1.6.1 tag

.gitattributes

@@ -9,6 +9,8 @@
 /NEWS -text
 /README -text
 /autogen.sh -text
+/config.guess -text
+/config.sub -text
 /configure-crayxt -text
 /configure.ac -text
 /depcomp -text
@@ -16,9 +18,6 @@ doc/Doxyfile -text
 doc/H5X_File_Format.txt -text
 doc/Makefile.am -text
 doc/doxyfooter -text
-examples/core_vfd.c -text
-examples/fields.c -text
-examples/particles.c -text
 examples/simplef.F90 -text
 examples/stridedf.F90 -text
 examples/write_setview.c -text
@@ -77,7 +76,6 @@ test/H5test.cc -text
 test/H5testF.f -text
 test/H5testFpar.F90 -text
 test/Makefile.am -text
-test/coords.F90 -text
 test/params.h -text
 test/read.c -text
 test/test.c -text

.gitignore

@@ -1,13 +0,0 @@
-/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

AUTHORS

@@ -8,4 +8,4 @@ John Shalf (NERSC/LBNL)
 Cristina Siegerist (NERSC/LBNL)
 Mark Howison (NERSC/LBNL)
 
-Please use h5part@lists.psi.ch for communication.
+Please use h5part@lists.psi.ch for communicaion.

Makefile.am

@@ -1,4 +1,5 @@
-ACLOCAL_AMFLAGS=-I m4
+# Trial by Antino Kim
+# Top level Makefile.am
 
 SUBDIRS = \
 	doc \
@@ -6,6 +7,8 @@ SUBDIRS = \
 	test \
 	tools
 
+EXTRA_DIST = configure-crayxt
+
 MAINTAINERCLEANFILES = \
 	config.h \
 	config.log \

NEWS

@@ -1,50 +1,3 @@
-#### H5PART 1.6.6 ############################################################
-
-Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
-interface.
-
-Added missing type normalization for int32 type.
-
-Rewrite of h5pAttrib tool.
-
-#### 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.
-
-Fixed a bug that incorrectly identifies the number of selected points in a view
-when using H5PartSetViewIndices.
-
-Fixed bug in Fortran test reported by several people, as well as several
-incorrect views set in the C test that were causing segfaults.
-
-Fixed name mismatches in the Fortran interface, and an off-by-one indexing
-problem.
-
-#### H5PART 1.6.2 ############################################################
-
-Removed H5PartSetViewEmpty
---------------------------
-
-An empty view can now be selected with:
-H5PartSetNumParticles(file, 0);
-
-Bug Fixes to Attribute Calls in Fortran API
--------------------------------------------
-
-Fixed a problem where attribute values were reverting to zero.
-
 #### H5PART 1.6.1 ############################################################
 
 Chunking in the H5Part API

autogen.sh

@@ -1,48 +1,46 @@
 #!/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 [ "$LIBTOOLIZE" = "" ]; then
-        echo "libtoolize not found" 1>&2
-        exit 1
-fi
-
 echo "+ making misc files ..."
 touch NEWS README AUTHORS ChangeLog
 echo
-$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
+echo
-	echo "libtoolize failed"
-	exit 1
-}
 echo
 echo "+ running aclocal ..."
 aclocal $ACLOCAL_FLAGS || {
-	echo "aclocal failed - check that all needed development files are present on system"
+  echo
-	exit 1
+  echo "aclocal failed - check that all needed development files are present on system"
+  exit 1
 }
 echo
+echo
+echo
+echo
 echo "+ running autoheader ... "
 autoheader || {
-	echo "autoheader failed"
+  echo
-	exit 1
+  echo "autoheader failed"
+  exit 1
 }
 echo
+echo
+echo
 echo "+ running autoconf ... "
 autoconf || {
-	echo "autoconf failed"
+  echo
-	exit 1
+  echo "autoconf failed"
+  exit 1
 }
 echo
+echo
+echo
 echo "+ running automake ... "
-automake $AUTOMAKE_FLAGS || {
+automake -a -c --foreign || {
-	echo "automake failed"
+  echo
-	exit 1
+  echo "automake failed"
+  exit 1
 }
+echo
+echo
+echo
 

configure-crayxt

@@ -1,20 +1,18 @@
 #!/bin/sh
 
-F90=gfortran
-
  ./configure \
         $@ \
         --enable-parallel \
         --enable-fortran \
         --enable-tools \
-        CC=cc CXX=CC FC=$F90 \
+        CC=cc CXX=CC FC=pgf90 \
         MPICC=cc MPICXX=CC MPIFC=ftn
-sed -e 's/$F90/ftn/g' <Makefile > newMakefile
+sed -e 's/pgf90/ftn/g' <Makefile > newMakefile
 mv newMakefile Makefile
-sed -e 's/$F90/ftn/g' <src/Makefile > newMakefile
+sed -e 's/pgf90/ftn/g' <src/Makefile > newMakefile
 mv newMakefile src/Makefile
-sed -e 's/$F90/ftn/g' <test/Makefile > newMakefile
+sed -e 's/pgf90/ftn/g' <test/Makefile > newMakefile
 mv newMakefile test/Makefile
-sed -e 's/$F90/ftn/g' <tools/Makefile > newMakefile
+sed -e 's/pgf90/ftn/g' <tools/Makefile > newMakefile
 mv newMakefile tools/Makefile
 

configure.ac

@@ -1,24 +1,18 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.6.6], [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. 
 # If the version of Autoconf being used to create configure is earlier than version, 
 # print an error message to the standard error output and do not create configure.
-AC_PREREQ(2.59)
+#AC_PREREQ(2.59)
+
 
 # should be called right after AC_INIT.
 # configure scripts can create a C header file containing `#define' directives. 
 # The AC_CONFIG_HEADERS macro selects this kind of output.
-AC_CONFIG_HEADERS(config.h)
+AC_CONFIG_HEADER(config.h)
-
-AC_CONFIG_MACRO_DIR([m4])
-
-# AM_INIT_AUTOMAKE is required to use autoconf with automake
-AM_INIT_AUTOMAKE
-
-BUILD_LIBS='libH5Part'
-BUILD_TESTS='test'
 
 ###############################################################################
 ################# --enable-xxx and --with-xxx Argument ########################
@@ -27,20 +21,32 @@ BUILD_TESTS='test'
 AC_ARG_ENABLE(
 	[debug],
 	[AC_HELP_STRING([--enable-debug],
-	[Compile with debug flags [default=no]])],
+	[Compile with debug support [default=no]])],
 	[USE_DEBUG=$enableval])
 
+AC_ARG_ENABLE(
+	[shared],
+	[AC_HELP_STRING([--enable-shared],
+	[Compile with shared library support [default=no]])],
+	[USE_SHARED=$enableval])
+
+AC_ARG_ENABLE(
+	[64],
+	[AC_HELP_STRING([--enable-64],
+	[Compile using 64-bit flags [default=no]])],
+	[USE_64=$enableval])
+
 AC_ARG_ENABLE(
 	[fortran],
-	[AC_HELP_STRING([--enable-fortran],
+        [AC_HELP_STRING([--enable-fortran],
 	[Compile the Fortran interface [default=no]])],
-	[USE_FORTRAN=$enableval])
+        [USE_FORTRAN=$enableval])
 
 AC_ARG_ENABLE(
 	[parallel],
-	[AC_HELP_STRING([--enable-parallel],
+        [AC_HELP_STRING([--enable-parallel],
 	[Compile the MPI/IO interface [default=no]])],
-	[USE_PARALLEL=$enableval])
+        [USE_PARALLEL=$enableval])
 
 AC_ARG_ENABLE(
 	[tools],
@@ -49,11 +55,35 @@ AC_ARG_ENABLE(
         [USE_TOOLS=$enableval])
 
 AC_ARG_WITH(
-	[hdf5],
+	[mpipath],
-	[AC_HELP_STRING([--with-hdf5],
+	[AC_HELP_STRING([--with-mpipath],
+	[path to MPI installation [default=""]])],
+        [MPIPATH=$withval], [MPIPATH=""])
+
+AC_ARG_WITH(
+	[hdf5path],
+	[AC_HELP_STRING([--with-hdf5path],
 	[path to HDF5 installation [default=""]])],
 	[HDF5PATH=$withval], [HDF5PATH=""])
 
+###############################################################################
+################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
+###############################################################################
+
+SAVE_CC=$CC
+SAVE_CXX=$CXX
+SAVE_FC=$FC
+SAVE_MPICC=$MPICC
+SAVE_MPICXX=$MPICXX
+SAVE_MPIFC=$MPIFC
+SAVE_MPILIB=$MPILIB
+SAVE_MPIINC=$MPIINC
+SAVE_CFLAGS=$CFLAGS
+SAVE_FFLAGS=$FFLAGS
+SAVE_MPIROOT=$MPIROOT
+SAVE_HDF5ROOT=$HDF5ROOT
+SAVE_LDFLAGS=$LDFLAGS
+
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -66,26 +96,35 @@ AC_ARG_WITH(
 #   @enddesc
 #@@*/
 
-PATH_Search() {
+PATH_Search()
-	eval  $1=""
+{
-	if test $# -lt 4 ; then
+  eval  $1=""
-		h5part_basedir=""
+  if test $# -lt 4 ; then
-	else
+    h5part_basedir=""
-		h5part_basedir="$4/"
+  else
-	fi
+    h5part_basedir="$4/"
-	for h5part_place in $2; do
+  fi
-		AC_MSG_CHECKING([looking in $h5part_place ... ])
+  for h5part_place in $2
-		if test -r "$h5part_basedir$h5part_place/$3" ; then
+    do
-			AC_MSG_RESULT([found])
+      echo -n "looking in $h5part_place ... $ac_c" #1>&6
-			eval $1="$h5part_place"
+      if test -r "$h5part_basedir$h5part_place/$3" ; then
-			break
+        echo "$ac_t"" found" #1>&6
-		fi
+        eval $1="$h5part_place"
-		AC_MSG_RESULT([no])
+        break
-	done
+      fi
-	return
+      if test -d "$h5part_basedir$h5part_place/$3" ; then
+        echo "$ac_t"" found" #1>&6
+        eval $1="$h5part_place"
+        break
+      fi
+      echo "$ac_t"" no" #1>&6
+    done
+
+  return
 }
 
 
+
 ###############################################################################
 ############# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING ################
 ###############################################################################
@@ -93,37 +132,82 @@ PATH_Search() {
 # individual parts host_cpu, host_vendor, and host_os.
 AC_CANONICAL_HOST
 
-AC_PROG_MAKE_SET
 
-# Determine a C/C++ compiler to use. 
+uname=`uname -s`
+if test $uname = "AIX"; then
+  AC_MSG_CHECKING([if system is AIX])
+  AC_MSG_RESULT([OK])
+
+  # If on AIX, define _ALL_SOURCE. Allows the use of some BSD functions. 
+  # Should be called before any macros that run the C compiler.
+  AC_AIX
+fi
+
+
+# DAVINCI SPECIFIC!!!
+if test `uname -n` = "davinci"; then
+   echo "DAVINCI SPECIFIC TESTING FOR STDC++ LIBRARY!"
+   PATH_Search STDCXX_CHECK '/usr/lib64 /usr/lib' libstdc++.a
+
+   # if STDCXX_CHECK is set...
+   if test "$STDCXX_CHECK" = "/usr/lib64"; then
+      echo "STDCXX setting ..."
+      echo "STDCXX_CHECK = $STDCXX_CHECK ..."
+      STDCXX="-L/usr/lib64 -lstdc++"
+      echo "STDCXX =  $STDCXX ..."
+   elif test "$STDCXX_CHECK" = "/usr/lib"; then
+      echo "STDCXX setting ..."
+      echo "STDCXX_CHECK = $STDCXX_CHECK ..."
+      STDCXX="-L/usr/lib -lstdc++"
+      echo "STDCXX =  $STDCXX ..."
+   fi 
+fi
+
+
+# Determine a C compiler to use. 
 # If CC is not already set in the environment, check for gcc and cc, then
 # for other C compilers. 
 # Set output variable CC to the name of the compiler found.
-if test "x$USE_PARALLEL" = "xyes"; then
+AC_PROG_CC(pgcc pathcc icc cc_r gcc cc)
-   	CCOMPILERS="mpicc cc"
+
-   	CXXCOMPILERS="mpic++ mpicxx CC"
+# AC_PROG_CC doesn't pick up cc_r in Bassi. The following AC_PATH_PROGS
-else
+# is the fix.
-	CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
+AC_PATH_PROGS([BAS_CC], [cc_r], [], [$PATH])
-   	CXXCOMPILERS="pgCC pathCC icpc g++"
+
+# if BAS_CC not empty
+if test -n "$BAS_CC"; then
+  echo "CC setting for Bassi ..."
+  CC=$BAS_CC
+  echo "CC =  $CC ..."
 fi 
 
-AC_PROG_CC($CCOMPILERS)
 
-# Only need C++ for some of the tools
+# Determine a C++ compiler to use. 
-#if test "x$USE_TOOLS" = "xyes"; then
+# Check if the environment variable CXX or CCC (in that order) is set; 
-	AC_PROG_CXX($CXXCOMPILERS)
+# if so, then set output variable CXX to its value.
-#fi
+# Otherwise, if the macro is invoked without an argument, 
+# 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(pgCC pathCC icc cc_r g++ gcc cc)
+
 
 # Set output variable INSTALL to the path of a BSD-compatible install program,
 # if one is found in the current PATH. 
 # Otherwise, set INSTALL to `dir/install-sh -c`
 AC_PROG_INSTALL
 
-AC_PROG_AWK
+
+# AM_INIT_AUTOMAKE is required to use autoconf with automake
+AM_INIT_AUTOMAKE()
+
+
+AC_PROG_RANLIB
 
 # Default prefix for bindir, etc... (eg >> ./build/bin)
 AC_PREFIX_DEFAULT(`pwd`/build)
 
+
 # AC_DEFINE_UNQUOTED (variable, value, [description])
 # Define the C preprocessor variable variable to value
 # Use this macro instead of AC_DEFINE when variable or value is a shell variable. 
@@ -134,6 +218,7 @@ AC_DEFINE_UNQUOTED(MY_GNUNAME, "${host_cpu}-${host_vendor}-${host_os}", "")
 AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 
 
+
 ###############################################################################
 ######################## CONFIGURE LINE OPTIONS ###############################
 ###############################################################################
@@ -143,92 +228,216 @@ AC_MSG_CHECKING([if debug is enabled])
 if test "X$USE_DEBUG" = "Xyes"; then
     AC_MSG_RESULT([yes])
     CFLAGS="$CFLAGS -g"
-    CXXFLAGS="$CXXFLAGS -g"
-    FFLAGS="$FFLAGS -g"
 else
     AC_MSG_RESULT([no])
 fi
 
-############################ fortran enabled ##################################
+# shared library
-AC_MSG_CHECKING([if fortran interface enabled])
+AC_MSG_CHECKING([if shared libraries are enabled])
-if test "X$USE_FORTRAN" = "Xyes"; then
-	AC_MSG_RESULT([yes])
-	LIB_FORTRAN="libH5PartF.la"
-        BUILD_LIBS="$BUILD_LIBS libH5PartF"
-	BUILD_TESTS="$BUILD_TESTS testf"
-
-	if test "X$USE_PARALLEL" = "Xyes"; then
-		AC_PROG_FC(mpif90 mpif77 ftn)
-	else
-		AC_PROG_FC(pgf90 pathf90 ifort ftn xlf_r g95 g90 gfortran)
-	fi
-
-	if test -z "$FC" ; then
-		AC_MSG_ERROR([Cannot find a Fortran compiler!])
-		exit 1
-	fi
-
-	if test $FC = "g90"; then
-		FFLAGS="${FFLAGS} -fno-second-underscore"
-	fi
-
-	if test $FC = "g95"; then
-		FFLAGS="${FFLAGS} -fno-second-underscore"
-	fi
-
-	AC_MSG_CHECKING([symbol convention in object files])
-	`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
-	`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
-	`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-	`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
-
-	if test -f src/TestUnderscore ; then
-		UNDERSCORE_H=Underscore.h
-		`cd src && ./TestUnderscore > Underscore.h`
-		AC_MSG_RESULT([ok])
-	else
-		AC_MSG_RESULT([nok])
-		AC_MSG_ERROR([Cannot determine the symbon convention for Fortran object files!])
-		exit 1
-	fi
 
+if test "X$USE_SHARED" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    CFLAGS="$CFLAGS -fPIC"
+    FFLAGS="$FFLAGS -fPIC"
 else
-	AC_MSG_RESULT([no])
+    AC_MSG_RESULT([no])
+fi
+
+###################### 64-bit compilation enabled #############################
+AC_MSG_CHECKING([if 64-bit compilation is enabled])
+
+
+# If --enable-64 is set in the configure line
+if test "X$USE_64:/f90
+" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    if test $uname = "AIX"; then
+        CFLAGS="$CFLAGS -q64"
+        FFLAGS="$FFLAGS -q64"
+    fi
+
+    if test $uname = "IRIX64"; then
+        CFLAGS="$CFLAGS -64"
+        FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
+    fi
+else
+    AC_MSG_RESULT([no])
 fi
 
 
-# Disable shared libraries by default: can be enabled with --enable-shared
+############################ fortran enabled ##################################
-LT_INIT([disable-shared])
+AC_MSG_CHECKING([if fortran interface enabled])
-AC_PROG_LIBTOOL
+if test "X$USE_FORTRAN" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+
+    AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
+    if test -z "$FC" ; then
+        AC_MSG_ERROR([Cannot find a fortran compiler!!!])
+        exit 1
+    fi
+
+    if test ! $uname = "AIX"; then
+        FFLAGS="${FFLAGS} -fPIC"
+    fi
+
+    if test $FC = "g90"; then
+	FFLAGS="${FFLAGS} -fno-second-underscore"
+    fi
+
+    if test $FC = "g95"; then
+	FFLAGS="${FFLAGS} -fno-second-underscore"
+    fi
+
+    if test $FC = "gfortran"; then
+        FFLAGS="${FFLAGS} -DHAVE_GFORTRAN"
+    fi
+
+    AC_MSG_CHECKING([symbol convention in object files])
+    `cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
+    `cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
+    `cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
+    `cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o -lc`
+
+    if test -f src/TestUnderscore ; then
+        UNDERSCORE_H=Underscore.h
+        `cd src && ./TestUnderscore > Underscore.h`
+        AC_MSG_RESULT([ok])
+    else
+        AC_MSG_RESULT([nok])
+        AC_MSG_ERROR([Cannot build fortran executables!!!])
+        exit 1
+    fi
+else
+    AC_MSG_RESULT([no])
+fi
 
 
 ######################## parallel interface enabled ###########################
 AC_MSG_CHECKING([if parallel interface enabled])
 if test "X$USE_PARALLEL" = "Xyes"; then
-	AC_MSG_RESULT([yes])
+    AC_MSG_RESULT([yes])
 
-	CFLAGS="${CFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+    CFLAGS="${CFLAGS} -DPARALLEL_IO -DH5_HAVE_PARALLEL -DMPICH_IGNORE_CXX_SEEK"
-	CXXFLAGS="${CXXFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
-	FFLAGS="${FFLAGS} -DPARALLEL_IO"
 
-	AC_MSG_CHECKING([if we can compile MPI code without setting flags])
+    AC_MSG_CHECKING([if we can compile MPI code without setting flags])
-	AC_TRY_LINK([#include "mpi.h"], [
+    AC_TRY_LINK([#include "mpi.h"], [
-		MPI_Comm comm;
+        MPI_Comm comm;
-		int n;
+	int n;
-		MPI_Comm_size( comm, &n ); ], 
+	MPI_Comm_size( comm, &n ); ], 
-		[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
+	[echo 'yes'; r='yes'], [echo "no"; r='no'] )
 
-	if test "X$r" = "Xno"; then
+    if test "X$r" = "Xno"; then
-		AC_MSG_ERROR([MPI wrapper can't compile or link MPI program! Please set the INCLUDE and LIBS variables manually.])
+        AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
-		exit 1
+        AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
+        if test -z "$MPICC" -o -z "$MPICXX"; then 
+            AC_MSG_CHECKING([for MPI root ])
+            AC_MSG_RESULT([])
+            if test -n "$MPIROOT"; then
+                P=${MPIROOT}
+            elif test -n "$MPIHOME"; then
+                P=${MPIHOME}
+            elif test -n "$MPIPATH"; then
+                P=${MPIPATH}
+            else
+                P=''
+                P="$P /usr"
+                P="$P /usr/local"
+                P="$P /usr/local/mpi"
+                P="$P /usr/local/packages/mpi"
+                P="$P /usr/local/mpich2"
+                P="$P /usr/local/mpich"
+                P="$P /opt/xt-mpt/default/mpich2-64/P2"
+            fi
+            PATH_Search MPIROOT "$P" include/mpi.h
+            if test ! -n "$MPIROOT"; then
+		AC_MSG_ERROR([Cannot determine MPI root!!!])
+                exit 1
+            fi
+
+	    if test -e "${MPIROOT}/bin/mpicc"; then
+	       MPICC=${MPIROOT}/bin/mpicc
+	    fi
+
+	    if test -e "${MPIROOT}/bin/mpicxx"; then
+	       MPICXX=${MPIROOT}/bin/mpicxx
+	    fi
 	fi
 
+        if test -z "$MPICC" -o -z "$MPICXX"; then 
+            MPIINC="${MPIINC} -I${MPIROOT}/include"
+            FFLAGS="${FFLAGS} -I${MPIROOT}/include"
+            AC_MSG_CHECKING([for name of MPI lib ])
+            if test -e ${MPIROOT}/lib/libmpi.a; then
+                MPILIB="-L${MPIROOT}/lib -lmpi"
+            elif test -e ${MPIROOT}/lib/libmpi.so; then
+                MPILIB="-L${MPIROOT}/lib -lmpi"
+            elif test -e ${MPIROOT}/lib/libmpich.a; then
+                MPILIB="-L${MPIROOT}/lib -lmpich"
+            elif test -e ${MPIROOT}/lib/libmpich.so; then
+                MPILIB="-L${MPIROOT}/lib -lmpich"
+            else
+                AC_MSG_RESULT([not found])
+                exit 1
+            fi
+            AC_MSG_RESULT([${MPILIB}])
+	fi
+
+        if test -n "$MPICC"; then
+	    CC=${MPICC}
+        fi 
+  
+        if test -n "$MPICXX"; then
+	    CXX=${MPICXX}
+        fi
+    fi
+
+    H5P_LIB_NAME="-lpH5Part"
+    MTARGET="libpH5Part.a"
+    TTARGET="test"
+
+
+    # parallel + fortran
+    if test "X$USE_FORTRAN" = "Xyes"; then
+        AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
+
+        FFLAGS="${FFLAGS} -DPARALLEL_IO"
+
+	if test -z "${MPIFC}" ; then
+	    if test -e "${MPIROOT}/bin/mpif90"; then
+	       MPIFC=${MPIROOT}/bin/mpif90
+	    fi
+	fi
+ 
+        # if MPIFC empty
+        if test ! -n "$MPIFC"; then
+            AC_MSG_CHECKING([ No MPIFC detected. Setting MPIFC to FC.])
+            MPIFC=$FC
+            echo "MPIFC =  $MPIFC ..."
+        fi 
+
+	if test -n "$MPIFC"; then
+	    FC=${MPIFC}
+	fi
+ 
+        H5P_LIB_NAME="-lpH5PartF"
+        MTARGET="${MTARGET} libpH5PartF.a"
+        TTARGET="${TTARGET} testf"
+    fi
+
 else  # --enable-parallel=no
-	AC_MSG_RESULT([no])
+    AC_MSG_RESULT([no])
+
+    H5P_LIB_NAME="-lH5Part"
+    MTARGET="libH5Part.a"
+    TTARGET="test"
+
+    if test "X$USE_FORTRAN" = "Xyes"; then
+        H5P_LIB_NAME="-lH5PartF"
+        MTARGET="${MTARGET} libH5PartF.a"
+        TTARGET="${TTARGET} testf"
+    fi
 fi
 
-
-######################## tools enabled ###########################
 AC_MSG_CHECKING([whether tools are enabled])
 if test "X$USE_TOOLS" = "Xyes"; then
     AC_MSG_RESULT([yes])
@@ -241,96 +450,171 @@ else
     AC_MSG_RESULT([no])
 fi
 
-
 ###############################################################################
 ######################### PATH CHECKING & SETTING #############################
 ###############################################################################
 
 AC_MSG_CHECKING([for HDF5 root ])
 AC_MSG_RESULT([])
-if test -n "${HDF5PATH}" ; then
+if test -n "${HDF5ROOT}"; then
-	P=${HDF5PATH}
+    P=${HDF5ROOT}
-elif test -n "${HDF5ROOT}"; then
-	P=${HDF5ROOT}
 elif test -n "${HDF5HOME}" ; then
-	P=${HDF5HOME}
+    P=${HDF5HOME}
-elif test -n "${HDF5_DIR}" ; then
+elif test -n "${HDF5PATH}" ; then
-	P=${HDF5_DIR}
+    P=${HDF5PATH}
 else
-	P=''
+    P=''
-	P="$P /usr"
+    P="$P /usr"
-	P="$P /usr/local"
+    P="$P /usr/local"
-	P="$P /usr/local/hdf5"
+    P="$P /usr/local/hdf5"
-	P="$P /usr/local/packages/hdf5"
+    P="$P /usr/local/packages/hdf5"
-	P="$P /apps/hdf5"
+    P="$P /apps/hdf5"
-	P="$P /opt/hdf5"
+
+    if test "X$USE_PARALLEL" = "Xyes"; then
+        P="$P /usr/local/phdf5"
+        P="$P /usr/local/hdf5/hdf5_par"
+        if test "X$USE_64" = "Xyes"; then
+            P="$P /usr/common/usg/hdf5/64/default/parallel"
+        else
+            P="$P /usr/common/usg/hdf5/32/default/parallel"
+        fi
+    else
+        P="$P /usr/local/hdf5/hdf5_serial"
+        if test "X$USE_64" = "Xyes"; then
+            P="$P /usr/common/usg/hdf5/64/default/serial"
+        else
+            P="$P /usr/common/usg/hdf5/32/default/serial"
+        fi
+    fi
 fi
 PATH_Search HDF5ROOT "$P" include/hdf5.h
 if test -z "$HDF5ROOT"; then
-	AC_MSG_ERROR([Cannot find an HDF5 library!])
+    AC_MSG_ERROR([Cannot determine HDF5 root!!!])
-	exit 1
+    exit 1
 fi
 
-INCLUDES="$INCLUDES -I$HDF5ROOT/include"
-LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
-LIBS="$LIBS -lhdf5"
-
 AC_MSG_CHECKING([if we need to link to libsz ])
 if test -n "$HDF5ROOT"; then
-	if test -f $HDF5ROOT/lib/libsz.a; then
+    if test -f $HDF5ROOT/lib/libsz.a; then
-		AC_MSG_RESULT([yes])
+	AC_MSG_RESULT([yes])
-		LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
+        SZLIB="-L$HDF5ROOT/lib/ -lsz"
-                LIBS="$LIBS -lsz"
+    else
-	else
+	AC_MSG_RESULT([no])
-		AC_MSG_RESULT([no])
+        SZLIB=""
-	fi
+    fi
 fi
 
-LIBS="$LIBS -lz -lm"
+AC_MSG_CHECKING([for static zlib root ])
+echo
+PATH_Search ZLIBROOT '/apps/zlib' lib/libz.a
+if test -n "$ZLIBROOT"; then
+    LDFLAGS="$LDFLAGS -L$ZLIBROOT/lib"
+fi
+
+FCFLAGS=${FFLAGS}
+CXXFLAGS=${CFLAGS}
 
 
-# Checks for header files.
+###############################################################################
-AC_CHECK_HEADERS([fcntl.h stdlib.h string.h unistd.h])
+#################### MISC SETTINGS - path, flags, etc #########################
+###############################################################################
 
-# Checks for typedefs, structures, and compiler characteristics.
+H5P_LIB_LOC=`pwd`/src
-AC_HEADER_STDBOOL
-AC_TYPE_INT64_T
-AC_TYPE_SIZE_T
-AC_TYPE_SSIZE_T
 
-# Checks for library functions.
+###############################################################################
-AC_FUNC_MALLOC
+################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-AC_CHECK_FUNCS([memset pow strchr strdup])
+###############################################################################
+
+#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 "$SAVE_MPICC"; then
+MPICC=$SAVE_MPICC
+fi
+
+if test -n "$SAVE_MPICXX"; then
+MPICXX=$SAVE_MPICXX
+fi
+
+if test -n "$SAVE_MPIFC"; then
+MPIFC=$SAVE_MPIFC
+fi
+
+if test -n "$SAVE_MPILIB"; then
+MPILIB=$SAVE_MPILIB
+fi
+
+if test -n "$SAVE_MPIINC"; then
+MPIINC=$SAVE_MPIINC
+fi
+
+if test -n "$SAVE_CFLAGS"; then
+CFLAGS="$SAVE_CFLAGS ${CFLAGS}"
+fi
+
+if test -n "$SAVE_FFLAGS"; then
+FFLAGS=$SAVE_FFLAGS
+fi
+
+if test -n "$SAVE_MPIROOT"; then
+MPIROOT=$SAVE_MPIROOT
+fi
+
+if test -n "$SAVE_HDF5ROOT"; then
+HDF5ROOT=$SAVE_HDF5ROOT
+fi
+
+if test -n "$SAVE_LDFLAGS"; then
+LDFLAGS=$SAVE_LDFLAGS
+fi
 
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################
 # AC_SUBST (variable, [value])
-# Create an output variable from a shell variable.  Make AC_OUTPUT substitute
+# Create an output variable from a shell variable. 
-# the variable variable into output files (typically one or more `Makefile's).
+# Make AC_OUTPUT substitute the variable variable into output files (typically one or more `Makefile's). 
-# This means that AC_OUTPUT will replace instances of `@variable@' in input
+# This means that AC_OUTPUT will replace instances of `@variable@' in input files with the value that 
-# files with the value that the shell variable variable has when AC_OUTPUT is
+# the shell variable variable has when AC_OUTPUT is called. 
-# called.  This value of variable should not contain literal newlines.  If
+# This value of variable should not contain literal newlines.
-# value is given, in addition assign it to variable. 
+# If value is given, in addition assign it to variable. 
+AC_SUBST(MPIROOT)
+AC_SUBST(HDF5ROOT)
+AC_SUBST(MPIINC)
+AC_SUBST(MPILIB)
+AC_SUBST(MPICC)
+AC_SUBST(MPICXX)
+AC_SUBST(MPIFC)
+AC_SUBST(MTARGET)
+AC_SUBST(TTARGET)
+AC_SUBST(SZLIB)
 AC_SUBST(CFLAGS)
-AC_SUBST(CXXFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(INCLUDES)
+AC_SUBST(STDCXX)
-AC_SUBST(LDFLAGS)
+AC_SUBST(H5P_LIB_LOC)
-AC_SUBST(LIBS)
+AC_SUBST(H5P_LIB_NAME)
 AC_SUBST(UNDERSCORE_H)
-AC_SUBST(LIB_FORTRAN)
-AC_SUBST(BUILD_TESTS)
 AC_SUBST(BUILD_TOOLS)
+AC_SUBST(LDFLAGS)
 
 # Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
 # substituting the output variable values.
 AC_CONFIG_FILES([
-	Makefile
+Makefile
-	src/Makefile
+doc/Makefile
-	doc/Makefile
+src/Makefile
-	test/Makefile
+test/Makefile
-	tools/Makefile
+tools/Makefile
 ])
 
 AC_OUTPUT
@@ -338,23 +622,27 @@ AC_OUTPUT
 ###############################################################################
 ########################## PRINTING SUMMARY ###################################
 ###############################################################################
-AC_MSG_RESULT([ ])
+echo
-AC_MSG_RESULT([Summary:])
+echo
-AC_MSG_RESULT([ ])
+echo "Summary for `(hostname || uname -n) 2>/dev/null | sed 1q`:"
-AC_MSG_RESULT([Host OS:             $host_os])
+echo
-AC_MSG_RESULT([Host CPU:            $host_cpu])
+echo "Host OS:             $host_os"
-AC_MSG_RESULT([Host vendor:         $host_vendor])
+echo "Host CPU:            $host_cpu"
-AC_MSG_RESULT([Build libraries:     $BUILD_LIBS])
+echo "Host vendor:         $host_vendor"
-AC_MSG_RESULT([Build test programs: $BUILD_TESTS])
+echo "Build libraries:     $MTARGET"
-AC_MSG_RESULT([Build tools:         $BUILD_TOOLS])
+echo "Build test programs: $TTARGET"
-AC_MSG_RESULT([CC =                 $CC])
+echo "Build tools:         $BUILD_TOOLS"
-AC_MSG_RESULT([CXX =                $CXX])
+echo "CC =                 $CC"
-AC_MSG_RESULT([FC =                 $FC])
+echo "CXX =                $CXX"
-AC_MSG_RESULT([CFLAGS =             $CFLAGS])
+echo "FC =                 $FC"
-AC_MSG_RESULT([CXXFLAGS =           $CXXFLAGS])
+echo "MPICC =              $MPICC"
-AC_MSG_RESULT([FFLAGS =             $FFLAGS])
+echo "MPICXX =             $MPICXX"
-AC_MSG_RESULT([INCLUDES =           $INCLUDES])
+echo "MPIFC =              $MPIFC"
-AC_MSG_RESULT([LDFLAGS =            $LDFLAGS])
+echo "CFLAGS =             $CFLAGS"
-AC_MSG_RESULT([LIBS =               $LIBS])
+echo "FFLAGS =             $FFLAGS"
-AC_MSG_RESULT([HDF5ROOT =           $HDF5ROOT])
+echo "MPILIB =             $MPILIB"
-AC_MSG_RESULT([ ])
+echo "MPIINC =             $MPIINC"
+echo "MPIROOT =            $MPIROOT"
+echo "HDF5ROOT =           $HDF5ROOT"
+echo "LDFLAGS =            $LDFLAGS"
+echo

doc/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.6.6
+PROJECT_NUMBER         = 1.6.1
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English

examples/core_vfd.c

@@ -1,51 +0,0 @@
-#include <stdlib.h>
-#include <assert.h>
-#include <mpi.h>
-#include <H5Part.h>
-
-#define DATASIZE 32
-
-int main(int argc, char** argv)
-{
-    int i, rank, nprocs;
-    h5part_int32_t data[DATASIZE];
-    h5part_int64_t stat;
-    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);
-
-    char filename[8];
-    sprintf (filename, "%d.h5", rank);
-
-    file = H5PartOpenFileParallel(
-            filename,
-            H5PART_WRITE | H5PART_VFD_CORE,
-            MPI_COMM_SELF);
-    assert (file != NULL);
-
-    stat = H5PartSetStep(file, 0);
-    assert (stat == H5PART_SUCCESS);
-
-    stat = H5PartSetNumParticles(file, DATASIZE);
-    assert (stat == H5PART_SUCCESS);
-
-    // create fake data
-    for (i=0; i<DATASIZE; i++) {
-        data[i] = i + rank * DATASIZE;
-    }
-
-    // write the data
-    stat = H5PartWriteDataInt32(file, "data", data);
-    assert (stat == H5PART_SUCCESS);
-
-    H5PartCloseFile(file);
-
-    MPI_Finalize();
-    return EXIT_SUCCESS;
-}
-

examples/fields.c

@@ -1,45 +0,0 @@
-#include <stdlib.h>
-#include <assert.h>
-#include <mpi.h>
-#include <H5Part.h>
-
-#define XSIZE 8
-#define YSIZE 8
-#define ZSIZE 8
-#define DATASIZE XSIZE*YSIZE*ZSIZE
-#define H5OpenFileParallel H5PartOpenFileParallel
-#define H5SetStep H5PartSetStep
-#define H5Block3dSetLayout H5BlockDefine3DFieldLayout
-#define H5CloseFile H5PartCloseFile
-
-int main(int argc, char** argv)
-{
-    int rank, nprocs;
-    h5part_float64_t ex[DATASIZE];
-    h5part_float64_t ey[DATASIZE];
-    h5part_float64_t ez[DATASIZE];
-    h5part_float64_t q[DATASIZE];
-    h5part_int64_t nparticles = DATASIZE;
-    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 = H5OpenFileParallel("fields.h5", H5PART_WRITE, MPI_COMM_WORLD);
-    H5SetStep(file, 0);
-    H5Block3dSetLayout(file,
-            rank*XSIZE, (rank+1)*XSIZE - 1,
-            0, YSIZE - 1,
-            0, ZSIZE - 1);
-    H5Block3dWriteScalarFieldFloat64(file, "Q", q);
-    H5Block3dWrite3dVectorFieldFloat64(file, "E", ex, ez, ey);
-    H5CloseFile(file);
-
-    MPI_Finalize();
-    return EXIT_SUCCESS;
-}
-

examples/particles.c

@@ -1,41 +0,0 @@
-#include <stdlib.h>
-#include <assert.h>
-#include <mpi.h>
-#include <H5Part.h>
-
-#define DATASIZE 32
-
-int main(int argc, char** argv)
-{
-    int rank, nprocs;
-    h5part_float64_t x[DATASIZE];
-    h5part_float64_t y[DATASIZE];
-    h5part_float64_t z[DATASIZE];
-    h5part_float64_t px[DATASIZE];
-    h5part_float64_t py[DATASIZE];
-    h5part_float64_t pz[DATASIZE];
-    h5part_int64_t nparticles = DATASIZE;
-    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("particles.h5", H5PART_WRITE, MPI_COMM_WORLD);
-    H5PartSetStep(file, 0);
-    H5PartSetNumParticles(file, nparticles);
-    H5PartWriteDataFloat64(file, "x", x);
-    H5PartWriteDataFloat64(file, "y", y);
-    H5PartWriteDataFloat64(file, "z", z);
-    H5PartWriteDataFloat64(file, "px", px);
-    H5PartWriteDataFloat64(file, "py", py);
-    H5PartWriteDataFloat64(file, "pz", pz);
-    H5PartCloseFile(file);
-
-    MPI_Finalize();
-    return EXIT_SUCCESS;
-}
-

examples/simplef.F90

@@ -8,15 +8,12 @@ program H5PartTest
   integer*8 :: file_id, status, npoints, i
   real*8, allocatable :: particles(:)
   integer*8, allocatable :: id(:)
-  real*8 :: r8val
-  integer*8 :: i8val
 
   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_set_verbosity_level(5)
   file_id = h5pt_openw_par('test.h5', comm)
 
   ! in the Fortran API, time steps start at 1
@@ -25,10 +22,6 @@ program H5PartTest
   ! write an attribute to the file
   status = h5pt_writefileattrib_string(file_id, 'desc', 'This is a test.')
 
-  r8val = 0.5
-  i8val = 1
-  status = h5pt_writefileattrib_r8(file_id, 'double', r8val, i8val)
-
   ! create fake data
   npoints = 99
   allocate(particles(npoints), id(npoints))

src/H5Block.c

@@ -269,16 +269,17 @@ static h5part_int64_t
 _allgather (
 	const H5PartFile *f		/*!< IN: file handle */
 	) {
+	struct H5BlockPartition *partition = &f->block->user_layout[f->myproc];
 	struct H5BlockPartition *layout = f->block->user_layout;
 
 	MPI_Datatype    partition_m;
 	size_t n = sizeof (struct H5BlockPartition) / sizeof (h5part_int64_t);
 
 	MPI_Type_contiguous ( n, MPI_LONG_LONG, &partition_m );
-	MPI_Type_commit ( &partition_m );
+	  MPI_Type_commit ( &partition_m );
 
-	MPI_Allgather ( MPI_IN_PLACE, 0, MPI_DATATYPE_NULL,
+	MPI_Allgather ( partition, 1, partition_m, layout, 1, partition_m,
-			layout, 1, partition_m, f->comm );
+			f->comm );
 
 	return H5PART_SUCCESS;
 }
@@ -2009,250 +2010,6 @@ H5Block3dSetFieldSpacing (
 		3 );
 }
 
-/*!
-  \ingroup h5block_attrib
-
-  Get the explicit list of X coordinates for field \c field_name in the current
-  time step. The coordinates are read into the 1D array \c coords which has
-  length \c coords_len.
-
-  By convention, the \c coords array should have the same length as the X
-  dimension of the field, and a warning will be printed if they differ.
-
-
-  \return \c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5Block3dGetFieldXCoords(
-	H5PartFile *f,				/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	h5part_float64_t *coords,		/*!< OUT: X coordinates */
-	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
-	) {
-
-	SET_FNAME ( "H5BlockGetFieldXCoords" );
-	BLOCK_INIT ( f );
-	CHECK_TIMEGROUP( f );
-	CHECK_LAYOUT( f );
-
-	struct H5BlockStruct *b = f->block;
-
-	if (coords_len != b->i_max + 1)
-	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
-		    (long long)coords_len, (long long)b->i_max + 1);
-
-	return _read_field_attrib (
-		f,
-		field_name,
-		H5BLOCK_FIELD_XCOORD_NAME,
-		coords );
-}
-
-/*!
-  \ingroup h5block_attrib
-
-  Set an explicit list of X coordinates for field \c field_name in the current
-  time step. The coordinates are a 1D array of floating point values with
-  dimension \c coords_len.
-
-  By convention, the \c coords array should have the same length as the X
-  dimension of the field, and a warning will be printed if not.
-
-  \return \c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5Block3dSetFieldXCoords (
-	H5PartFile *f,				/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	const h5part_float64_t *coords,		/*!< IN: X coordinates */
-	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
-	) {
-
-	SET_FNAME ( "H5BlockSetFieldXCoords" );
-	BLOCK_INIT ( f );
-	CHECK_WRITABLE_MODE( f );
-	CHECK_TIMEGROUP( f );
-	CHECK_LAYOUT( f );
-
-	struct H5BlockStruct *b = f->block;
-
-	if (coords_len != b->i_max + 1)
-	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
-		    (long long)coords_len, (long long)b->i_max + 1);
-
-	return _write_field_attrib (
-		f,
-		field_name,
-		H5BLOCK_FIELD_XCOORD_NAME,
-		(const hid_t)H5PART_FLOAT64, 
-		coords,
-		coords_len
-		 );
-}
-
-/*!
-  \ingroup h5block_attrib
-
-  Get the explicit list of Y coordinates for field \c field_name in the current
-  time step. The coordinates are read into the 1D array \c coords which has
-  length \c coords_len.
-
-  By convention, the \c coords array should have the same length as the Y
-  dimension of the field, and a warning will be printed if they differ.
-
-
-  \return \c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5Block3dGetFieldYCoords(
-	H5PartFile *f,				/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	h5part_float64_t *coords,		/*!< OUT: Y coordinates */
-	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
-	) {
-
-	SET_FNAME ( "H5BlockGetFieldYCoords" );
-	BLOCK_INIT ( f );
-	CHECK_TIMEGROUP( f );
-	CHECK_LAYOUT( f );
-
-	struct H5BlockStruct *b = f->block;
-
-	if (coords_len != b->j_max + 1)
-	    _H5Part_print_warn( "Coordinate array length (%lld) does not match Y dimension (%lld)",
-		    (long long)coords_len, (long long)b->j_max + 1);
-
-	return _read_field_attrib (
-		f,
-		field_name,
-		H5BLOCK_FIELD_YCOORD_NAME,
-		coords );
-}
-
-
-/*!
-  \ingroup h5block_attrib
-
-  Set an explicit list of Y coordinates for field \c field_name in the current
-  time step. The coordinates are a 1D array of floating point values with
-  dimension \c coords_len.
-
-  By convention, the \c coords array should have the same length as the Y
-  dimension of the field, and a warning will be printed if not.
-
-  \return \c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5Block3dSetFieldYCoords (
-	H5PartFile *f,				/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	const h5part_float64_t *coords,		/*!< IN: Y coordinates */
-	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
-	) {
-
-	SET_FNAME ( "H5BlockSetFieldYCoords" );
-	BLOCK_INIT ( f );
-	CHECK_WRITABLE_MODE( f );
-	CHECK_TIMEGROUP( f );
-	CHECK_LAYOUT( f );
-
-	struct H5BlockStruct *b = f->block;
-
-	if (coords_len != b->j_max + 1)
-	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
-		    (long long)coords_len, (long long)b->j_max + 1);
-
-	return _write_field_attrib (
-		f,
-		field_name,
-		H5BLOCK_FIELD_YCOORD_NAME,
-		(const hid_t)H5PART_FLOAT64, 
-		coords,
-		coords_len
-		 );
-}
-
-/*!
-  \ingroup h5block_attrib
-
-  Get the explicit list of Z coordinates for field \c field_name in the current
-  time step. The coordinates are read into the 1D array \c coords which has
-  length \c coords_len.
-
-  By convention, the \c coords array should have the same length as the Z
-  dimension of the field, and a warning will be printed if they differ.
-
-
-  \return \c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5Block3dGetFieldZCoords(
-	H5PartFile *f,				/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	h5part_float64_t *coords,		/*!< OUT: Z coordinates */
-	const h5part_int64_t coords_len		/*!< IN: length of coordinates */
-	) {
-
-	SET_FNAME ( "H5BlockGetFieldZCoords" );
-	BLOCK_INIT ( f );
-	CHECK_TIMEGROUP( f );
-	CHECK_LAYOUT( f );
-
-	struct H5BlockStruct *b = f->block;
-
-	if (coords_len != b->k_max + 1)
-	    _H5Part_print_warn( "Coordinate array length (%lld) does not match Z dimension (%lld)",
-		    (long long)coords_len, (long long)b->k_max + 1);
-
-	return _read_field_attrib (
-		f,
-		field_name,
-		H5BLOCK_FIELD_ZCOORD_NAME,
-		coords );
-}
-
-/*!
-  \ingroup h5block_attrib
-
-  Set an explicit list of Z coordinates for field \c field_name in the current
-  time step. The coordinates are a 1D array of floating point values with
-  dimension \c coords_len.
-
-  By convention, the \c coords array should have the same length as the Z
-  dimension of the field, and a warning will be printed if not.
-
-  \return \c H5PART_SUCCESS or error code
-*/
-h5part_int64_t
-H5Block3dSetFieldZCoords (
-	H5PartFile *f,				/*!< IN: file handle */
-	const char *field_name,			/*!< IN: field name */
-	const h5part_float64_t *coords,		/*!< IN: Z coordinates */
-	const h5part_int64_t coords_len		/*!< IN: number of coordinates */
-	) {
-
-	SET_FNAME ( "H5BlockSetFieldZCoords" );
-	BLOCK_INIT ( f );
-	CHECK_WRITABLE_MODE( f );
-	CHECK_TIMEGROUP( f );
-	CHECK_LAYOUT( f );
-
-	struct H5BlockStruct *b = f->block;
-
-	if (coords_len != b->k_max + 1)
-	    _H5Part_print_warn( "Coordinate array length (%lld) does not match X dimension (%lld)",
-		    (long long)coords_len, (long long)b->k_max  + 1);
-
-	return _write_field_attrib (
-		f,
-		field_name,
-		H5BLOCK_FIELD_ZCOORD_NAME,
-		(const hid_t)H5PART_FLOAT64, 
-		coords,
-		coords_len
-		 );
-}
-
 /*!
   \ingroup h5block_model
 

src/H5Block.f90

@@ -232,69 +232,4 @@ INTEGER*8 FUNCTION h5bl_3d_set_field_origin ( filehandle, name, x, y, z )
     REAL*8, INTENT(IN) :: z
 END FUNCTION
   
-!> \ingroup h5blockf_attrib
-!! See \ref H5Block3dGetFieldXCoords
-!! \return 0 on success or error code
-!<
-INTEGER*8 FUNCTION h5bl_3d_get_field_xcoords ( filehandle, name, coords )
-    INTEGER*8, INTENT(IN) :: filehandle
-    CHARACTER(LEN=*), INTENT(IN) :: name
-    REAL*8, INTENT(OUT) :: coords(*)
-    INTEGER*8, INTENT(IN) :: coords_len
-END FUNCTION
-  
-!> \ingroup h5blockf_attrib
-!! See \ref H5Block3dSetFieldXCoords
-!! \return 0 on success or error code
-!<
-INTEGER*8 FUNCTION h5bl_3d_set_field_xcoords ( filehandle, name, coords )
-    INTEGER*8, INTENT(IN) :: filehandle
-    CHARACTER(LEN=*), INTENT(IN) :: name
-    REAL*8, INTENT(IN) :: coords(*)
-    INTEGER*8, INTENT(IN) :: coords_len
-END FUNCTION
-
-!> \ingroup h5blockf_attrib
-!! See \ref H5Block3dGetFieldYCoords
-!! \return 0 on success or error code
-!<
-INTEGER*8 FUNCTION h5bl_3d_get_field_ycoords ( filehandle, name, coords )
-    INTEGER*8, INTENT(IN) :: filehandle
-    CHARACTER(LEN=*), INTENT(IN) :: name
-    REAL*8, INTENT(OUT) :: coords(*)
-    INTEGER*8, INTENT(IN) :: coords_len
-END FUNCTION
-  
-!> \ingroup h5blockf_attrib
-!! See \ref H5Block3dSetFieldYCoords
-!! \return 0 on success or error code
-!<
-INTEGER*8 FUNCTION h5bl_3d_set_field_ycoords ( filehandle, name, coords )
-    INTEGER*8, INTENT(IN) :: filehandle
-    CHARACTER(LEN=*), INTENT(IN) :: name
-    REAL*8, INTENT(IN) :: coords(*)
-    INTEGER*8, INTENT(IN) :: coords_len
-END FUNCTION
-
-!> \ingroup h5blockf_attrib
-!! See \ref H5Block3dGetFieldZCoords
-!! \return 0 on success or error code
-!<
-INTEGER*8 FUNCTION h5bl_3d_get_field_zcoords ( filehandle, name, coords )
-    INTEGER*8, INTENT(IN) :: filehandle
-    CHARACTER(LEN=*), INTENT(IN) :: name
-    REAL*8, INTENT(OUT) :: coords(*)
-    INTEGER*8, INTENT(IN) :: coords_len
-END FUNCTION
-  
-!> \ingroup h5blockf_attrib
-!! See \ref H5Block3dSetFieldZCoords
-!! \return 0 on success or error code
-!<
-INTEGER*8 FUNCTION h5bl_3d_set_field_zcoords ( filehandle, name, coords )
-    INTEGER*8, INTENT(IN) :: filehandle
-    CHARACTER(LEN=*), INTENT(IN) :: name
-    REAL*8, INTENT(IN) :: coords(*)
-    INTEGER*8, INTENT(IN) :: coords_len
-END FUNCTION
   

src/H5Block.h

@@ -13,9 +13,6 @@ extern "C" {
 
 #define H5BLOCK_FIELD_ORIGIN_NAME	"__Origin__"
 #define H5BLOCK_FIELD_SPACING_NAME	"__Spacing__"
-#define H5BLOCK_FIELD_XCOORD_NAME	"__X_Coordinates__"
-#define H5BLOCK_FIELD_YCOORD_NAME	"__Y_Coordinates__"
-#define H5BLOCK_FIELD_ZCOORD_NAME	"__Z_Coordinates__"
 
 /*! 
   Interface for block structured field data.
@@ -141,54 +138,6 @@ H5Block3dSetFieldSpacing (
 	const h5part_float64_t z_spacing
 	);
 
-h5part_int64_t
-H5Block3dGetFieldXCoords (
-	H5PartFile *f,
-	const char *field_name,
-	h5part_float64_t *coords,
-	const h5part_int64_t coords_len
-	);
-
-h5part_int64_t
-H5Block3dSetFieldXCoords (
-	H5PartFile *f,
-	const char *field_name,
-	const h5part_float64_t *coords,
-	const h5part_int64_t coords_len
-	);
-
-h5part_int64_t
-H5Block3dGetFieldYCoords (
-	H5PartFile *f,
-	const char *field_name,
-	h5part_float64_t *coords,
-	const h5part_int64_t coords_len
-	);
-
-h5part_int64_t
-H5Block3dSetFieldYCoords (
-	H5PartFile *f,
-	const char *field_name,
-	const h5part_float64_t *coords,
-	const h5part_int64_t coords_len
-	);
-
-h5part_int64_t
-H5Block3dGetFieldZCoords (
-	H5PartFile *f,
-	const char *field_name,
-	h5part_float64_t *coords,
-	const h5part_int64_t coords_len
-	);
-
-h5part_int64_t
-H5Block3dSetZCoords (
-	H5PartFile *f,
-	const char *field_name,
-	const h5part_float64_t *coords,
-	const h5part_int64_t coords_len
-	);
-
 h5part_int64_t
 H5BlockWriteFieldAttrib (
 	H5PartFile *f,

src/H5BlockF.c

@@ -68,24 +68,6 @@
 #define h5bl_3d_get_field_origin F77NAME (				\
 					h5bl_3d_get_field_origin_,	\
 					H5BL_3D_GET_FIELD_origin )
-#define h5bl_3d_get_field_xcoords F77NAME (				\
-					h5bl_3d_get_field_xcoords_,	\
-					H5BL_3D_GET_FIELD_XCOORDS )
-#define h5bl_3d_set_field_xcoords F77NAME (				\
-					h5bl_3d_set_field_xcoords_,	\
-					H5BL_3D_SET_FIELD_XCOORDS )
-#define h5bl_3d_get_field_ycoords F77NAME (				\
-					h5bl_3d_get_field_ycoords_,	\
-					H5BL_3D_GET_FIELD_YCOORDS )
-#define h5bl_3d_set_field_ycoords F77NAME (				\
-					h5bl_3d_set_field_ycoords_,	\
-					H5BL_3D_SET_FIELD_YCOORDS )
-#define h5bl_3d_get_field_zcoords F77NAME (				\
-					h5bl_3d_get_field_zcoords_,	\
-					H5BL_3D_GET_FIELD_ZCOORDS )
-#define h5bl_3d_set_field_zcoords F77NAME (				\
-					h5bl_3d_set_field_zcoords_,	\
-					H5BL_3D_SET_FIELD_ZCOORDS )
 #endif
 
 h5part_int64_t
@@ -383,7 +365,7 @@ h5bl_has_fielddata (
 }
 
 h5part_int64_t
-h5bl_3d_get_field_spacing (
+h5b_3d_get_field_spacing (
 	h5part_int64_t *f,
 	const char *field_name,
 	h5part_float64_t *x,
@@ -404,7 +386,7 @@ h5bl_3d_get_field_spacing (
 }
 
 h5part_int64_t
-h5bl_3d_set_field_spacing (
+h5b_3d_set_field_spacing (
 	h5part_int64_t *f,
 	const char *field_name,
 	const h5part_float64_t *x,
@@ -425,7 +407,7 @@ h5bl_3d_set_field_spacing (
 }
 
 h5part_int64_t
-h5bl_3d_get_field_origin (
+h5b_3d_get_field_origin (
 	h5part_int64_t *f,
 	const char *field_name,
 	h5part_float64_t *x,
@@ -446,7 +428,7 @@ h5bl_3d_get_field_origin (
 }
 
 h5part_int64_t
-h5bl_3d_set_field_origin (
+h5b_3d_set_field_origin (
 	h5part_int64_t *f,
 	const char *field_name,
 	const h5part_float64_t *x,
@@ -465,123 +447,3 @@ h5bl_3d_set_field_origin (
 	free ( field_name2 );
 	return herr;
 }
-
-h5part_int64_t
-h5bl_3d_set_field_xcoords (
-	h5part_int64_t *f,
-	const char *field_name,
-	const h5part_float64_t *coords,
-	const h5part_int64_t *coords_len,
-	const int l_field_name
-	) {
-
-	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
-
-	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
-
-	h5part_int64_t herr = H5Block3dSetFieldXCoords (
-		filehandle, field_name2, coords, *coords_len );
-
-	free ( field_name2 );
-	return herr;
-}
-
-h5part_int64_t
-h5bl_3d_get_field_xcoords (
-	h5part_int64_t *f,
-	const char *field_name,
-	h5part_float64_t *coords,
-	const h5part_int64_t *coords_len,
-	const int l_field_name
-	) {
-
-	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
-
-	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
-
-	h5part_int64_t herr = H5Block3dGetFieldXCoords (
-		filehandle, field_name2, coords, *coords_len );
-
-	free ( field_name2 );
-	return herr;
-}
-
-h5part_int64_t
-h5bl_3d_set_field_ycoords (
-	h5part_int64_t *f,
-	const char *field_name,
-	const h5part_float64_t *coords,
-	const h5part_int64_t *coords_len,
-	const int l_field_name
-	) {
-
-	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
-
-	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
-
-	h5part_int64_t herr = H5Block3dSetFieldYCoords (
-		filehandle, field_name2, coords, *coords_len );
-
-	free ( field_name2 );
-	return herr;
-}
-
-h5part_int64_t
-h5bl_3d_get_field_ycoords (
-	h5part_int64_t *f,
-	const char *field_name,
-	h5part_float64_t *coords,
-	const h5part_int64_t *coords_len,
-	const int l_field_name
-	) {
-
-	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
-
-	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
-
-	h5part_int64_t herr = H5Block3dGetFieldYCoords (
-		filehandle, field_name2, coords, *coords_len );
-
-	free ( field_name2 );
-	return herr;
-}
-
-h5part_int64_t
-h5bl_3d_set_field_zcoords (
-	h5part_int64_t *f,
-	const char *field_name,
-	const h5part_float64_t *coords,
-	const h5part_int64_t *coords_len,
-	const int l_field_name
-	) {
-
-	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
-
-	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
-
-	h5part_int64_t herr = H5Block3dSetFieldZCoords (
-		filehandle, field_name2, coords, *coords_len );
-
-	free ( field_name2 );
-	return herr;
-}
-
-h5part_int64_t
-h5bl_3d_get_field_zcoords (
-	h5part_int64_t *f,
-	const char *field_name,
-	h5part_float64_t *coords,
-	const h5part_int64_t *coords_len,
-	const int l_field_name
-	) {
-
-	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
-
-	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
-
-	h5part_int64_t herr = H5Block3dGetFieldZCoords (
-		filehandle, field_name2, coords, *coords_len );
-
-	free ( field_name2 );
-	return herr;
-}

src/H5BlockReadWriteF.c

@@ -57,7 +57,7 @@ h5bl_3d_read_scalar_field_r8 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dReadScalarFieldFloat64 (
+	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat64 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );
@@ -161,7 +161,7 @@ h5bl_3d_read_scalar_field_r4 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dReadScalarFieldFloat32 (
+	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat32 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );
@@ -265,7 +265,7 @@ h5bl_3d_read_scalar_field_i8 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dReadScalarFieldInt64 (
+	h5part_int64_t herr = H5Block3dWriteScalarFieldInt64 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );
@@ -369,7 +369,7 @@ h5bl_3d_read_scalar_field_i4 (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block3dReadScalarFieldInt32 (
+	h5part_int64_t herr = H5Block3dWriteScalarFieldInt32 (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );

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 = (char*) malloc ( bufsize );
+	send_buffer = malloc ( bufsize );
 	if ( send_buffer == NULL ) return HANDLE_H5PART_NOMEM_ERR;
 
-	recv_buffer = (char*) malloc ( bufsize );
+	recv_buffer = malloc ( bufsize );
 	if ( recv_buffer == NULL ) return HANDLE_H5PART_NOMEM_ERR;
 
 	/* forward */

src/H5Part.c

@@ -199,7 +199,7 @@ _H5Part_open_file (
 		{
 			/* extend the btree size so that metadata pieces are
 		 	* close to the alignment value */
-			if ( align > 16384 )
+			if ( align > 0 )
 			{
 				unsigned int btree_ik = (align - 4096) / 96;
 				unsigned int btree_bytes = 64 + 96*btree_ik;
@@ -252,7 +252,7 @@ _H5Part_open_file (
 			}
 		} else if (flags & H5PART_VFD_CORE) {
 			_H5Part_print_info ( "Selecting CORE VFD" );
-			if (H5Pset_fapl_core ( f->access_prop, align, 1 ) < 0) {
+			if (H5Pset_fapl_core ( f->access_prop, comm, 0 ) < 0) {
 				HANDLE_H5P_SET_FAPL_ERR;
 				goto error_cleanup;
 			}
@@ -291,15 +291,15 @@ _H5Part_open_file (
 
 	if ( align != 0 ) {
 		_H5Part_print_info (
-			"Setting HDF5 alignment to %lld bytes with threshold at half that many bytes",
+			"Setting HDF5 alignment to %ld bytes",
-			(long long)align );
+			align );
-		if (H5Pset_alignment ( f->access_prop, align/2, align ) < 0) {
+		if (H5Pset_alignment ( f->access_prop, 0, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
 		}
 		_H5Part_print_info (
-			"Setting HDF5 meta block to %lld bytes",
+			"Setting HDF5 meta block to %ld bytes",
-			(long long)align );
+			align );
 		if (H5Pset_meta_block_size ( f->access_prop, align ) < 0) {
 			HANDLE_H5P_SET_FAPL_ERR;
 			goto error_cleanup;
@@ -713,11 +713,7 @@ _set_num_particles (
 	register int i;
 #endif
 
-#ifdef PARALLEL_IO
-	if ( nparticles < 0 )
-#else
 	if ( nparticles <= 0 )
-#endif
 		return HANDLE_H5PART_INVALID_ERR ( "nparticles", nparticles );
 
 	/* prevent invalid stride value */	
@@ -730,8 +726,6 @@ _set_num_particles (
 		stride = (hsize_t) _stride;
 	}
 
-	if ( nparticles == 0 ) stride = 1;
-
 #ifndef PARALLEL_IO
 	/*
 	  if we are not using parallel-IO, there is enough information
@@ -757,14 +751,11 @@ _set_num_particles (
 
 	f->nparticles = (hsize_t) nparticles;
 
-	if ( f->nparticles > 0 )
+	/* declare local memory datasize with striding */
-	{
+	count = f->nparticles * stride;
-		/* declare local memory datasize with striding */
+	f->memshape = H5Screate_simple ( 1, &count, &dmax );
-		count = f->nparticles * stride;
+	if ( f->memshape < 0 )
-		f->memshape = H5Screate_simple ( 1, &count, &dmax );
+		return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );
-		if ( f->memshape < 0 )
-			return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );
-	}
 
 	/* we need a hyperslab selection if there is striding
 	 * (otherwise, the default H5S_ALL selection is ok)
@@ -805,7 +796,7 @@ _set_num_particles (
 	*/
 
 	ret = MPI_Allgather (
-		(void*)&nparticles, 1, MPI_LONG_LONG,
+		&nparticles, 1, MPI_LONG_LONG,
 		f->pnparticles, 1, MPI_LONG_LONG,
 		f->comm );
 	if ( ret != MPI_SUCCESS) return HANDLE_MPI_ALLGATHER_ERR;
@@ -842,16 +833,12 @@ _set_num_particles (
 
 	count = nparticles;
 	stride = 1;
-	if ( count > 0 ) {
+	herr = H5Sselect_hyperslab (
-		herr = H5Sselect_hyperslab (
+		f->diskshape,
-			f->diskshape,
+		H5S_SELECT_SET,
-			H5S_SELECT_SET,
+		&start,
-			&start,
+		&stride,
-			&stride,
+		&count, NULL );
-			&count, NULL );
-	} else {
-		herr = H5Sselect_none ( f->diskshape );
-	}
 	if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
 #endif
 
@@ -1314,9 +1301,6 @@ _H5Part_normalize_h5_type (
 		if ( size==8 ) {
 			return H5PART_INT64;
 		}
-	  	else if ( size==4 ) {
-			return H5PART_INT32;
-		}
 	  	else if ( size==1 ) {
 			return H5PART_CHAR;
 		}
@@ -1346,7 +1330,9 @@ _H5Part_read_attrib (
 	) {
 
 	herr_t herr;
+	h5part_int64_t h5err;
 	hid_t attrib_id;
+	hid_t space_id;
 	hid_t type_id;
 
 #ifdef H5PART_HAVE_HDF5_18
@@ -1362,9 +1348,15 @@ _H5Part_read_attrib (
 	type_id = H5Aget_type ( attrib_id );
 	if ( type_id < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
 
+	space_id = H5Aget_space ( attrib_id );
+	if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;
+
 	herr = H5Aread ( attrib_id, type_id, attrib_value );
 	if ( herr < 0 ) return HANDLE_H5A_READ_ERR;
 
+	herr = H5Sclose ( space_id );
+	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
+
 	herr = H5Tclose ( type_id );
 	if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
 
@@ -1642,9 +1634,9 @@ H5PartWriteStepAttrib (
 	h5part_int64_t herr = _H5Part_write_step_attrib (
 		f,
 		name,
-		(hid_t)type,
+		(const hid_t)type,
 		data,
-		(hsize_t)nelem );
+		nelem );
 	if ( herr < 0 ) return herr;
 
 	return H5PART_SUCCESS;
@@ -1686,9 +1678,9 @@ H5PartWriteFileAttrib (
 	h5part_int64_t herr = _H5Part_write_file_attrib (
 		f,
 		name,
-		(hid_t)type,
+		(const hid_t)type,
 		data,
-		(hsize_t)nelem );
+		nelem );
 	if ( herr < 0 ) return herr;
 
 	return H5PART_SUCCESS;
@@ -2081,6 +2073,9 @@ _H5Part_iteration_operator2 (
 	void *operator_data		/*!< [in,out] data passed to the iterator */
 	) {
 
+  struct _iter_op_data *data = (struct _iter_op_data*)operator_data;
+  herr_t herr = 0;
+
   switch (linfo->type) {
     case H5L_TYPE_HARD: {
 
@@ -2274,12 +2269,7 @@ _H5Part_get_num_objects_matching_pattern (
 	data.pattern = pattern;
 
 #ifdef H5PART_HAVE_HDF5_18
-	hid_t child_id = H5Gopen( group_id, group_name
+	hid_t child_id = H5Gopen( group_id, group_name, H5P_DEFAULT );
-#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 );
@@ -2324,11 +2314,7 @@ _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
+	hid_t child_id = H5Gopen ( group_id, group_name, H5P_DEFAULT );
-#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 );
@@ -2581,30 +2567,7 @@ _H5Part_get_num_particles (
 		0,
 		dataset_name, H5PART_DATANAME_LEN );
 	if ( herr < 0 ) return herr;
-
+	/* returns 0 if there are no datasets on disk */
-	/* if a view exists, use its size as the number of particles */
-	if ( _H5Part_has_view ( f ) )
-	{
-		nparticles = H5Sget_select_npoints ( f->diskshape );
-		if ( nparticles < 0 ) return HANDLE_H5S_GET_SELECT_NPOINTS_ERR;
-
-		_H5Part_print_debug (
-			"Found %lld points with H5Sget_select_npoints",
-			(long long)nparticles );
-
-#if 0 // this does not work for indices
-		/* double check that the size of the diskshape agrees with
-		 * the size of the view */
-		if ( nparticles != f->viewend - f->viewstart + 1 ) {
-			_H5Part_print_warn (
-				"Number of particles (%lld) does not agree "
-				"with view range.", (long long)nparticles );
-			return HANDLE_H5PART_BAD_VIEW_ERR (
-					f->viewstart, f->viewend);
-		}
-#endif
-	}
-	/* herr is 0 if there are no datasets on disk */
 	else if ( herr == 0 )
 	{
 		/* try to recover number of particles from a previous
@@ -2633,6 +2596,29 @@ _H5Part_get_num_particles (
 			return 0;
 		}
 	}
+
+	/* if a view exists, use its size as the number of particles */
+	if ( _H5Part_has_view ( f ) )
+	{
+		nparticles = H5Sget_select_npoints ( f->diskshape );
+		if ( nparticles < 0 ) return HANDLE_H5S_GET_SELECT_NPOINTS_ERR;
+
+		_H5Part_print_debug (
+			"Found %lld points with H5Sget_select_npoints",
+			(long long)nparticles );
+
+#if 0 // this does not work for indices
+		/* double check that the size of the diskshape agrees with
+		 * the size of the view */
+		if ( nparticles != f->viewend - f->viewstart + 1 ) {
+			_H5Part_print_warn (
+				"Number of particles (%lld) does not agree "
+				"with view range.", (long long)nparticles );
+			return HANDLE_H5PART_BAD_VIEW_ERR (
+					f->viewstart, f->viewend);
+		}
+#endif
+	}
 	/* otherwise, report all particles on disk in the first dataset
 	 * for this timestep */
 	else
@@ -2786,7 +2772,10 @@ _set_view (
 	  end==-1 to mean end of file
 	*/
 	total = (hsize_t) _H5Part_get_num_particles ( f );
-	if ( total == 0 ) {
+	if ( total < 0 ) {
+		return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total );
+	}
+	else 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
 		 * many particles there should be! */
@@ -2851,9 +2840,9 @@ _set_view_indices (
 	herr = _reset_view ( f );
 	if ( herr < 0 ) return herr;
 
-	if ( indices == NULL || nelems < 0 ) {
+	if ( indices == NULL ) {
 		_H5Part_print_warn (
-			"View indices array is null or size is < 0: reseting view." );
+			"View indices array is null: reseting view." );
 		return H5PART_SUCCESS;
 	}
 
@@ -2865,7 +2854,10 @@ _set_view_indices (
 	  end==-1 to mean end of file
 	*/
 	total = (hsize_t) _H5Part_get_num_particles ( f );
-	if ( total == 0 ) {
+	if ( total < 0 ) {
+		return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total );
+	}
+	else 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
 		 * many particles there should be! */
@@ -2876,7 +2868,15 @@ _set_view_indices (
 
 	if ( total == 0 ) return H5PART_SUCCESS;
 
-	f->nparticles = (hsize_t) nelems;
+	/* check length of list */
+	if ( nelems < 0 ) {
+		_H5Part_print_warn (
+			"Array of view indices has length < 0: "
+			"resetting view.");
+		f->nparticles = 0;
+	} else {
+		f->nparticles = (hsize_t) nelems;
+	}
 
 	/* declare overall data size  but then will select a subset */
 	f->diskshape = H5Screate_simple ( 1, &total, NULL );
@@ -2982,6 +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
 
@@ -3129,7 +3157,7 @@ _read_data (
 	) {
 
 	h5part_int64_t herr;
-	hssize_t ndisk, nread, nmem;
+	hsize_t ndisk, nread, nmem;
 	hid_t dataset_id;
 	hid_t space_id;
 	hid_t memspace_id;
@@ -3191,7 +3219,7 @@ _read_data (
 
 	if ( f->memshape != H5S_ALL )
 	{
-		nmem = H5Sget_simple_extent_npoints ( f->memshape );
+		nmem = H5Sget_select_npoints ( f->memshape );
 		if ( nmem <  0 ) return HANDLE_H5S_GET_SELECT_NPOINTS_ERR;
 
 		/* make sure the memory space selected by the view has
@@ -3206,6 +3234,7 @@ _read_data (
 				"elements selected (%lld) than are available "
 				"in memory (%lld).",
 				name2, (long long)nread, (long long)nmem );
+			memspace_id == H5S_ALL;
 		}
 	}
 

src/H5Part.f90

@@ -115,10 +115,9 @@ END FUNCTION
 !! - \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
 !<
-INTEGER*8 FUNCTION h5pt_openr_par_align ( filename, mpi_communicator, align, flags )
+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
@@ -266,6 +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	"1.6.6"
+#define H5PART_VER_STRING	"1.6.2"
 #define H5PART_VER_MAJOR	1
 #define H5PART_VER_MINOR	6
-#define H5PART_VER_RELEASE	6
+#define H5PART_VER_RELEASE	2
 
 /* error values */
 #define H5PART_SUCCESS		0
@@ -220,6 +220,11 @@ H5PartSetViewIndices (
 	h5part_int64_t nelems		/*!< [in]  Size of list */
 	);
 
+h5part_int64_t
+H5PartSetViewEmpty (
+	H5PartFile *f
+	);
+
 h5part_int64_t
 H5PartGetView (
 	H5PartFile *f,

src/H5PartAttribF.c

@@ -23,7 +23,7 @@ h5pt_writefileattrib_r8 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float64_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float64_t *nelem,
 	const int l_name
 	) {
 
@@ -39,9 +39,9 @@ h5pt_writefileattrib_r8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_r8 F77NAME ( \
+#define h5pt_writefileattrib_r8 F77NAME ( \
-	h5pt_readfileattrib_r8_, \
+	h5pt_writefileattrib_r8_, \
-	H5PT_READFILEATTRIB_R8 )
+	H5PT_WRITEFILEATTRIB_R8 )
 #endif
 
 h5part_int64_t
@@ -74,7 +74,7 @@ h5pt_writefileattrib_r4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float32_t *nelem,
 	const int l_name
 	) {
 
@@ -90,9 +90,9 @@ h5pt_writefileattrib_r4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_r4 F77NAME ( \
+#define h5pt_writefileattrib_r4 F77NAME ( \
-	h5pt_readfileattrib_r4_, \
+	h5pt_writefileattrib_r4_, \
-	H5PT_READFILEATTRIB_R4 )
+	H5PT_WRITEFILEATTRIB_R4 )
 #endif
 
 h5part_int64_t
@@ -141,9 +141,9 @@ h5pt_writefileattrib_i8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_i8 F77NAME ( \
+#define h5pt_writefileattrib_i8 F77NAME ( \
-	h5pt_readfileattrib_i8_, \
+	h5pt_writefileattrib_i8_, \
-	H5PT_READFILEATTRIB_I8 )
+	H5PT_WRITEFILEATTRIB_I8 )
 #endif
 
 h5part_int64_t
@@ -176,7 +176,7 @@ h5pt_writefileattrib_i4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_int32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_int32_t *nelem,
 	const int l_name
 	) {
 
@@ -192,9 +192,9 @@ h5pt_writefileattrib_i4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readfileattrib_i4 F77NAME ( \
+#define h5pt_writefileattrib_i4 F77NAME ( \
-	h5pt_readfileattrib_i4_, \
+	h5pt_writefileattrib_i4_, \
-	H5PT_READFILEATTRIB_I4 )
+	H5PT_WRITEFILEATTRIB_I4 )
 #endif
 
 h5part_int64_t
@@ -227,7 +227,7 @@ h5pt_writestepattrib_r8 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float64_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float64_t *nelem,
 	const int l_name
 	) {
 
@@ -243,9 +243,9 @@ h5pt_writestepattrib_r8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_r8 F77NAME ( \
+#define h5pt_writestepattrib_r8 F77NAME ( \
-	h5pt_readstepattrib_r8_, \
+	h5pt_writestepattrib_r8_, \
-	H5PT_READSTEPATTRIB_R8 )
+	H5PT_WRITESTEPATTRIB_R8 )
 #endif
 
 h5part_int64_t
@@ -278,7 +278,7 @@ h5pt_writestepattrib_r4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_float32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_float32_t *nelem,
 	const int l_name
 	) {
 
@@ -294,9 +294,9 @@ h5pt_writestepattrib_r4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_r4 F77NAME ( \
+#define h5pt_writestepattrib_r4 F77NAME ( \
-	h5pt_readstepattrib_r4_, \
+	h5pt_writestepattrib_r4_, \
-	H5PT_READSTEPATTRIB_R4 )
+	H5PT_WRITESTEPATTRIB_R4 )
 #endif
 
 h5part_int64_t
@@ -345,9 +345,9 @@ h5pt_writestepattrib_i8 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_i8 F77NAME ( \
+#define h5pt_writestepattrib_i8 F77NAME ( \
-	h5pt_readstepattrib_i8_, \
+	h5pt_writestepattrib_i8_, \
-	H5PT_READSTEPATTRIB_I8 )
+	H5PT_WRITESTEPATTRIB_I8 )
 #endif
 
 h5part_int64_t
@@ -380,7 +380,7 @@ h5pt_writestepattrib_i4 (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_int32_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_int32_t *nelem,
 	const int l_name
 	) {
 
@@ -396,9 +396,9 @@ h5pt_writestepattrib_i4 (
 }
 
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_readstepattrib_i4 F77NAME ( \
+#define h5pt_writestepattrib_i4 F77NAME ( \
-	h5pt_readstepattrib_i4_, \
+	h5pt_writestepattrib_i4_, \
-	H5PT_READSTEPATTRIB_I4 )
+	H5PT_WRITESTEPATTRIB_I4 )
 #endif
 
 h5part_int64_t

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 )
@@ -623,7 +626,7 @@ h5pt_setview (
 
 	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
 
-	return H5PartSetView ( filehandle, (*start)-1, (*end)-1 );
+	return H5PartSetView ( filehandle, *start, *end );
 }
 
 h5part_int64_t
@@ -638,6 +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

@@ -116,24 +116,6 @@ _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,

src/H5PartTypes.h

@@ -19,9 +19,11 @@ __attribute__ ((format (printf, 3, 4)))
 #endif
  ;
 
-#ifndef PARALLEL_IO
+#ifndef MPI_INCLUDED
+#ifndef OPEN_MPI
 typedef unsigned long		MPI_Comm;
 #endif
+#endif
 
 #define H5PART_STEPNAME_LEN	64
 #define H5PART_DATANAME_LEN	64

src/Makefile.am

@@ -2,6 +2,8 @@
 
 OBJEXT=o
 
+INCLUDES = -I@HDF5ROOT@/include @MPIINC@
+
 EXTRA_HEADERS = 	H5PartPrivate.h \
 			H5BlockPrivate.h \
 			H5MultiBlockPrivate.h \
@@ -23,10 +25,10 @@ EXTRA_DIST =		TestUnderscoreC.c \
 nodist_include_HEADERS = H5PartF.h @UNDERSCORE_H@
 
 # What to build... Will be determined by configure script.
-lib_LTLIBRARIES = libH5Part.la @LIB_FORTRAN@
+lib_LIBRARIES = @MTARGET@
 
 # Listing of all possible targets that I may build.
-EXTRA_LTLIBRARIES = libH5PartF.la
+EXTRA_LIBRARIES = libH5Part.a libH5PartF.a
 
 # Header files that I wish to install in $(prefix)/include
 include_HEADERS = 	H5Part.h \
@@ -45,28 +47,27 @@ include_HEADERS = 	H5Part.h \
 			@UNDERSCORE_H@
 
 # Listing of sources
-libH5Part_la_SOURCES =	H5Part.c \
+libH5Part_a_SOURCES =	H5Part.c \
 			H5PartAttrib.c \
 			H5Block.c \
 			H5BlockReadWrite.c \
 			H5MultiBlock.c \
 			H5MultiBlockReadWrite.c
 
-libH5Part_la_LDFLAGS = -version-info 0:0:0
+libH5PartF_a_SOURCES =	$(libH5Part_a_SOURCES) \
-
-libH5PartF_la_SOURCES =	H5Part.c \
-			H5PartAttrib.c \
-			H5Block.c \
-			H5BlockReadWrite.c \
-			H5MultiBlock.c \
-			H5MultiBlockReadWrite.c \
 			H5PartF.c \
 			H5PartAttribF.c \
 			H5BlockF.c \
 			H5BlockReadWriteF.c
 
-libH5PartF_la_LDFLAGS = -version-info 0:0:0 -rpath '$(libdir)'
-
 H5PartF.h: H5Part.f90 H5PartAttrib.f90 H5Block.f90 H5BlockReadWrite.f90
 	awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >$@
 
+libpH5Part.a: libH5Part.a
+	$(RM) $@
+	ln -s $^ $@
+
+libpH5PartF.a: libH5PartF.a
+	$(RM) $@
+	ln -s $^ $@
+

src/generate-attr.py

@@ -113,7 +113,7 @@ h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# (
 	h5part_int64_t *f,
 	const char *name,
 	const h5part_#TYPE_H5P#_t *data,
-	const h5part_int64_t *nelem,
+	const h5part_#TYPE_H5P#_t *nelem,
 	const int l_name
 	) {
 
@@ -143,9 +143,9 @@ END FUNCTION
 
 read_attr_fc = """
 #if ! defined(F77_NO_UNDERSCORE)
-#define h5pt_read#LEVELLC#attrib_#TYPE_F90_ABV# F77NAME ( \\
+#define h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV# F77NAME ( \\
-	h5pt_read#LEVELLC#attrib_#TYPE_F90_ABV#_, \\
+	h5pt_write#LEVELLC#attrib_#TYPE_F90_ABV#_, \\
-	H5PT_READ#LEVELUC#ATTRIB_#TYPE_F90_ABVC# )
+	H5PT_WRITE#LEVELUC#ATTRIB_#TYPE_F90_ABVC# )
 #endif
 
 h5part_int64_t

src/generate-h5bl-readwrite.py

@@ -214,7 +214,7 @@ h5bl_#DIM#d_read_scalar_field_#TYPE_F90_ABV# (
 
 	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
 
-	h5part_int64_t herr = H5Block#DIM#dReadScalarField#TYPE_ABV# (
+	h5part_int64_t herr = H5Block#DIM#dWriteScalarField#TYPE_ABV# (
 		filehandle, field_name2, data );
 
 	free ( field_name2 );

test/Makefile.am

@@ -2,12 +2,15 @@
 
 OBJEXT=o
 
-INCLUDES = -I../src @INCLUDES@
+HDFLIB = -L@HDF5ROOT@/lib -lhdf5 -lz @SZLIB@
+LIBS = -L@H5P_LIB_LOC@ @H5P_LIB_NAME@ $(HDFLIB) -lm
 
-noinst_PROGRAMS = @BUILD_TESTS@
+INCLUDES = -I@H5P_LIB_LOC@ -I@HDF5ROOT@/include @MPIINC@
+
+noinst_PROGRAMS = @TTARGET@
 
 TESTS_ENVIRONMENT = env LD_LIBRARY_PATH=@HDF5ROOT@/lib:$(LD_LIBRARY_PATH)
-TESTS = @BUILD_TESTS@
+TESTS = @TTARGET@
 
 EXTRA_PROGRAMS = test testf
 
@@ -17,11 +20,9 @@ test_SOURCES =	test.c \
 		read.c \
 		testframe.h \
 		params.h
-test_LDADD   =  ../src/libH5Part.la
 
 testf_SOURCES = testf.F90
-testf_LDADD   =  ../src/libH5PartF.la
 
-clean-local:
+clean: clean-am
-	$(RM) -f *.h5
+	rm -f *.h5
 

test/coords.F90

@@ -1,97 +0,0 @@
-program H5BlockCoordsTest
-  implicit none
-
-#ifdef PARALLEL_IO
-  include 'mpif.h'
-#endif
-  include 'H5PartF.h'
-
-#ifdef PARALLEL_IO
-  integer :: ierr, comm
-#endif
-  integer*8 :: file_id, status, i
-  real*8, allocatable :: r8buf(:,:,:), r8buf3(:,:,:,:), coords(:)
-  real*8 :: x, y, z
-
-#ifdef PARALLEL_IO
-  call MPI_INIT(ierr)
-  comm = MPI_COMM_WORLD
-#endif
-
-  ! this enables level 4 ("debug") messages to be
-  ! printed by the H5Part library
-  ! (4_8 is the literal for an integer*8 with value 4)
-  status = h5pt_set_verbosity_level (4_8)
-
-  ! open the a file called 'test.h5' in parallel for writing
-#ifdef PARALLEL_IO
-  file_id = h5pt_openw_par_align ('test.h5', comm, 1048576_8, "vfd_mpiposix")
-#else
-  file_id = h5pt_openw_align ('test.h5', 1048576_8, "vfd_mpiposix")
-#endif
-
-  status = h5bl_define3dlayout(file_id, 1_8, 30_8, 1_8, 30_8, 1_8, 30_8)
-
-  ! in the Fortran API, steps start at 1
-  status = h5pt_setstep (file_id, 1_8)
-
-  ! create fake data
-  allocate(r8buf(30,30,30))
-  allocate(r8buf3(30,30,30,3))
-  allocate(coords(30))
-  x = 1.0
-  y = 2.0
-  z = 3.0
-
-  ! write the data
-  status = h5bl_3d_write_scalar_field_r8(file_id, "x", r8buf(1,1,1))
-  status = h5bl_3d_set_field_origin(file_id, "x", x, y, z)
-  status = h5bl_3d_set_field_spacing(file_id, "x", x, y, z)
-
-  status = h5bl_3d_write_3dvector_field_r8(file_id, "v", r8buf3(1,1,1,1), r8buf3(1,1,1,2), r8buf3(1,1,1,3))
-  status = h5bl_3d_set_field_origin(file_id, "v", x, y, z)
-  status = h5bl_3d_set_field_spacing(file_id, "v", x, y, z)
-
-  ! create fake coordinates
-  do i = 1, 30
-    coords(i) = 3*i
-  enddo
-  status = h5bl_3d_set_field_xcoords(file_id, "v", coords, 30_8)
-  do i = 1, 30
-    coords(i) = 3*i + 1
-  enddo
-  status = h5bl_3d_set_field_ycoords(file_id, "v", coords, 30_8)
-  do i = 1, 30
-    coords(i) = 3*i + 2
-  enddo
-  status = h5bl_3d_set_field_zcoords(file_id, "v", coords, 30_8)
-
-  ! read fake coordinates
-  do i = 1, 30
-    coords(i) = -1
-  enddo
-  status = h5bl_3d_get_field_xcoords(file_id, "v", coords, 30_8)
-  write(*, *) coords
-  !write(*, "I3") ( coords(i), i=1, 30 )
-  do i = 1, 30
-    coords(i) = -1
-  enddo
-  status = h5bl_3d_get_field_ycoords(file_id, "v", coords, 30_8)
-  write(*, *) coords
-  !write(*, "I3") ( coords(i), i=1, 30 )
-  do i = 1, 30
-    coords(i) = -1
-  enddo
-  status = h5bl_3d_get_field_zcoords(file_id, "v", coords, 30_8)
-  write(*, *) coords
-  !write(*, "I3") ( coords(i), i=1, 30 )
-
-  ! close the file
-  status = h5pt_close (file_id)
-
-#ifdef PARALLEL_IO
-  call MPI_FINALIZE(ierr)
-#endif
-
-end program H5BlockCoordsTest
-

test/read.c

@@ -1,4 +1,3 @@
-#include <string.h>
 #include <H5Part.h>
 
 #include "testframe.h"
@@ -176,6 +175,10 @@ test_read_data64(H5PartFile *file, int nparticles, int step)
 		status = H5PartSetView(file, start, end);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetView");
 
+		status = H5PartReadDataFloat64(file, "x", x);
+		RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
+		FVALUE(x[rank], (double)(start+rank+nparticles*t), "x data");
+
 		val = H5PartGetView(file, &start, &end);
 		IVALUE(val, nprocs*nparticles-start, "particle count");
 		IVALUE(start, rank, "view start");
@@ -184,60 +187,51 @@ test_read_data64(H5PartFile *file, int nparticles, int step)
 		status = H5PartSetView(file, -1, -1);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetView");
 
-		status = H5PartSetView(file, 0, nparticles-1);
-		RETURN(status, H5PART_SUCCESS, "H5PartSetView");
-
-		val = H5PartGetNumParticles(file);
-		IVALUE(val, nparticles, "particle count");
-
 		status = H5PartReadDataFloat64(file, "x", x);
 		RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
 		IVALUE(x[rank], (double)(rank+nparticles*t), "x data");
 
-		status = H5PartResetView(file);
-		RETURN(status, H5PART_SUCCESS, "H5PartResetView");
-
-		val = H5PartGetNumParticles(file);
-		IVALUE(val, nprocs*nparticles, "particle count");
-
 		indices[0] = rank*2 + 0;
 		indices[1] = rank*2 + 3;
 		indices[2] = rank*2 + 9;
 		indices[3] = rank*2 + 7;
 
+		status = H5PartSetViewIndices(file, indices, -1);
+		RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
+
+		status = H5PartReadDataFloat64(file, "x", x);
+		RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
+		FVALUE(x[2*rank], (double)(2*rank+nparticles*t), "x data");
+
+		status = H5PartResetView(file);
+		RETURN(status, H5PART_SUCCESS, "H5PartResetView");
+
 		status = H5PartSetViewIndices(file, indices, 4);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
 
 		val = H5PartGetNumParticles(file);
 		IVALUE(val, 4, "particle count");
 
-		double x2[4];
+		status = H5PartReadDataFloat64(file, "x", x);
-		status = H5PartReadDataFloat64(file, "x", x2);
 		RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
-		FVALUE(x2[0], (double)(2*rank+0+nparticles*t), "x data");
+		FVALUE(x[2], (double)(rank*2+9+nparticles*t), "x data");
-		FVALUE(x2[1], (double)(2*rank+3+nparticles*t), "x data");
-		FVALUE(x2[2], (double)(2*rank+9+nparticles*t), "x data");
-		FVALUE(x2[3], (double)(2*rank+7+nparticles*t), "x data");
-
-		status = H5PartSetViewIndices(file, indices, -1);
-		RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
 
 		val = H5PartGetNumParticles(file);
-		IVALUE(val, nprocs*nparticles, "particle count");
+		IVALUE(val, 4, "particle count");
+
+		status = H5PartSetViewIndices(file, NULL, 4);
+		RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
+
+		status = H5PartReadDataFloat64(file, "x", x);
+		RETURN(status, H5PART_SUCCESS, "H5PartReadDataFloat64");
 
 		status = H5PartSetCanonicalView(file);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetCanonicalView");
 
-		val = H5PartGetNumParticles(file);
-		IVALUE(val, nparticles, "particle count");
-
                 status = H5PartReadParticleStep (
                         file, t, x, y, z, px, py, pz, id);
 		RETURN(status, H5PART_SUCCESS, "H5PartReadParticleStep");
 
-		status = H5PartSetViewIndices(file, NULL, 4);
-		RETURN(status, H5PART_SUCCESS, "H5PartSetViewIndices");
-
 		for (i=0; i<nparticles; i++)
 		{
 			FVALUE(x[i] , 0.0 + (double)(i+nparticles*t), " x data");

test/testf.F90

@@ -7,9 +7,9 @@ program H5PartTest
   include 'H5PartF.h'
 
 #ifdef PARALLEL_IO
-  integer :: comm, ierr
+  integer :: comm, ierr, i
+  integer*8 :: file_id, status, npoints
 #endif
-  integer*8 :: file_id, status, npoints, i
   real*8, allocatable :: x(:),y(:),z(:),px(:),py(:),pz(:)
   integer*8, allocatable :: id(:)
 
@@ -18,10 +18,10 @@ program H5PartTest
   comm = MPI_COMM_WORLD
 #endif
 
-  ! this enables level 4 ("debug") messages to be
+  ! this enables level 3 ("info") messages to be
   ! printed by the H5Part library
-  ! (4_8 is the literal for an integer*8 with value 4)
+  ! (3_8 is the literal for an integer*8 with value 3)
-  status = h5pt_set_verbosity_level (4_8)
+  status = h5pt_set_verbosity_level (3_8)
 
   ! open the a file called 'test.h5' in parallel for writing
 #ifdef PARALLEL_IO

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 = (char*)malloc(strlen(format)+8);
+	char *format2 = 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 = (char*)malloc(strlen(format)+8);
+	char *format2 = malloc(strlen(format)+8);
 	sprintf(format2, "[%d] %s", nproc, format);
 	va_start(arglist, format);
 	ret_value = vfprintf(stderr, format2, arglist);
@@ -661,7 +661,7 @@ test_open_objects(H5PartFile *file, int max_objects)
 				"at line %4d in %s\n", nopen, max_objects,
 				(int)__LINE__, __FILE__ );
 
-		hid_t *list = (hid_t)malloc(sizeof(hid_t)*nopen);
+		hid_t *list = malloc(sizeof(hid_t)*nopen);
 		H5Fget_obj_ids(file->file, H5F_OBJ_ALL, nopen, list);
 
                 H5O_info_t info;

test/testframe.h

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

tools/Makefile.am

@@ -2,7 +2,10 @@
 
 OBJEXT=o
 
-INCLUDES = -I../src @INCLUDES@
+HDFLIB = -L@HDF5ROOT@/lib -lhdf5 -lz @SZLIB@
+LIBS = -L@H5P_LIB_LOC@ @H5P_LIB_NAME@ $(HDFLIB) -lm @STDCXX@
+
+INCLUDES = -I@H5P_LIB_LOC@ -I@HDF5ROOT@/include @MPIINC@
 
 # What to build... make install will place these files in the $(prefix)/bin directory.
 bin_PROGRAMS = @BUILD_TOOLS@
@@ -16,17 +19,8 @@ EXTRA_PROGRAMS =	h5pAttrib \
 
 # Listing of sources
 h5pAttrib_SOURCES =	h5pAttrib.cc
-h5pAttrib_LDADD   =  ../src/libH5Part.la
-
 h5pToGNUplot_SOURCES =	h5pToGNUplot.cc
-h5pToGNUplot_LDADD   =  ../src/libH5Part.la
-
 homdynToH5p_SOURCES =	homdynToH5p.cc
-homdynToH5p_LDADD   =  ../src/libH5Part.la
-
 H5PartBench_SOURCES =	H5PartBench.c
-H5PartBench_LDADD   =  ../src/libH5Part.la
-
 H5BlockBench_SOURCES =	H5BlockBench.c
-H5BlockBench_LDADD   =  ../src/libH5Part.la