1.6.5 release: Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.

.gitattributes

@@ -9,8 +9,6 @@
 /NEWS -text
 /README -text
 /autogen.sh -text
-/config.guess -text
-/config.sub -text
 /configure-crayxt -text
 /configure.ac -text
 /depcomp -text

.gitignore

@@ -0,0 +1,13 @@
+/Makefile.in
+/aclocal.m4
+/autom4te.cache
+/build
+/config.h.in
+/configure
+doc/Makefile.in
+/ltmain.sh
+/m4
+src/H5PartF.h
+src/Makefile.in
+test/Makefile.in
+tools/Makefile.in

Makefile.am

@@ -1,5 +1,3 @@
-# Trial by Antino Kim
-# Top level Makefile.am
 ACLOCAL_AMFLAGS=-I m4
 
 SUBDIRS = \

NEWS

@@ -1,3 +1,15 @@
+#### H5PART 1.6.5 ############################################################
+
+Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
+
+#### H5PART 1.6.4 ############################################################
+
+Fixed bug where H5PartSetViewIndices was not setting an empty view when the
+number of elements is 0.
+
+Set a threshold on the HDF5 alignment parameter so that small metadata writes
+are not aligned, which causes large gaps in the file.
+
 #### H5PART 1.6.3 ############################################################
 
 New build system uses libtool and can build shared libraries.

autogen.sh

@@ -1,54 +1,48 @@
 #!/bin/sh
 # Run this to generate all the initial makefiles, etc.
 
+ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
+LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
+AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
+
+LIBTOOLIZE=`which libtoolize`
+if [ "$LIBTOOLIZE" = "" ]; then
+        LIBTOOLIZE=`which glibtoolize`
+fi
+if [ "$LIBTOOLIZE" = "" ]; then
+        echo "libtoolize not found" 1>&2
+        exit 1
+fi
+
 echo "+ making misc files ..."
 touch NEWS README AUTHORS ChangeLog
 echo
-echo
+$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
+	echo "libtoolize failed"
+	exit 1
+}
 echo
 echo "+ running aclocal ..."
 aclocal $ACLOCAL_FLAGS || {
-  echo
+	echo "aclocal failed - check that all needed development files are present on system"
-  echo "aclocal failed - check that all needed development files are present on system"
+	exit 1
-  exit 1
 }
 echo
-echo
-echo
 echo "+ running autoheader ... "
 autoheader || {
-  echo
+	echo "autoheader failed"
-  echo "autoheader failed"
+	exit 1
-  exit 1
 }
 echo
-echo
-echo
-echo "+ running libtoolize ... "
-libtoolize --force || {
-  echo
-  echo "libtoolize failed"
-  exit 1
-}
-echo
-echo
-echo
 echo "+ running autoconf ... "
 autoconf || {
-  echo
+	echo "autoconf failed"
-  echo "autoconf failed"
+	exit 1
-  exit 1
 }
 echo
-echo
-echo
 echo "+ running automake ... "
-automake -a -c --foreign || {
+automake $AUTOMAKE_FLAGS || {
-  echo
+	echo "automake failed"
-  echo "automake failed"
+	exit 1
-  exit 1
 }
-echo
-echo
-echo
 

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], [1.6.3], [h5part@lists.psi.ch], H5Part)
+AC_INIT([H5Part], [1.6.5], [h5part@lists.psi.ch], H5Part)
 
 # Ensure that a recent enough version of Autoconf is being used. 
 # If the version of Autoconf being used to create configure is earlier than version, 
@@ -54,20 +54,6 @@ AC_ARG_WITH(
 	[path to HDF5 installation [default=""]])],
 	[HDF5PATH=$withval], [HDF5PATH=""])
 
-###############################################################################
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-###############################################################################
-
-SAVE_CC=$CC
-SAVE_CXX=$CXX
-SAVE_FC=$FC
-SAVE_CFLAGS=$CFLAGS
-SAVE_CXXFLAGS=$CXXFLAGS
-SAVE_FFLAGS=$FFLAGS
-SAVE_INCLUDES=$INCLUDES
-SAVE_LDFLAGS=$LDFLAGS
-SAVE_LIBS=$LIBS
-
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -316,48 +302,6 @@ AC_TYPE_SSIZE_T
 AC_FUNC_MALLOC
 AC_CHECK_FUNCS([memset pow strchr strdup])
 
-
-###############################################################################
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-###############################################################################
-
-#if there was an external input for the variable...
-if test -n "$SAVE_CC"; then
-	CC="$SAVE_CC"
-fi
-
-if test -n "$SAVE_CXX"; then
-	CXX="$SAVE_CXX"
-fi
-
-if test -n "$SAVE_FC"; then
-	FC="$SAVE_FC"
-fi
-
-if test -n "$SAVE_CFLAGS"; then
-	CFLAGS="$SAVE_CFLAGS"
-fi
-
-if test -n "$SAVE_CXXFLAGS"; then
-	CFLAGS="$SAVE_CXXFLAGS"
-fi
-
-if test -n "$SAVE_FFLAGS"; then
-	FFLAGS="$SAVE_FFLAGS"
-fi
-
-if test -n "$SAVE_INCLUDES"; then
-	INCLUDES="$SAVE_INCLUDES"
-fi
-
-if test -n "$SAVE_LDFLAGS"; then
-	LDFLAGS="$SAVE_LDFLAGS"
-fi
-
-if test -n "$SAVE_LIBS"; then
-	LIBS="$SAVE_LIBS"
-fi
-
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################

src/H5MultiBlock.c

@@ -567,10 +567,10 @@ _halo_exchange_buffers (
 	ibufsize = (int)bufsize;
 	if ( (h5part_int64_t)ibufsize != bufsize ) return HANDLE_MPI_INT64_ERR;
 
-	send_buffer = malloc ( bufsize );
+	send_buffer = (char*) malloc ( bufsize );
 	if ( send_buffer == NULL ) return HANDLE_H5PART_NOMEM_ERR;
 
-	recv_buffer = malloc ( bufsize );
+	recv_buffer = (char*) malloc ( bufsize );
 	if ( recv_buffer == NULL ) return HANDLE_H5PART_NOMEM_ERR;
 
 	/* forward */

src/H5Part.c

@@ -291,9 +291,9 @@ _H5Part_open_file (
 
 	if ( align != 0 ) {
 		_H5Part_print_info (
-			"Setting HDF5 alignment to %ld bytes",
+			"Setting HDF5 alignment to %ld bytes with threshold at half that many bytes",
 			align );
-		if (H5Pset_alignment ( f->access_prop, 0, align ) < 0) {
+		if (H5Pset_alignment ( f->access_prop, align/2, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
 		}
@@ -2332,7 +2332,11 @@ _H5Part_get_object_name (
 	data.len = (size_t)len_obj_name;
 
 #ifdef H5PART_HAVE_HDF5_18
-	hid_t child_id = H5Gopen ( group_id, group_name, H5P_DEFAULT );
+	hid_t child_id = H5Gopen ( group_id, group_name
+#ifndef H5_USE_16_API
+		, H5P_DEFAULT
+#endif
+		);
 	if ( child_id < 0 ) return child_id;
  	herr = H5Literate ( child_id, H5_INDEX_NAME, H5_ITER_INC, 0,
  			_H5Part_iteration_operator2, &data );
@@ -2855,9 +2859,9 @@ _set_view_indices (
 	herr = _reset_view ( f );
 	if ( herr < 0 ) return herr;
 
-	if ( indices == NULL || nelems <= 0 ) {
+	if ( indices == NULL || nelems < 0 ) {
 		_H5Part_print_warn (
-			"View indices array is null or size is <= 0: reseting view." );
+			"View indices array is null or size is < 0: reseting view." );
 		return H5PART_SUCCESS;
 	}
 

src/H5Part.h

@@ -16,10 +16,10 @@ extern "C" {
 #include "H5MultiBlock.h"
 #endif
 
-#define H5PART_VER_STRING	"1.6.3"
+#define H5PART_VER_STRING	"1.6.5"
 #define H5PART_VER_MAJOR	1
 #define H5PART_VER_MINOR	6
-#define H5PART_VER_RELEASE	3
+#define H5PART_VER_RELEASE	5
 
 /* error values */
 #define H5PART_SUCCESS		0

src/H5PartPrivate.h

@@ -116,6 +116,24 @@ _H5Part_write_attrib (
 	const hsize_t attrib_nelem
 	);
 
+h5part_int64_t
+_H5Part_write_file_attrib (
+	H5PartFile *f,
+	const char *name,
+	const hid_t type,
+	const void *value,
+	const hsize_t nelem
+	);
+
+h5part_int64_t
+_H5Part_write_step_attrib (
+	H5PartFile *f,
+	const char *name,
+	const hid_t type,
+	const void *value,
+	const hsize_t nelem
+	);
+
 h5part_int64_t
 _H5Part_get_attrib_info (
 	hid_t id,

test/Makefile.am

@@ -22,6 +22,6 @@ test_LDADD   =  ../src/libH5Part.la
 testf_SOURCES = testf.F90
 testf_LDADD   =  ../src/libH5PartF.la
 
-clean: clean-am
+clean-local:
-	rm -f *.h5
+	$(RM) -f *.h5
 

test/read.c

@@ -1,3 +1,4 @@
+#include <string.h>
 #include <H5Part.h>
 
 #include "testframe.h"

test/testframe.c

@@ -536,7 +536,7 @@ TestPrintf(const char *format, ...)
     int nproc;
     MPI_Comm_rank(MPI_COMM_WORLD, &nproc);
     if ( nproc == 0 || VERBOSE_HI ) {
-	char *format2 = malloc(strlen(format)+8);
+	char *format2 = (char*)malloc(strlen(format)+8);
 	sprintf(format2, "[%d] %s", nproc, format);
 	va_start(arglist, format);
 	ret_value = vprintf(format2, arglist);
@@ -570,7 +570,7 @@ TestErrPrintf(const char *format, ...)
     int nproc;
     MPI_Comm_rank(MPI_COMM_WORLD, &nproc);
     if ( nproc == 0 || VERBOSE_HI ) {
-	char *format2 = malloc(strlen(format)+8);
+	char *format2 = (char*)malloc(strlen(format)+8);
 	sprintf(format2, "[%d] %s", nproc, format);
 	va_start(arglist, format);
 	ret_value = vfprintf(stderr, format2, arglist);

test/testframe.h

@@ -6,6 +6,8 @@
 #ifndef _H5PART_TESTFRAME_H_
 #define _H5PART_TESTFRAME_H_
 
+#include <string.h>
+
 #ifdef PARALLEL_IO
 #define OPEN(file,mode) \
     H5PartOpenFileParallel(file,mode,MPI_COMM_WORLD)