bugfix

.gitattributes

@@ -2,7 +2,6 @@
 /AUTHORS -text
 /COPYING -text
 /ChangeLog -text
-/GNUmakefile.orig -text
 /Makefile.am -text
 /NEWS -text
 /README -text
@@ -368,12 +367,6 @@ src/C++/Makefile.am -text
 src/C/H5.c -text
 src/C/H5Block.c -text
 src/C/H5Block_readwrite.c -text
-src/C/H5Fed.c -text
-src/C/H5Fed_adjacency.c -text
-src/C/H5Fed_inquiry.c -text
-src/C/H5Fed_retrieve.c -text
-src/C/H5Fed_store.c -text
-src/C/H5Fed_tags.c -text
 src/C/H5Part.c -text
 src/C/H5_attachments.c -text
 src/C/H5_attribs.c -text
@@ -558,7 +551,6 @@ tools/H5PartMerge/INSTALL -text
 tools/H5PartMerge/NEWS -text
 tools/H5PartMerge/README -text
 tools/H5PartMerge/autogen.sh -text
-tools/H5PartMerge/configure -text
 tools/H5PartMerge/configure.ac -text
 tools/H5PartMerge/makefile.am -text
 tools/H5PartMerge/src/H5merge.cpp -text
@@ -566,6 +558,8 @@ tools/H5PartMerge/src/optparse.cpp -text
 tools/H5PartMerge/src/optparse.hh -text
 tools/Makefile.am -text
 tools/README -text
+tools/h5PartDcToVtk.cc -text
+tools/h5PartSurfaceToVtk.cc -text
 tools/h5hutcc.in -text
 tools/h5pAttrib.cc -text
 tools/h5pToGNUplot.cc -text

.gitignore

@@ -1,8 +1,10 @@
+/H5hut
 /INSTALL
 /Makefile
 /Makefile.in
 /aclocal.m4
 /autom4te.cache
+/build
 /config.guess
 /config.h
 /config.h.in
@@ -14,6 +16,9 @@
 doc/Makefile
 doc/Makefile.in
 /install-sh
+/libtool
+/ltmain.sh
+/m4
 /missing
 src/.deps
 src/C++/Makefile

GNUmakefile.orig

@@ -1,133 +0,0 @@
-UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
-# for host specific options
-HOST := $(shell hostname)
-
-# for processor-specific options
-ifeq ($(UNAME), Linux)
-PROC := $(shell uname -p)
-endif
-
-CXX = c++
-CC = cc
-H5HOME = /usr/local/hdf5
-CFLAGS = -g -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-
-# MacOS-X Serial
-ifeq ($(UNAME), Darwin)
-ifeq ($(PARALLEL), yes)
-CXX = g++
-CC = mpicc
-H5HOME = /usr/local
-CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
-LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
-else
-CXX = c++
-CC = cc
-F90 = xlf
-H5HOME = /usr/local
-CFLAGS = -O -g -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-endif
-endif
-
-# SGI MIPS/Irix
-ifeq ($(UNAME), IRIX64)
-CXX = CC
-CC = cc
-F90 = f90
-ifeq ($(PARALLEL), yes)
-H5HOME = $(HDF5_DIR)
-CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
-LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
-else
-H5HOME = /usr/local
-CFLAGS = -O3 -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-endif
-endif
-
-# AIX/SP-2 Parallel/serial : Seaborg
-ifeq ($(UNAME), AIX)
-ifeq ($(PARALLEL), yes) # parallel
-CXX = mpCC_r
-CC = mpxlc_r
-# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
-H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
-# /usr/common/usg/hdf5/1.4.4/parallel
-H4HOME = /usr/common/usg/hdf/default
-OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
-CFLAGS = -q64 -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
-else # serial
-CXX = xlC
-CC = xlc
-H5HOME = /usr/common/usg/hdf5/1.4.4/serial
-H4HOME = /usr/common/usg/hdf/default
-OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
-CFLAGS = -g -bmaxdata:800000000  -bmaxstack:256000000 -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
-endif
-endif
-
-# Linux
-ifeq ($(UNAME), Linux)
-# if this machine is NERSC/Davinci Altix system
-ifeq ($(PROC), ia64)
-CC = icc 
-CXX = icc
-
-ifeq ($(PARALLEL), yes)
-# IA64 Linux Parallel
-ifeq ($(HOST), davinci)
-H5HOME = $(HDF5_PAR)
-MPILIB = -lmpi
-else
-H5HOME = /usr/local
-HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
-HDF5_PAR_INCLUDE = -I$(H5HOME)/include
-MPIHOME = /usr/local
-MPILIB = -lmpich
-endif # HOST
-CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE) 
-LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
-else # IA64 Linux Serial
-CFLAGS = -O3 $(HDF5_INCLUDE)
-LDFLAGS = $(HDF5_LIB) -lm
-endif # PARALLEL
-
-# else this is standard IA32 linux
-else
-ifeq ($(PARALLEL), yes)
-# Linux Parallel
-CC = gcc
-CXX = g++
-H5HOME = /usr/local
-MPIHOME = /usr/local
-CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include 
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
-else # Linux Serial
-CXX = g++
-CC = gcc
-CFLAGS = -O -g -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-endif # !PARALLEL
-endif # PROC!ia64
-
-endif # !Linux
-
-ifeq ($(PARALLEL), yes) #parallel
-ifdef F90
-all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
-else
-all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
-endif
-else
-ifdef F90
-all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
-else
-all: H5PartTest H5PartTest.o H5Part.o
-endif
-endif
-
-include rules.make

Makefile.am

@@ -1,3 +1,5 @@
+ACLOCAL_AMFLAGS = -I m4
+
 SUBDIRS = \
 	src \
 	test \

autogen.sh

@@ -1,46 +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
 echo "+ running autoheader ... "
 autoheader || {
-  echo
+	echo "autoheader failed"
-  echo "autoheader failed"
+	exit 1
-  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

@@ -8,13 +8,17 @@ AC_INIT([H5hut], [1.99.1], [h5part@lists.psi.ch], H5hut)
 # print an error message to the standard error output and do not create configure.
 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_HEADER(config.h)
+AC_CONFIG_HEADERS(config.h)
 
-BUILD_LIBS='libH5hut.a'
+AC_CONFIG_MACRO_DIR([m4])
+
+# AM_INIT_AUTOMAKE is required to use autoconf with automake
+AM_INIT_AUTOMAKE
+
+BUILD_LIBS='libH5hut'
 USE_C='yes'
 
 ###############################################################################
@@ -27,12 +31,6 @@ AC_ARG_ENABLE(
 	[Compile with debug flags [default=no]])],
 	[USE_DEBUG=$enableval])
 
-AC_ARG_ENABLE(
-	[64],
-	[AC_HELP_STRING([--enable-64],
-	[Compile using 64-bit flags [default=no]])],
-	[USE_64=$enableval])
-
 AC_ARG_ENABLE(
 	[c],
 	[AC_HELP_STRING([--enable-c],
@@ -51,12 +49,6 @@ AC_ARG_ENABLE(
 	[Compile the MPI/IO interface [default=no]])],
 	[USE_PARALLEL=$enableval])
 
-AC_ARG_WITH(
-	[mpi],
-	[AC_HELP_STRING([--with-mpi],
-	[path to MPI installation [default=""]])],
-	[MPIPATH=$withval], [MPIPATH=""])
-
 AC_ARG_WITH(
 	[hdf5],
 	[AC_HELP_STRING([--with-hdf5],
@@ -69,17 +61,6 @@ AC_ARG_WITH(
 	[path to lustre user API [default=""]])],
 	[LUSTREPATH=$withval], [LUSTREPATH=""])
 
-###############################################################################
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-###############################################################################
-
-SAVE_CC=$CC
-SAVE_CXX=$CXX
-SAVE_MPICC=$MPICC
-SAVE_MPICXX=$MPICXX
-SAVE_MPIROOT=$MPIROOT
-SAVE_HDF5ROOT=$HDF5ROOT
-
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -119,35 +100,31 @@ PATH_Search() {
 # individual parts host_cpu, host_vendor, and host_os.
 AC_CANONICAL_HOST
 
-
+AC_PROG_MAKE_SET
-uname=`uname -s`
-if test "x$uname" = "xAIX"; then
-	AC_MSG_CHECKING([if system is AIX])
-	AC_MSG_RESULT([OK])
-
-	# If on AIX, define _ALL_SOURCE. Allows the use of some BSD functions. 
-	# Should be called before any macros that run the C compiler.
-	AC_AIX
-fi
-
-#if test -n "$MPIPATH"; then
-#   	PATH="$MPIPATH/bin:$PATH"
-#fi
 
 # Determine a C/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(mpicc)
+   	CCOMPILERS="mpicc cc"
-   	AC_PROG_CXX(mpicxx)
-	CC=`which $CC`
-	CXX=`which $CXX`
 else
-	AC_PROG_CC(pgcc pathcc icc cc_r gcc cc)
+	CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
-	AC_PROG_CXX(pgCC pathCC icc cc_r g++ gcc cc)
+fi
-	CC=`which $CC`
+
-	CXX=`which $CXX`
+AC_PROG_CC($CCOMPILERS)
+AC_PROG_CXX
+
+# Use macro to set C99 mode instead of checking for gcc, which breaks with
+# parallel builds.
+AC_PROG_CC_C99
+#if test "x$CC" = "xgcc"; then
+#	CFLAGS="$CFLAGS -std=c99"
+#fi
+
+if test "x$ac_cv_prog_cc_c99" = "xno"; then
+	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
+	exit 1
 fi
 
 # Set output variable INSTALL to the path of a BSD-compatible install program,
@@ -155,18 +132,35 @@ fi
 # Otherwise, set INSTALL to `dir/install-sh -c`
 AC_PROG_INSTALL
 
-if test "x$CC" = "xgcc"; then
+AC_PROG_AWK
-	CFLAGS="$CFLAGS -std=c99"
-fi
 
-# AM_INIT_AUTOMAKE is required to use autoconf with automake
+# Disable shared libraries by default: can be enabled with --enable-shared
-AM_INIT_AUTOMAKE()
+LT_INIT([disable-shared])
-
+AC_PROG_LIBTOOL
-AC_PROG_RANLIB
 
 # Default prefix for bindir, etc... (eg >> ./build/bin)
 AC_PREFIX_DEFAULT(`pwd`/build)
 
+# Checks for header files.
+AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_INT16_T
+AC_TYPE_INT32_T
+AC_TYPE_INT64_T
+AC_TYPE_SIZE_T
+AC_TYPE_SSIZE_T
+AC_TYPE_UINT16_T
+AC_TYPE_UINT32_T
+AC_TYPE_UINT64_T
+AC_CHECK_TYPES([ptrdiff_t])
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
 
 # AC_DEFINE_UNQUOTED (variable, value, [description])
 # Define the C preprocessor variable variable to value
@@ -187,6 +181,7 @@ AC_MSG_CHECKING([if debug is enabled])
 if test "X$USE_DEBUG" = "Xyes"; then
     AC_MSG_RESULT([yes])
     CFLAGS="$CFLAGS -g"
+    FFLAGS="$FFLAGS -g"
 else
     AC_MSG_RESULT([no])
 fi
@@ -196,10 +191,10 @@ AC_MSG_CHECKING([if C interface enabled])
 if test "X$USE_C" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 	BINDINGS="$BINDINGS C"
-	LIB_C="../lib/libH5hutC.a"
+	LIB_C="libH5hutC.la"
-	BUILD_LIBS="$BUILD_LIBS libH5hutC.a"
+	BUILD_LIBS="$BUILD_LIBS libH5hutC"
 	BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
-	BUILD_TOOLS="$BUILD_TOOLS h5hutcc"
+	BUILD_TOOLS="$BUILD_TOOLS h5hutcc h5PartDcToVtk h5PartSurfaceToVtk"
 fi
 
 ############################ fortran enabled ##################################
@@ -207,17 +202,18 @@ AC_MSG_CHECKING([if fortran interface enabled])
 if test "X$USE_FORTRAN" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 	BINDINGS="$BINDINGS Fortran"
-	LIB_FORTRAN="../lib/libH5hutF.a"
+	LIB_FORTRAN="libH5hutF.la"
-        BUILD_LIBS="$BUILD_LIBS libH5hutF.a"
+        BUILD_LIBS="$BUILD_LIBS libH5hutF"
 
-	AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
+	if test "X$USE_PARALLEL" = "Xyes"; then
-	if test -z "$FC" ; then
+		AC_PROG_FC(mpif90 mpif77)
-		AC_MSG_ERROR([Cannot find a fortran compiler!!!])
+	else
-		exit 1
+		AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
 	fi
 
- 	if test ! $uname = "AIX"; then
+	if test -z "$FC" ; then
-		FFLAGS="${FFLAGS} -fPIC"
+		AC_MSG_ERROR([Cannot find a Fortran compiler!])
+		exit 1
 	fi
 
 	if test $FC = "g90"; then
@@ -240,7 +236,7 @@ if test "X$USE_FORTRAN" = "Xyes"; then
 		AC_MSG_RESULT([ok])
 	else
 		AC_MSG_RESULT([nok])
-		AC_MSG_ERROR([Cannot build fortran executables!!!])
+		AC_MSG_ERROR([Cannot determine the symbon convention for Fortran object files!])
 		exit 1
 	fi
 
@@ -264,67 +260,8 @@ if test "X$USE_PARALLEL" = "Xyes"; then
 		[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
 
 	if test "X$r" = "Xno"; then
-		AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
+		AC_MSG_ERROR([MPI wrapper can't compile or link MPI program! Please set the INCLUDE and LIBS variables manually.])
-		AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
+		exit 1
-		if test -z "$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 
-			INCLUDES="${INCLUDES} -I${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
 
 	TPTARGET="${TPTARGET} H5PartTestP H5PartAndreasTest Bench"
@@ -333,25 +270,6 @@ if test "X$USE_PARALLEL" = "Xyes"; then
 
 	# parallel + fortran
 	if test "X$USE_FORTRAN" = "Xyes"; then
-		AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
-
-		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
-			AC_MSG_RESULT([MPIFC =  $MPIFC])
-		fi 
-
-		if test -n "$MPIFC"; then
-			FC=${MPIFC}
-		fi
-
 		TPTARGET="${TPTARGET} H5testFpar"
 		TBTARGET="${TBTARGET} H5BlockParTestScalarFieldF"
 	fi
@@ -374,12 +292,14 @@ fi
 
 AC_MSG_CHECKING([for HDF5 root ])
 AC_MSG_RESULT([])
-if test -n "${HDF5ROOT}"; then
+if test -n "${HDF5PATH}" ; then
+	P=${HDF5PATH}
+elif test -n "${HDF5ROOT}"; then
 	P=${HDF5ROOT}
 elif test -n "${HDF5HOME}" ; then
 	P=${HDF5HOME}
-elif test -n "${HDF5PATH}" ; then
+elif test -n "${HDF5_DIR}" ; then
-	P=${HDF5PATH}
+	P=${HDF5_DIR}
 else
 	P=''
 	P="$P /usr"
@@ -391,7 +311,7 @@ else
 fi
 PATH_Search HDF5ROOT "$P" include/hdf5.h
 if test -z "$HDF5ROOT"; then
-	AC_MSG_ERROR([Cannot determine HDF5 root!!!])
+	AC_MSG_ERROR([Cannot find an HDF5 library!])
 	exit 1
 fi
 
@@ -414,6 +334,10 @@ AC_MSG_CHECKING([for lustre API ])
 AC_MSG_RESULT([])
 if test -n "${LUSTREPATH}"; then
 	P=${LUSTREPATH}
+elif test -n "${LUSTREROOT}" ; then
+	P=${LUSTREROOT}
+elif test -n "${LUSTREHOME}" ; then
+	P=${LUSTREHOME}
 elif test -n "${LUSTRE_DIR}" ; then
 	P=${LUSTRE_DIR}
 else
@@ -435,40 +359,6 @@ fi
 
 LIBS="$LIBS -lz -lm"
 
-
-###############################################################################
-################# 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 "$SAVE_MPICC"; then
-	MPICC="$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 "$SAVE_MPIROOT"; then
-	MPIROOT="$SAVE_MPIROOT"
-fi
-
-if test -n "$SAVE_HDF5ROOT"; then
-	HDF5ROOT="$SAVE_HDF5ROOT"
-fi
-
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################
@@ -479,15 +369,8 @@ fi
 # files with the value that the shell variable variable has when AC_OUTPUT is
 # called.  This value of variable should not contain literal newlines.  If
 # value is given, in addition assign it to variable. 
-AC_SUBST(MPIROOT)
 AC_SUBST(HDF5ROOT)
 AC_SUBST(LUSTREROOT)
-AC_SUBST(MPICC)
-AC_SUBST(MPICXX)
-AC_SUBST(MPIFC)
-AC_SUBST(TPTARGET)
-AC_SUBST(TBTARGET)
-AC_SUBST(TFTARGET)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)
 AC_SUBST(INCLUDES)
@@ -526,20 +409,15 @@ AC_MSG_RESULT([Host OS:             $host_os])
 AC_MSG_RESULT([Host CPU:            $host_cpu])
 AC_MSG_RESULT([Host vendor:         $host_vendor])
 AC_MSG_RESULT([Build libraries:     $BUILD_LIBS])
-AC_MSG_RESULT([Build test programs: $TTARGET])
+AC_MSG_RESULT([Build test programs: $BUILD_TESTS])
 AC_MSG_RESULT([Build tools:         $BUILD_TOOLS])
 AC_MSG_RESULT([CC =                 $CC])
-AC_MSG_RESULT([CXX =                $CXX])
 AC_MSG_RESULT([FC =                 $FC])
-AC_MSG_RESULT([MPICC =              $MPICC])
-AC_MSG_RESULT([MPICXX =             $MPICXX])
-AC_MSG_RESULT([MPIFC =              $MPIFC])
 AC_MSG_RESULT([CFLAGS =             $CFLAGS])
 AC_MSG_RESULT([FFLAGS =             $FFLAGS])
 AC_MSG_RESULT([INCLUDES =           $INCLUDES])
 AC_MSG_RESULT([LDFLAGS =            $LDFLAGS])
 AC_MSG_RESULT([LIBS =               $LIBS])
-AC_MSG_RESULT([MPIROOT =            $MPIROOT])
 AC_MSG_RESULT([HDF5ROOT =           $HDF5ROOT])
 AC_MSG_RESULT([LUSTREROOT =         $LUSTREROOT])
 AC_MSG_RESULT([ ])

src/C/H5.c

@@ -77,7 +77,7 @@ h5_err_t
 H5CloseFile (
 	h5_file_t* const f		/*!< file handle		*/
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_close_file (f));
 }
 
@@ -92,10 +92,27 @@ h5_err_t
 H5CheckFile (
 	h5_file_t* const f		/*!< file handle		*/
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_check_filehandle (f));
 }
 
+
+h5_err_t
+H5FlushStep (
+	h5_file_t* const f		/*!< file handle		*/
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
+	H5_API_RETURN (h5_flush_step (f));
+}
+
+h5_err_t
+H5FlushFile (
+	h5_file_t* const f		/*!< file handle		*/
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
+	H5_API_RETURN (h5_flush_file (f));
+}
+
 /*!
   \ingroup h5hut_model
 
@@ -113,7 +130,7 @@ H5SetStepNameFormat (
 	const h5_int64_t width		/*!< Width of the number	*/
 	) {
 	H5_API_ENTER3 (h5_err_t,
-		       "f=0x%p, name=\"%s\", width=%lld",
+		       "f=%p, name=\"%s\", width=%lld",
 		       f, name, (long long) width);
 	H5_API_RETURN (h5_set_stepname_fmt (f, name, width));
 }
@@ -134,7 +151,7 @@ H5GetStepNameFormat (
 	int* width			/*!< OUT: Width of the number	*/
 	) {
 	H5_API_ENTER4 (h5_err_t,
-		       "f=0x%p, name=0x%p, l_name=%llu, width=0x%p",
+		       "f=%p, name=%p, l_name=%llu, width=%p",
 		       f, name, (unsigned long long)l_name, width);
 	H5_API_RETURN (h5_get_stepname_fmt (f, name, l_name, width));
 }
@@ -151,7 +168,7 @@ H5SetStep (
 	h5_file_t* const f,		/*!< [in]  Handle to open file */
 	const h5_id_t step		/*!< [in]  Step to set. */
 	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, step=%lld", f, (long long)step);
+	H5_API_ENTER2 (h5_err_t, "f=%p, step=%lld", f, (long long)step);
 	H5_API_RETURN (h5_set_step (f, step));
 }
 
@@ -166,7 +183,7 @@ h5_id_t
 H5GetStep (
 	h5_file_t* const f		/*!< Handle to open file */
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_get_step (f));
 }
 
@@ -184,7 +201,7 @@ int
 H5GetNumProcs (
 	h5_file_t* const f
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_get_num_procs(f));
 }
 
@@ -205,7 +222,7 @@ h5_ssize_t
 H5GetNumSteps (
 	h5_file_t* const f
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_get_num_steps(f));
 }
 
@@ -225,7 +242,7 @@ H5HasStep (
 	h5_id_t stepno
 	) {
 	H5_API_ENTER2 (h5_err_t,
-		       "f=0x%p, stepno=%lld",
+		       "f=%p, stepno=%lld",
 		       f,
 		       (long long)stepno);
 	H5_API_RETURN (h5_has_step (f, stepno));
@@ -242,7 +259,7 @@ h5_err_t
 H5StartTraverseSteps (
 	h5_file_t* const f		/*!< Handle to open file */
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_start_traverse_steps (f));
 }
 
@@ -257,7 +274,7 @@ h5_err_t
 H5TraverseSteps (
 	h5_file_t* const f		/*!< Handle to open file */
 	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_ENTER1 (h5_err_t, "f=%p", f);
 	H5_API_RETURN (h5_traverse_steps (f));
 }
 
@@ -283,7 +300,7 @@ H5SetThrottle (
 	h5_file_t* f,
 	int factor
 	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, factor=%d", f, factor);
+	H5_API_ENTER2 (h5_err_t, "f=%p, factor=%d", f, factor);
 	H5_API_RETURN (h5_set_throttle(f, factor));
 }
 #endif // PARALLEL_IO
@@ -314,7 +331,7 @@ h5_err_t
 H5SetErrorHandler (
 	h5_errorhandler_t handler
 	) {
-	H5_API_ENTER1 (h5_err_t, "handler=0x%p", handler);
+	H5_API_ENTER1 (h5_err_t, "handler=%p", handler);
 	H5_API_RETURN (h5_set_errorhandler (handler));
 }
 

src/C/H5Fed.c

@@ -1,43 +0,0 @@
-/*
-  Copyright 2007-2009
- 	Paul Scherrer Institut, Villigen, Switzerland;
- 	Benedikt Oswald;
- 	Achim Gsell
- 	All rights reserved.
- 
-  Authors
- 	Achim Gsell
-  
-  Warning
-	This code is under development.
- 
- */
-#include "h5core/h5_core.h"
-#include "H5Fed.h"
-
-
-h5_err_t
-H5FedCloseMesh (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_close_mesh (f));
-}
-
-h5_err_t
-H5FedSetLevel (
-	h5_file_t* const f,
-	const h5t_lvl_idx_t level_id
-	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, level_id=%d", f, level_id);
-	H5_API_RETURN (h5t_set_level (f, level_id));
-}
-
-h5_err_t
-H5FedLinkMeshToStep (
-	h5_file_t* const f,
-	const h5_id_t mesh_id
-	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, mesh_id=%lld", f, (long long)mesh_id);
-	H5_API_RETURN (h5_error_not_implemented ());
-}

src/C/H5Fed_adjacency.c

@@ -1,46 +0,0 @@
-/*
-  Copyright 2006-2010
- 	Paul Scherrer Institut, Villigen, Switzerland;
- 	Benedikt Oswald;
- 	Achim Gsell
- 	All rights reserved.
- 
-  Authors
- 	Achim Gsell
-  
-  Warning
-	This code is under development.
- 
- */
-
-#include "h5core/h5_core.h"
-#include "H5Fed.h"
-
-/******	UPWARD ADJACENCY routines *********************************************/
-
-/*!
-  \return	number of upward adjacent edges 
- */
-h5_err_t
-H5FedGetAdjacencies (
-	h5_file_t* const f,
-	const h5_loc_id_t entity_id,
-	const h5_int32_t dim,
-	h5_loc_idlist_t** list
-	) {
-	H5_API_ENTER4 (h5_err_t,
-		       "f=0x%p, entity_id=%lld, dim=%d, list=0x%p",
-		       f, (long long)entity_id, dim, list);
-	H5_API_RETURN (h5t_get_adjacencies (f, entity_id, dim, list));
-}
-
-h5_err_t
-H5FedReleaseListOfAdjacencies (
-	h5_file_t* const f,
-	h5_loc_idlist_t** list
-	) {
-	H5_API_ENTER2 (h5_err_t,
-		       "f=0x%p, list=0x%p",
-		       f, list);
-	H5_API_RETURN (h5t_release_list_of_adjacencies (f, list));
-}

src/C/H5Fed_inquiry.c

@@ -1,154 +0,0 @@
-/*
-  Copyright 2007-2008
- 	Paul Scherrer Institut, Villigen, Switzerland;
- 	Benedikt Oswald;
- 	Achim Gsell
- 	All rights reserved.
- 
-  Authors
- 	Achim Gsell
-  
-  Warning
-	This code is under development.
- 
- */
-/*!
-  \ingroup h5fed_c_api
-  \defgroup h5fed_mesh_inquiry
-*/
-
-#include "h5core/h5_core.h"
-#include "H5Fed.h"
-
-
-/*!
-  Get the number of hierarchical mesh levels.
-
-  \param[in]	f	File handle
-
-  \return	Number of hierarchical mesh levels or error code.
- */
-h5_ssize_t
-H5FedGetNumLevels (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_get_num_leaf_levels (f));
-}
-
-/*!
-  Get current mesh levels.
-
-  \param[in]	f	File handle
-
-  \return	ID of current mesh levels or error code.
- */
-h5t_lvl_idx_t
-H5FedGetLevel (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5t_lvl_idx_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_get_level (f));
-}
-
-/*!
-  Returns the number of vertices used for defining the (sub-)mesh
-  at current level on this compute node.
-
-  \param[in]	f	file handle
-
-  \return	Number of vertices or error code.
-*/
-h5_ssize_t
-H5FedGetNumVertices (
-	h5_file_t* const f		/*!< file handle		*/
-	) {
-	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_get_num_vertices (f, -1));
-}
-
-/*!
-  Returns the number of vertices used for defining the (sub-)mesh
-  at current level on compute node \c cnode.
-
-  \param[in]	f	file handle
-  \param[in]	cnode	compute node
-
-  \return	Number of vertices or error code.
-*/
-h5_ssize_t
-H5FedGetNumVerticesCnode (
-	h5_file_t* const f,
-	const int cnode
-	) {
-	H5_API_ENTER2 (h5_ssize_t, "f=0x%p, cnode=%d", f, cnode);
-	H5_API_RETURN (h5t_get_num_vertices (f, cnode));
-}
-
-/*!
-  Returns the number of vertices used for defining the (sub-)mesh
-  at current level overl all compute nodes.
-
-  \param[in]	f	file handle
-
-  \return	Total number of vertices or error code.
-*/
-h5_ssize_t
-H5FedGetNumVerticesTotal (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_get_num_vertices (f, -1));
-}
-
-/*!
-  Returns the number of elements present in the (sub-)mesh
-  at current level on this compute node.
-
-  \param[in]	f	file handle
-
-  \return	Number of elements or error code.
-*/
-h5_ssize_t
-H5FedGetNumElements (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
-	// MLH: can't use field from opaque h5_file_t!
-	//h5_ssize_t num = h5t_get_num_elems (f, f->myproc);
-	H5_API_RETURN (h5t_get_num_elems (f, -1));
-}
-
-/*!
-  Returns the number of elements present in the (sub-)mesh
-  at current level on compute node \c cnode.
-
-  \param[in]	f	file handle
-  \param[in]	cnode	Compute node
-
-  \return	Number of elements or error code.
-*/
-h5_ssize_t
-H5FedGetNumElementsCnode (
-	h5_file_t* const f,
-	const int cnode
-	) {
-	H5_API_ENTER2 (h5_ssize_t, "f=0x%p, cnode=%d", f, cnode);
-	H5_API_RETURN (h5t_get_num_elems (f, cnode));
-}
-
-/*!
-  Returns the number of elements present in the mesh
-  at current level over all compute nodes.
-
-  \param[in]	f	File handle.
-
-  \return	Number of elements or error code.
-*/
-h5_ssize_t
-H5FedGetNumElementsTotal (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_get_num_elems (f, -1));
-}

src/C/H5Fed_retrieve.c

@@ -1,176 +0,0 @@
-/******	RETRIEVAL routines **************************************************/
-/*
-  Copyright 2007-2008
- 	Paul Scherrer Institut, Villigen, Switzerland;
- 	Benedikt Oswald;
- 	Achim Gsell
- 	All rights reserved.
- 
-  Authors
- 	Achim Gsell
-  
-  Warning
-	This code is under development.
- 
- */
-
-#include "h5core/h5_core.h"
-#include "H5Fed.h"
-
-/*!
-  Begin traverse over all entities on this compute node. 
-  Initialize internal data structures.
-
-  \remark
-  Entities might be on processor boundaries! Therefore the same entity might be
-  processed on several compute nodes.
-
-  \param[in]	f	file handle
-  \param[in]	codim	co-dimension of entity to traverse
-
-  \return	H5_SUCCESS or error code
-*/
-
-h5t_iterator_p
-H5FedBeginTraverseEntities (
-	h5_file_t* const f,
-	const int codim
-	) {
-	H5_API_ENTER2 (h5t_iterator_p, "f=0x%p, codim=%d", f, codim);
-	h5t_iterator_p iter;
-	TRY2 (iter = h5_calloc (1, sizeof (*iter)));
-	TRY2 (h5t_init_leaf_iterator (f, iter, codim));
-	H5_API_RETURN (iter);
-}
-
-h5t_iterator_p
-H5FedBeginTraverseBoundaryFaces (
-	h5_file_t* const f,
-	const int codim
-	) {
-	H5_API_ENTER2 (h5t_iterator_p, "f=0x%p, codim=%d", f, codim);
-	h5t_iterator_p iter;
-	TRY2 (iter = h5_calloc (1, sizeof (*iter)));
-	TRY2 (h5t_init_boundary_face_iterator (f, iter, codim));
-	H5_API_RETURN (iter);
-}
-
-/*!
-  Get next local entity ID.
-
-  \param[in]		f	file handle
-  \param[in/out]	iter	iterator
-
-  \return		Local entity ID
-  \return		-1, if done
-  \return		error code on error
-  */
-h5_loc_id_t
-H5FedTraverseEntities (
-	h5_file_t* const f,
-	h5t_iterator_t* iter
-	) {
-	H5_API_ENTER2 (h5_loc_id_t, "f=0x%p, iter=0x%p", f, iter);
-	H5_API_RETURN (h5t_iterate_entities (f, iter));
-}
-
-/*!
-  End of traversing. Release internal data structures.
-
-  \param[in]	f	File handle
-
-  \return	H5_SUCCESS or error code
- 
- */
-h5_err_t
-H5FedEndTraverseEntities (
-	h5_file_t* const f,
-	h5t_iterator_t* iter
-	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, iter=0x%p", f, iter);
-	H5_API_RETURN (h5t_release_entity_iterator (f, iter));
-}
-
-
-/*!
-  Get coordinates of vertex given by local index
-
-  \param[in]	f		file handle
-  \param[in]	vertex_idx	local index of vertex
-  \param[out]	P		3-dimensional coordinates
-
-  \return	H5_SUCCESS or error code
-  */
-h5_err_t
-H5FedGetVertexCoordsByIndex (
-	h5_file_t* const f,
-	h5_loc_idx_t vertex_index,
-	h5_float64_t P[3]
-	) {
-	H5_API_ENTER3 (h5_err_t, 
-		       "f=0x%p, vertex_index=%lld, P=0x%p",
-		       f, (long long)vertex_index, P);
-	H5_API_RETURN (h5t_get_vertex_coords_by_index (f, vertex_index, P));
-}
-
-h5_err_t
-H5FedGetVertexCoordsByID (
-	h5_file_t* const f,
-	h5_loc_id_t vertex_id,
-	h5_float64_t P[3]
-	) {
-	H5_API_ENTER3 (h5_err_t, 
-		       "f=0x%p, vertex_id=%lld, P=0x%p",
-		       f, (long long)vertex_id, P);
-	H5_API_RETURN (h5t_get_vertex_coords_by_id (f, vertex_id, P));
-}
-
-h5_err_t
-H5FedGetVertexIndicesOfEdge (
-	h5_file_t* const f,
-	h5_loc_id_t entity_id,
-	h5_loc_idx_t* vertex_indices
-	) {
-	H5_API_ENTER3 (h5_err_t,
-		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
-		       f, (long long)entity_id, vertex_indices);
-	H5_API_RETURN (h5t_get_vertex_indices_of_edge (f, entity_id, vertex_indices));
-}
-
-h5_err_t
-H5FedGetVertexIndicesOfTriangle (
-	h5_file_t* const f,
-	h5_loc_id_t entity_id,
-	h5_loc_idx_t* vertex_indices
-	) {
-	H5_API_ENTER3 (h5_err_t,
-		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
-		       f, (long long)entity_id, vertex_indices);
-	H5_API_RETURN (h5t_get_vertex_indices_of_triangle (f, entity_id, vertex_indices));
-}
-
-h5_err_t
-H5FedGetVertexIndicesOfTet (
-	h5_file_t* const f,
-	h5_loc_id_t entity_id,
-	h5_loc_idx_t* vertex_indices
-	) {
-	H5_API_ENTER3 (h5_err_t,
-		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
-		       f, (long long)entity_id, vertex_indices);
-	H5_API_RETURN (h5t_get_vertex_indices_of_tet (f, entity_id, vertex_indices));
-}
-
-h5_err_t
-H5FedGetVertexIndicesOfEntity (
-	h5_file_t* const f,
-	h5_loc_id_t entity_id,
-	h5_loc_idx_t* vertex_indices
-	) {
-	H5_API_ENTER3 (h5_err_t,
-		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
-		       f, (long long)entity_id, vertex_indices);
-	H5_API_RETURN (h5t_get_vertex_indices_of_entity (f, entity_id, vertex_indices));
-}
-
-

src/C/H5Fed_store.c

@@ -1,168 +0,0 @@
-/*
-  Copyright 2007-2008
- 	Paul Scherrer Institut, Villigen, Switzerland;
- 	Benedikt Oswald;
- 	Achim Gsell
- 	All rights reserved.
- 
-  Authors
- 	Achim Gsell
-  
-  Warning
-	This code is under development.
- 
- */
-
-#include "h5core/h5_core.h"
-#include "H5Fed.h"
-
-
-
-/*!
-  \ingroup h5fed_c_api
-
-  Add a new level with \c num_elems elements. The number of elements must be the
-  real number of elements to add the level. If you want to refine \c n tetrahedra
-  \c n*8 elements must be added.
-
-  \param[in]	f			File handle.
-  \param[in]	num_elems_to_refine	Number of elements which will be refined.
-
-  \return ID of new level.
-
-  \note
-  values for f->t.num_levels:
-  \c -1		unknown: after opening the file. This is equivalent to
-		"topological data has not been initialized".
-  \c 0		no levels: HDF5 group for meshes may already exist but must not!
-  \c > 0	number of mesh levels
- 
-*/
-h5t_lvl_idx_t
-H5FedAddLevel (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5t_lvl_idx_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_add_level (f));
-}
-
-h5_err_t
-H5FedBeginStoreVertices (
-	h5_file_t* const f,
-	const h5_size_t num
-	) {
-	H5_API_ENTER2 (h5_err_t,
-		       "f=0x%p, num=%llu",
-		       f, (long long unsigned)num);
-	H5_API_RETURN (h5t_begin_store_vertices (f, num));
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Stores the the coordinates of a specific vertex at level \c level
-  with id \c vertex_id of the tetrahedral mesh.
-
-  \return local vertex id on success
-  \return errno on error
-*/
-h5_loc_idx_t
-H5FedStoreVertex (
-	h5_file_t* const f,		/*!< file handle		*/
-	const h5_glb_id_t vertex_id,	/*!< id from mesher or -1	*/
-	const h5_float64_t P[3]		/*!< coordinates		*/
-	) {
-	H5_API_ENTER3 (h5_loc_idx_t,
-		       "f=0x%p, vertex_id=%lld, P=0x%p",
-		       f, (long long)vertex_id, P);
-	if (h5t_get_level (f) != 0) {
-		H5_API_LEAVE (
-			h5_error (
-				H5_ERR_INVAL,
-				"Vertices can be added to level 0 only!"));
-	}
-	H5_API_RETURN (h5t_store_vertex (f, vertex_id, P));
-}
-
-h5_err_t
-H5FedEndStoreVertices (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_end_store_vertices (f));
-}
-
-h5_err_t
-H5FedBeginStoreElements (
-	h5_file_t* const f,
-	const h5_size_t num
-	) {
-	H5_API_ENTER2 (h5_err_t,
-		       "f=0x%p, num=%llu",
-		       f, (long long unsigned)num);
-	H5_API_RETURN (h5t_begin_store_elems (f, num));
-}
-
-/*!
-  \ingroup h5fed_c_api
-
-  Stores the 4-tuple, that contains the specific indices describing
-  a tetrahedron with id \c tet_id at level \c level of the tetrahedral
-  mesh.
-
-  Errors:
-  * current level not yet defined
-  * to many tets stored on level
-
-  \return local tetrahedron id
-  \return \c errno on error
-*/
-h5_loc_idx_t
-H5FedStoreElement (
-	h5_file_t* const f,		/*!< file handle		*/
-	const h5_loc_idx_t local_vids[]	/*!< tuple with vertex id's	*/
-	) {
-	H5_API_ENTER2 (h5_loc_idx_t, "f=0x%p, local_vids=0x%p", f, local_vids);
-	if (h5t_get_level (f) != 0) {
-		H5_API_LEAVE (
-			h5_error (
-				H5_ERR_INVAL,
-				"Elements can be added to level 0 only!"));
-	}
-	H5_API_RETURN (h5t_store_elem (f, -1, local_vids));
-}
-
-h5_err_t
-H5FedEndStoreElements (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_end_store_elems (f));
-}
-
-h5_err_t
-H5FedBeginRefineElements (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_begin_refine_elems (f));
-}
-
-h5_loc_idx_t
-H5FedRefineElement (
-	h5_file_t* const f,		/*!< file handle		*/
-	const h5_loc_id_t local_eid	/*!< local element id		*/
-	) {
-	H5_API_ENTER2 (h5_loc_idx_t,
-		       "f=0x%p, local_eid=%lld",
-		       f, (long long)local_eid);
-	H5_API_RETURN (h5t_mark_entity (f, local_eid));
-}
-
-h5_err_t
-H5FedEndRefineElements (
-	h5_file_t* const f
-	) {
-	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
-	H5_API_RETURN (h5t_end_refine_elems (f));
-}

src/C/H5Fed_tags.c

@@ -1,154 +0,0 @@
-/*
-  Copyright 2007-2011
- 	Paul Scherrer Institut, Villigen, Switzerland;
- 	Achim Gsell
- 	All rights reserved.
- 
-  Authors
- 	Achim Gsell
-  
-  Warning
-	This code is under development.
- 
- */
-#include "h5core/h5_core.h"
-#include "H5Fed.h"
-
-/*!
-  Add a tagset to the current mesh.
-
-  \param[in]	f	file handle
-  \param[in]	name	name of tagset
-  \param[in]	type	data type of tagset
-
-  \return	H5_SUCCESS or error code
- */
-h5_err_t
-H5FedAddMTagset (
-	h5_file_t* const f,
-	char* name,
-	h5_id_t type
-	) {
-	H5_API_ENTER3 (h5_err_t, "f=0x%p, name=\"%s\", type=%lld",
-		       f, name, (long long)type);
-	H5_API_RETURN (h5t_add_mtagset (f, name, type));
-}
-
-/*!
-  Remove a tagset from the current mesh.
-
-  \param[in]	f	file handle
-  \param[in]	name	name of tagset to remove
-
-  \return	H5_SUCCESS or error code
- */
-h5_err_t
-H5FedRemoveMTagset (
-	h5_file_t* const f,
-	char name[]
-	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, name=\"%s\"", f, name);
-	H5_API_RETURN (h5t_remove_mtagset (f, name));
-}
-
-/*!
-  Get available tagsets in current mesh.
-
-  \param[in]	f	file handle
-  \param[out]	names	names of available tagsets
-
-  \return	Number of tagsets or error code
- */
-h5_ssize_t
-H5FedGetMTagsets (
-	h5_file_t* const f,
-	char** names[]
-	) {
-	H5_API_ENTER2 (h5_ssize_t, "f=0x%p, names=0x%p", f, names);
-	H5_API_RETURN (h5t_get_mtagsets (f, names));
-}
-
-/*!
-  Get type of tagset in current mesh.
-
-  \param[in]	f	file handle
-  \param[in]	name	name of tagset
-
-  \return	H5_SUCCESS or error code
- */
-h5_id_t
-H5FedGetTypeOfMTagset (
-	h5_file_t* const f,
-	char name[]
-	) {
-	H5_API_ENTER2 (h5_err_t, "f=0x%p, name=\"%s\"", f, name);
-	H5_API_RETURN (h5t_get_mtagset_type_by_name (f, name));
-}
-
-/*!
-  Set tag for entity in current mesh.
-
-  \param[in]	f	file handle
-  \param[in]	name	names of tagset
-  \param[in]	id	id of entity
-  \param[in]	dim	dimension of value
-  \param[in]	val	tag value
-
-  \return	H5_SUCCESS or error code
- */
-h5_err_t
-H5FedSetMTag (
-	h5_file_t* const f,
-	char name[],
-	h5_loc_id_t id,
-	const size_t dim,
-	void* buffer
-	) {
-	H5_API_ENTER5 (h5_err_t,
-		       "f=0x%p, name=\"%s\", id=%lld, dim=%lld, val=0x%p",
-		       f, name, (long long)id, (long long)dim, buffer);
-	H5_API_RETURN (h5t_set_mtag_by_name (f, name, id, dim, buffer));
-}
-
-/*!
-  Set tag for entity in current mesh.
-
-  \param[in]	f	file handle
-  \param[in]	name	names of tagset
-  \param[in]	id	id of entity
-  \param[out]	dim	dimension of value
-  \param[out]	val	tag value
-
-  \return	H5_SUCCESS or error code
- */
-h5_err_t
-H5FedGetMTag (
-	h5_file_t* const f,
-	const char name[],
-	const h5_loc_id_t id,
-	size_t* dim,
-	void* buffer
-	) {
-	H5_API_ENTER5 (h5_err_t,
-		       "f=0x%p, name=\"%s\", id=%lld, dim=0x%p, val=0x%p",
-		       f, name, (long long)id, dim, buffer);
-	H5_API_RETURN (h5t_get_mtag_by_name (f, name, id, dim, buffer));
-}
-
-/*!
-  Remove tag for entity in current mesh.
-
-  \param[in]	f	file handle
-  \param[in]	name	names of tagset
-  \param[in]	id	id of entity
-*/
-h5_err_t
-H5FedRemoveMTag (
-	h5_file_t* const f,
-	const char name[],
-	const h5_loc_id_t id
-	) {
-	H5_API_ENTER3 (h5_err_t, "f=0x%p, name=\"%s\", id=%lld",
-		       f, name, (long long)id);
-	H5_API_RETURN (h5t_remove_mtag_by_name (f, name, id));
-}

src/C/Makefile.am

@@ -2,14 +2,13 @@
 
 OBJEXT=o
 
-LIBS = @LIBS@
 INCLUDES = -I../include @INCLUDES@
 
 # What to build... Will be determined by configure script.
-lib_LIBRARIES = @LIB_C@
+lib_LTLIBRARIES = @LIB_C@
 
 # Listing of all possible targets that I may build.
-EXTRA_LIBRARIES = ../lib/libH5hutC.a
+EXTRA_LTLIBRARIES = libH5hutC.la
 
 # Header files that I wish to install in $(prefix)/include
 include_HEADERS =				\
@@ -31,21 +30,16 @@ include_HEADERS =				\
 EXTRA_HEADERS =
 
 # Listing of sources
-___lib_libH5hutC_a_SOURCES =			\
+libH5hutC_la_SOURCES =				\
 	H5.c					\
 	H5_attribs.c				\
 	H5_attachments.c			\
 	H5Part.c                                \
 	H5Block.c				\
-	H5Block_readwrite.c			\
+	H5Block_readwrite.c
-	H5Fed.c					\
-	H5Fed_adjacency.c			\
-	H5Fed_inquiry.c				\
-	H5Fed_retrieve.c			\
-	H5Fed_store.c				\
-	H5Fed_tags.c
 
-all: all-am
+libH5hutC_la_LDFLAGS = -version-info 2:0:0 -rpath '$(libdir)'
 
-clean: clean-am
+all-local:
+	$(INSTALL) -m644 .libs/libH5hutC.a ../lib
 

src/Fortran/Makefile.am

@@ -2,7 +2,6 @@
 
 OBJEXT=o
 
-LIBS = @LIBS@
 INCLUDES = -I../include @INCLUDES@
 
 F90_FILES =     	H5.f90 \
@@ -23,19 +22,21 @@ EXTRA_DIST =		TestUnderscoreC.c \
 nodist_include_HEADERS = ../include/H5hutF.h
 
 # What to build... Will be determined by configure script.
-lib_LIBRARIES = @LIB_FORTRAN@
+lib_LTLIBRARIES = @LIB_FORTRAN@
 
 # Listing of all possible targets that I may build.
-EXTRA_LIBRARIES = ../lib/libH5hutF.a
+EXTRA_LTLIBRARIES = libH5hutF.la
 
-___lib_libH5hutF_a_SOURCES = 	\
+libH5hutF_la_SOURCES = 	\
 	H5_F.c			\
 	H5_attribs_F.c		\
 	H5Part_F.c		\
 	H5Block_F.c		\
 	H5Block_readwrite_F.c
 
-___lib_libH5hutF_a_DEPENDENCIES = ../include/H5hutF.h
+libH5hutF_la_DEPENDENCIES = ../include/H5hutF.h
+
+libH5hutF_la_LDFLAGS = -version-info 2:0:0 -rpath '$(libdir)'
 
 ../include/H5hutF.h: $(F90_FILES)
 	awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >$@

src/h5core/Makefile.am

@@ -2,7 +2,6 @@
 
 OBJEXT=o
 
-LIBS = @LIBS@
 INCLUDES = -I../include @INCLUDES@
 
 EXTRA_HEADERS =					\
@@ -69,13 +68,10 @@ EXTRA_HEADERS =					\
 EXTRA_DIST = $(EXTRA_HEADERS)
 
 # What to build... Will be determined by configure script.
-lib_LIBRARIES = ../lib/libH5hut.a
+lib_LTLIBRARIES = libH5hut.la
-
-# Listing of all possible targets that I may build.
-EXTRA_LIBRARIES = ../lib/libH5hut.a
 
 # Listing of sources
-___lib_libH5hut_a_SOURCES =			\
+libH5hut_la_SOURCES =			\
 	h5_attach.c				\
 	h5_attribs.c				\
 	h5_errorhandling.c			\
@@ -118,13 +114,17 @@ ___lib_libH5hut_a_SOURCES =			\
 	h5t_store_trim.c			\
 	h5t_tags.c
 
-___lib_libH5hut_a_DEPENDENCIES = $(EXTRA_HEADERS)
+libH5hut_la_DEPENDENCIES = $(EXTRA_HEADERS)
 
-all: all-am
+libH5hut_la_LDFLAGS = -version-info 2:0:0
+
+all-local:
+	$(INSTALL) -m644 .libs/libH5hut.a ../lib
 
 install-exec-local:
 	@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core
 	@$(INSTALL) -m644 ../include/h5core/*.h $(DESTDIR)$(includedir)/h5core/
 
-clean: clean-am
+clean-local:
+	$(RM) -f ../lib/libH5hut.*
 

src/h5core/h5_attribs.c

@@ -81,7 +81,7 @@ h5_read_attrib (
 
 	if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
 
-	hid_t id;
+	hid_t id = 0;
 	TRY (get_hdf5_obj_id(f, mode, &id));
 	TRY (h5priv_read_attrib (id, attrib_name, attrib_type, attrib_value));
 	H5_CORE_API_RETURN (H5_SUCCESS);
@@ -161,7 +161,7 @@ h5_write_attrib (
 	if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
 	CHECK_WRITABLE_MODE( f );
 
-	hid_t id;
+	hid_t id = 0;
 	TRY (get_hdf5_obj_id(f, mode, &id));
 	TRY (h5priv_write_attrib (id, attrib_name, attrib_type,
 				  attrib_value, attrib_nelem));
@@ -245,7 +245,7 @@ h5_get_attrib_info (
 
 	if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
 
-	hid_t id;
+	hid_t id = 0;
 	TRY (get_hdf5_obj_id(f, mode, &id));
 	TRY (h5priv_get_attrib_info (id, attrib_idx, attrib_name, len_attrib_name,
 				     attrib_type, attrib_nelem));
@@ -267,7 +267,7 @@ h5_get_num_attribs (
 	H5_CORE_API_ENTER2 (h5_ssize_t,
 			    "f=%p, mode=%d", f, mode);
 	if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
-	hid_t id;
+	hid_t id = 0;
 	TRY (get_hdf5_obj_id(f, mode, &id));
 	H5_CORE_API_RETURN (hdf5_get_num_attribute (id));
 }

src/h5core/h5_core_private.h

@@ -81,6 +81,22 @@
 #define MALLOC_WRAPPER_LEAVE(value)	__FUNC_LEAVE(value)
 #define MALLOC_WRAPPER_RETURN(value)	__FUNC_RETURN(value, H5_DEBUG_MALLOC)
 
+#define MPI_WRAPPER_ENTER(type)	__FUNC_ENTER(type)
+#define MPI_WRAPPER_ENTER0(type)		\
+	__FUNC_ENTER0(type, H5_DEBUG_MPI)
+#define MPI_WRAPPER_ENTER1(type, fmt, a1)		\
+	__FUNC_ENTER1(type, fmt, a1, H5_DEBUG_MPI)
+#define MPI_WRAPPER_ENTER2(type, fmt, a1, a2)		\
+	__FUNC_ENTER2(type, fmt, a1, a2, H5_DEBUG_MPI)
+#define MPI_WRAPPER_ENTER3(type, fmt, a1, a2, a3)		\
+	__FUNC_ENTER3(type, fmt, a1, a2, a3, H5_DEBUG_MPI)
+#define MPI_WRAPPER_ENTER4(type, fmt, a1, a2, a3, a4)		\
+	__FUNC_ENTER4(type, fmt, a1, a2, a3, a4, H5_DEBUG_MPI)
+#define MPI_WRAPPER_ENTER5(type, fmt, a1, a2, a3, a4, a5)	\
+	__FUNC_ENTER5(type, fmt, a1, a2, a3, a4, a5, H5_DEBUG_MPI)
+#define MPI_WRAPPER_LEAVE(value)	__FUNC_LEAVE(value)
+#define MPI_WRAPPER_RETURN(value)	__FUNC_RETURN(value, H5_DEBUG_MPI)
+
 /* WARNING! Changing these values will alter the data model and introduce
  * file incompatibilities with previous versions. */
 #define H5_DATANAME_LEN		64

src/h5core/h5_maps.c

@@ -105,18 +105,18 @@ h5priv_find_idlist (
 	if (!list) {
 		H5_PRIV_API_LEAVE (-1);
 	}
-	register h5_loc_idx_t low = 0;
+	register size_t low = 0;
-	register h5_loc_idx_t high = list->num_items - 1;
+	register size_t mid;
-	register h5_loc_id_t diff;
+	register size_t high = list->num_items - 1;
-	register h5_loc_id_t mid;
+	register h5_loc_idx_t diff;
-	const h5_loc_id_t face_idx =  h5tpriv_get_face_idx(item);
+	const h5_loc_id_t face_id =  h5tpriv_get_face_id(item);
-	const h5_loc_id_t elem_idx =  h5tpriv_get_elem_idx(item);
+	const h5_loc_idx_t elem_idx =  h5tpriv_get_elem_idx(item);
 	while (low <= high) {
 		mid = (low + high) / 2;
 		diff = h5tpriv_get_elem_idx(list->items[mid]) - elem_idx;
 		// if element indices are equal, we decide on the face indices
 		if (diff == 0) {
-			diff = h5tpriv_get_face_idx(list->items[mid]) - face_idx;
+			diff = h5tpriv_get_face_id (list->items[mid]) - face_id;
 		}
            	if ( diff > 0 )
                		high = mid - 1;

src/h5core/h5_mpi.c

@@ -12,6 +12,9 @@ h5priv_mpi_recv(
 	const int tag,
 	const MPI_Comm comm
 	) {
+	MPI_WRAPPER_ENTER4 (h5_err_t,
+			   "buf=0x%p, count=%d, type=?, from=%d, tag=%d, comm=?",
+			   buf, count, from, tag);
 	int err = MPI_Recv(
 		buf,
 		count,
@@ -22,8 +25,8 @@ h5priv_mpi_recv(
 		MPI_STATUS_IGNORE
 		);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot receive data");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot receive data"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -35,6 +38,9 @@ h5priv_mpi_send(
 	const int tag,
 	const MPI_Comm comm
 	) {
+	MPI_WRAPPER_ENTER4 (h5_err_t,
+			   "buf=0x%p, count=%d, type=?, to=%d, tag=%d, comm=?",
+			   buf, count, to, tag);
 	int err = MPI_Send(
 		buf,
 		count,
@@ -44,8 +50,8 @@ h5priv_mpi_send(
 		comm
 		);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot send data");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot send data"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -56,6 +62,9 @@ h5priv_mpi_bcast (
 	const int root,
 	const MPI_Comm comm
 	) {
+	MPI_WRAPPER_ENTER3 (h5_err_t,
+			   "buf=0x%p, count=%d, type=?, root=%d, comm=?",
+			   buf, count, root);
 	int err = MPI_Bcast(
 		buf,
 		count,
@@ -64,8 +73,8 @@ h5priv_mpi_bcast (
 		comm
 		);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot perform broadcast");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot perform broadcast"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 
@@ -78,6 +87,9 @@ h5priv_mpi_sum (
 	const MPI_Datatype type,
 	const MPI_Comm comm
 	) {
+	MPI_WRAPPER_ENTER3 (h5_err_t,
+			   "sendbuf=0x%p, recvbuf=0x%p, count=%d, type=?, comm=?",
+			    sendbuf, recvbuf, count);
 	int err = MPI_Allreduce(
 		sendbuf,
 		recvbuf,
@@ -87,8 +99,8 @@ h5priv_mpi_sum (
 		comm
 		);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot perform sum reduction");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot perform sum reduction"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -99,6 +111,9 @@ h5priv_mpi_prefix_sum (
 	const MPI_Datatype type,
 	const MPI_Comm comm
 	) {
+	MPI_WRAPPER_ENTER3 (h5_err_t,
+			   "sendbuf=0x%p, recvbuf=0x%p, count=%d, type=?, comm=?",
+			    sendbuf, recvbuf, count);
 	int err = MPI_Scan(
 		sendbuf,
 		recvbuf,
@@ -108,8 +123,8 @@ h5priv_mpi_prefix_sum (
 		comm
 		);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot perform prefix sum");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot perform prefix sum"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -122,6 +137,9 @@ h5priv_mpi_allgather (
 	const MPI_Datatype recvtype,
 	const MPI_Comm comm
 	) {
+	MPI_WRAPPER_ENTER4 (h5_err_t,
+			   "sendbuf=0x%p, sendcount=%d, sendtype=?, recvbuf=0x%p, recvcount=%d, recvtype=?, comm=?",
+			    sendbuf, sendcount, recvbuf, recvcount);
 	int err = MPI_Allgather (
 		sendbuf,
 		sendcount,
@@ -131,8 +149,8 @@ h5priv_mpi_allgather (
 		recvtype,
 		comm);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot gather data");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot gather data"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -140,10 +158,12 @@ h5priv_mpi_comm_size (
 	MPI_Comm comm,
 	int* size
 	) {
+	MPI_WRAPPER_ENTER1 (h5_err_t,
+			    "comm=?, size=0x%p", size);
 	int err = MPI_Comm_size (comm, size);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot get communicator size");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot get communicator size"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 
@@ -152,10 +172,12 @@ h5priv_mpi_comm_rank (
 	MPI_Comm comm,
 	int* rank
 	) {
+	MPI_WRAPPER_ENTER1 (h5_err_t,
+			    "comm=?, rank=0x%p", rank);
 	int err = MPI_Comm_rank (comm, rank);
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot get this task's rank");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot get this task's rank"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -164,24 +186,26 @@ h5priv_mpi_type_contiguous (
 	const MPI_Datatype oldtype,
 	MPI_Datatype *const newtype
 	) {
+	MPI_WRAPPER_ENTER1 (h5_err_t, "nelems=%lu, oldtype=?, newtype=?", (long unsigned)nelems);
 	int err;
 	err = MPI_Type_contiguous ( nelems, oldtype, newtype );
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot create new MPI type");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot create new MPI type"));
 	err = MPI_Type_commit ( newtype );
 	if (err != MPI_SUCCESS)
-		return h5_error (H5_ERR_MPI, "Cannot commit new MPI type");
+		MPI_WRAPPER_LEAVE (h5_error (H5_ERR_MPI, "Cannot commit new MPI type"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
 h5priv_mpi_type_free (
 	MPI_Datatype *type
 	) {
+	MPI_WRAPPER_ENTER1 (h5_err_t, "type=0x%p", type);
 	int err = MPI_Type_free( type );
 	if (err != MPI_SUCCESS)
-		return h5_error(H5_ERR_MPI, "Cannot free MPI type");
+		MPI_WRAPPER_LEAVE (h5_error(H5_ERR_MPI, "Cannot free MPI type"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -193,11 +217,13 @@ h5priv_mpi_cart_create (
 	int reorder,
 	MPI_Comm *new_comm
 	) {
+	MPI_WRAPPER_ENTER5 (h5_err_t, "old_comm=?, ndims=%d, dims=0x%p, period=0x%p, reorder=%d, new_comm=0x%p",
+			    ndims, dims, period, reorder, new_comm);
 	int err = MPI_Cart_create(
 		old_comm, ndims, dims, period, reorder, new_comm);
 	if (err != MPI_SUCCESS)
-		return h5_error(H5_ERR_MPI, "Cannot create cartesian grid");
+		MPI_WRAPPER_LEAVE (h5_error(H5_ERR_MPI, "Cannot create cartesian grid"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 h5_err_t
@@ -207,10 +233,12 @@ h5priv_mpi_cart_coords (
 	int maxdim,
 	int *coords
 	) {
+	MPI_WRAPPER_ENTER3 (h5_err_t, "comm=?, rank=%d, maxdim=%d, coords=0x%p",
+			    rank, maxdim, coords);
 	int err = MPI_Cart_coords( comm, rank, maxdim, coords );
 	if (err != MPI_SUCCESS)
-		return h5_error(H5_ERR_MPI, "Cannot create cartesian grid");
+		MPI_WRAPPER_LEAVE (h5_error(H5_ERR_MPI, "Cannot create cartesian grid"));
-	return H5_SUCCESS;
+	MPI_WRAPPER_RETURN (H5_SUCCESS);
 }
 
 #endif // PARALLEL_IO

src/h5core/h5_openclose.c

@@ -325,6 +325,23 @@ h5_close_file (
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
 
+h5_err_t
+h5_flush_step (
+	h5_file_t * const f
+	) {
+	H5_CORE_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_CORE_API_RETURN (hdf5_flush (f->step_gid, H5F_SCOPE_LOCAL));
+}
+
+h5_err_t
+h5_flush_file (
+	h5_file_t * const f
+	) {
+	H5_CORE_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_CORE_API_RETURN (hdf5_flush (f->file, H5F_SCOPE_GLOBAL));
+}
+
+
 /*!
   \ingroup h5_core_filehandling
 

src/h5core/h5t_adjacencies_trim.c

@@ -582,13 +582,13 @@ update_internal_structs (
 	clock_t t1 = clock();
 	TRY( compute_elems_of_vertices (f, from_lvl) );
 	clock_t t2 = clock();
-	fprintf (stderr, "compute_elems_of_vertices(): %f\n",
+	//	fprintf (stderr, "compute_elems_of_vertices(): %f\n",
-		 (float)(t2-t1)/CLOCKS_PER_SEC);
+	//	 (float)(t2-t1)/CLOCKS_PER_SEC);
 	t1 = clock();
 	TRY( compute_elems_of_edges (f, from_lvl ) );
 	t2 = clock();
-	fprintf (stderr, "compute_elems_of_edge(): %f\n",
+	//	fprintf (stderr, "compute_elems_of_edge(): %f\n",
-		 (float)(t2-t1)/CLOCKS_PER_SEC);
+	//	 (float)(t2-t1)/CLOCKS_PER_SEC);
 	h5_debug ("%s (%lld): done", __func__, (long long)from_lvl);
 	H5_PRIV_FUNC_RETURN (H5_SUCCESS);
 }

src/h5core/h5t_core_private.h

@@ -57,19 +57,22 @@
 #define H5T_FACE_MASK		(0x0f)
 #define H5T_TYPE_MASK		(0x70)
 
-#define h5tpriv_set_entity_type( type, elem_idx )	\
+#if 0
-	(((type) << (BITS_OF(elem_idx)-4)) | (elem_idx))
+enum elem_types {
-				 
+	vertex = 1,	// 1 vertex
-#define h5tpriv_get_entity_type( entity_id )	\
+	edge,		// 2 vertices
-	((entity_id >> (BITS_OF(entity_id)-8)) & H5T_TYPE_MASK)
+	triangle,	// 3 vertices
+	quadrangle,	// 4 vertices
+	tetrahedron,	// 4 vertices
+	pyramid,	// 5 vertices
+	prism,		// 6 vertices
+	hexahedron	// 8 vertices
+};
+#endif
 
 #define h5tpriv_build_entity_id( type, face_idx, elem_idx )	\
 	(((type) | (face_idx)) << (BITS_OF(elem_idx)-8) | (elem_idx))
 
-#define h5tpriv_build_entity_id2( face_id, elem_idx )		\
-	(((face_id) << (BITS_OF(elem_idx)-8)) |		\
-	 (elem_idx))
-
 #define h5tpriv_build_vertex_id( face_idx, elem_idx )			\
 	(h5tpriv_build_entity_id (H5T_TYPE_VERTEX, face_idx, elem_idx))
 
@@ -82,6 +85,9 @@
 #define h5tpriv_build_tet_id( face_idx, elem_idx )			\
 	(h5tpriv_build_entity_id (H5T_TYPE_TET, face_idx, elem_idx))
 
+#define h5tpriv_get_entity_type( entity_id )	\
+	((entity_id >> (BITS_OF(entity_id)-8)) & H5T_TYPE_MASK)
+
 #define h5tpriv_get_face_idx( entity_id )				\
 	(((entity_id) >> (BITS_OF(entity_id)-8)) & H5T_FACE_MASK)
 

src/h5core/h5t_model_tetm.c

@@ -72,15 +72,19 @@ h5t_open_tetrahedral_mesh (
 	t->dsinfo_elems.type_id = t->dtypes.h5_tet_t;
 	t->methods = tet_funcs;
 	t->ref_elem = &h5t_tet_ref_elem;
-	TRY (open_tetmesh_group (f, id));
 
-	if (id == -1) {			// append new
+	if (id == -1) {			// add new
-		id = t->num_meshes;
+		id = 0;
-		t->num_meshes++;
+		t->num_meshes = 1;
-		t->mesh_changed = id;
+		t->cur_mesh = 0;
+		t->mesh_changed = 0;
+		t->leaf_level = 0;
 		t->num_leaf_levels = 0;
+		TRY (open_tetmesh_group (f, id));
 	} else {			// read existing
+		TRY (open_tetmesh_group (f, id));
 		TRY (h5tpriv_read_mesh (f));
+		t->leaf_level = 0;
 	} 
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }

src/h5core/h5t_model_trim.c

@@ -9,7 +9,9 @@ static struct h5t_methods tri_funcs = {
 	&h5tpriv_trim_adjacency_methods
 };
 
-
+/*
+  Open container of triangle meshes
+ */
 static inline h5_err_t
 open_trimeshes_group (
 	h5_file_t* const f
@@ -30,7 +32,7 @@ open_trimeshes_group (
 }
 
 /*
-  open HDF5 group with data of specific mesh.
+  Open container of triangle mesh with \c id 
  */
 static inline h5_err_t
 open_trimesh_group (
@@ -73,15 +75,19 @@ h5t_open_triangle_mesh (
 	t->dsinfo_elems.type_id = t->dtypes.h5_triangle_t;
 	t->methods = tri_funcs;
 	t->ref_elem = &h5t_tri_ref_elem;
-	TRY (open_trimesh_group (f, id));
 
 	if (id == -1) {			// add new
-		id = t->num_meshes;
+		id = 0;
-		t->num_meshes++;
+		t->num_meshes = 1;
-		t->mesh_changed = id;
+		t->cur_mesh = 0;
+		t->mesh_changed = 0;
+		t->leaf_level = 0;
 		t->num_leaf_levels = 0;
+		TRY (open_trimesh_group (f, 0));
 	} else {			// read existing
+		TRY (open_trimesh_group (f, 0));
 		TRY (h5tpriv_read_mesh (f));
+		t->leaf_level = 0;
 	}
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
@@ -124,8 +130,6 @@ h5t_open_triangle_mesh_by_name (
 
 	TRY (h5t_close_mesh (f));
 
-
-
 	t->dsinfo_elems.type_id = t->dtypes.h5_triangle_t;
 	t->methods = tri_funcs;
 	t->ref_elem = &h5t_tri_ref_elem;

src/h5core/h5t_tags.c

@@ -861,8 +861,8 @@ write_tagset (
 		for (ti_idx = 0; eleminfo && ti_idx < eleminfo->num_tags; ti_idx++) {
 			h5t_taginfo_t* ti = eleminfo->ti+ti_idx;
 			h5_glb_idx_t glb_elem_idx = h5tpriv_get_loc_elem_glb_idx (f, elem_idx);
-			entity->eid = h5tpriv_build_entity_id2 (
+			entity->eid = h5tpriv_build_entity_id (
-				(h5_glb_id_t)ti->face_id, glb_elem_idx);
+				0, (h5_glb_id_t)ti->face_id, glb_elem_idx);
 			entity->idx = val_idx;
 
 			// copy values 

src/h5core/h5u_model.c

@@ -6,11 +6,10 @@ h5u_get_num_particles (
 	h5_file_t *const f      /*!< [in]  Handle to open file */
 	) {
 	H5_CORE_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
-	h5_int64_t nparticles;
+	h5_ssize_t nparticles;
 
 	/* if a view exists, use its size as the number of particles */
-	if ( h5u_has_view ( f ) )
+	if (h5u_has_view (f)) {
-	{
 		TRY (nparticles = hdf5_get_selected_npoints_of_dataspace(
 			    f->u->diskshape));
 		h5_debug(
@@ -22,8 +21,7 @@ h5u_get_num_particles (
 		h5_debug(
 			"Found %lld particles from previous H5PartSetNumParticles call.",
 			(long long)nparticles );
-	}
+	} else {
-	else {
 		/* otherwise, report all particles on disk in the first dataset
 		 * for this timestep */
 		char dataset_name[H5_DATANAME_LEN];
@@ -33,20 +31,20 @@ h5u_get_num_particles (
 				0,
 				dataset_name,
 				H5_DATANAME_LEN);
-		if ( exists < 0 )
+		if (exists < 0)
 			H5_CORE_API_LEAVE (
-				h5_error(
+				h5_error (
 					H5_ERR_INVAL,
 					"Cannot determine the number of particles: "
 					"H5PartSetNumParticles has not been called, "
 					"no view has been set, and there are no "
 					"data sets for this time step!"));
-		TRY( nparticles = hdf5_get_npoints_of_dataset_by_name(
+		TRY (nparticles = hdf5_get_npoints_of_dataset_by_name(
-			f->step_gid,
+			     f->step_gid,
-			dataset_name) );
+			     dataset_name) );
-		h5_debug(
+		h5_debug (
 			"Found %lld particles in the first data set of this time step.",
-			(long long)nparticles );
+			(long long)nparticles);
 	}
 
 	H5_CORE_API_RETURN (nparticles);
@@ -63,21 +61,19 @@ h5u_set_num_particles (
 			    f, (long long unsigned)nparticles,
 			    (long long unsigned)stride);
 	struct h5u_fdata *u = f->u;
-	hsize_t hstride;
-	hsize_t count;
 	hsize_t start;
 	hsize_t total;
 	hsize_t dmax = H5S_UNLIMITED;
 
-	if ( nparticles <= 0 )
+	if (nparticles < 0)
 		H5_CORE_API_LEAVE (
 			h5_error(
 				H5_ERR_INVAL,
 				"Invalid number particles: %lld!\n",
 				(long long)nparticles));
 
-	hstride = (hsize_t)stride;
+	hsize_t hstride = (hsize_t)stride;
-	if ( hstride > 1 )
+	if (hstride > 1)
 		h5_debug ("Striding by %lld elements.", (long long)hstride);
 
 #ifndef PARALLEL_IO
@@ -100,14 +96,13 @@ h5u_set_num_particles (
 	u->nparticles = (hsize_t)nparticles;
 
 	/* declare local memory datasize with striding */
-	count = u->nparticles * stride;
+	hsize_t count = u->nparticles * stride;
 	TRY (u->memshape = hdf5_create_dataspace (1, &count, &dmax));
 
 	/* we need a hyperslab selection if there is striding
 	 * (otherwise, the default H5S_ALL selection is ok)
 	 */
-	if ( hstride > 1 )
+	if (hstride > 1) {
-	{
 		start = 0;
 		count = u->nparticles;
 		TRY (hdf5_select_hyperslab_of_dataspace(
@@ -159,11 +154,15 @@ h5u_set_num_particles (
 
 	count = nparticles;
 	hstride = 1;
-	TRY( hdf5_select_hyperslab_of_dataspace(
+	if (count > 0) {
-			u->diskshape,
+		TRY( hdf5_select_hyperslab_of_dataspace(
-			H5S_SELECT_SET,
+			     u->diskshape,
-			&start, &hstride, &count,
+			     H5S_SELECT_SET,
-			NULL) );
+			     &start, &hstride, &count,
+			     NULL) );
+	} else {
+		TRY (hdf5_select_none (u->diskshape));
+	}
 #endif
 	H5_CORE_API_RETURN (H5_SUCCESS);
 }
@@ -205,7 +204,6 @@ h5u_set_view (
 			    f, (long long)start, (long long)end);
 	hsize_t total;
 	hsize_t stride = 1;
-	hsize_t hstart;
 	hsize_t dmax = H5S_UNLIMITED;
 	struct h5u_fdata *u = f->u;
 
@@ -260,7 +258,7 @@ h5u_set_view (
 	TRY (u->diskshape = hdf5_create_dataspace ( 1, &total, NULL ));
 
 	total = (hsize_t)u->nparticles;
-	hstart = (size_t)start;
+	hsize_t hstart = (hsize_t)start;
 
 	TRY (hdf5_select_hyperslab_of_dataspace ( 
 		     u->diskshape,
@@ -319,11 +317,14 @@ h5u_set_view_indices (
 	/* declare local memory datasize */
 	total = u->nparticles;
 	TRY (u->memshape = hdf5_create_dataspace (1, &total, &dmax));
-	TRY (hdf5_select_elements_of_dataspace ( 
+	if (nelems > 0) {
-		u->diskshape,
+		TRY (hdf5_select_elements_of_dataspace ( 
-		H5S_SELECT_SET,
+			     u->diskshape,
-		(hsize_t)nelems, (hsize_t*)indices ) );
+			     H5S_SELECT_SET,
-
+			     (hsize_t)nelems, (hsize_t*)indices ) );
+	} else {
+		TRY (hdf5_select_none (u->diskshape));
+	}
 	u->viewindexed = 1;
 
 	H5_CORE_API_RETURN (H5_SUCCESS);

src/h5core/h5u_readwrite.c

@@ -36,7 +36,7 @@ h5u_read_data (
 	TRY (ndisk = hdf5_get_npoints_of_dataspace (space_id));
 
 	if (u->diskshape != H5S_ALL) {
-		TRY (nread = hdf5_get_npoints_of_dataspace(u->diskshape));
+		TRY (nread = hdf5_get_selected_npoints_of_dataspace (u->diskshape));
 
 		/* make sure the disk space selected by the view doesn't
 		 * exceed the size of the dataset */
@@ -155,6 +155,9 @@ h5u_write_data (
 #ifdef PARALLEL_IO
 	TRY (h5_end_throttle (f));
 #endif
+	if (f->mode & H5_O_FLUSHSTEP)
+		TRY (hdf5_flush (f->step_gid, H5F_SCOPE_LOCAL));
+
 	TRY (hdf5_close_dataset (dset_id));
 
 	f->empty = 0;

src/include/H5Fed.h

@@ -49,22 +49,31 @@ H5FedOpenTriangleMesh (
 	H5_API_RETURN (h5t_open_triangle_mesh (f, mesh_id));
 }
 
-h5_err_t
+static inline h5_err_t
 H5FedCloseMesh (
-	h5_file_t * const f
+	h5_file_t* const f
-	);
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_close_mesh (f));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedSetLevel (
-	h5_file_t * f,
+	h5_file_t* const f,
 	const h5t_lvl_idx_t level_id
-	);
+	) {
+	H5_API_ENTER2 (h5_err_t, "f=0x%p, level_id=%d", f, level_id);
+	H5_API_RETURN (h5t_set_level (f, level_id));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedLinkMeshToStep (
-	h5_file_t * f,
+	h5_file_t* const f,
 	const h5_id_t mesh_id
-	);
+	) {
+	H5_API_ENTER2 (h5_err_t, "f=0x%p, mesh_id=%lld", f, (long long)mesh_id);
+	H5_API_RETURN (h5_error_not_implemented ());
+}
 
 #ifdef __cplusplus
 }

src/include/H5Fed_adjacency.h

@@ -5,19 +5,29 @@
 extern "C" {
 #endif
 
-h5_err_t
+static inline h5_err_t
 H5FedGetAdjacencies (
 	h5_file_t* const f,
 	const h5_loc_id_t entity_id,
 	const h5_int32_t dim,
 	h5_loc_idlist_t** list
-	);
+	) {
+	H5_API_ENTER4 (h5_err_t,
+		       "f=0x%p, entity_id=%lld, dim=%d, list=0x%p",
+		       f, (long long)entity_id, dim, list);
+	H5_API_RETURN (h5t_get_adjacencies (f, entity_id, dim, list));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedReleaseListOfAdjacencies (
-	h5_file_t * const f,
+	h5_file_t* const f,
-	h5_loc_idlist_t **list
+	h5_loc_idlist_t** list
-	);
+	) {
+	H5_API_ENTER2 (h5_err_t,
+		       "f=0x%p, list=0x%p",
+		       f, list);
+	H5_API_RETURN (h5t_release_list_of_adjacencies (f, list));
+}
 
 #ifdef __cplusplus
 }

src/include/H5Fed_inquiry.h

@@ -46,14 +46,137 @@ H5FedGetNumTriangleMeshes (
 	H5_API_RETURN (h5t_get_num_trimeshes (f));
 }
 
-h5_ssize_t H5FedGetNumLevels ( h5_file_t * const f );
+/*!
-h5t_lvl_idx_t H5FedGetLevel ( h5_file_t * const f );
+  Get the number of hierarchical mesh levels.
-h5_ssize_t H5FedGetNumVertices ( h5_file_t * const f );
+
-h5_ssize_t H5FedGetNumVerticesCnode ( h5_file_t * const f, const int cnode );
+  \param[in]	f	File handle
-h5_ssize_t H5FedGetNumVerticesTotal ( h5_file_t * const f );
+
-h5_ssize_t H5FedGetNumElements ( h5_file_t * const f );
+  \return	Number of hierarchical mesh levels or error code.
-h5_ssize_t H5FedGetNumElementsCnode ( h5_file_t * const f, const int cnode );
+ */
-h5_ssize_t H5FedGetNumElementsTotal ( h5_file_t * const f );
+static inline h5_ssize_t
+H5FedGetNumLevels (
+	h5_file_t* const f
+	) {
+	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_get_num_leaf_levels (f));
+}
+
+/*!
+  Get current mesh levels.
+
+  \param[in]	f	File handle
+
+  \return	ID of current mesh levels or error code.
+ */
+static inline h5t_lvl_idx_t
+H5FedGetLevel (
+	h5_file_t* const f
+	) {
+	H5_API_ENTER1 (h5t_lvl_idx_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_get_level (f));
+}
+
+/*!
+  Returns the number of vertices used for defining the (sub-)mesh
+  at current level on this compute node.
+
+  \param[in]	f	file handle
+
+  \return	Number of vertices or error code.
+*/
+static inline h5_ssize_t
+H5FedGetNumVertices (
+	h5_file_t* const f		/*!< file handle		*/
+	) {
+	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_get_num_vertices (f, -1));
+}
+
+/*!
+  Returns the number of vertices used for defining the (sub-)mesh
+  at current level on compute node \c cnode.
+
+  \param[in]	f	file handle
+  \param[in]	cnode	compute node
+
+  \return	Number of vertices or error code.
+*/
+static inline h5_ssize_t
+H5FedGetNumVerticesCnode (
+	h5_file_t* const f,
+	const int cnode
+	) {
+	H5_API_ENTER2 (h5_ssize_t, "f=0x%p, cnode=%d", f, cnode);
+	H5_API_RETURN (h5t_get_num_vertices (f, cnode));
+}
+
+/*!
+  Returns the number of vertices used for defining the (sub-)mesh
+  at current level overl all compute nodes.
+
+  \param[in]	f	file handle
+
+  \return	Total number of vertices or error code.
+*/
+static inline h5_ssize_t
+H5FedGetNumVerticesTotal (
+	h5_file_t* const f
+	) {
+	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_get_num_vertices (f, -1));
+}
+
+/*!
+  Returns the number of elements present in the (sub-)mesh
+  at current level on this compute node.
+
+  \param[in]	f	file handle
+
+  \return	Number of elements or error code.
+*/
+static inline h5_ssize_t
+H5FedGetNumElements (
+	h5_file_t* const f
+	) {
+	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
+	// MLH: can't use field from opaque h5_file_t!
+	//h5_ssize_t num = h5t_get_num_elems (f, f->myproc);
+	H5_API_RETURN (h5t_get_num_elems (f, -1));
+}
+
+/*!
+  Returns the number of elements present in the (sub-)mesh
+  at current level on compute node \c cnode.
+
+  \param[in]	f	file handle
+  \param[in]	cnode	Compute node
+
+  \return	Number of elements or error code.
+*/
+static inline h5_ssize_t
+H5FedGetNumElementsCnode (
+	h5_file_t* const f,
+	const int cnode
+	) {
+	H5_API_ENTER2 (h5_ssize_t, "f=0x%p, cnode=%d", f, cnode);
+	H5_API_RETURN (h5t_get_num_elems (f, cnode));
+}
+
+/*!
+  Returns the number of elements present in the mesh
+  at current level over all compute nodes.
+
+  \param[in]	f	File handle.
+
+  \return	Number of elements or error code.
+*/
+static inline h5_ssize_t
+H5FedGetNumElementsTotal (
+	h5_file_t* const f
+	) {
+	H5_API_ENTER1 (h5_ssize_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_get_num_elems (f, -1));
+}
 
 #ifdef __cplusplus
 }

src/include/H5Fed_retrieve.h

@@ -19,73 +19,162 @@
 extern "C" {
 #endif
 
-h5t_iterator_t*
+
+/*!
+  Begin traverse over all entities on this compute node. 
+  Initialize internal data structures.
+
+  \remark
+  Entities might be on processor boundaries! Therefore the same entity might be
+  processed on several compute nodes.
+
+  \param[in]	f	file handle
+  \param[in]	codim	co-dimension of entity to traverse
+
+  \return	H5_SUCCESS or error code
+*/
+
+static inline h5t_iterator_p
 H5FedBeginTraverseEntities (
 	h5_file_t* const f,
-	int codim
+	const int codim
-	);
+	) {
-h5t_iterator_t*
+	H5_API_ENTER2 (h5t_iterator_p, "f=0x%p, codim=%d", f, codim);
+	h5t_iterator_p iter;
+	TRY3 (h5t_iterator_p, iter = (h5t_iterator_p)h5_calloc (1, sizeof (*iter)));
+	TRY3 (h5t_iterator_p, h5t_init_leaf_iterator (f, iter, codim));
+	H5_API_RETURN (iter);
+}
+
+static inline h5t_iterator_p
 H5FedBeginTraverseBoundaryFaces (
 	h5_file_t* const f,
-	int codim
+	const int codim
-	);
+	) {
-h5_loc_id_t
+	H5_API_ENTER2 (h5t_iterator_p, "f=0x%p, codim=%d", f, codim);
+	h5t_iterator_p iter;
+	TRY3 (h5t_iterator_p, iter = (h5t_iterator_p)h5_calloc (1, sizeof (*iter)));
+	TRY3 (h5t_iterator_p, h5t_init_boundary_face_iterator (f, iter, codim));
+	H5_API_RETURN (iter);
+}
+
+/*!
+  Get next local entity ID.
+
+  \param[in]		f	file handle
+  \param[in/out]	iter	iterator
+
+  \return		Local entity ID
+  \return		-1, if done
+  \return		error code on error
+  */
+static inline h5_loc_id_t
 H5FedTraverseEntities (
 	h5_file_t* const f,
 	h5t_iterator_t* iter
-	);
+	) {
-h5_err_t
+	H5_API_ENTER2 (h5_loc_id_t, "f=0x%p, iter=0x%p", f, iter);
+	H5_API_RETURN (h5t_iterate_entities (f, iter));
+}
+
+/*!
+  End of traversing. Release internal data structures.
+
+  \param[in]	f	File handle
+
+  \return	H5_SUCCESS or error code
+ 
+ */
+static inline h5_err_t
 H5FedEndTraverseEntities (
 	h5_file_t* const f,
 	h5t_iterator_t* iter
-	);
+	) {
-h5_err_t
+	H5_API_ENTER2 (h5_err_t, "f=0x%p, iter=0x%p", f, iter);
+	H5_API_RETURN (h5t_release_entity_iterator (f, iter));
+}
+
+
+/*!
+  Get coordinates of vertex given by local index
+
+  \param[in]	f		file handle
+  \param[in]	vertex_idx	local index of vertex
+  \param[out]	P		3-dimensional coordinates
+
+  \return	H5_SUCCESS or error code
+  */
+static inline h5_err_t
 H5FedGetVertexCoordsByIndex (
 	h5_file_t* const f,
 	h5_loc_idx_t vertex_index,
 	h5_float64_t P[3]
-	);
+	) {
-h5_err_t
+	H5_API_ENTER3 (h5_err_t, 
+		       "f=0x%p, vertex_index=%lld, P=0x%p",
+		       f, (long long)vertex_index, P);
+	H5_API_RETURN (h5t_get_vertex_coords_by_index (f, vertex_index, P));
+}
+
+static inline h5_err_t
 H5FedGetVertexCoordsByID (
 	h5_file_t* const f,
 	h5_loc_id_t vertex_id,
 	h5_float64_t P[3]
-	);
+	) {
+	H5_API_ENTER3 (h5_err_t, 
+		       "f=0x%p, vertex_id=%lld, P=0x%p",
+		       f, (long long)vertex_id, P);
+	H5_API_RETURN (h5t_get_vertex_coords_by_id (f, vertex_id, P));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedGetVertexIndicesOfEdge (
 	h5_file_t* const f,
 	h5_loc_id_t entity_id,
-	h5_loc_idx_t* const vertex_indices
+	h5_loc_idx_t* vertex_indices
-	);
+	) {
+	H5_API_ENTER3 (h5_err_t,
+		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
+		       f, (long long)entity_id, vertex_indices);
+	H5_API_RETURN (h5t_get_vertex_indices_of_edge (f, entity_id, vertex_indices));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedGetVertexIndicesOfTriangle (
 	h5_file_t* const f,
 	h5_loc_id_t entity_id,
-	h5_loc_idx_t* const vertex_indices
+	h5_loc_idx_t* vertex_indices
-	);
+	) {
+	H5_API_ENTER3 (h5_err_t,
+		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
+		       f, (long long)entity_id, vertex_indices);
+	H5_API_RETURN (h5t_get_vertex_indices_of_triangle (f, entity_id, vertex_indices));
+}
 
-h5_err_t
+static inline h5_err_t
-H5FedGetVertexIndicesOfTriangleCClockwise (
-	h5_file_t* const f,
-	h5_loc_id_t entity_id,
-	h5_loc_idx_t* const vertex_indices
-	);
-
-h5_err_t
 H5FedGetVertexIndicesOfTet (
 	h5_file_t* const f,
 	h5_loc_id_t entity_id,
-	h5_loc_idx_t* const vertex_indices
+	h5_loc_idx_t* vertex_indices
-	);
+	) {
+	H5_API_ENTER3 (h5_err_t,
+		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
+		       f, (long long)entity_id, vertex_indices);
+	H5_API_RETURN (h5t_get_vertex_indices_of_tet (f, entity_id, vertex_indices));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedGetVertexIndicesOfEntity (
 	h5_file_t* const f,
 	h5_loc_id_t entity_id,
-	h5_loc_idx_t* const vertex_indices
+	h5_loc_idx_t* vertex_indices
-	);
+	) {
+	H5_API_ENTER3 (h5_err_t,
+		       "f=0x%p, entity_id=%lld, vertex_indices=0x%p",
+		       f, (long long)entity_id, vertex_indices);
+	H5_API_RETURN (h5t_get_vertex_indices_of_entity (f, entity_id, vertex_indices));
+}
 
 #ifdef __cplusplus
 }

src/include/H5Fed_store.h

@@ -39,62 +39,154 @@ H5FedAddTriangleMesh (
 	H5_API_RETURN (h5t_add_triangle_mesh (f));
 }
 
-h5t_lvl_idx_t
+/*!
+  \ingroup h5fed_c_api
+
+  Add a new level with \c num_elems elements. The number of elements must be the
+  real number of elements to add the level. If you want to refine \c n tetrahedra
+  \c n*8 elements must be added.
+
+  \param[in]	f			File handle.
+  \param[in]	num_elems_to_refine	Number of elements which will be refined.
+
+  \return ID of new level.
+
+  \note
+  values for f->t.num_levels:
+  \c -1		unknown: after opening the file. This is equivalent to
+		"topological data has not been initialized".
+  \c 0		no levels: HDF5 group for meshes may already exist but must not!
+  \c > 0	number of mesh levels
+ 
+*/
+static inline h5t_lvl_idx_t
 H5FedAddLevel (
-	h5_file_t * const f
+	h5_file_t* const f
-	);
+	) {
+	H5_API_ENTER1 (h5t_lvl_idx_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_add_level (f));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedBeginStoreVertices (
-	h5_file_t * const f,
-	const h5_size_t num
-	);
-
-h5_loc_idx_t
-H5FedStoreVertex (
-	h5_file_t * const f,
-	const h5_glb_idx_t id,
-	const h5_float64_t P[3]
-	);
-
-h5_err_t
-H5FedEndStoreVertices (
-	h5_file_t * const f
-	);
-
-h5_err_t
-H5FedBeginStoreElements (
-	h5_file_t * const f,
-	const h5_size_t num
-	);
-
-
-h5_loc_idx_t
-H5FedStoreElement (
 	h5_file_t* const f,
-	const h5_loc_idx_t local_vids[]
+	const h5_size_t num
-	);
+	) {
+	H5_API_ENTER2 (h5_err_t,
+		       "f=0x%p, num=%llu",
+		       f, (long long unsigned)num);
+	H5_API_RETURN (h5t_begin_store_vertices (f, num));
+}
 
-h5_err_t
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the the coordinates of a specific vertex at level \c level
+  with id \c vertex_id of the tetrahedral mesh.
+
+  \return local vertex id on success
+  \return errno on error
+*/
+static inline h5_loc_idx_t
+H5FedStoreVertex (
+	h5_file_t* const f,		/*!< file handle		*/
+	const h5_glb_id_t vertex_id,	/*!< id from mesher or -1	*/
+	const h5_float64_t P[3]		/*!< coordinates		*/
+	) {
+	H5_API_ENTER3 (h5_loc_idx_t,
+		       "f=0x%p, vertex_id=%lld, P=0x%p",
+		       f, (long long)vertex_id, P);
+	if (h5t_get_level (f) != 0) {
+		H5_API_LEAVE (
+			h5_error (
+				H5_ERR_INVAL,
+				"Vertices can be added to level 0 only!"));
+	}
+	H5_API_RETURN (h5t_store_vertex (f, vertex_id, P));
+}
+
+static inline h5_err_t
+H5FedEndStoreVertices (
+	h5_file_t* const f
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_end_store_vertices (f));
+}
+
+static inline h5_err_t
+H5FedBeginStoreElements (
+	h5_file_t* const f,
+	const h5_size_t num
+	) {
+	H5_API_ENTER2 (h5_err_t,
+		       "f=0x%p, num=%llu",
+		       f, (long long unsigned)num);
+	H5_API_RETURN (h5t_begin_store_elems (f, num));
+}
+
+/*!
+  \ingroup h5fed_c_api
+
+  Stores the 4-tuple, that contains the specific indices describing
+  a tetrahedron with id \c tet_id at level \c level of the tetrahedral
+  mesh.
+
+  Errors:
+  * current level not yet defined
+  * to many tets stored on level
+
+  \return local tetrahedron id
+  \return \c errno on error
+*/
+static inline h5_loc_idx_t
+H5FedStoreElement (
+	h5_file_t* const f,		/*!< file handle		*/
+	const h5_loc_idx_t local_vids[]	/*!< tuple with vertex id's	*/
+	) {
+	H5_API_ENTER2 (h5_loc_idx_t, "f=0x%p, local_vids=0x%p", f, local_vids);
+	if (h5t_get_level (f) != 0) {
+		H5_API_LEAVE (
+			h5_error (
+				H5_ERR_INVAL,
+				"Elements can be added to level 0 only!"));
+	}
+	H5_API_RETURN (h5t_store_elem (f, -1, local_vids));
+}
+
+static inline h5_err_t
 H5FedEndStoreElements (
-	h5_file_t * const f
+	h5_file_t* const f
-	);
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_end_store_elems (f));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedBeginRefineElements (
-	h5_file_t * const f
+	h5_file_t* const f
-	);
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_begin_refine_elems (f));
+}
 
-h5_loc_idx_t
+static inline h5_loc_idx_t
 H5FedRefineElement (
-	h5_file_t * const f,
+	h5_file_t* const f,		/*!< file handle		*/
-	const h5_loc_idx_t elem_idx
+	const h5_loc_id_t local_eid	/*!< local element id		*/
-	);
+	) {
+	H5_API_ENTER2 (h5_loc_idx_t,
+		       "f=0x%p, local_eid=%lld",
+		       f, (long long)local_eid);
+	H5_API_RETURN (h5t_mark_entity (f, local_eid));
+}
 
-h5_err_t
+static inline h5_err_t
 H5FedEndRefineElements (
-	h5_file_t * const f
+	h5_file_t* const f
-	);
+	) {
+	H5_API_ENTER1 (h5_err_t, "f=0x%p", f);
+	H5_API_RETURN (h5t_end_refine_elems (f));
+}
 
 #ifdef __cplusplus
 }

src/include/H5Fed_tags.h

@@ -5,49 +5,144 @@
 extern "C" {
 #endif
 
-h5_err_t
+/*!
+  Add a tagset to the current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	name of tagset
+  \param[in]	type	data type of tagset
+
+  \return	H5_SUCCESS or error code
+ */
+static inline h5_err_t
 H5FedAddMTagset (
 	h5_file_t* const f,
 	char* name,
 	h5_id_t type
-	);
+	) {
-h5_err_t
+	H5_API_ENTER3 (h5_err_t, "f=0x%p, name=\"%s\", type=%lld",
+		       f, name, (long long)type);
+	H5_API_RETURN (h5t_add_mtagset (f, name, type));
+}
+
+/*!
+  Remove a tagset from the current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	name of tagset to remove
+
+  \return	H5_SUCCESS or error code
+ */
+static inline h5_err_t
 H5FedRemoveMTagset (
 	h5_file_t* const f,
 	char name[]
-	);
+	) {
-h5_ssize_t
+	H5_API_ENTER2 (h5_err_t, "f=0x%p, name=\"%s\"", f, name);
+	H5_API_RETURN (h5t_remove_mtagset (f, name));
+}
+
+/*!
+  Get available tagsets in current mesh.
+
+  \param[in]	f	file handle
+  \param[out]	names	names of available tagsets
+
+  \return	Number of tagsets or error code
+ */
+static inline h5_ssize_t
 H5FedGetMTagsets (
 	h5_file_t* const f,
 	char** names[]
-	);
+	) {
-h5_id_t
+	H5_API_ENTER2 (h5_ssize_t, "f=0x%p, names=0x%p", f, names);
+	H5_API_RETURN (h5t_get_mtagsets (f, names));
+}
+
+/*!
+  Get type of tagset in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	name of tagset
+
+  \return	H5_SUCCESS or error code
+ */
+static inline h5_id_t
 H5FedGetTypeOfMTagset (
 	h5_file_t* const f,
 	char name[]
-	);
+	) {
-h5_err_t
+	H5_API_ENTER2 (h5_err_t, "f=0x%p, name=\"%s\"", f, name);
+	H5_API_RETURN (h5t_get_mtagset_type_by_name (f, name));
+}
+
+/*!
+  Set tag for entity in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	names of tagset
+  \param[in]	id	id of entity
+  \param[in]	dim	dimension of value
+  \param[in]	val	tag value
+
+  \return	H5_SUCCESS or error code
+ */
+static inline h5_err_t
 H5FedSetMTag (
 	h5_file_t* const f,
 	char name[],
-	h5_loc_id_t entity_id,
+	h5_loc_id_t id,
-	const size_t dims,
+	const size_t dim,
-	void* val
+	void* buffer
-	);
+	) {
-h5_err_t
+	H5_API_ENTER5 (h5_err_t,
+		       "f=0x%p, name=\"%s\", id=%lld, dim=%lld, val=0x%p",
+		       f, name, (long long)id, (long long)dim, buffer);
+	H5_API_RETURN (h5t_set_mtag_by_name (f, name, id, dim, buffer));
+}
+
+/*!
+  Set tag for entity in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	names of tagset
+  \param[in]	id	id of entity
+  \param[out]	dim	dimension of value
+  \param[out]	val	tag value
+
+  \return	H5_SUCCESS or error code
+ */
+static inline h5_err_t
 H5FedGetMTag (
 	h5_file_t* const f,
 	const char name[],
 	const h5_loc_id_t id,
-	size_t* dims,
+	size_t* dim,
-	void* val
+	void* buffer
-	);
+	) {
-h5_err_t
+	H5_API_ENTER5 (h5_err_t,
+		       "f=0x%p, name=\"%s\", id=%lld, dim=0x%p, val=0x%p",
+		       f, name, (long long)id, dim, buffer);
+	H5_API_RETURN (h5t_get_mtag_by_name (f, name, id, dim, buffer));
+}
+
+/*!
+  Remove tag for entity in current mesh.
+
+  \param[in]	f	file handle
+  \param[in]	name	names of tagset
+  \param[in]	id	id of entity
+*/
+static inline h5_err_t
 H5FedRemoveMTag (
 	h5_file_t* const f,
 	const char name[],
 	const h5_loc_id_t id
-	);
+	) {
+	H5_API_ENTER3 (h5_err_t, "f=0x%p, name=\"%s\", id=%lld",
+		       f, name, (long long)id);
+	H5_API_RETURN (h5t_remove_mtag_by_name (f, name, id));
+}
 
 #ifdef __cplusplus
 }

src/include/h5core/h5_core.h

@@ -13,15 +13,32 @@ extern "C" {
 #define H5_DEBUG_PRIV_API	(1<<5)
 #define H5_DEBUG_PRIV_FUNC	(1<<6)
 #define H5_DEBUG_HDF5		(1<<7)
-#define H5_DEBUG_MALLOC		(1<<8)
+#define H5_DEBUG_MPI		(1<<8)
-#define H5_DEBUG_CLIB		(1<<9)
+#define H5_DEBUG_MALLOC		(1<<9)
+#define H5_DEBUG_CLIB		(1<<10)
+
 #define H5_DEBUG_ALL		(-1)
 
 extern char* h5_rfmts[];
+
 #define __FUNC_ENTER(type)			\
 	h5_call_stack_push (__func__,e_##type); \
 	type ret_value = (type)H5_ERR;
 
+#if defined(NDEBUG)
+
+#define __FUNC_ARGS0(mask)
+#define __FUNC_ARGS1(fmt, a1, mask)
+#define __FUNC_ARGS2(fmt, a1, a2, mask)
+#define __FUNC_ARGS3(fmt, a1, a2, a3, mask)
+#define __FUNC_ARGS4(fmt, a1, a2, a3, a4, mask)
+#define __FUNC_ARGS5(fmt, a1, a2, a3, a4, a5, mask)
+#define __FUNC_ARGS6(fmt, a1, a2, a3, a4, a5, a6, mask)
+#define __FUNC_ARGS7(fmt, a1, a2, a3, a4, a5, a6, a7, mask)
+#define __FUNC_ARGS8(fmt, a1, a2, a3, a4, a5, a6, a7, a8, mask)
+
+#else
+
 #define __FUNC_ARGS0(mask)			\
 	if (h5_debug_level & mask ) {		\
 		h5_debug ("(void)");		\
@@ -66,6 +83,7 @@ extern char* h5_rfmts[];
 	if (h5_debug_level & mask ) {			\
 		h5_debug ("(" fmt ")", a1, a2, a3, a4, a5, a6, a7, a8);	\
 	}
+#endif
 
 #define __FUNC_ENTER0(type, mask)		\
 	__FUNC_ENTER(type);			\
@@ -108,6 +126,17 @@ extern char* h5_rfmts[];
 	goto done;				\
 }
 
+#if defined(NDEBUG)
+
+#define __FUNC_RETURN(expr, mask)		\
+	ret_value = expr;			\
+	goto done;						\
+done:								\
+	h5_call_stack_pop();					\
+	return ret_value;
+
+#else
+
 #define __FUNC_RETURN(expr, mask)		\
 	ret_value = expr;			\
 	goto done;				\
@@ -121,6 +150,7 @@ done:								\
 	h5_call_stack_pop();					\
 	return ret_value;
 
+#endif
 
 #define H5_API_ENTER_(type)					\
 	if (!h5_initialized) {					\
@@ -180,12 +210,11 @@ done:								\
 		goto done;						\
 	}
 
-#define TRY3( expr, ret_val )						\
+#define TRY3( type, expr )						\
 	if ((int64_t)(ptrdiff_t)(expr) <= (int64_t)H5_ERR) {		\
-		ret_value = ret_val;					\
+		ret_value = (type) H5_ERR;				\
 		goto done;						\
 	}
-#define ON_ERROR
 
 #ifdef __cplusplus
 }

src/include/h5core/h5_openclose.h

@@ -12,17 +12,27 @@ h5_open_file (
 	MPI_Comm comm
 	);
 
-h5_int64_t
+h5_err_t
 h5_check_filehandle (
 	h5_file_t * const f
 	);
 
-h5_int64_t
+h5_err_t
 h5_close_file (
 	h5_file_t * const f
 	);
 
-h5_int64_t
+h5_err_t
+h5_flush_step (
+	h5_file_t * const f
+	);
+
+h5_err_t
+h5_flush_file (
+	h5_file_t * const f
+	);
+
+h5_err_t
 h5_set_stepname_fmt (
 	h5_file_t * const f,
 	const char *name,

src/include/h5core/h5_types.h

@@ -24,6 +24,8 @@ extern "C" {
 #define H5_VFD_MPIPOSIX         0x10
 #define H5_VFD_INDEPENDENT      0x20
 
+#define H5_O_FLUSHSTEP		0x40
+
 #define H5_ID_T			H5T_NATIVE_INT64
 #define H5_FLOAT64_T		H5T_NATIVE_DOUBLE
 #define H5_FLOAT32_T		H5T_NATIVE_FLOAT

test/Makefile.am

@@ -5,9 +5,6 @@ SUBDIRS = H5Fed
 
 OBJEXT=o
 
-AM_LDFLAGS = -L../src/lib @LDFLAGS@
-LIBS = -lH5hutC -lH5hut @LIBS@
-
 INCLUDES = -I../src/include @INCLUDES@
 
 noinst_PROGRAMS = @BUILD_TESTS@
@@ -25,6 +22,10 @@ h5u_test_SOURCES =	\
 		testframe.h \
 		params.h
 
+h5u_test_LDADD = \
+		../src/h5core/libH5hut.la \
+		../src/C/libH5hutC.la
+
 h5b_test_SOURCES =	\
 		h5b_test.c \
 		h5b_write.c \
@@ -33,16 +34,16 @@ h5b_test_SOURCES =	\
 		testframe.h \
 		params.h
 
-h5b_test_DEPENDENCIES = \
+h5b_test_LDADD = \
-		../src/lib/libH5hut.a \
+		../src/h5core/libH5hut.la \
-		../src/lib/libH5hutC.a
+		../src/C/libH5hutC.la
 
 h5_attach_test_SOURCES = \
 		h5_attach_test.c
 
-h5_attach_test_DEPENDENCIES = \
+h5_attach_test_LDADD = \
-		../src/h5core/libH5hut.a \
+		../src/h5core/libH5hut.la \
-		../src/C/libH5hutC.a
+		../src/C/libH5hutC.la
 
 clean: clean-am
 	rm -f *.h5

test/h5u_read.c

@@ -175,10 +175,6 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
 		status = H5PartSetView(file, start, end);
 		RETURN(status, H5_SUCCESS, "H5PartSetView");
 
-		status = H5PartReadDataFloat64(file, "x", x);
-		RETURN(status, H5_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");
@@ -212,10 +208,13 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
 		val = H5PartGetNumParticles(file);
 		IVALUE(val, 4, "particle count");
 
-                x[3] = 0;
+		double x2[4];
-		status = H5PartReadDataFloat64(file, "x", x);
+		status = H5PartReadDataFloat64(file, "x", x2);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
-		FVALUE(x[3], (double)(rank*2+3+nparticles*t), "x data");
+		FVALUE(x2[0], (double)(2*rank+0+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");
 
 		val = H5PartGetNumParticles(file);
 		IVALUE(val, 4, "particle count");
@@ -347,7 +346,7 @@ test_read_data32(h5_file_t *file, int nparticles, int step)
 		RETURN(status, H5_SUCCESS, "H5PartSetCanonicalView");
 
                 test_read_step_attribs(file, t);
-
+return;
 		status = H5PartReadDataFloat32(file, "x", x);
 		RETURN(status, H5_SUCCESS, "H5PartReadDataFloat32");
 

tools/H5PartMerge/autogen.sh

@@ -3,7 +3,5 @@
 aclocal
 autoconf
 automake -a -c
-./configure --prefix=$HOME --with-h5part=$HOME --enable-boost
+
-make
-#make install
 

tools/H5PartMerge/configure.ac

@@ -69,32 +69,40 @@ AC_LANG_PUSH(C)
     [AC_MSG_ERROR(hdf5 library not found!)]
   )
 
-  H5PART_PREFIX=""
+  H5HUT_PREFIX=""
-  H5PART_INCL_PATH=""
+  H5HUT_INCL_PATH=""
-  H5PART_LIB_PATH=""
+  H5HUT_LIB_PATH=""
   AC_ARG_WITH(
-    [h5part],
+    [h5hut],
-    AC_HELP_STRING([--with-h5part=PREFIX],
+    AC_HELP_STRING([--with-h5hut=PREFIX],
-      [prefix, parent directory, where the serial(!) h5part library and header files can be found]),
+      [prefix, parent directory, where the serial(!) h5hut library and header files can be found]),
-    [H5PART_PREFIX=$withval
+    [H5HUT_PREFIX=$withval
-     H5PART_INCL_PATH=${H5PART_PREFIX}"/include "
+     H5HUT_INCL_PATH=${H5HUT_PREFIX}"/include "
-     H5PART_LIB_PATH=${H5PART_PREFIX}"/lib "]
+     H5HUT_LIB_PATH=${H5HUT_PREFIX}"/lib "]
   )
-  if test "${H5PART_PREFIX}" != ""; then
+  if test "${H5HUT_PREFIX}" != ""; then
-    CPPFLAGS=${CPPFLAGS}" -I"${H5PART_INCL_PATH};
+    CPPFLAGS=${CPPFLAGS}" -I"${H5HUT_INCL_PATH};
-    LDFLAGS=${LDFLAGS}" -L"${H5PART_LIB_PATH};
+    LDFLAGS=${LDFLAGS}" -L"${H5HUT_LIB_PATH};
   fi
   AC_CHECK_HEADERS(
-    [H5Part.h],
+    [H5hut.h],
     [],
-    [AC_MSG_ERROR(H5Part.h not found!)]
+    [AC_MSG_ERROR(H5hut.h not found!)]
   )
   AC_CHECK_LIB(
-    [H5Part],
+    [H5hut],
     [main],
     [],
-    [AC_MSG_ERROR(H5Part library not found!)]
+    [AC_MSG_ERROR(H5hut library not found!)]
   )
+  AC_CHECK_LIB(
+    [H5hutC],
+    [main],
+    [],
+    [AC_MSG_ERROR(H5hut library not found!)]
+  )
+
+
 AC_LANG_POP
 AC_LANG(C++)
 
@@ -139,7 +147,7 @@ AC_C_CONST
 AC_TYPE_SIZE_T
 
 # Checks for library functions.
-AC_FUNC_MALLOC
+#AC_FUNC_MALLOC
 
 CPPFLAGS=$CPPFLAGS" -m64 -mtune=k8"
 LDFLAGS=$LDFLAGS" -lm"

tools/Makefile.am

@@ -2,13 +2,14 @@
 
 OBJEXT=o
 
-AM_LDFLAGS = -L../src/lib @LFLAGS@
+AM_LDFLAGS = -L../src/lib @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 
 INCLUDES = -I../src/include @INCLUDES@
 
 # What to build... make install will place these files in the $(prefix)/bin directory.
-bin_SCRIPTS = @BUILD_TOOLS@
+bin_PROGRAMS = @BUILD_TOOLS@
+EXTRA_PROGRAMS = h5pAttrib h5PartDcToVtk h5PartSurfaceToVtk
 
 # Listing of all programs that maybe built. (Has to know statically...)
 EXTRA_SCRIPTS = h5hutcc
@@ -17,11 +18,15 @@ EXTRA_SCRIPTS = h5hutcc
 #EXTRA_DIST = h5pAttrib.cc h5pToGNUplot.cc## TO BE TAILORED LATER...
 
 # Listing of sources
-#h5pAttrib_SOURCES = h5pAttrib.cc
+h5pAttrib_SOURCES = h5pAttrib.cc
 
 #h5pToGNUplot_SOURCES = h5pToGNUplot.cc
 
 #homdynToH5p_SOURCES = homdynToH5p.cc
 
+h5PartDcToVtk_SOURCES = h5PartDcToVtk.cc
+
+h5PartSurfaceToVtk_SOURCES = h5PartSurfaceToVtk.cc
+
 clean: clean-am
 

tools/h5PartDcToVtk.cc

@@ -0,0 +1,653 @@
+/* h5ToVtk.cc
+   Andreas Adelmann
+
+*/
+
+#include <hdf5.h>
+#include "H5hut.h"
+
+#include <cmath>
+#include <stdio.h>
+#include <stdlib.h>
+#include <cctype>
+#include <string.h>
+#include <set>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <vector>
+#include <sstream>
+#include <iomanip>
+#include <cassert>
+//#include <string>
+//#include <cstdlib>
+using namespace std;
+
+#define MAX_LEN 100
+
+/* Function headers */
+int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts);
+static void print_help();
+static void variable_assign(int argc, const char *argv[]);
+
+/* Global variables */
+static char* input_name      = NULL;
+static char* output_name      = NULL;
+static bool flg_alive = false;
+static double z_pos = 0.0; 
+static int print_all = 0;
+
+/* `get_option' variables */
+int         opt_err = 1;    /*get_option prints errors if this is on */
+int         opt_ind = 1;    /*token pointer                          */
+const char *opt_arg = NULL;        /*flag argument (or value)               */
+
+/* indication whether the flag (option) requires an argument or not */
+enum {
+  no_arg = 0,         /* doesn't take an argument     */
+  require_arg,        /* requires an argument	        */
+};
+
+/* struct for flags (options) */
+typedef struct long_options
+{
+  const char  *name;          /* name of the long option              */
+  int          has_arg;       /* whether we should look for an arg    */
+  char         shortval;      /* the shortname equivalent of long arg
+			       * this gets returned from get_option   */
+} long_options;
+
+/* List of options in single characters */
+static const char *s_opts = "h1:2:i:o:a:";
+
+/* List of options in full words */
+static struct long_options l_opts[] =
+  {
+    { "help", no_arg, 'h' },         // Print help page
+    { "input", require_arg, 'i' },        // Takes input file name
+    { "output", require_arg, 'o' },   // Takes output file name (without this flag, the program will print to stdout)
+    { "alive ", no_arg , 'a' }, // also generate the alive dark current to display the dark current source
+    { NULL, 0, '\0' }
+  };
+
+
+
+/************************************************************************************
+ ***********************************  FUNCTIONS  *************************************
+ *************************************************************************************/
+
+
+string convert2Int(int number) {
+  stringstream ss;
+  ss <<   setw(5) << setfill('0') <<  number; 
+  return ss.str(); 
+}
+
+
+/* get_option is the parsing function that was majorly ported from h5dump utility */
+int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts) {
+  static int sp = 1;    /* character index in current token */
+  int opt_opt = '?';    /* option character passed back to user */
+
+  if (sp == 1) 
+    {
+      /* check for more flag-like tokens */
+      if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0') 
+	{
+	  return EOF;
+	}
+      else if (strcmp(argv[opt_ind], "--") == 0)
+	{
+	  opt_ind++;
+	  return EOF;
+	}
+    }
+
+  if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') 
+    {
+      /* long command line option */
+      const char *arg = &argv[opt_ind][2];
+      int i;
+
+      for (i = 0; l_opts && l_opts[i].name; i++)
+	{
+	  size_t len = strlen(l_opts[i].name);
+
+	  if (strncmp(arg, l_opts[i].name, len) == 0)
+	    {
+	      /* we've found a matching long command line flag */
+	      opt_opt = l_opts[i].shortval;
+
+	      if (l_opts[i].has_arg != no_arg)
+		{
+		  if (arg[len] == '=')
+		    {
+		      opt_arg = &arg[len + 1];
+		    }
+		  else if (opt_ind < (argc - 1) && argv[opt_ind + 1][0] != '-')
+		    {
+		      opt_arg = argv[++opt_ind];
+		    }
+		  else if (l_opts[i].has_arg == require_arg)
+		    {
+		      if (opt_err)
+			fprintf(stderr, "%s: option required for \"--%s\" flag\n", argv[0], arg);
+
+		      opt_opt = '?';
+		    }
+		}
+	      else
+		{
+		  if (arg[len] == '=')
+		    {
+		      if (opt_err)
+			fprintf(stderr, "%s: no option required for \"%s\" flag\n", argv[0], arg);
+
+		      opt_opt = '?';
+		    }
+
+		  opt_arg = NULL;
+		}
+
+	      break;
+	    }
+	}
+
+      if (l_opts[i].name == NULL)
+	{
+	  /* exhausted all of the l_opts we have and still didn't match */
+	  if (opt_err)
+	    fprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
+
+	  opt_opt = '?';
+	}
+
+      opt_ind++;
+      sp = 1;
+    }
+  else
+    {
+      register char *cp;    /* pointer into current token */
+
+      /* short command line option */
+      opt_opt = argv[opt_ind][sp];
+
+      if (opt_opt == ':' || (cp = strchr(opts, opt_opt)) == 0)
+	{
+
+	  if (opt_err)
+	    fprintf(stderr, "%s: unknown option \"%c\"\n", argv[0], opt_opt);
+	  /* if no chars left in this token, move to next token */
+	  if (argv[opt_ind][++sp] == '\0')
+	    {
+	      opt_ind++;
+	      sp = 1;
+	    }
+
+	  return '?';
+	}
+
+      if (*++cp == ':')
+	{
+
+	  /* if a value is expected, get it */
+	  if (argv[opt_ind][sp + 1] != '\0')
+	    {
+	      /* flag value is rest of current token */
+	      opt_arg = &argv[opt_ind++][sp + 1];
+	    }
+	  else if (++opt_ind >= argc)
+	    {
+	      if (opt_err)
+		{
+		  fprintf(stderr, "%s: value expected for option \"%c\"\n", argv[0], opt_opt);
+		}
+	      opt_opt = '?';
+	    }
+	  else
+	    {
+	      /* flag value is next token */
+	      opt_arg = argv[opt_ind++];
+	    }
+
+	  sp = 1;
+	}
+      else 
+	{
+	  /* set up to look at next char in token, next time */
+	  if (argv[opt_ind][++sp] == '\0')
+	    {
+	      /* no more in current token, so setup next token */
+	      opt_ind++;
+	      sp = 1;
+	    }
+
+	  opt_arg = NULL;
+	}
+    }
+
+  /* return the current flag character found */
+  return opt_opt;
+}
+
+/* Assigns functions according to the parsed result */
+static void variable_assign(int argc, const char *argv[])
+{
+  int option;
+
+  /* set options according to the command line */
+  while ((option = get_option(argc, argv, s_opts, l_opts)) != EOF)
+    {
+      switch ((char)option)
+	{
+	case 'h': // Print help page
+	  print_help();
+	  exit(1);
+	case 'o': // Print number of steps
+	  output_name = strdup(opt_arg);
+	  break;
+	case 'i': // Print shorter version without the values
+	  input_name = strdup(opt_arg);
+	  break;
+	case 'a': // 
+	  { flg_alive = true;
+	    z_pos = atof(strdup(opt_arg));
+	  }
+	  break;  
+	default:
+	  print_help();
+	  exit(1);
+	}
+    }
+}
+
+/* For printing help page */
+static void print_help()
+{
+  fflush(stdout);
+  fprintf(stdout, "\nusage: h5ToVtk  -i INPUTFILE -o OUTPUTFILE [OPTIONAL_FLAGS] -a ZVALUE\n");
+  fprintf(stdout, "\n");
+  fprintf(stdout, "  FLAGS\n");
+  fprintf(stdout, "   -h, --help                 Print help page\n");
+  fprintf(stdout, "   -i file, --input file      (REQUIRED) Takes input base file name to \"file\" (extension h5 is assumed \n");
+  fprintf(stdout, "   -o file, --output file     (REQUIRED) Takes output base file name to \"file\" (extension vtk is added)\n");
+  fprintf(stdout, "   -a zvalue                  Only display particles which have servived and reached z value  \n");
+
+  fprintf(stdout, "\n");
+  fprintf(stdout, "  Examples:\n");
+  fprintf(stdout, "\n");
+  fprintf(stdout, "        /h5ToVtk -i ctf3-injector-darkcurrent-1 -o ctf3-injector-darkcurrent-1- \n");
+  fprintf(stdout, "\n");
+  fprintf(stdout, "        /h5ToVtk -i ctf3-injector-darkcurrent-1 -o ctf3-injector-darkcurrent-1- -a 0.19 \n");
+  fprintf(stdout, "\n");
+}
+
+
+int main(int argc, const char *argv[])
+{
+
+  h5_file_t *h5file = NULL;
+
+  std::ofstream of, ofalive, ofenergy, ofpnum;
+   
+  int j;
+
+  int num_dataset;
+
+  int ntime_step = 0;
+
+  variable_assign(argc, argv);
+
+  if(input_name == NULL)  {
+    fprintf(stdout, "missing input file name\n");
+    print_help();
+    exit(1);
+  }
+   
+  if(output_name == NULL) {
+    fprintf(stdout, "missing output file name\n");
+    print_help();
+    exit(1);
+  }
+   
+  string ifn = string(input_name) + string(".h5");
+
+  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, NULL);
+   
+  if( h5file == NULL ) {
+    fprintf(stdout, "unable to open file %s\n", input_name);
+    print_help();
+    exit(1);
+  }
+   
+  ntime_step = H5GetNumSteps(h5file);
+
+  string ffenergy = string(output_name) + string("energy") + string(".dat");//new
+  ofenergy.open(ffenergy.c_str());//new
+  assert(ofenergy.is_open());//new
+  ofenergy  << setprecision(10)//new
+	    << "# Energy" << endl;//new
+  string ffpnum = string(output_name) + string("pnum") + string(".dat");//new
+  ofpnum.open(ffpnum.c_str());//new
+  assert(ofpnum.is_open());//new
+  ofpnum  << setprecision(10)//new
+	  << "# time" <<" partNum"<< endl;//new
+
+  if (flg_alive) {
+       
+    set<h5_int64_t> idSet;
+      
+
+    H5SetStep(h5file, ntime_step-1);
+    num_dataset = H5PartGetNumDatasets(h5file);
+    h5_int64_t nparticles = H5PartGetNumParticles(h5file);
+     
+    h5_int64_t* larray = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+    H5PartReadDataInt64(h5file, "id", larray);
+
+    h5_float64_t* z = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+    H5PartReadDataFloat64(h5file, "z", z);
+
+    for(unsigned long int n = 0; n < nparticles; ++n) {
+      if (z[n] >= z_pos)
+	idSet.insert(larray[n]);
+    }
+       
+    cout << "Last timestep contains " << nparticles << " particles" << endl;
+       
+    for (size_t j = 0; j<ntime_step ; j ++) {
+
+      H5SetStep(h5file,j);
+      // char s_name[64]="ENERGY";//new
+      //h5_float64_t Etmp=0.0;//new
+      //int var_readE=H5PartReadStepAttrib(h5file,s_name,&Etmp);//new 	
+      //num_dataset = H5PartGetNumDatasets(h5file);//new 
+      //Etmp = (Etmp -  0.51099906)*1000000.0;//new eV
+      h5_int64_t nparticles = H5PartGetNumParticles(h5file);
+      //ofenergy<<Etmp<<" "<<nparticles<<endl;//new
+      //cout<<"Read mean energy in step: "<<j<<" Energy: "<<Etmp<<endl;//new
+            
+      h5_int64_t* larray = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+      H5PartReadDataInt64(h5file, "id", larray);
+	   
+      h5_float64_t* x = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "x", x);
+      vector<h5_float64_t> x_alive;
+
+      h5_float64_t* y = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "y", y);
+      vector<h5_float64_t> y_alive;
+
+      h5_float64_t* z = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "z", z);
+      vector<h5_float64_t> z_alive;
+
+      h5_int64_t* ptype = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+      H5PartReadDataInt64(h5file, "ptype", ptype);
+      vector<h5_int64_t> ptype_alive;
+
+      for (size_t i = 0; i < nparticles ; i ++) {
+	if ( idSet.find(larray[i]) != idSet.end() ) {
+	  x_alive.push_back(x[i]);
+	  y_alive.push_back(y[i]);
+	  z_alive.push_back(z[i]);
+	  ptype_alive.push_back(ptype[i]);
+	}
+      }
+      cout<<" ptype_alive size = "<< ptype_alive.size()<<endl;
+      string ffnlive = string("vtk/") + string(output_name) + string("-alive-") + convert2Int(j) + string(".vtk");
+      ofalive.open(ffnlive.c_str());
+      assert(ofalive.is_open());
+      ofalive.precision(6);
+
+      size_t alive_num =  x_alive.size();           
+
+      ofalive  << setprecision(5)
+	       << "# vtk DataFile Version 2.0" << endl
+	       << "unstructured grid and vector field on the nodes" << endl
+	       << "ASCII" << endl
+	       << "DATASET UNSTRUCTURED_GRID" << endl
+	       << "POINTS " <<  alive_num << " float" << endl;
+           
+      // Particle positions
+
+
+      for(size_t i = 0; i < alive_num; i++)
+	ofalive << x_alive[i] << "  " << y_alive[i] << "  " << z_alive[i] << endl;
+           
+      ofalive << endl;            // defining VTK_poly_vertex
+           
+      ofalive << "CELLS " << alive_num << " " << 2 * alive_num << endl;
+           
+      for(size_t i = 0; i < alive_num; i++)
+	ofalive << "1 " << i << endl;
+      ofalive << endl;
+           
+      // defining Cell_types
+      ofalive << "CELL_TYPES " << alive_num << endl;
+      for(size_t i = 0; i < alive_num; i++)
+	ofalive << "2" << endl;
+           
+      // defining Cell_types
+      ofalive << "POINT_DATA " << alive_num << endl;
+      ofalive << "SCALARS " << "Pointtype" << " float " << "1" << endl;
+      ofalive << "LOOKUP_TABLE " << "mytable" << endl ;
+      for(size_t i = 0; i < alive_num ; i ++) {
+	if (ptype_alive[i] == 0) {
+	  ofalive << 0.0 << endl;
+	}
+	else if (ptype_alive[i] == 1) {
+	  ofalive << 0.5 << endl;
+	}
+	else if (ptype_alive[i] == 2) {
+	  ofalive << 1.0 << endl;
+	}
+	else  {
+	  ofalive << ptype_alive[i] << endl;
+	}
+
+      }
+           
+      ofalive << "LOOKUP_TABLE " << "mytable " << 3 << endl ;
+      ofalive << 1.0 <<" "<< 0.0 <<" "<< 0.0 <<" "<< 1.0 << endl;
+      ofalive << 0.0 <<" "<< 1.0 <<" "<< 0.0 <<" "<< 1.0 << endl;
+      ofalive << 0.0 <<" "<< 0.0 <<" "<< 1.0 <<" "<< 1.0 << endl;
+      ofalive << endl;
+      ofalive.close();
+
+      free(x);
+      free(y);
+      free(z);
+      free(ptype);
+
+      x_alive.clear();
+      y_alive.clear();
+      z_alive.clear();
+      ptype_alive.clear();
+
+      cout <<"Done time step "<< j << endl;
+    }
+  }
+
+       
+  else {
+    vector<double>Esmall;//smaller than 28eV
+    vector<double>Emultip;//Energy zone of SEY>1.
+    vector<double>Elarge;//larger than 2100eV
+    double sey_num;//sey total number
+    int remained_num;//
+    for (size_t j=0; j<ntime_step; j++) {
+      set<h5_int64_t> idSet;
+      H5SetStep(h5file,j);
+      // char s_name[64]="ENERGY";//new
+      //h5_float64_t Etmp=0.0;//new
+      //int var_readE=H5PartReadStepAttrib(h5file,s_name,&Etmp);//new 	
+      //num_dataset = H5PartGetNumDatasets(h5file);//new 
+      num_dataset = H5PartGetNumDatasets(h5file);
+      h5_int64_t nparticles = H5PartGetNumParticles(h5file);
+      //Etmp = (Etmp -  0.51099906)*1000000.0;//new eV
+      //ofenergy<<Etmp<<" "<<nparticles<<endl;//new          
+      //cout<<"Read mean energy in step: "<<j<<" Energy: "<<Etmp<<endl;//new
+          
+      cout << "Working on timestep " << j << " expecting " << nparticles << " particles " << endl;
+      ofpnum  << j <<" "<<nparticles<<endl;//new
+            
+	   
+      h5_float64_t* x = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "x", x);
+
+      h5_float64_t* y = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "y", y);
+
+      h5_float64_t* z = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "z", z);
+
+      h5_int64_t* ptype = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+      H5PartReadDataInt64(h5file, "ptype", ptype);
+
+      string ffn = string("vtk/") + string(output_name)  + convert2Int(j) + string(".vtk");
+      
+      of.open(ffn.c_str());
+      assert(of.is_open());
+      of.precision(6);
+       
+      of  << setprecision(5)
+	  << "# vtk DataFile Version 2.0" << endl
+	  << "unstructured grid and vector field on the nodes" << endl
+	  << "ASCII" << endl
+	  << "DATASET UNSTRUCTURED_GRID" << endl
+	  << "POINTS " << nparticles << " float" << endl;
+       
+      // Particle positions
+      for(size_t i = 0; i < nparticles; i++)
+	of << x[i] << "  " << y[i] << "  " << z[i] << endl;
+
+      of << endl;            // defining VTK_poly_vertex
+       
+      of << "CELLS " << nparticles << " " << 2 * nparticles << endl;
+
+      for(size_t i = 0; i < nparticles; i++)
+	of << "1 " << i << endl;
+      of << endl;
+       
+      // defining Cell_types
+      of << "CELL_TYPES " << nparticles << endl;
+      for(size_t i = 0; i < nparticles; i++)
+	of << "2" << endl;
+
+      // defining Cell_types
+      of << "POINT_DATA " << nparticles << endl;
+      of << "SCALARS " << "Pointtype" << " float " << "1" << endl;
+      of << "LOOKUP_TABLE " << "mytable" << endl ;
+      for(size_t i = 0; i < nparticles ; i ++) {
+	if (ptype[i] == 0) {
+	  of << 0.0 << endl;
+	}
+	else if (ptype[i] == 1) {
+	  of << 0.5 << endl;
+	}
+	else if (ptype[i] >= 2) {
+	  of << 1.0 << endl;
+	}
+	else  {
+	  cout<< "Step " <<j<<" error occurs while determine particle type integer ptype should be >=0 "<< endl;
+	}
+      }
+
+      of << "LOOKUP_TABLE " << "mytable " << 3 << endl ;
+      of << 1.0 <<" "<< 0.0 <<" "<< 0.0 <<" "<< 1.0 << endl;
+      of << 0.0 <<" "<< 1.0 <<" "<< 0.0 <<" "<< 1.0 << endl;
+      of << 0.0 <<" "<< 0.0 <<" "<< 1.0 <<" "<< 1.0 << endl;
+      of << endl;
+      of.close();
+
+      h5_int64_t* larray = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+      H5PartReadDataInt64(h5file, "id", larray);
+
+      h5_float64_t* larrayPx = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "px", larrayPx);
+            
+      h5_float64_t* larrayPy = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "py", larrayPy);
+
+      h5_float64_t* larrayPz = (h5_float64_t*)malloc(sizeof(h5_float64_t)*nparticles);
+      H5PartReadDataFloat64(h5file, "pz", larrayPz);
+      if(j!=(ntime_step-1)) {
+	H5SetStep(h5file,j+1);
+	int num_dataset_temp = H5PartGetNumDatasets(h5file);
+	h5_int64_t nparticles_temp = H5PartGetNumParticles(h5file);
+
+	h5_int64_t* larray_temp = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles_temp);
+	H5PartReadDataInt64(h5file, "id", larray_temp);
+
+               
+                                
+	for (size_t i = 0; i < nparticles_temp ; i ++) {
+	  idSet.insert(larray_temp[i]);
+	}
+	for (size_t i = 0; i < nparticles ; i ++) {
+
+	  if(idSet.find(larray[i])==idSet.end()) {
+	    double Etemp=0.51099906*1000000.0*(sqrt(1.0+larrayPx[i]*larrayPx[i]+larrayPy[i]*larrayPy[i]+larrayPz[i]*larrayPz[i])-1);
+
+	    double sey_temp=2.469*exp(-0.0004644*Etemp)-1.9*exp(-0.01054*Etemp);
+	    sey_num+=sey_temp;
+	    if ( std::isinf(Etemp)){
+
+	      cout<<"Etemp in time step: "<<j<<" is infinity "<<Etemp<<endl;
+	      if ( std::isinf(larrayPx[i])){
+
+		cout<<"Px in time step: "<<j<<" is infinity "<<Etemp<<endl;
+	      }else  if ( std::isinf(larrayPy[i])){
+
+		cout<<"Py in time step: "<<j<<" is infinity "<<Etemp<<endl;
+	      }else  if ( std::isinf(larrayPz[i])){
+
+		cout<<"Pz in time step: "<<j<<" is infinity "<<Etemp<<endl;
+	      }else {
+		cout<<"Px,Py,Pz in time step: "<<j<<" are "<<larrayPx[i]<<" "<<larrayPy[i]<<" "<<larrayPz[i]<<endl;
+	      }
+	    }
+	    ofenergy<<Etemp<<endl;
+	    if(Etemp<28.0) {
+	      Esmall.push_back(Etemp);
+	    }else if (Etemp<2100) {
+	      Emultip.push_back(Etemp);
+	    }else {
+	      Elarge.push_back(Etemp);
+	    }
+                       
+
+	  }
+
+	}
+	free(larray_temp);
+      }
+
+    
+      //cout <<"ptype size = "<< sizeof(ptype) << endl;
+      free(x);
+      free(y);
+      free(z);
+      free(ptype);
+      free(larrayPx);
+      free(larrayPy);
+      free(larrayPz);
+      free(larray);
+      if(j==(ntime_step-1)) {
+	remained_num = nparticles;
+      }
+    }
+    ofenergy<<Esmall.size()<<endl;//new
+    ofenergy<<Emultip.size()<<endl;//new   
+    ofenergy<<Elarge.size()<<endl;//new
+    ofenergy<<sey_num<<endl;
+    ofenergy<<sey_num-int(Esmall.size()+Emultip.size()+Elarge.size())+1000<<endl;
+    ofenergy<<remained_num<<endl;
+    ofpnum.close();
+  }
+
+
+  H5CloseFile(h5file);   
+  return 0;
+}

tools/h5PartSurfaceToVtk.cc

@@ -0,0 +1,528 @@
+/* h5PartSurfaceToVtk.cc
+   Andreas Adelmann & Chuan Wang
+   2010-2011
+*/
+
+#include <hdf5.h>
+#include "H5hut.h"
+
+#include <cmath>
+#include <stdio.h>
+#include <stdlib.h>
+#include <cctype>
+#include <string.h>
+
+#include <set>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <vector>
+#include <sstream>
+#include <iomanip>
+#include <cassert>
+
+using namespace std;
+
+#define MAX_LEN 100
+
+/* Function headers */
+int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts);
+
+static void print_help();
+
+static void variable_assign(int argc, const char *argv[]);
+
+/* Global variables */
+
+static char* input_name      = NULL;
+static char* mytemp          = NULL;
+static char* geo_name        = NULL;
+static char* output_name     = NULL;
+
+static bool flg_alive = false;
+static double z_pos = 0.0; 
+static int print_all = 0;
+static int step_ini = 1;
+static int dump_freq = 1;
+
+
+/* `get_option' variables */
+int         opt_err = 1;    /*get_option prints errors if this is on */
+int         opt_ind = 1;    /*token pointer                          */
+const char *opt_arg = NULL;        /*flag argument (or value)               */
+
+/* indication whether the flag (option) requires an argument or not */
+enum {
+  no_arg = 0,         /* doesn't take an argument     */
+  require_arg,        /* requires an argument	        */
+};
+
+/* struct for flags (options) */
+typedef struct long_options
+{
+  const char  *name;          /* name of the long option              */
+  int          has_arg;       /* whether we should look for an arg    */
+  char         shortval;      /* the shortname equivalent of long arg
+			       * this gets returned from get_option   */
+} long_options;
+
+/* List of options in single characters */
+static const char *s_opts = "h1:2:i:g:o:f:d:";
+
+/* List of options in full words */
+static struct long_options l_opts[] =
+  {
+    { "help", no_arg, 'h' },         // Print help page
+    { "input", require_arg, 'i' },        // Takes input file name
+    { "geometry", require_arg, 'g' },        // Takes input geometry file name
+    { "output", require_arg, 'o' },   // Takes output file name (without this flag, the program will print to stdout)
+    { "first", require_arg, 'f' },   // first step
+    { "dumpfreq", require_arg, 'd' },   // dump frequency of the
+    { NULL, 0, '\0' }
+  };
+
+/************************************************************************************
+ ***********************************  FUNCTIONS  *************************************
+ *************************************************************************************/
+
+
+string convert2Int(int number) {
+  stringstream ss;
+  ss <<   setw(5) << setfill('0') <<  number; 
+  return ss.str(); 
+}
+
+
+/* get_option is the parsing function that was majorly ported from h5dump utility */
+int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts) {
+  static int sp = 1;    /* character index in current token */
+  int opt_opt = '?';    /* option character passed back to user */
+
+  if (sp == 1) 
+    {
+      /* check for more flag-like tokens */
+      if (opt_ind >= argc || argv[opt_ind][0] != '-' || argv[opt_ind][1] == '\0') 
+	{
+	  return EOF;
+	}
+      else if (strcmp(argv[opt_ind], "--") == 0)
+	{
+	  opt_ind++;
+	  return EOF;
+	}
+    }
+
+  if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') 
+    {
+      /* long command line option */
+      const char *arg = &argv[opt_ind][2];
+      int i;
+
+      for (i = 0; l_opts && l_opts[i].name; i++)
+	{
+	  size_t len = strlen(l_opts[i].name);
+
+	  if (strncmp(arg, l_opts[i].name, len) == 0)
+	    {
+	      /* we've found a matching long command line flag */
+	      opt_opt = l_opts[i].shortval;
+
+	      if (l_opts[i].has_arg != no_arg)
+		{
+		  if (arg[len] == '=')
+		    {
+		      opt_arg = &arg[len + 1];
+		    }
+		  else if (opt_ind < (argc - 1) && argv[opt_ind + 1][0] != '-')
+		    {
+		      opt_arg = argv[++opt_ind];
+		    }
+		  else if (l_opts[i].has_arg == require_arg)
+		    {
+		      if (opt_err)
+			fprintf(stderr, "%s: option required for \"--%s\" flag\n", argv[0], arg);
+
+		      opt_opt = '?';
+		    }
+		}
+	      else
+		{
+		  if (arg[len] == '=')
+		    {
+		      if (opt_err)
+			fprintf(stderr, "%s: no option required for \"%s\" flag\n", argv[0], arg);
+
+		      opt_opt = '?';
+		    }
+
+		  opt_arg = NULL;
+		}
+
+	      break;
+	    }
+	}
+
+      if (l_opts[i].name == NULL)
+	{
+	  /* exhausted all of the l_opts we have and still didn't match */
+	  if (opt_err)
+	    fprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
+
+	  opt_opt = '?';
+	}
+
+      opt_ind++;
+      sp = 1;
+    }
+  else
+    {
+      register char *cp;    /* pointer into current token */
+
+      /* short command line option */
+      opt_opt = argv[opt_ind][sp];
+
+      if (opt_opt == ':' || (cp = strchr(opts, opt_opt)) == 0)
+	{
+
+	  if (opt_err)
+	    fprintf(stderr, "%s: unknown option \"%c\"\n", argv[0], opt_opt);
+	  /* if no chars left in this token, move to next token */
+	  if (argv[opt_ind][++sp] == '\0')
+	    {
+	      opt_ind++;
+	      sp = 1;
+	    }
+
+	  return '?';
+	}
+
+      if (*++cp == ':')
+	{
+
+	  /* if a value is expected, get it */
+	  if (argv[opt_ind][sp + 1] != '\0')
+	    {
+	      /* flag value is rest of current token */
+	      opt_arg = &argv[opt_ind++][sp + 1];
+	    }
+	  else if (++opt_ind >= argc)
+	    {
+	      if (opt_err)
+		{
+		  fprintf(stderr, "%s: value expected for option \"%c\"\n", argv[0], opt_opt);
+		}
+	      opt_opt = '?';
+	    }
+	  else
+	    {
+	      /* flag value is next token */
+	      opt_arg = argv[opt_ind++];
+	    }
+
+	  sp = 1;
+	}
+      else 
+	{
+	  /* set up to look at next char in token, next time */
+	  if (argv[opt_ind][++sp] == '\0')
+	    {
+	      /* no more in current token, so setup next token */
+	      opt_ind++;
+	      sp = 1;
+	    }
+
+	  opt_arg = NULL;
+	}
+    }
+
+  /* return the current flag character found */
+  return opt_opt;
+}
+
+/* Assigns functions according to the parsed result */
+static void variable_assign(int argc, const char *argv[])
+{
+  int option;
+
+  /* set options according to the command line */
+  while ((option = get_option(argc, argv, s_opts, l_opts)) != EOF)
+    {
+      switch ((char)option)
+	{
+	case 'h': // Print help page
+	  print_help();
+	  exit(1);
+	case 'o': // Print number of steps
+	  output_name = strdup(opt_arg);
+	  break;
+	case 'i': // Print shorter version without the values
+	  input_name = strdup(opt_arg);
+	  break;
+	case 'g': // 
+	  { geo_name = strdup(opt_arg);
+                        
+	  }
+	  break;  
+	case 'f': // 
+	  { 	
+	    mytemp = strdup(opt_arg);
+	    step_ini = (int)strtod(mytemp,NULL);
+	    fprintf(stdout,"string=%s, %s \n",opt_arg, mytemp);
+	    fprintf(stdout,"step_ini=%i \n",step_ini);                        
+	  }
+	  break;  
+	case 'd': // 
+	  { 	
+	    fprintf(stdout,"string=%s \n",opt_arg);
+	    mytemp = strdup(opt_arg);
+	    dump_freq = (int)strtod(mytemp,NULL);
+	    fprintf(stdout,"string=%s \n",opt_arg);
+	    fprintf(stdout,"dump_freq=%i \n",dump_freq);
+	  }
+	  break;  
+	default:
+	  print_help();
+	  exit(1);
+	}
+    }
+}
+
+/* For printing help page */
+static void print_help()
+{
+  fflush(stdout);
+  fprintf(stdout, "\nusage: h5PartSurfaceToVtk  -i INPUTFILE -g GEOMETRYFILE -o OUTPUTFILE\n");
+  fprintf(stdout, "\n");
+  fprintf(stdout, "  FLAGS\n");
+  fprintf(stdout, "   -h, --help                 Print help page\n");
+  fprintf(stdout, "   -i file, --input file      (REQUIRED) Takes input base file name to \"file\" (extension h5 is assumed \n");
+  fprintf(stdout, "   -g file, --input geometry file      (REQUIRED) Takes input base file name to \"file\" (extension h5 is assumed \n");
+  fprintf(stdout, "   -o file, --output file     (REQUIRED) Takes output base file name to \"file\" (extension vtk is added)\n");
+    
+  fprintf(stdout, "\n");
+  fprintf(stdout, "  Examples first dump step 100 and dump frequency 100:\n");
+  fprintf(stdout, "\n");
+  fprintf(stdout, "        /h5SurfaceVtk -i Cavity_Mag_Surface -g ../10 -o p- -f 100 -d 100 \n");
+  fprintf(stdout, "\n");
+    
+}
+
+
+int main(int argc, const char *argv[])
+{
+  h5_file_t *h5file = NULL;
+    
+  std::ofstream of, ofalive, ofenergy, ofpnum;
+   
+  int j;
+
+  int num_dataset;
+
+  int ntime_step = 0;
+
+  variable_assign(argc, argv);
+
+  if(input_name == NULL)  {
+    fprintf(stdout, "missing input file name\n");
+    print_help();
+    exit(1);
+  }
+   
+  if(output_name == NULL) {
+    fprintf(stdout, "missing output file name\n");
+    print_help();
+    exit(1);
+  }
+   
+  string ifn = string(input_name) + string(".h5");
+   
+  h5file = H5OpenFile(ifn.c_str(), H5_O_WRONLY, NULL);
+     
+  if( h5file == NULL ) {
+    fprintf(stdout, "unable to open file %s\n", input_name);
+    print_help();
+    exit(1);
+  }
+
+  string gfn = string(geo_name) + string(".h5");
+  hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS); //Property list identifier
+  //    H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);
+  // Create a new file collectively and release property list identifier.
+  hid_t file_id = H5Fopen(gfn.c_str(), H5F_ACC_RDONLY, plist_id);
+  assert(file_id >= 0);
+  H5Pclose(plist_id);
+  int     numbfaces_global_m;
+  /////////////////////////////////////////////
+    //   Read dataset "surface" from .h5 file
+    ////////////////////////////////////////////
+
+    hsize_t dimsf[2];//dataset dimensions
+    herr_t  status;
+
+    hid_t dset_id = H5Dopen(file_id, "/surface",H5P_DEFAULT);
+    assert(dset_id >= 0);
+    // Create the dataspace for the dataset.
+    hid_t x = H5Dget_space(dset_id);
+    H5Sget_simple_extent_dims(x, dimsf, NULL);
+    hid_t filespace = H5Screate_simple(2, dimsf, NULL);
+
+    numbfaces_global_m = dimsf[0];
+    int *allbfaces_m = (int*)malloc(numbfaces_global_m * 4*sizeof(int));
+
+    int *bfaces_idx_m = (int*)malloc(numbfaces_global_m*sizeof(int));
+
+    //Tribarycent_m = new Vector_t[numbfaces_global_m];
+    // Create property list for collective dataset write.
+    hid_t plist_id2 = H5Pcreate(H5P_DATASET_XFER);
+    //H5Pset_dxpl_mpio(plist_id2, H5FD_MPIO_COLLECTIVE);
+    status = H5Dread(dset_id, H5T_NATIVE_INT, H5S_ALL, filespace, plist_id2, allbfaces_m);
+    assert(status >= 0);
+    // Store local boundary faces, discard others
+    int nof_sym_m = 0; // Count number of symmetry planes.
+    int const nogeosym_flag = 0; // heronion outputs a index, case 0 indicates no symmetry plane, 1 for (x,y) sym, 2 for (y,z), 3 for (z,x),none 0 means the current triangle is not on a real surface of geometry but on a symmetry plane.
+
+   
+    for(int i = 0; i < numbfaces_global_m; i ++) {
+      bfaces_idx_m[i] = i;
+      if(allbfaces_m[4 * i] > nogeosym_flag) {
+	nof_sym_m += 1;
+	if(i < numbfaces_global_m - 1) {
+	  for(int j = 0; j < numbfaces_global_m - i; j ++) {
+	    allbfaces_m[4*(i+j)] = allbfaces_m[4*(i+j+1)];
+	    allbfaces_m[4*(i+j)+1] = allbfaces_m[4*(i+j+1)+1];
+	    allbfaces_m[4*(i+j)+2] = allbfaces_m[4*(i+j+1)+2];
+	    allbfaces_m[4*(i+j)+3] = allbfaces_m[4*(i+j+1)+3];
+	  }
+	} else
+	  numbfaces_global_m = numbfaces_global_m - 1;
+      }
+    }
+    H5Dclose(dset_id);
+    H5Sclose(filespace);
+    ////////////////////////////////
+    //  Also read dataset "coords"
+    ////////////////////////////////
+    hsize_t dimsf_c[2];
+    herr_t status_c;
+    hid_t dset_id_c = H5Dopen(file_id, "/coords",H5P_DEFAULT);
+    assert(dset_id_c >= 0);
+
+    // Create the dataspace for the dataset.
+    hid_t cp_space = H5Dget_space(dset_id_c);
+    H5Sget_simple_extent_dims(cp_space, dimsf_c, NULL);
+    hid_t filespace_c = H5Screate_simple(2, dimsf_c, NULL);
+
+    int numpoints_global_m = dimsf_c[0];
+    double *point_coords = (double*)malloc(3 * numpoints_global_m*sizeof(double));
+    hid_t plist_id3 = H5Pcreate(H5P_DATASET_XFER);
+    //H5Pset_dxpl_mpio(plist_id3, H5FD_MPIO_COLLECTIVE);
+    status_c = H5Dread(dset_id_c, H5T_NATIVE_DOUBLE, H5S_ALL, filespace_c, plist_id3, point_coords);
+    assert(status_c >= 0);
+    
+
+    
+    
+    double **geo3Dcoords_m;//=  malloc(sizeof(double)*numpoints_global_m*3);
+    geo3Dcoords_m = (double**)malloc(sizeof(double)*numpoints_global_m);
+    for (int i=0;i<numpoints_global_m;i++) {
+      geo3Dcoords_m[i] = (double*)malloc(sizeof(double)*3);
+    }
+    
+    for(int i = 0; i < numpoints_global_m; i++) {
+      geo3Dcoords_m[i][0] = point_coords[3*i];
+      geo3Dcoords_m[i][1] = point_coords[3*i+1];
+      geo3Dcoords_m[i][2] = point_coords[3*i+2];
+    }
+   
+    
+    
+    // Close HDF5 stuff
+    H5Dclose(dset_id_c);
+    H5Sclose(filespace_c);
+
+
+    ntime_step = H5GetNumSteps(h5file);
+    cout<<"step number: "<<ntime_step<<endl;
+    double sey_num;//sey total number
+    int remained_num;//
+    for (size_t j=1; j<=ntime_step; j++) {
+      set<h5_int64_t> idSet;
+      size_t step_local = step_ini + (j-1)*dump_freq;
+      H5SetStep(h5file,step_local);
+      num_dataset = H5PartGetNumDatasets(h5file);
+      h5_int64_t triNum = H5PartGetNumParticles(h5file);
+      double    qi = 0.0;
+      H5ReadStepAttribFloat64(h5file,"qi",&qi);
+      cout << "Working on timestep " << step_local  << endl;
+		
+      h5_float64_t* PrimaryLoss = (h5_float64_t*)malloc(sizeof(h5_float64_t)*triNum);
+      H5PartReadDataFloat64(h5file, "PrimaryLoss", PrimaryLoss);
+	
+      h5_float64_t* SecondaryLoss = (h5_float64_t*)malloc(sizeof(h5_float64_t)*triNum);
+      H5PartReadDataFloat64(h5file, "SecondaryLoss", SecondaryLoss);
+	
+      h5_float64_t* FNEmissionLoss = (h5_float64_t*)malloc(sizeof(h5_float64_t)*triNum);
+      H5PartReadDataFloat64(h5file, "FNEmissionLoss", FNEmissionLoss);
+	
+      h5_int64_t* TriID = (h5_int64_t*)malloc(sizeof(h5_int64_t)*triNum);
+      H5PartReadDataInt64(h5file, "TriangleID", TriID);
+	
+      string ffn = string("vtk/") + string(output_name) + string("Surface-") + convert2Int(j) + string(".vtk");
+	
+      of.open(ffn.c_str());
+      assert(of.is_open());
+      of.precision(6);
+      of << "# vtk DataFile Version 2.0" << endl;  // first line of a vtk file
+      of << "generated using DataSink::writeGeoToVtk" << endl;   // header
+      of << "ASCII" << endl << endl;   // file format
+      of << "DATASET UNSTRUCTURED_GRID" << endl;  // dataset structrue
+      of << "POINTS " << numpoints_global_m << " float" << endl;   // data num and type
+      for(int i = 0; i < numpoints_global_m ; i ++)
+	of << geo3Dcoords_m[i][0] << " " << geo3Dcoords_m[i][1] << " " << geo3Dcoords_m[i][2] << endl;
+      of << endl;
+
+      of << "CELLS " << numbfaces_global_m << " " << 4 * numbfaces_global_m << endl;
+      for(int i = 0; i < numbfaces_global_m ; i ++)
+	of << "3 " << allbfaces_m[4*i+1] << " " << allbfaces_m[4*i+2] << " " << allbfaces_m[4*i+3] << endl;
+      of << "CELL_TYPES " << numbfaces_global_m << endl;
+      for(int i = 0; i < numbfaces_global_m ; i ++)
+	of << "5" << endl;
+      of << "CELL_DATA " << numbfaces_global_m << endl;
+      of << "SCALARS " << "PrimaryLoss" << " float " << "1" << endl;
+      of << "LOOKUP_TABLE " << "default" << endl ;
+      for(int i = 0; i < numbfaces_global_m ; i ++)
+	of << fabs(PrimaryLoss[i]/qi) << endl;
+      of << "SCALARS " << "SecondaryLoss" << " float " << "1" << endl;
+      of << "LOOKUP_TABLE " << "default" << endl ;
+      for(int i = 0; i < numbfaces_global_m ; i ++)
+	of << fabs(SecondaryLoss[i]/qi) << endl;
+      of << "SCALARS " << "FNEmissionLoss" << " float " << "1" << endl;
+      of << "LOOKUP_TABLE " << "default" << endl ;
+      for(int i = 0; i < numbfaces_global_m ; i ++)
+	of << fabs(FNEmissionLoss[i]/qi) << endl;
+      of << "SCALARS " << "TotalLoss" << " float " << "1" << endl;
+      of << "LOOKUP_TABLE " << "default" << endl ;
+      for(int i = 0; i < numbfaces_global_m ; i ++)
+	of << fabs((FNEmissionLoss[i]+SecondaryLoss[i]+PrimaryLoss[i])/qi) << endl;
+      of << endl;
+	
+      of.close();
+	   
+      //cout <<"ptype size = "<< sizeof(ptype) << endl;
+	
+      free(PrimaryLoss);
+      free(SecondaryLoss);
+      free(FNEmissionLoss);
+      free(TriID);
+    }
+    free(point_coords);
+    for (int i=0;i<numpoints_global_m;i++) {
+      free(geo3Dcoords_m[i]);
+    }
+    free(geo3Dcoords_m);
+    free(allbfaces_m);
+    free(bfaces_idx_m);
+
+    H5CloseFile(h5file);   
+    return 0;
+}