));
+  cfile.write(c_tail)
   cfile.close()
   hfile.write(h_tail)
   hfile.close()

test/read.c

@@ -509,7 +509,7 @@ void test_read4(void)
 	status = H5PartSetStep(file2, NTIMESTEPS);
 	RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
 
-	test_read_data64(file2, NPARTICLES, NTIMESTEPS);
+	test_read_data64(file2, NPARTICLES, NTIMESTEPS-2);
 
 	status = H5PartCloseFile(file1);
 	RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");

test/test.c

@@ -23,9 +23,10 @@ int main(int argc, char **argv)
 	int procs;
 	MPI_Comm_size(MPI_COMM_WORLD, &procs);
 	if (procs > MAX_MPI_TASKS) {
-		fprintf(stderr, "ERROR: please use <= %d MPI tasks for the test.",
+		fprintf(stderr,
+			"ERROR: please use <= %d MPI tasks for the test.\n",
 			MAX_MPI_TASKS);
-		MPI_Abort(MPI_COMM_WORLD, -1);
+                exit(EXIT_FAILURE);
 	}
 #endif
 
@@ -62,9 +63,10 @@ int main(int argc, char **argv)
         //    TestCleanup();
 
 #ifdef PARALLEL_IO
-	return MPI_Finalize();
-#else
-	return GetTestNumErrs();
+	TestPrintf ("reached end\n");
+        fflush(stdout);
+        MPI_Finalize();
 #endif
+	return GetTestNumErrs();
 }
 

test/testframe.c

@@ -31,6 +31,7 @@
 #include <string.h>
 #include <H5Part.h>
 #include "testframe.h"
+#include "../src/H5PartPrivate.h"
 
 /*
  * Definitions for the testing structure.
@@ -652,6 +653,7 @@ test_is_valid(H5PartFile *file)
 void
 test_open_objects(H5PartFile *file, int max_objects)
 {
+#ifndef H5_USE_16_API
 	ssize_t nopen = H5Fget_obj_count(file->file, H5F_OBJ_ALL);
 	if (nopen > max_objects)
 	{
@@ -682,5 +684,6 @@ test_open_objects(H5PartFile *file, int max_objects)
 		}
 		free(list);
 	}
+#endif
 }
 

test/write.c

@@ -65,7 +65,7 @@ static void
 test_write_data64(H5PartFile *file, int nparticles, int step)
 {
 	int i,t;
-	h5part_int64_t status;
+	h5part_int64_t status, val;
 
 	double *x,*y,*z;
 	double *px,*py,*pz;
@@ -108,10 +108,12 @@ test_write_data64(H5PartFile *file, int nparticles, int step)
 			id[i] = i + nparticles*t;
 		}
 
+		val = H5PartHasStep(file, t);
+
 		status = H5PartSetStep(file, t);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
 
-		test_write_step_attribs(file, t);
+		if (val == 0) test_write_step_attribs(file, t);
 
 		status = H5PartSetNumParticles(file, nparticles);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticles");
@@ -198,7 +200,7 @@ static void
 test_write_data32(H5PartFile *file, int nparticles, int step)
 {
 	int i,t;
-	h5part_int32_t status;
+	h5part_int32_t status, val;
 	int rank, nprocs;
 
 	float *x,*y,*z;
@@ -244,8 +246,11 @@ test_write_data32(H5PartFile *file, int nparticles, int step)
 			id[i] = i + nparticles*t;
 		}
 
-		status = H5PartSetStep(file, t);
-		RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
+		val = H5PartHasStep(file, t);
+		if (val == 0) {
+			status = H5PartSetStep(file, t);
+			RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
+		}
 
 		/* test a two-part write using views */
 		status = H5PartSetView(file,
@@ -370,8 +375,6 @@ void test_write1(void)
 	test_write_data32(file1, NPARTICLES, 1);
 	test_write_file_attribs(file1, 0);
 
-	_H5Part_close_hdf_ids(file1);
-	test_open_objects(file1, 1);
 	status = H5PartCloseFile(file1);
 	RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
 }
@@ -405,10 +408,10 @@ void test_write3(void)
 	h5part_int64_t status;
 
 	TEST(	"Opening file once, write-truncate, lustre filesyste, "
-		"MPI-POSIX VFD, 64KB alignment");
+		"MPI-POSIX VFD, 1KB alignment");
 	file1 = OPENALIGN(FILENAME,
 		H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE,
-		65536);
+		1024);
 	test_is_valid(file1);
 
 	TEST("Redefining step name");
@@ -430,14 +433,14 @@ void test_write4(void)
 	h5part_int64_t status;
 
 	TEST(	"Opening file twice, write-append + read-only, "
-		"lustre filesystem, MPI-IO Independent VFD, 64K alignment");
+		"lustre filesystem, MPI-IO Independent VFD, 1K alignment");
 	file1 = OPENALIGN(FILENAME,
 		H5PART_APPEND | H5PART_VFD_MPIIO_IND | H5PART_FS_LUSTRE,
-		65536);
+		1024);
 	test_is_valid(file1);
 	file2 = OPENALIGN(FILENAME,
 		H5PART_READ | H5PART_VFD_MPIIO_IND | H5PART_FS_LUSTRE,
-		65536);
+		1024);
 	test_is_valid(file2);
 
 	TEST("Redefining step name");
@@ -447,7 +450,10 @@ void test_write4(void)
 	status = H5PartDefineStepName(file2, LONGNAME, 16);
 	RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
 
-	test_write_data64(file1, NPARTICLES, NTIMESTEPS);
+	status = H5PartSetChunkSize(file1, NPARTICLES);
+	RETURN(status, H5PART_SUCCESS, "H5PartSetChunkSize");
+
+	test_write_data64(file1, NPARTICLES, NTIMESTEPS-2);
 	test_write_file_attribs(file1, 1);
 
 	status = H5PartCloseFile(file1);