updated h5_lustre.c to user new macros; changed library targets to ../lib/lib*.a to avoid the mv and mkdir hacks in Makefile.am; fixed problem in h5u_test with H5PartSetViewIndices; OPEN BUG with h5u_test for >1 MPI task (strange pthread setfault?)

configure.ac

@@ -194,8 +194,8 @@ AC_MSG_CHECKING([if C interface enabled])
 if test "X$USE_C" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 	BINDINGS="$BINDINGS C"
-	LIB_C="libH5hutC.a"
-	BUILD_LIBS="$BUILD_LIBS $LIB_C"
+	LIB_C="../lib/libH5hutC.a"
+	BUILD_LIBS="$BUILD_LIBS libH5hutC.a"
 	BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
 	BUILD_TOOLS="$BUILD_TOOLS h5hutcc"
 fi
@@ -205,8 +205,8 @@ AC_MSG_CHECKING([if fortran interface enabled])
 if test "X$USE_FORTRAN" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 	BINDINGS="$BINDINGS Fortran"
-	LIB_FORTRAN="libH5hutF.a"
-        BUILD_LIBS="$BUILD_LIBS $LIB_FORTRAN"
+	LIB_FORTRAN="../lib/libH5hutF.a"
+        BUILD_LIBS="$BUILD_LIBS libH5hutF.a"
 
 	AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
 	if test -z "$FC" ; then
@@ -507,8 +507,7 @@ AC_CONFIG_FILES([
 	src/h5core/Makefile
         src/Fortran/Makefile
 	test/Makefile
-	test/H5Fed/Makefile
-	test/H5Part/Makefile
+        test/H5Fed/Makefile
 	tools/Makefile
 	tools/h5hutcc
 ])

src/C/H5.c

@@ -41,6 +41,16 @@
   Open file with name \c filbename. This function is available in the parallel
   and serial version. In the serial case \c comm may have any value.
 
+  File mode flags are:
+  - H5_O_RDONLY: only reading allowed
+  - H5_O_WRONLY: create new file, dataset must not exist
+  - H5_O_APPEND: allows to append a new datasets to an existing file
+  - H5_O_RDWR:   dataset may exist
+
+  You can also select a "virtual file driver" in the HDF5 layer using:
+  - H5_VFD_INDEPENDENT: MPI-IO in independent (asynchronous) mode
+  - H5_VFD_MPIPOSIX: parallel I/O implemented directly by HDF5, bypassing MPI-IO
+
   \return File handle.
   \return NULL on error.
 */
@@ -59,7 +69,7 @@ H5OpenFile (
 /*!
   \ingroup h5hut_file
 
-  Close file.
+  Close file and free all memory associated with the file handle.
 
   \return \c H5_SUCCESS or error code
 */
@@ -74,7 +84,7 @@ H5CloseFile (
 /*!
   \ingroup h5hut_file
 
-  Close file.
+  Verify that the file handle points to a valid H5hut file structure.
 
   \return \c H5_SUCCESS or error code
 */

src/C/H5Part.c

@@ -539,6 +539,11 @@ H5PartSetView (
   is set, or the number of particles in a dataset changes, or the view is
   "unset" by calling \c H5PartSetViewIndices(NULL,0);
 
+  When you perform a read or write on a view consisting of indices, it
+  is assumed that your buffer is \b unpacked, meaning that there is room
+  for all the intermediate values (which will not be touched by the read
+  or write).
+
   Before you set a view, the \c H5PartGetNumParticles() 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
@@ -549,7 +554,7 @@ H5PartSetView (
 h5_err_t
 H5PartSetViewIndices (
 	h5_file_t *f,			/*!< [in]  Handle to open file */
-	const h5_id_t *indices,		/*!< [in]  List of indices */
+	const h5_size_t *indices,	/*!< [in]  List of indices */
 	h5_size_t nelems		/*!< [in]  Size of list */
 	) {
 	H5_API_ENTER3 (h5_err_t,

src/C/Makefile.am

@@ -9,7 +9,7 @@ INCLUDES = -I../include @INCLUDES@
 lib_LIBRARIES = @LIB_C@
 
 # Listing of all possible targets that I may build.
-EXTRA_LIBRARIES = libH5hutC.a
+EXTRA_LIBRARIES = ../lib/libH5hutC.a
 
 # Header files that I wish to install in $(prefix)/include
 include_HEADERS =				\
@@ -31,7 +31,7 @@ include_HEADERS =				\
 EXTRA_HEADERS =
 
 # Listing of sources
-libH5hutC_a_SOURCES =				\
+___lib_libH5hutC_a_SOURCES =			\
 	H5.c					\
 	H5_attribs.c				\
 	H5_attachments.c			\
@@ -45,10 +45,7 @@ libH5hutC_a_SOURCES =				\
 	H5Fed_store.c				\
 	H5Fed_tags.c
 
-all: all-am install-libs-local
-
-install-libs-local:
-	-cp ${lib_LIBRARIES} ../lib
+all: all-am
 
 clean: clean-am
 

src/Fortran/H5Part_F.c

@@ -146,7 +146,7 @@ h5pt_setview (
 
 	h5_file_t *filehandle = (h5_file_t*)(size_t)*f;
 	h5_set_funcname( filehandle, __func__ );
-	return h5u_set_view ( filehandle, *start, *end );
+	return h5u_set_view ( filehandle, (*start)-1, (*end)-1 );
 }
 
 h5_err_t

src/Fortran/H5_F.c

@@ -78,7 +78,7 @@ h5_openr (
 	) {
 
 	char *file_name2 = h5_strdupfor2c ( file_name, l_file_name );
-	h5_file_t* f = h5_open_file ( file_name2, H5_O_RDONLY, 0, __func__ );
+	h5_file_t* f = h5_open_file ( file_name2, H5_O_RDONLY, 0 );
 	free ( file_name2 );
 	return (h5_int64_t)(size_t)f; 
 }
@@ -90,7 +90,7 @@ h5_openw (
 	) {
 
 	char *file_name2 = h5_strdupfor2c ( file_name, l_file_name );
-	h5_file_t* f = h5_open_file ( file_name2, H5_O_WRONLY, 0, __func__ );
+	h5_file_t* f = h5_open_file ( file_name2, H5_O_WRONLY, 0 );
 	free ( file_name2 );
 	return (h5_int64_t)(size_t)f; 
 }
@@ -102,7 +102,7 @@ h5pt_opena (
 	) {
 	
 	char *file_name2 = h5_strdupfor2c ( file_name, l_file_name );
-	h5_file_t* f = h5_open_file ( file_name2, H5_O_APPEND, 0, __func__ );
+	h5_file_t* f = h5_open_file ( file_name2, H5_O_APPEND, 0 );
 	free ( file_name2 );
 	return (h5_int64_t)(size_t)f;
 }
@@ -123,7 +123,7 @@ h5_openr_par (
 
 	h5_int32_t fbits = H5_O_RDONLY | _flagsfor2c ( flags2 );
 
-	h5_file_t* f = h5_open_file ( file_name2, fbits, ccomm, __func__  );
+	h5_file_t* f = h5_open_file ( file_name2, fbits, ccomm );
 
 	free ( file_name2 );
 	free ( flags2 );
@@ -145,7 +145,7 @@ h5_openw_par (
 
 	h5_int32_t fbits = H5_O_WRONLY | _flagsfor2c ( flags2 );
 
-	h5_file_t* f = h5_open_file ( file_name2, ccomm, fbits, __func__ );
+	h5_file_t* f = h5_open_file ( file_name2, ccomm, fbits );
 
 	free ( file_name2 );
 	free ( flags2 );
@@ -168,7 +168,7 @@ h5pt_opena_par_align (
        
 	h5_int32_t fbits = H5_O_APPEND | _flagsfor2c ( flags2 );
 
-	h5_file_t* f = h5_open_file( file_name2, ccomm, fbits, __func__ );
+	h5_file_t* f = h5_open_file( file_name2, ccomm, fbits );
 
 	free ( file_name2 );
 	free ( flags2 );

src/Fortran/Makefile.am

@@ -26,15 +26,16 @@ nodist_include_HEADERS = ../include/H5hutF.h
 lib_LIBRARIES = @LIB_FORTRAN@
 
 # Listing of all possible targets that I may build.
-EXTRA_LIBRARIES = libH5hutF.a
+EXTRA_LIBRARIES = ../lib/libH5hutF.a
 
-libH5hutF_a_SOURCES =	H5_F.c \
-			H5_attribs_F.c \
-			H5Part_F.c \
-			H5Block_F.c \
-			H5Block_readwrite_F.c
+___lib_libH5hutF_a_SOURCES = 	\
+	H5_F.c			\
+	H5_attribs_F.c		\
+	H5Part_F.c		\
+	H5Block_F.c		\
+	H5Block_readwrite_F.c
 
-libH5hutF_a_DEPENDENCIES = ../include/H5hutF.h
+___lib_libH5hutF_a_DEPENDENCIES = ../include/H5hutF.h
 
 ../include/H5hutF.h: $(F90_FILES)
 	awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >$@

src/h5core/Makefile.am

@@ -32,19 +32,22 @@ EXTRA_HEADERS =					\
 	../include/h5core/h5t_retrieve.h	\
 	../include/h5core/h5t_storemesh.h	\
 	../include/h5core/h5t_tags.h		\
-	h5b_errorhandling_private.h		\
-	h5b_model_private.h			\
-	h5b_types_private.h			\
+	h5_attribs_private.h			\
 	h5_core_private.h			\
 	h5_errorhandling_private.h		\
 	h5_fcmp_private.h			\
 	h5_hdf5_private.h			\
 	h5_hsearch_private.h			\
 	h5_lustre_private.h			\
+	h5_maps_private.h			\
 	h5_mpi_private.h			\
 	h5_qsort_private.h			\
 	h5_readwrite_private.h			\
 	h5_syscall_private.h			\
+	h5_types_private.h			\
+	h5b_errorhandling_private.h		\
+	h5b_model_private.h			\
+	h5b_types_private.h			\
 	h5t_access_private.h			\
 	h5t_adjacencies_private.h		\
 	h5t_consts_private.h			\
@@ -60,7 +63,6 @@ EXTRA_HEADERS =					\
 	h5t_store_trim_private.h		\
 	h5t_tags_private.h			\
 	h5t_types_private.h			\
-	h5_types_private.h			\
 	h5u_errorhandling_private.h		\
 	h5u_types_private.h
 
@@ -68,13 +70,13 @@ EXTRA_HEADERS =					\
 EXTRA_DIST = $(EXTRA_HEADERS)
 
 # What to build... Will be determined by configure script.
-lib_LIBRARIES = libH5hut.a
+lib_LIBRARIES = ../lib/libH5hut.a
 
 # Listing of all possible targets that I may build.
-EXTRA_LIBRARIES = libH5hut.a
+EXTRA_LIBRARIES = ../lib/libH5hut.a
 
 # Listing of sources
-libH5hut_a_SOURCES =				\
+___lib_libH5hut_a_SOURCES =			\
 	h5_attach.c				\
 	h5_attribs.c				\
 	h5_errorhandling.c			\
@@ -117,12 +119,9 @@ libH5hut_a_SOURCES =				\
 	h5t_store_trim.c			\
 	h5t_tags.c
 
-libH5hut_a_DEPENDENCIES = $(EXTRA_HEADERS)
+___lib_libH5hut_a_DEPENDENCIES = $(EXTRA_HEADERS)
 
-all: all-am install-libs-local
-
-install-libs-local:
-	-cp ${lib_LIBRARIES} ../lib
+all: all-am
 
 install-exec-local:
 	@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core

src/h5core/h5_errorhandling.c

@@ -83,7 +83,7 @@ h5_set_debuglevel (
 
   \return current debug level
 */
-h5_id_t
+h5_err_t
 h5_get_debuglevel (
 	void
 	) {

src/h5core/h5_hdf5.c

@@ -262,7 +262,7 @@ hdf5_close_dataset (
 			     "dataset_id=%d (%s)", 
 			    dataset_id,
 			    hdf5_get_objname (dataset_id));
-	if (dataset_id == 0 || dataset_id == -1)
+	if (dataset_id < 0)
 		HDF5_WRAPPER_LEAVE (H5_SUCCESS); 
 
 	if (H5Dclose (dataset_id) < 0) {
@@ -537,7 +537,7 @@ hdf5_select_elements_of_dataspace (
 		herr = H5Sselect_elements (
 			space_id,
 			op,
-			nelems,
+			(size_t)nelems,
 			indices);
 	} else {
 		herr = H5Sselect_none ( space_id );

src/h5core/h5_lustre.c

@@ -8,6 +8,7 @@
 #define __USE_GNU
 #include <fcntl.h>
 #undef __USE_GNU
+#include <unistd.h>
 #include <lustre/liblustreapi.h>
 
 #include "h5core/h5_core.h"
@@ -32,25 +33,29 @@ _get_lustre_stripe_size(h5_file_t *const f,  const char *path )
 {
 	size_t nbytes = sizeof(struct lov_user_md) +
 				INIT_ALLOC_NUM_OSTS * sizeof(struct lov_user_ost_data);
-	struct lov_user_md *lum;
-	TRY( lum = h5_calloc (1, nbytes) );
+	struct lov_user_md *lum = h5_calloc(1, nbytes);
+	if (!lum) {
+		h5_error(H5_ERR_INTERNAL, MSG_HEADER
+			"cannot allocate lustre struct");
+		return -1;
+	}
 	lum->lmm_magic = LOV_USER_MAGIC;
 
-	int fd = open64(path, O_RDONLY);
+	int fd = open(path, O_RDONLY);
 	if (fd < 0) {
 		extern int errno;
 		if (errno == EINVAL)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
-				"open64: a flag is invalid!");
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
+				"open: a flag is invalid!");
 		else if (errno == EACCES)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
-				"open64: access denied or file does not exist!");
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
+				"open: access denied or file does not exist!");
 		else if (errno == ENAMETOOLONG)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
-				"open64: path is too long!");
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
+				"open: path is too long!");
 		else
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
-				"open64: unspecific error!");
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
+				"open: unspecific error!");
 		return -1;
 	}
 		
@@ -58,22 +63,22 @@ _get_lustre_stripe_size(h5_file_t *const f,  const char *path )
 	if (ret == -1) {
 		extern int errno;
 		if (errno == EBADF)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
 				"ioctl: bad file handle!");
 		else if (errno == EINVAL)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
 				"ioctl: invalid argument!");
 		else if (errno == EIO)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
 				"ioctl: physical I/O problem!");
 		else if (errno == ENOTTY)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
 				"ioctl: file handle does not accept control functions!");
 		else if (errno == ENODEV)
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
 				"ioctl: driver doesn't support control functions!");
 		else
-			h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
+			h5_error(H5_ERR_INTERNAL, MSG_HEADER
 				"ioctl: unspecific error!");
 		return -1;
 	}
@@ -95,6 +100,7 @@ h5_optimize_for_lustre (
 	const char *filename
 	) {
 
+	H5_CORE_API_ENTER2 (h5_err_t, "f=0x%p, filename=\"%s\"", f, filename);
 	ssize_t stripe_size;
 	if ( f->myproc == 0 )
 	{
@@ -119,23 +125,23 @@ h5_optimize_for_lustre (
 		h5_free(path);
 	}
 
-	TRY( h5priv_mpi_bcast(f, &stripe_size, 1, MPI_LONG_LONG, 0, f->comm) );
-	h5_info(f, MSG_HEADER
+	TRY( h5priv_mpi_bcast(&stripe_size, 1, MPI_LONG_LONG, 0, f->comm) );
+	h5_info(MSG_HEADER
 		"Found lustre stripe size of %lld bytes",
 		(long long)stripe_size);
 
 	hsize_t btree_ik = (stripe_size - 4096) / 96;
 	hsize_t btree_bytes = 64 + 96*btree_ik;
-	h5_info(f, MSG_HEADER
+	h5_info(MSG_HEADER
 		"Setting HDF5 btree ik to %lld (= %lld bytes at rank 3)",
 		(long long)btree_ik, (long long)btree_bytes);
-	TRY( hdf5_set_btree_ik_property(f, f->create_prop, btree_ik) );
+	TRY( hdf5_set_btree_ik_property(f->create_prop, btree_ik) );
 
 	/* set alignment to lustre stripe size */
-	TRY( hdf5_set_alignment_property(f,
+	TRY( hdf5_set_alignment_property(
 				f->access_prop, 0, stripe_size) );
 
-	h5_info(f, MSG_HEADER "Disabling metadata cache flushes.");
+	h5_info(MSG_HEADER "Disabling metadata cache flushes.");
 	/* disable metadata cache flushes */
 	/* defer metadata writes */
 	H5AC_cache_config_t config;
@@ -149,7 +155,7 @@ h5_optimize_for_lustre (
 	config.flash_incr_mode = H5C_flash_incr__off;
 	TRY( H5Pset_mdc_config( f->access_prop, &config ) );
 
-	return H5_SUCCESS;
+	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
 #endif // H5_USE_LUSTRE

src/h5core/h5_openclose.c

@@ -348,7 +348,8 @@ h5_set_stepname_fmt (
 	strncpy (
 		f->prefix_step_name,
 		name,
-		H5_STEPNAME_LEN - 1);
+		//H5_STEPNAME_LEN - 1);
+		63);
 	f->width_step_idx = width;
 
 	H5_CORE_API_RETURN (H5_SUCCESS);
@@ -474,10 +475,11 @@ h5_strdupfor2c (
 
 	char *dup = (char*)malloc ( len + 1 );
 	strncpy ( dup, s, len );
-	char *p = dup + len;
-	do {
-		*p-- = '\0';
-	} while ( *p == ' ' );
+	dup[len] = '\0';
+	for (int i=len-1; i>=0; i--) {
+		if (dup[i] == ' ') dup[i] = '\0';
+		else break;
+	}
 	return dup;
 }
 

src/h5core/h5_readwrite.c

@@ -269,7 +269,7 @@ h5_normalize_dataset_name (
 	H5_CORE_API_ENTER2 (h5_err_t,
 			    "name=\"%s\", name2=\"%s\"",
 			    name, name2);
-	if ( strlen(name) > H5_DATANAME_LEN ) {
+	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);

src/h5core/h5u_model.c

@@ -275,8 +275,8 @@ h5u_set_view (
 h5_err_t
 h5u_set_view_indices (
 	h5_file_t *const f,	        	/*!< [in]  Handle to open file */
-	const h5_id_t *const indices,		/*!< [in]  List of indices */
-	const h5_size_t nelems		        /*!< [in]  Size of list */
+	const h5_size_t *const indices,		/*!< [in]  List of indices */
+	h5_size_t nelems		        /*!< [in]  Size of list */
 	) {
 	H5_CORE_API_ENTER3 (h5_err_t,
 			    "f=0x%p, indices=0x%p, nelems=%llu",
@@ -299,7 +299,7 @@ h5u_set_view_indices (
 	  For now, we interpret start=-1 to mean 0 and 
 	  end==-1 to mean end of file
 	*/
-	TRY ( total = (hsize_t) h5u_get_num_particles ( f ) );
+	TRY ( total = h5u_get_num_particles ( f ) );
 	if ( total == 0 ) {
 		/* No datasets have been created yet and no veiws are set.
 		 * We have to leave the view empty because we don't know how
@@ -309,19 +309,19 @@ h5u_set_view_indices (
 
 	if ( total == 0 ) return H5_SUCCESS;
 
-	u->nparticles = (hsize_t) nelems;
+	u->nparticles = nelems;
 	h5_debug ("This view selected %lld particles.", (long long)u->nparticles );
 
 	/* declare overall data size  but then will select a subset */
 	TRY (u->diskshape = hdf5_create_dataspace (1, &total, NULL));
 
 	/* declare local memory datasize */
-	total = (size_t)u->nparticles;
+	total = u->nparticles;
 	TRY (u->memshape = hdf5_create_dataspace (1, &total, &dmax));
 	TRY (hdf5_select_elements_of_dataspace ( 
-		     u->diskshape,
-		     H5S_SELECT_SET,
-		     nelems, (hsize_t*)indices ) );
+		u->diskshape,
+		H5S_SELECT_SET,
+		nelems, indices ) );
 
 	u->viewindexed = 1;
 

src/include/H5Part.h

@@ -129,7 +129,7 @@ H5PartSetView (
 h5_err_t
 H5PartSetViewIndices (
 	h5_file_t *f,			/*!< [in]  Handle to open file */
-	const h5_id_t *indices,		/*!< [in]  List of indices */
+	const h5_size_t *indices,	/*!< [in]  List of indices */
 	h5_size_t nelems		/*!< [in]  Size of list */
 	);
 

src/include/h5core/h5u_model.h

@@ -33,8 +33,8 @@ h5u_set_view (
 h5_err_t
 h5u_set_view_indices (
 	h5_file_t *const f,
-	const h5_id_t *const indices,
-	const h5_size_t nelems
+	const h5_size_t *const indices,
+	h5_size_t nelems
 	);
 
 h5_err_t 

test/H5Fed/Makefile.am

@@ -2,15 +2,6 @@
 
 OBJEXT = o
 
-# COMPILER SETTING
-CC = @CC@
-CXX = @CXX@
-FC = @FC@
-
-# COMPILER FLAG SETTING
-AM_CFLAGS = @CFLAGS@
-FFLAGS = @FFLAGS@
-
 AM_LDFLAGS = -L../../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 INCLUDES = -I../../src/include @INCLUDES@
@@ -35,7 +26,7 @@ EXTRA_DIST =					\
 		tetmesh_adjacencies.c		\
 		tetmesh_read.c			\
 		tetmesh_read_tags.c		\
-g		tetmesh_write.c			\
+		tetmesh_write.c			\
 		tetmesh_write2.c		\
 		tetmesh_write_tags.c		\
 		trimesh_adjacencies.c		\
@@ -47,8 +38,6 @@ g		tetmesh_write.c			\
 #		map_triangle2globalid.c \
 #		$(bin_SCRIPTS)
 
-all:	$(noinst_PROGRAMS)
-
 clean: clean-am
 	rm -f *.h5
 

test/H5Part/Bench.c

@@ -10,7 +10,7 @@
 #endif
 
 #ifndef DISABLE_H5PART
-#include "H5Part.h"
+#include "H5hut.h"
 #endif
 
 #define FILENAME "testio"
@@ -217,7 +217,7 @@ int main(int argc,char *argv[]){
     if(rank==0) unlink(filename);
     MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
 
-    f = H5PartOpenFileParallel(filename,H5PART_WRITE,MPI_COMM_WORLD);
+    f = H5OpenFile(filename,H5_O_WRONLY,MPI_COMM_WORLD);
     MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
     /* start the timer */
     starttime=endtime=MPI_Wtime();
@@ -228,7 +228,7 @@ int main(int argc,char *argv[]){
 	for(n=0;n<localnp;n++)
 	  (data[j])[n]=(double)rank;
       }
-      H5PartSetStep(f,i);
+      H5SetStep(f,i);
       H5PartWriteDataFloat64(f,"x",x);
       H5PartWriteDataFloat64(f,"y",y);
       H5PartWriteDataFloat64(f,"z",z);
@@ -239,7 +239,7 @@ int main(int argc,char *argv[]){
       curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
       MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
     }
-    H5PartCloseFile(f);
+    H5CloseFile(f);
     MPI_Barrier(MPI_COMM_WORLD);
     endtime=MPI_Wtime();
     if(rank==0){

test/Makefile.am

@@ -1,10 +1,11 @@
 # test level Makefile.am
 
 #SUBDIRS = H5Block H5Fed H5Part
+SUBDIRS = H5Fed
 
 OBJEXT=o
 
-AM_LDFLAGS = -L../src/h5core -L../src/C @LDFLAGS@
+AM_LDFLAGS = -L../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 
 INCLUDES = -I../src/include @INCLUDES@
@@ -25,8 +26,8 @@ h5u_test_SOURCES =	\
 		params.h
 
 h5u_test_DEPENDENCIES = \
-		../src/h5core/libH5hut.a \
-		../src/C/libH5hutC.a
+		../src/lib/libH5hut.a \
+		../src/lib/libH5hutC.a
 
 h5b_test_SOURCES =	\
 		h5b_test.c \
@@ -37,8 +38,8 @@ h5b_test_SOURCES =	\
 		params.h
 
 h5b_test_DEPENDENCIES = \
-		../src/h5core/libH5hut.a \
-		../src/C/libH5hutC.a
+		../src/lib/libH5hut.a \
+		../src/lib/libH5hutC.a
 
 clean: clean-am
 	rm -f *.h5

test/h5u_read.c

@@ -96,7 +96,7 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
         h5_int64_t val, start, end, type;
 	char name1[4];
 	char name2[8];
-	h5_id_t indices[8];
+	h5_size_t indices[8];
         h5_size_t size;
 
 	double *x,*y,*z;
@@ -212,9 +212,10 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
 		val = H5PartGetNumParticles(file);
 		IVALUE(val, 4, "particle count");
 
+                x[3] = 0;
 		status = H5PartReadDataFloat64(file, "x", x);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
-		FVALUE(x[2], (double)(rank*2+9+nparticles*t), "x data");
+		FVALUE(x[3], (double)(rank*2+3+nparticles*t), "x data");
 
 		val = H5PartGetNumParticles(file);
 		IVALUE(val, 4, "particle count");
@@ -330,7 +331,7 @@ test_read_data32(h5_file_t *file, int nparticles, int step)
 	px=(float*)malloc(nparticles*sizeof(float));
 	py=(float*)malloc(nparticles*sizeof(float));
 	pz=(float*)malloc(nparticles*sizeof(float));
-	id=(int*)malloc(nparticles*sizeof(int));
+	id=(h5_int32_t*)malloc(nparticles*sizeof(h5_int32_t));
 
 	TEST("Reading 32-bit data");
 
@@ -365,7 +366,7 @@ test_read_data32(h5_file_t *file, int nparticles, int step)
 		status = H5PartReadDataFloat32(file, "pz", pz);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataFloat32");
 		
-		status = H5PartReadDataInt32(file, LONGNAME, id);
+		status = H5PartReadDataInt32(file, LONGNAME2, id);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataInt32");
 
 		for (i=0; i<nparticles; i++)

test/h5u_write.c

@@ -278,7 +278,7 @@ test_write_data32(h5_file_t *file, int nparticles, int step)
 		status = H5PartWriteDataFloat32(file, "pz", pz);
 		RETURN(status, H5_SUCCESS, "H5PartWriteDataFloat32");
 		
-		status = H5PartWriteDataInt32(file, LONGNAME, id);
+		status = H5PartWriteDataInt32(file, LONGNAME2, id);
 		RETURN(status, H5_SUCCESS, "H5PartWriteDataInt32");
 
 		/* the second write phase... */

test/params.h

@@ -3,6 +3,7 @@
 
 #define FILENAME "test.h5"
 #define LONGNAME "thisisaverylongnamethatshouldexceedthelimitof64charcausingawarningtoprint"
+#define LONGNAME2 "thisisaverylongnamethatshouldexceedthelimitof64charcausingawarni"
 #define NTIMESTEPS 10
 
 /* do not decrease this value below 99, or it will break assumptions