doc/Downloading.html

- update H5Part download instructions

configure.ac

@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.3.1], [vis@hpcrdm.lbl.gov])
+AC_INIT([H5Part], [1.3.2], [vis@hpcrdm.lbl.gov], H5Part)
 
 
 # Ensure that a recent enough version of Autoconf is being used. 
@@ -14,6 +14,45 @@ AC_INIT([H5Part], [1.3.1], [vis@hpcrdm.lbl.gov])
 # The AC_CONFIG_HEADERS macro selects this kind of output.
 AC_CONFIG_HEADER(config.h)
 
+###############################################################################
+################# --enable-xxx and --with-xxx Argument ########################
+###############################################################################
+
+AC_ARG_ENABLE(
+	[64],
+	[AC_HELP_STRING([--enable-64],
+	[Compile using 64-bit flags [default=no]])],
+	[USE_64=$enableval])
+
+AC_ARG_ENABLE(
+	[fortran],
+        [AC_HELP_STRING([--enable-fortran],
+	[Compile the Fortran interface [default=no]])],
+        [USE_FORTRAN=$enableval])
+
+AC_ARG_ENABLE(
+	[parallel],
+        [AC_HELP_STRING([--enable-parallel],
+	[Compile the MPI/IO interface [default=no]])],
+        [USE_PARALLEL=$enableval])
+
+AC_ARG_ENABLE(
+	[tools],
+        [AC_HELP_STRING([--enable-tools],
+	[Compile h5part tools [default=no]])],
+        [USE_TOOLS=$enableval])
+
+AC_ARG_WITH(
+	[mpipath],
+	[AC_HELP_STRING([--with-mpipath],
+	[path to MPI installation [default=""]])],
+        [MPIPATH=$withval], [MPIPATH=""])
+
+AC_ARG_WITH(
+	[hdf5path],
+	[AC_HELP_STRING([--with-hdf5path],
+	[path to HDF5 installation [default=""]])],
+	[HDF5PATH=$withval], [HDF5PATH=""])
 
 ###############################################################################
 ################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
@@ -56,18 +95,18 @@ PATH_Search()
   fi
   for h5part_place in $2
     do
-      echo -n "Looking in $h5part_place ... $ac_c" #1>&6
+      echo -n "looking in $h5part_place ... $ac_c" #1>&6
       if test -r "$h5part_basedir$h5part_place/$3" ; then
-        echo "$ac_t"" Found" #1>&6
+        echo "$ac_t"" found" #1>&6
         eval $1="$h5part_place"
         break
       fi
       if test -d "$h5part_basedir$h5part_place/$3" ; then
-        echo "$ac_t"" Found" #1>&6
+        echo "$ac_t"" found" #1>&6
         eval $1="$h5part_place"
         break
       fi
-      echo "$ac_t"" No" #1>&6
+      echo "$ac_t"" no" #1>&6
     done
 
   return
@@ -176,85 +215,63 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 ###################### 64-bit compilation enabled #############################
 AC_MSG_CHECKING([if 64-bit compilation is enabled])
 
-AC_ARG_ENABLE([64],
-	[AC_HELP_STRING([--enable-64],
-	[Compile using 64-bit flags [default=no]])],
-	[USE_64=$enableval])
-
 
 # If --enable-64 is set in the configure line
 if test "X$USE_64" = "Xyes"; then
-   echo "YES, 64-BIT ENABLED"
+    AC_MSG_RESULT([yes])
-   if test $uname = "AIX"; then
+    if test $uname = "AIX"; then
-      CFLAGS="$CFLAGS -q64"
+        CFLAGS="$CFLAGS -q64"
-      FFLAGS="$FFLAGS -q64"
+        FFLAGS="$FFLAGS -q64"
-   fi
+    fi
 
-   if test $uname = "IRIX64"; then
+    if test $uname = "IRIX64"; then
-      CFLAGS="$CFLAGS -64"
+        CFLAGS="$CFLAGS -64"
-      FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
+        FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
-   fi
+    fi
 else
-   echo "NO, 64-BIT NOT ENABLED"
+    AC_MSG_RESULT([no])
 fi
 
 
 ############################ fortran enabled ##################################
 AC_MSG_CHECKING([if fortran interface enabled])
-AC_MSG_RESULT([])
-AC_ARG_ENABLE([fortran],
-              [AC_HELP_STRING([--enable-fortran],
-	       [Compile the Fortran interface [default=no]])],
-              [USE_FORTRAN=$enableval])
-
-
 if test "X$USE_FORTRAN" = "Xyes"; then
-   echo "YES, FORTRAN ENABLED"
+    AC_MSG_RESULT([yes])
 
-   # Start looking for ifort first
+    AC_PROG_FC(ifort xlf_r pathf90 g95 g90 ftn gfortran)
-   AC_PROG_FC(ifort xlf_r pathf90 g95 g90 ftn gfortran)
+    if test -z "$FC" ; then
+        AC_MSG_ERROR([Cannot find a fortran compiler!!!])
+        exit 1
+    fi
 
-   if test -n "$FC" ; then
+    if test ! $uname = "AIX"; then
-      if test "X$FC" = "Xg95"; then
+        FFLAGS="${FFLAGS} -fPIC -fno-second-underscore"
-          FFLAGS="${FFLAGS} -fno-second-underscore"
+    fi
-      fi
-      AC_MSG_CHECKING([Test Number of FC Underscores])
-      AC_MSG_RESULT([OK])
-      `cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
-      `cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
-      `cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-      `cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o -lc`
 
-      if test -f src/TestUnderscore ; then
+    AC_MSG_CHECKING([symbol convention in object files])
-         UNDERSCORE_H=Underscore.h
+    `cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
-         `cd src && cat COPYRIGHT > Underscore.h`
+    `cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
-         `cd src && ./TestUnderscore >> Underscore.h`
+    `cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-         echo "==== Underscore.h contains ============="
+    `cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o -lc`
-         cat src/Underscore.h
+
-         echo "========================================"
+    if test -f src/TestUnderscore ; then
-      else
+        UNDERSCORE_H=Underscore.h
-         AC_MSG_ERROR(could not build fortran executable)
+        `cd src && ./TestUnderscore > Underscore.h`
-         USE_FORTRAN = "no"
+        AC_MSG_RESULT([ok])
-      fi
+    else
-   else
+        AC_MSG_RESULT([nok])
-      AC_MSG_ERROR(could not find a fortran compiler)
+        AC_MSG_ERROR([Cannot build fortran executables!!!])
-      USE_FORTRAN = "no"
+        exit 1
-      exit 1
+    fi
-   fi
 else
-   echo "NO, FORTRAN NOT ENABLED"
+    AC_MSG_RESULT([no])
 fi
 
 
 ######################## parallel interface enabled ###########################
 AC_MSG_CHECKING([if parallel interface enabled])
-AC_ARG_ENABLE([parallel],
-              [AC_HELP_STRING([--enable-parallel],
-	       [Compile the MPI/IO interface [default=no]])],
-              [USE_PARALLEL=$enableval])
-
 if test "X$USE_PARALLEL" = "Xyes"; then
-    AC_MSG_RESULT([YES, PARALLEL ENABLED])
+    AC_MSG_RESULT([yes])
 
     CFLAGS="${CFLAGS} -DPARALLEL_IO -DH5_HAVE_PARALLEL -DMPICH_IGNORE_CXX_SEEK"
 
@@ -269,13 +286,15 @@ if test "X$USE_PARALLEL" = "Xyes"; then
         AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
         AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
         if test -z "$MPICC" -o -z "$MPICXX"; then 
-            AC_ARG_WITH([mpipath],
+            AC_MSG_CHECKING([for MPI root ])
-                [AC_HELP_STRING([--with-mpipath],
+            AC_MSG_RESULT([])
-		 [path to MPI installation [default=""]])],
+            if test -n "$MPIROOT"; then
-                [MPIROOT=$withval], [MPIROOT=""])
+                P=${MPIROOT}
-            if test -z "$MPIROOT"; then 
+            elif test -n "$MPIHOME"; then
-                AC_MSG_CHECKING([for MPI root ])
+                P=${MPIHOME}
-                echo
+            elif test -n "$MPIPATH"; then
+                P=${MPIPATH}
+            else
                 P=''
                 P="$P /usr"
                 P="$P /usr/local"
@@ -284,10 +303,10 @@ if test "X$USE_PARALLEL" = "Xyes"; then
                 P="$P /usr/local/mpich2"
                 P="$P /usr/local/mpich"
                 P="$P /opt/xt-mpt/default/mpich2-64/P2"
-                PATH_Search MPIROOT "$P" include/mpi.h
             fi
+            PATH_Search MPIROOT "$P" include/mpi.h
             if test ! -n "$MPIROOT"; then
-                AC_MSG_RESULT([Cannot determine MPIROOT])
+		AC_MSG_ERROR([Cannot determine MPI root!!!])
                 exit 1
             fi
 
@@ -335,8 +354,6 @@ if test "X$USE_PARALLEL" = "Xyes"; then
 
     # parallel + fortran
     if test "X$USE_FORTRAN" = "Xyes"; then
-        echo "PARALLEL ENABLED WITH FORTRAN"
- 
         AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
 
 	if test -z "${MPIFC}" ; then
@@ -359,97 +376,78 @@ if test "X$USE_PARALLEL" = "Xyes"; then
         MTARGET="${MTARGET} libpH5PartF.a"
         TTARGET="${TTARGET} H5testFpar"
 	TTARGET="${TTARGET} H5BlockParTestScalarFieldF"
-    else
-        echo "PARALLEL ENABLED WITHOUT FORTRAN"
     fi
 
-else
+else  # --enable-parallel=no
-    echo "NO, PARALLEL NOT ENABLED"
+    AC_MSG_RESULT([no])
 
     MTARGET="libH5Part.a"
     TTARGET="H5PartTest H5test"
     TTARGET="${TTARGET} H5BlockTestAttributes"
 
     if test "X$USE_FORTRAN" = "Xyes"; then
-        echo "PARALLEL NOT ENABLED WITH FORTRAN ENABLED"
-
         MTARGET="${MTARGET} libH5PartF.a"
         TTARGET="${TTARGET} H5testF"
 	TTARGET="${TTARGET} H5BlockTestAttributesF"
-   else
-        echo "BOTH PARALLEL & FORTRAN NOT ENABLED"
    fi
 fi
 
-AC_MSG_CHECKING([for h5pTools file: ])
+AC_MSG_CHECKING([wheter tools are enabled])
-AC_MSG_RESULT([OK])
-AC_ARG_ENABLE([tools],
-              [AC_HELP_STRING([--enable-tools], [Compile h5part tools [default=no]])],
-              [USE_TOOLS=$enableval])
-
-
 if test "X$USE_TOOLS" = "Xyes"; then
-    BUILD_TOOLS="h5pAttrib h5pToGNUplot homdynToH5p"
+    AC_MSG_RESULT([yes])
+    BUILD_TOOLS="h5pAttrib h5pToGNUplot # homdynToH5p"
+else
+    AC_MSG_RESULT([no])
 fi
 
 ###############################################################################
 ######################### PATH CHECKING & SETTING #############################
 ###############################################################################
 
-AC_ARG_WITH([hdf5path],
+AC_MSG_CHECKING([for HDF5 root ])
-    [AC_HELP_STRING([--with-hdf5path],
+AC_MSG_RESULT([])
-     [path to HDF5 installation [default=""]])],
+if test -n "${HDF5ROOT}"; then
-    [XROOT=$withval], [XROOT=""])
+    P=${HDF5ROOT}
+elif test -n "${HDF5HOME}" ; then
+    P=${HDF5HOME}
+elif test -n "${HDF5PATH}" ; then
+    P=${HDF5PATH}
+else
+    P=''
+    P="$P /usr"
+    P="$P /usr/local"
+    P="$P /usr/local/hdf5"
+    P="$P /usr/local/packages/hdf5"
+    P="$P /apps/hdf5"
 
-HDF5ROOT=$XROOT
+    if test "X$USE_PARALLEL" = "Xyes"; then
-
-if test "X$USE_PARALLEL" = "Xyes"; then
-    if test -z "$HDF5ROOT"; then
-        AC_MSG_CHECKING([for Parallel HDF5 root ])
-        AC_MSG_RESULT([])
-        P=''
-        P="$P /usr"
-        P="$P /usr/local"
         P="$P /usr/local/phdf5"
-        P="$P /usr/local/hdf5"
-        P="$P /usr/local/packages/hdf5"
         P="$P /usr/local/hdf5/hdf5_par"
-        P="$P /apps/hdf5"
- 
         if test "X$USE_64" = "Xyes"; then
             P="$P /usr/common/usg/hdf5/64/default/parallel"
         else
             P="$P /usr/common/usg/hdf5/32/default/parallel"
         fi
-        PATH_Search HDF5ROOT "$P" include/hdf5.h
+    else
-	XROOT=$HDF5ROOT
-    fi
-else
-    if test -z "$HDF5ROOT"; then
-        AC_MSG_CHECKING([for HDF5 library location ])
-        AC_MSG_RESULT([])
-        P=''
-        P="$P /usr"
-        P="$P /usr/local"
-        P="$P /usr/local/hdf5"
-        P="$P /usr/local/packages/hdf5"
         P="$P /usr/local/hdf5/hdf5_serial"
-        P="$P /apps/hdf5"
         if test "X$USE_64" = "Xyes"; then
             P="$P /usr/common/usg/hdf5/64/default/serial"
         else
             P="$P /usr/common/usg/hdf5/32/default/serial"
         fi
-        PATH_Search HDF5ROOT "$P" include/hdf5.h
-	XROOT=$HDF5ROOT
     fi
 fi
+PATH_Search HDF5ROOT "$P" include/hdf5.h
+if test -z "$HDF5ROOT"; then
+    AC_MSG_ERROR([Cannot determine HDF5 root!!!])
+    exit 1
+fi
 
 AC_MSG_CHECKING([if we need to link to libsz ])
-if test -n "$XROOT"; then
+if test -n "$HDF5ROOT"; then
-    if test -f $XROOT/lib/libsz.a; then
+    if test -f $HDF5ROOT/lib/libsz.a; then
 	AC_MSG_RESULT([yes])
-        SZLIB="-L$XROOT/lib/ -lsz"
+        SZLIB="-L$HDF5ROOT/lib/ -lsz"
     else
 	AC_MSG_RESULT([no])
         SZLIB=""
@@ -468,14 +466,6 @@ fi
 #################### MISC SETTINGS - path, flags, etc #########################
 ###############################################################################
 
-# if not AIX
-if test ! $uname = "AIX"; then
-# Additional flags
-echo "SETTING ADDITIONAL FLAGS"
-ADDFLAGS="-fPIC -fno-second-underscore"
-fi
-
-
 H5P_LIB_LOC=`pwd`/src
 
 ###############################################################################
@@ -545,36 +535,6 @@ TOOLS_H5PART_LIB="-lH5Part"
 TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5"
 fi
 
-###############################################################################
-########################## PRINTING SUMMARY ###################################
-###############################################################################
-echo "+++++++++++++++++++++++++++++++"
-echo "+++++++++ SUMMARY for `(hostname || uname -n) 2>/dev/null | sed 1q` +++++++++"
-echo "CC = $CC"
-echo "CXX = $CXX"
-echo "FC = $FC"
-echo "MPICC = $MPICC"
-echo "MPICXX = $MPICXX"
-echo "MPIFC = $MPIFC"
-echo "CFLAGS = $CFLAGS"
-echo "FFLAGS = $FFLAGS"
-echo "MPILIB = $MPILIB"
-echo "MPIINC = $MPIINC"
-echo "MPIROOT = $MPIROOT"
-echo "HDF5ROOT = $HDF5ROOT"
-echo "LDFLAGS = $LDFLAGS"
-echo "host_os = $host_os"
-echo "host_cpu = $host_cpu"
-echo "host_vendor = $host_vendor"
-echo "Will Be Building Libraries ... : $MTARGET"
-echo "Will Be Building Test Programs ... : $TTARGET"
-echo "TOOLS_CXX = $TOOLS_CXX"
-echo "TOOLS_H5PART_LIB = $TOOLS_H5PART_LIB"
-echo "TOOLS_HDFLIB = $TOOLS_HDFLIB"
-echo "BUILD_TOOLS = $BUILD_TOOLS"
-echo "+++++++++++++++++++++++++++++++"
-
-
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################
@@ -597,7 +557,6 @@ AC_SUBST(TTARGET)
 AC_SUBST(SZLIB)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(ADDFLAGS)
 AC_SUBST(STDCXX)
 AC_SUBST(H5P_LIB_LOC)
 AC_SUBST(UNDERSCORE_H)
@@ -617,5 +576,32 @@ test/Makefile
 tools/Makefile
 ])
 
-
 AC_OUTPUT
+
+###############################################################################
+########################## PRINTING SUMMARY ###################################
+###############################################################################
+echo
+echo
+echo "Summary for `(hostname || uname -n) 2>/dev/null | sed 1q`:"
+echo
+echo "Host OS:             $host_os"
+echo "Host CPU:            $host_cpu"
+echo "Host vendor:         $host_vendor"
+echo "Build libraries:     $MTARGET"
+echo "Build test programs: $TTARGET"
+echo "Build tools:         $BUILD_TOOLS"
+echo "CC =                 $CC"
+echo "CXX =                $CXX"
+echo "FC =                 $FC"
+echo "MPICC =              $MPICC"
+echo "MPICXX =             $MPICXX"
+echo "MPIFC =              $MPIFC"
+echo "CFLAGS =             $CFLAGS"
+echo "FFLAGS =             $FFLAGS"
+echo "MPILIB =             $MPILIB"
+echo "MPIINC =             $MPIINC"
+echo "MPIROOT =            $MPIROOT"
+echo "HDF5ROOT =           $HDF5ROOT"
+echo "LDFLAGS =            $LDFLAGS"
+echo

doc/Downloading.html

@@ -6,8 +6,6 @@
 <meta name="keywords" content="scientific visualization">
 <meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
 
-<!--#include virtual="/include/topIncludes.html"-->
-
 <div id="maincenter">
   <head>
     <title>Downloading HDF5 and H5Part</title>
@@ -39,12 +37,49 @@
 	ls
 	get zlib-1.2.1.tar.gz (get the current version, this as the one on April 20th, 2006)
 	</pre>
-	Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
 
-    <a name="hpart">
+ <P>
-    <h2>Downloading H5Part</h2></a>
+	Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
-	Please contact <address><a href="mailto:andreas.adelmann@psi.ch">Andreas Adelmann</a></address>.
+</P>
+
+<h4>Building Parallel HDF5</h4>
+<P>
+When you build HDF5, you will need to build an version with parallel I/O
+enabled. Here is a set of configure options that worked for us on a
+Linux workstation running SuSE 10.1 with MPICH installed in /usr/local/mpich.
+</p>
+
+<pre>
+./configure --prefix=/usr/local/hdf5-mpich --enable-parallel CC=mpicc CXX=mpicxx --disable-shared --enable-static --enable-stream-vfd
+</pre>
+
+<UL>
+<li> --prefix=/usr/local/hdf5-mpich : the location where the HDF5 libs and
+binaries will be installed.</LI>
+<li> --enable-parallel : contrary to the HDF5 documentation, which says that
+"--enable-parallel" is optional for building the parallel version of
+HDF5, you <b>must</b> have --enable-parallel to get the parallel-enabled
+build. See <a href="ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/release_docs/INSTALL_parallel">these notes from HDF5</a> where they claim that
+--enable-parallel is optional.</LI>
+<li> CC=mpicc CXX=mpicxx : contrary to the output from configure --help, the
+configure script seems to ignore the CC and CXX environment variables.
+We tried setting these environment variables to mpicc and mpicxx,
+respectively, and then ran configure with --enable-parallel. The configure
+script would faile with this error message: 	
+<pre>
+checking whether a simple MPI-IO program can be linked... no
+configure: error: unable to link a simple MPI-IO application
+</pre>
+</LI>
+<LI> --disable-shared and --enable-static: the HDF5 build failed for us
+w/o these options when attempting to read symbols from libmpich.a. The
+result of these options is that your parallel-enabled HDF5 libaries
+will be static rather than dynamic.
+
+</UL>
+
+
+    <h2 id="h5part">Downloading H5Part</h2>
+        H5Part is available for download from Berkeley Labs Codeforge system <a href="https://codeforge.lbl.gov/projects/h5part/">https://codeforge.lbl.gov/projects/h5part</a>.
  
 </div>
-
-<!--#include virtual="/include/dateFooter.html"-->

src/H5Part.c

@@ -93,36 +93,13 @@ _h5_error_handler (
 
 /*========== File Opening/Closing ===============*/
 
-/*!
+static H5PartFile*
-  \ingroup h5part_openclose
+_H5Part_open_file (
-
-  Opens file with specified filename. 
-
-  If you open with flag \c H5PART_WRITE, it will truncate any
-  file with the specified filename and start writing to it. If 
-  you open with \c H5PART_APPEND, then you can append new timesteps.
-  If you open with \c H5PART_READ, then it will open the file
-  readonly.
-
-  The typical extension for these files is \c .h5.
-  
-  H5PartFile should be treated as an essentially opaque
-  datastructure.  It acts as the file handle, but internally
-  it maintains several key state variables associated with 
-  the file.
-
-  \return	File handle or \c NULL
- */
-H5PartFile*
-H5PartOpenFileParallel (
 	const char *filename,	/*!< [in] The name of the data file to open. */
-	unsigned flags		/*!< [in] The access mode for the file. */
+	unsigned flags,		/*!< [in] The access mode for the file. */
-#ifdef PARALLEL_IO
+	MPI_Comm comm,		/*!< [in] MPI communicator */
-	,MPI_Comm comm		/*!< [in] MPI communicator */
+	int f_parallel		/*!< [in] 0 for serial io otherwise parallel */
-#endif
+	) {
-) {
-	SET_FNAME ( "H5PartOpenFileParallel" );
-
 	if ( _init() < 0 ) {
 		HANDLE_H5PART_INIT_ERR;
 		return NULL;
@@ -136,57 +113,71 @@ H5PartOpenFileParallel (
 		goto error_cleanup;
 	}
 	memset (f, 0, sizeof (H5PartFile));
-	f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
 
-#ifdef PARALLEL_IO
+	f->groupname_step = strdup ( H5PART_GROUPNAME_STEP );
-	/* for the SP2... perhaps different for linux */
+	if( f->groupname_step == NULL ) {
-	MPI_Info info = MPI_INFO_NULL;
-
-	if (MPI_Comm_size (comm, &f->nprocs) != MPI_SUCCESS) {
-		HANDLE_MPI_COMM_SIZE_ERR;
-		goto error_cleanup;
-	}
-	if (MPI_Comm_rank (comm, &f->myproc) != MPI_SUCCESS) {
-		HANDLE_MPI_COMM_RANK_ERR;
-		goto error_cleanup;
-	}
-
-	f->pnparticles = malloc (f->nprocs * sizeof (h5part_int64_t));
-	if (f->pnparticles == NULL) {
 		HANDLE_H5PART_NOMEM_ERR;
 		goto error_cleanup;
 	}
+	f->stepno_width = 0;
+
+	f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
+
+#ifdef PARALLEL_IO
+	if ( f_parallel ) {
+		/* for the SP2... perhaps different for linux */
+		MPI_Info info = MPI_INFO_NULL;
+
+		if (MPI_Comm_size (comm, &f->nprocs) != MPI_SUCCESS) {
+			HANDLE_MPI_COMM_SIZE_ERR;
+			goto error_cleanup;
+		}
+		if (MPI_Comm_rank (comm, &f->myproc) != MPI_SUCCESS) {
+			HANDLE_MPI_COMM_RANK_ERR;
+			goto error_cleanup;
+		}
+
+		f->pnparticles = malloc (f->nprocs * sizeof (h5part_int64_t));
+		if (f->pnparticles == NULL) {
+			HANDLE_H5PART_NOMEM_ERR;
+			goto error_cleanup;
+		}
 		
-	f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
+		f->access_prop = H5Pcreate (H5P_FILE_ACCESS);
-	if (f->access_prop < 0) {
+		if (f->access_prop < 0) {
-		HANDLE_H5P_CREATE_ERR;
+			HANDLE_H5P_CREATE_ERR;
-		goto error_cleanup;
+			goto error_cleanup;
-	}
+		}
 
-	if (H5Pset_fapl_mpio (f->access_prop, comm, info) < 0) {
+		if (H5Pset_fapl_mpio (f->access_prop, comm, info) < 0) {
-		HANDLE_H5P_SET_FAPL_MPIO_ERR;
+			HANDLE_H5P_SET_FAPL_MPIO_ERR;
-		goto error_cleanup;
+			goto error_cleanup;
-	}
+		}
 		
-	/* create_prop: tunable parameters like blocksize and btree sizes */
+		/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
-	/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
+		f->create_prop = H5P_DEFAULT;
-	f->create_prop = H5P_DEFAULT;
 
-	/* currently create_prop is empty */
+		/* currently create_prop is empty */
-	/* xfer_prop:  also used for parallel I/O, during actual writes
+		/* xfer_prop:  also used for parallel I/O, during actual writes
-	   rather than the access_prop which is for file creation. */
+		   rather than the access_prop which is for file creation. */
-	f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
+		f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
-	if (f->xfer_prop < 0) {
+		if (f->xfer_prop < 0) {
-		HANDLE_H5P_CREATE_ERR;
+			HANDLE_H5P_CREATE_ERR;
-		goto error_cleanup;
+			goto error_cleanup;
+		}
+
+		if (H5Pset_dxpl_mpio (f->xfer_prop,H5FD_MPIO_COLLECTIVE) < 0) {
+			HANDLE_H5P_SET_DXPL_MPIO_ERR;
+			goto error_cleanup;
+		}
+
+		f->comm = comm;
+	} else {
+		f->pnparticles = 0;
+		f->comm = MPI_COMM_WORLD;
+		f->nprocs = 1;
+		f->myproc = 0;
 	}
-
-	if (H5Pset_dxpl_mpio (f->xfer_prop, H5FD_MPIO_COLLECTIVE) < 0) {
-		HANDLE_H5P_SET_DXPL_MPIO_ERR;
-		goto error_cleanup;
-	}
-
-	f->comm = comm;
 #endif
 	if ( flags == H5PART_READ ) {
 		f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
@@ -194,12 +185,14 @@ H5PartOpenFileParallel (
 	else if ( flags == H5PART_WRITE ){
 		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
 				     f->access_prop);
+		f->empty = 1;
 	}
 	else if ( flags == H5PART_APPEND ) {
 		int fd = open (filename, O_RDONLY, 0);
 		if ( (fd == -1) && (errno == ENOENT) ) {
 			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
 					    f->create_prop, f->access_prop);
+			f->empty = 1;
 		}
 		else if (fd != -1) {
 			close (fd);
@@ -210,7 +203,7 @@ H5PartOpenFileParallel (
 			  if f->file < 0. But we can safely ignore this.
 			*/
 			f->timestep = _H5Part_get_num_objects_matching_pattern(
-				f->file, "/", H5G_GROUP, H5PART_GROUPNAME_STEP );
+				f->file, "/", H5G_GROUP, f->groupname_step );
 			if ( f->timestep < 0 ) goto error_cleanup;
 		}
 	}
@@ -241,6 +234,9 @@ H5PartOpenFileParallel (
 
  error_cleanup:
 	if (f != NULL ) {
+		if (f->groupname_step) {
+			free (f->groupname_step);
+		}
 		if (f->pnparticles != NULL) {
 			free (f->pnparticles);
 		}
@@ -249,6 +245,39 @@ H5PartOpenFileParallel (
 	return NULL;
 }
 
+#ifdef PARALLEL_IO
+/*!
+  \ingroup h5part_openclose
+
+  Opens file with specified filename. 
+
+  If you open with flag \c H5PART_WRITE, it will truncate any
+  file with the specified filename and start writing to it. If 
+  you open with \c H5PART_APPEND, then you can append new timesteps.
+  If you open with \c H5PART_READ, then it will open the file
+  readonly.
+
+  The typical extension for these files is \c .h5.
+  
+  H5PartFile should be treated as an essentially opaque
+  datastructure.  It acts as the file handle, but internally
+  it maintains several key state variables associated with 
+  the file.
+
+  \return	File handle or \c NULL
+ */
+H5PartFile*
+H5PartOpenFileParallel (
+	const char *filename,	/*!< [in] The name of the data file to open. */
+	unsigned flags,		/*!< [in] The access mode for the file. */
+	MPI_Comm comm		/*!< [in] MPI communicator */
+) {
+	int f_parallel = 1;	/* parallel i/o */
+
+	return _H5Part_open_file ( filename, flags, comm, f_parallel );
+}
+#endif
+
 /*!
   \ingroup  h5part_openclose
 
@@ -277,87 +306,11 @@ H5PartOpenFile (
 	) {
 
 	SET_FNAME ( "H5PartOpenFile" );
-	if ( _init() < 0 ) {
-		HANDLE_H5PART_INIT_ERR;
-		return NULL;
-	}
 
-	_errno = H5PART_SUCCESS;
+	MPI_Comm comm = 0;	/* dummy */
-	H5PartFile *f = NULL;
+	int f_parallel = 0;	/* serial open */
 
-	f = (H5PartFile*) malloc( sizeof (H5PartFile) );
+	return _H5Part_open_file ( filename, flags, comm, f_parallel );
-	if( f == NULL ) {
-		HANDLE_H5PART_NOMEM_ERR;
-		goto error_cleanup;
-	}
-	memset (f, 0, sizeof (H5PartFile));
-	f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
-
-#ifdef PARALLEL_IO
-	f->pnparticles = 0;
-	f->comm = MPI_COMM_WORLD;
-	f->nprocs = 1;
-	f->myproc = 0;
-#endif
-	if (flags == H5PART_READ) {
-		f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
-	}
-	else if (flags == H5PART_WRITE){
-		f->file = H5Fcreate (filename, H5F_ACC_TRUNC, f->create_prop,
-				     f->access_prop);
-	}
-	else if (flags == H5PART_APPEND) {
-		int fd = open (filename, O_RDONLY, 0);
-		if ( (fd == -1) && (errno == ENOENT) ) {
-			f->file = H5Fcreate(filename, H5F_ACC_TRUNC,
-					    f->create_prop, f->access_prop);
-		}
-		else if (fd != -1) {
-			close (fd);
-			f->file = H5Fopen (filename, H5F_ACC_RDWR,
-					   f->access_prop);
-			/*
-			  The following function call returns an error,
-			  if f->file < 0. But we can safely ignore it
-			*/
-			f->timestep = _H5Part_get_num_objects_matching_pattern(
-				f->file, "/", H5G_GROUP, H5PART_GROUPNAME_STEP );
-			if ( f->timestep < 0 ) goto error_cleanup;
-		}
-	}
-	else {
-		HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( flags );
-		goto error_cleanup;
-	}
-
-	if (f->file < 0) {
-		HANDLE_H5F_OPEN_ERR ( filename, flags );
-		goto error_cleanup;
-	}
-
-	f->mode = flags;
-	f->timegroup = -1;
-	f->shape = 0;
-	f->diskshape = H5S_ALL;
-	f->memshape = H5S_ALL;
-	f->viewstart = -1;
-	f->viewend = -1;
-
-	_H5Part_print_debug (
-		"Opened file \"%s\" val=%lld",
-		filename,
-		(long long)(size_t)f );
-
-	return f;
-
- error_cleanup:
-	if (f != NULL ) {
-		if (f->pnparticles != NULL) {
-			free (f->pnparticles);
-		}
-		free (f);
-	}
-	return NULL;
 }
 
 /*!
@@ -437,6 +390,9 @@ H5PartCloseFile (
 		if ( r < 0 ) HANDLE_H5F_CLOSE_ERR;
 		f->file = 0;
 	}
+	if (f->groupname_step) {
+		free (f->groupname_step);
+	}
 	if( f->pnparticles ) {
 		free( f->pnparticles );
 	}
@@ -447,6 +403,21 @@ H5PartCloseFile (
 
 /*============== File Writing Functions ==================== */
 
+h5part_int64_t
+H5PartDefineStepName (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int64_t width
+	) {
+	f->groupname_step = strdup ( name );
+	if( f->groupname_step == NULL ) {
+		return HANDLE_H5PART_NOMEM_ERR;
+	}
+	f->stepno_width = width;
+	
+	return H5PART_SUCCESS;
+}
+
 /*!
   \ingroup h5part_write
 
@@ -629,6 +600,8 @@ _write_data (
 	herr = H5Dclose ( dataset_id );
 	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
 
+	f->empty = 0;
+
 	return H5PART_SUCCESS;
 }
 
@@ -861,16 +834,16 @@ _H5Part_get_attrib_info (
 	attrib_id = H5Aopen_idx ( id, attrib_idx );
 	if ( attrib_id < 0 ) return HANDLE_H5A_OPEN_IDX_ERR ( attrib_idx );
 
-	mytype = H5Aget_type ( attrib_id );
-	if ( attrib_id < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
-
-	space_id =  H5Aget_space ( attrib_id );
-	if ( attrib_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;
-
 	if ( attrib_nelem ) {
+		space_id =  H5Aget_space ( attrib_id );
+		if ( space_id < 0 ) return HANDLE_H5A_GET_SPACE_ERR;
+
 		*attrib_nelem = H5Sget_simple_extent_npoints ( space_id );
 		if ( *attrib_nelem < 0 )
 			return HANDLE_H5S_GET_SIMPLE_EXTENT_NPOINTS_ERR;
+
+		herr = H5Sclose ( space_id );
+		if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
 	}
 	if ( attrib_name ) {
 		herr = H5Aget_name (
@@ -880,14 +853,14 @@ _H5Part_get_attrib_info (
 		if ( herr < 0 ) return HANDLE_H5A_GET_NAME_ERR;
 	}
 	if ( attrib_type ) {
+		mytype = H5Aget_type ( attrib_id );
+		if ( mytype < 0 ) return HANDLE_H5A_GET_TYPE_ERR;
+
 		*attrib_type = _H5Part_normalize_h5_type ( mytype );
+
+		herr = H5Tclose ( mytype );
+		if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
 	}
-	herr = H5Sclose ( space_id );
- 	if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
-
-	herr = H5Tclose ( mytype );
-	if ( herr < 0 ) return HANDLE_H5T_CLOSE_ERR;
-
 	herr = H5Aclose ( attrib_id);
 	if ( herr < 0 ) return HANDLE_H5A_CLOSE_ERR;
 
@@ -1303,7 +1276,10 @@ _H5Part_set_step (
 
 	char name[128];
 
-	sprintf ( name, "%s#%lld", H5PART_GROUPNAME_STEP, (long long) step );
+	sprintf (
+		name,
+		"%s#%0*lld",
+		f->groupname_step, f->stepno_width, (long long) step );
 	herr_t herr = H5Gget_objinfo( f->file, name, 1, NULL );
 	if ( (f->mode != H5PART_READ) && ( herr >= 0 ) ) {
 		return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
@@ -1387,11 +1363,13 @@ _H5Part_iteration_operator (
 	herr_t herr;
 	H5G_stat_t objinfo;
 
-	herr = H5Gget_objinfo ( group_id, member_name, 1, &objinfo );
+	if ( data->type != H5G_UNKNOWN ) {
-	if ( herr < 0 ) return HANDLE_H5G_GET_OBJINFO_ERR ( member_name );
+		herr = H5Gget_objinfo ( group_id, member_name, 1, &objinfo );
+		if ( herr < 0 ) return HANDLE_H5G_GET_OBJINFO_ERR ( member_name );
 
-	if ( objinfo.type != data->type )
+		if ( objinfo.type != data->type )
-		return 0;	/* don't count, continue iteration */
+			return 0;/* don't count, continue iteration */
+	}
 
 	if ( data->name && (data->stop_idx == data->count) ) {
 		memset ( data->name, 0, data->len );
@@ -1516,8 +1494,8 @@ H5PartGetNumSteps (
 	return _H5Part_get_num_objects_matching_pattern (
 		f->file,
 		"/",
-		H5G_GROUP,
+		H5G_UNKNOWN,
-		H5PART_GROUPNAME_STEP );
+		f->groupname_step );
 }
 
 /*!
@@ -1539,8 +1517,10 @@ H5PartGetNumDatasets (
 
 	CHECK_FILEHANDLE( f );
 
-	sprintf ( stepname, "%s#%lld",
+	sprintf (
-		  H5PART_GROUPNAME_STEP, (long long) f->timestep );
+		stepname,
+		"%s#%0*lld",
+		f->groupname_step, f->stepno_width, (long long) f->timestep );
 
 	return _H5Part_get_num_objects ( f->file, stepname, H5G_DATASET );
 }
@@ -1570,8 +1550,10 @@ H5PartGetDatasetName (
 	CHECK_FILEHANDLE ( f );
 	CHECK_TIMEGROUP ( f );
 
-	sprintf ( stepname, "%s#%lld",
+	sprintf (
-		  H5PART_GROUPNAME_STEP, (long long)f->timestep);
+		stepname,
+		"%s#%0*lld",
+		f->groupname_step, f->stepno_width, (long long) f->timestep );
 
 	return _H5Part_get_object_name (
 		f->file,
@@ -1613,8 +1595,10 @@ H5PartGetDatasetInfo (
 	CHECK_FILEHANDLE ( f );
 	CHECK_TIMEGROUP ( f );
 
-	sprintf ( step_name, "%s#%lld",
+	sprintf (
-		  H5PART_GROUPNAME_STEP, (long long)f->timestep);
+		step_name,
+		"%s#%0*lld",
+		f->groupname_step, f->stepno_width, (long long) f->timestep );
 
 	herr = _H5Part_get_object_name (
 		f->timegroup,
@@ -1734,8 +1718,10 @@ _H5Part_get_num_particles (
 
 	/* Get first dataset in current time-step */
 	sprintf (
-		step_name, "%s#%lld",
+		step_name,
-		H5PART_GROUPNAME_STEP, (long long) f->timestep );
+		"%s#%0*lld",
+		f->groupname_step, f->stepno_width, (long long) f->timestep );
+
 	herr = _H5Part_get_object_name (
 		f->file,
 		step_name,
@@ -1903,7 +1889,7 @@ _set_view (
 	/* setting up the new view */
 	f->viewstart =  start;
 	f->viewend =    end;
-	f->nparticles = end - start;
+	f->nparticles = end - start + 1;
 	
 	/* declare overall datasize */
 	f->shape = H5Screate_simple ( 1, &total, &total );

src/H5Part.h

@@ -61,6 +61,13 @@ H5PartCloseFile (
 
 
 /*============== File Writing Functions ==================== */
+h5part_int64_t
+H5PartDefineStepName (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int64_t width
+	);
+
 h5part_int64_t
 H5PartSetNumParticles ( 
 	H5PartFile *f, 

src/H5PartTypes.h

@@ -14,6 +14,10 @@ __attribute__ ((format (printf, 3, 4)))
 #endif
  ;
 
+#ifndef PARALLEL_IO
+typedef unsigned long		MPI_Comm;
+#endif
+
 struct H5BlockFile;
 
 /**
@@ -25,7 +29,11 @@ struct H5BlockFile;
    H5PartCloseFile().  
 */
 struct H5PartFile {
-	hid_t file;
+	hid_t	file;
+	char	*groupname_step;
+	int	stepno_width;
+	int	empty;
+	
 	h5part_int64_t timestep;
 	hsize_t nparticles;
 	
@@ -60,12 +68,12 @@ struct H5PartFile {
 	   The index of the processor this process is running on.
 	*/
 	int myproc;
-#ifdef PARALLEL_IO
+
 	/**
 	   MPI comnunicator
 	*/
 	MPI_Comm comm;
-#endif
+
 	struct H5BlockStruct *block;
 	h5part_int64_t (*close_block)(struct H5PartFile *f);
 };

test/Makefile.am

@@ -12,8 +12,7 @@ MPICC = @MPICC@
 
 # COMPILER FLAG SETTING
 CFLAGS = @CFLAGS@
-ADDFLAGS = @ADDFLAGS@
+FFLAGS = @FFLAGS@ @MPIINC@
-FFLAGS = @FFLAGS@ @MPIINC@ $(ADDFLAGS) 
 
 # LIBRARIES
 SZLIB = @SZLIB@

tools/Makefile.am

@@ -33,7 +33,7 @@ H5PINC = -I@H5P_LIB_LOC@
 bin_PROGRAMS = @BUILD_TOOLS@
 
 # Listing of all programs that maybe built. (Has to know statically...)
-EXTRA_PROGRAMS = h5pAttrib h5pToGNUplot homdynToH5p
+EXTRA_PROGRAMS = h5pAttrib h5pToGNUplot # homdynToH5p
 
 # Extra files that I wish to include in the dist tar ball.
 EXTRA_DIST = h5pAttrib.cc h5pToGNUplot.cc## TO BE TAILORED LATER...
@@ -43,7 +43,7 @@ h5pAttrib_SOURCES = h5pAttrib.cc
 
 h5pToGNUplot_SOURCES = h5pToGNUplot.cc
 
-homdynToH5p_SOURCES = homdynToH5p.cc
+#homdynToH5p_SOURCES = homdynToH5p.cc
 
 # Specific building instruction (What compilers to use...)
 # ------------ Build Tools ------------

tools/homdynToH5p.cc

@@ -31,6 +31,7 @@ int main(int argc,char *argv[]){
 
   double data[nCol][10000];
   string headers[nCol];
+  string units[nCol];
 
   string fnStr("HBUNCH.OUT");
 
@@ -75,15 +76,97 @@ int main(int argc,char *argv[]){
   }
 
   H5PartWriteFileAttribString(file,"File Description", "This file contains HOMDYN HBUNCH.OUT data");
+
+  H5PartWriteFileAttribString(file,"tUnit","s");
+  H5PartWriteFileAttribString(file,"xUnit","m");
+  H5PartWriteFileAttribString(file,"yUnit","m");
+  H5PartWriteFileAttribString(file,"zUnit","m");
+  H5PartWriteFileAttribString(file,"pxUnit","#beta#gamma");
+  H5PartWriteFileAttribString(file,"pyUnit","#beta#gamma");
+  H5PartWriteFileAttribString(file,"pzUnit","#beta#gamma");
+  H5PartWriteFileAttribString(file,"idUnit","1");
+  H5PartWriteFileAttribString(file,"SPOSUnit","m");
+  H5PartWriteFileAttribString(file,"TIMEUnit","s");
+  H5PartWriteFileAttribString(file,"#gammaUnit","1");
+  H5PartWriteFileAttribString(file,"ENERGYUnit","MeV");
+  H5PartWriteFileAttribString(file,"#varepsilonUnit","m rad");
+  H5PartWriteFileAttribString(file,"#varepsilonrUnit","m rad");
+
+  H5PartWriteFileAttribString(file,"#varepsilonr-geomUnit","m rad");
+  H5PartWriteFileAttribString(file,"RMSXUnit","m");
+  H5PartWriteFileAttribString(file,"RMSRUnit","m");
+  H5PartWriteFileAttribString(file,"RMSPUnit","#beta#gamma");
+
+  H5PartWriteFileAttribString(file,"maxdEUnit","MeV");
+  H5PartWriteFileAttribString(file,"max#phiUnit","deg");
+
+  H5PartWriteFileAttribString(file,"phizUnit","deg");
+  H5PartWriteFileAttribString(file,"enezUnit","keV");
   
-  for (int c=0;c<nCol;c++)	
+/*
-   int rc = H5PartWriteFileAttribString(file,(headers[c]+string("Unit")).c_str(), " ");	;
+1       Z_[m] 
+2	sigma_r_[mm] 
+3	sigma_z_[mm] 
+4	I_[A] 
+5	sigma_x_[mm]         
+6	enx_[um] 
+7	sigma_y_[mm] 
+8	eny_[um] 
+9	T_[MeV] 
+10	dg/g_[%] 
+11	DE_[MeV]          
+12	elz_[KeVmm] 	
+13	Ez_[MV/m] 
+14	Bz_[T] Bx_[G] By_[G] 	
+15	Qgrad_[T/m] 
+16	ByWig     
+17	BHOR_[T] 
+18	Time_[nsec] 
+19	beta 
+20	R/gL 
+21	Lplas_[m] 
+22	Zeq_[m] 
+23	EWsteady
+*/
 
   for (int t=0;t<nLines;t++)	{
-   H5PartSetStep(file,t); /* must set the current timestep in file */
+    H5PartSetStep(file,t); /* must set the current timestep in file */
-   for (int c=0;c<nCol;c++) {
+
-    int rc = H5PartWriteStepAttrib(file,headers[c].c_str(), H5T_NATIVE_DOUBLE,&data[c][t],1);
+    double d3[3];
-   }	
+    double dummy = 0.0;
+    int rc;
+	
+    rc = H5PartWriteStepAttrib(file,"SPOS", H5T_NATIVE_DOUBLE,&data[0][t],1);
+
+    dummy = data[1][t]/1000.0;
+    rc = H5PartWriteStepAttrib(file,"RMSR", H5T_NATIVE_DOUBLE,&dummy,1);
+    rc = H5PartWriteStepAttrib(file,"TIME", H5T_NATIVE_DOUBLE,&data[17][t],1);
+    rc = H5PartWriteStepAttrib(file,"ENERGY", H5T_NATIVE_DOUBLE,&data[8][t],1);
+
+    d3[0] = data[4][t]/1000.0;
+    d3[1] = data[6][t]/1000.0;
+    d3[2] = 0.0;
+    rc = H5PartWriteStepAttrib(file,"RMSX", H5T_NATIVE_DOUBLE,&d3,3);
+
+    d3[0] = data[5][t]/1000000.0;
+    d3[1] = data[7][t]/1000000.0;
+    d3[2] = 0.0;
+    rc = H5PartWriteStepAttrib(file,"#varepsilon", H5T_NATIVE_DOUBLE,&d3,3);
+
+
+    d3[0] = 0.0;
+    d3[1] = 0.0;
+    d3[2] = 0.0;
+
+    rc = H5PartWriteStepAttrib(file,"#gamma", H5T_NATIVE_DOUBLE,&dummy,1);
+    rc = H5PartWriteStepAttrib(file,"#varepsilonr", H5T_NATIVE_DOUBLE,&d3,3);
+    rc = H5PartWriteStepAttrib(file,"#varepsilonr-geom", H5T_NATIVE_DOUBLE,&d3,3);
+    rc = H5PartWriteStepAttrib(file,"RMSP", H5T_NATIVE_DOUBLE,&d3,3);
+
+    rc = H5PartWriteStepAttrib(file,"maxdE", H5T_NATIVE_DOUBLE,&dummy,1);
+    rc = H5PartWriteStepAttrib(file,"max#phi", H5T_NATIVE_DOUBLE,&dummy,1);
+    rc = H5PartWriteStepAttrib(file,"phiz", H5T_NATIVE_DOUBLE,&dummy,1);
+    rc = H5PartWriteStepAttrib(file,"enez", H5T_NATIVE_DOUBLE,&dummy,1);
   }
   H5PartCloseFile(file);
 } 

visit_plugins/databases/H5Part/avth5partFileFormat.C

@@ -24,7 +24,6 @@
 
 
 //h5part specific
-#include <H5Part.h>
 #include <stdio.h>
 #include <stdlib.h>
 
@@ -82,11 +81,11 @@ avth5partFileFormat::avth5partFileFormat(const char *filename)
     pointvarnames.resize(npointvars);
     cout << "constructor: nvariables: " << npointvars << "\n";
 
-		char name[64];
+		char name[128];
-		int status;
+		h5part_int64_t status;
     for (j=0; j < npointvars; j++){
-      status = H5PartGetDatasetName(file,j, name,64);
+      status = H5PartGetDatasetName(file,j, name,128);
-			if (status != 1){
+			if (status != H5PART_SUCCESS){
 				EXCEPTION1(VisItException, "could not read a variable name");
 			}
       pointvarnames[j] = name;
@@ -110,13 +109,13 @@ avth5partFileFormat::avth5partFileFormat(const char *filename)
 int
 avth5partFileFormat::GetNTimesteps(void)
 {
-    int nt;
+    h5part_int64_t nt;
     H5PartFile *file;
     file = H5PartOpenFile(fname.c_str(),H5PART_READ);
     H5PartSetStep(file,0);
     nt=H5PartGetNumSteps(file); /* get number of steps in file */
     H5PartCloseFile(file);
-    return nt;
+    return (int) nt;
 }
 
 
@@ -333,14 +332,15 @@ avth5partFileFormat::GetMesh(int timestate, int domain, const char *meshname)
 #ifdef PARALLEL_IO
  	nprocs = PAR_Size();	
 #endif
+
   H5PartSetStep(file,timestate);
 
   //points
   tnpoints= (int) H5PartGetNumParticles(file);
-  unsigned long long idStart = ((int)(tnpoints/nprocs))*domain;
+  h5part_int64_t idStart = (( h5part_int64_t)(tnpoints/nprocs))*domain;
-	unsigned long long idEnd;	
+	h5part_int64_t idEnd;	
 	if (domain < nprocs-1) 
-  	idEnd   = ((unsigned long int)(tnpoints/nprocs))*(domain+1);
+  	idEnd   = ((h5part_int64_t)(tnpoints/nprocs))*(domain+1);
 	else if (domain == nprocs - 1)
   	idEnd   = tnpoints;
 
@@ -358,21 +358,21 @@ avth5partFileFormat::GetMesh(int timestate, int domain, const char *meshname)
     EXCEPTION1(VisItException, "npoints is zero");
 
   points.resize(npoints*nspace);
-  double *x, *y, *z;
+  h5part_float64_t *x, *y, *z;
-  x = (double *) malloc(sizeof(double)*npoints);
+  x = (h5part_float64_t *) malloc(sizeof(h5part_float64_t)*npoints);
-  y = (double *) malloc(sizeof(double)*npoints);
+  y = (h5part_float64_t *) malloc(sizeof(h5part_float64_t)*npoints);
-  z = (double *) malloc(sizeof(double)*npoints);
+  z = (h5part_float64_t *) malloc(sizeof(h5part_float64_t)*npoints);
 
 
-  int status = 0;
+  h5part_int64_t status = H5PART_SUCCESS; 
   status = H5PartReadDataFloat64(file, "x", x);
-  if (status != 1)
+  if (status != H5PART_SUCCESS)
   EXCEPTION1(VisItException, "Could not read x coordinates");
   status = H5PartReadDataFloat64(file, "y", y);
-  if (status != 1)
+  if (status != H5PART_SUCCESS)
   EXCEPTION1(VisItException, "Could not read y coordinates");
   status = H5PartReadDataFloat64(file, "z", z);
-  if (status != 1)
+  if (status != H5PART_SUCCESS)
   EXCEPTION1(VisItException, "Could not read z coordinates");
   for (long int i = 0; i < npoints; i++){
     points[nspace*i] = (float) x[i];
@@ -464,8 +464,8 @@ avth5partFileFormat::GetVar(int timestate, int domain, const char *varname)
   if (!file)
     EXCEPTION1(InvalidFilesException, fname.c_str());
 
-  int status;
+	h5part_int64_t status;
-  long int tnpoints, npoints;
+  h5part_int64_t tnpoints, npoints;
 	int npointvars;
   int nspace = 3;
 	int nprocs = 1;
@@ -475,44 +475,44 @@ avth5partFileFormat::GetVar(int timestate, int domain, const char *varname)
 
   H5PartSetStep(file,timestate);
   //points
-  tnpoints= (long int) H5PartGetNumParticles(file);
+  tnpoints= H5PartGetNumParticles(file);
   //point vars
 
   char name[64];
-  long long *idvar;
+  h5part_int64_t *idvar;
   double *data;
-	unsigned long long idStart = ((int)(tnpoints/nprocs))*domain;
+	h5part_int64_t idStart = ((h5part_int64_t)(tnpoints/nprocs))*domain;
-  unsigned long long idEnd; 
+  h5part_int64_t idEnd; 
   if (domain < nprocs-1) 
-    idEnd   = ((unsigned long int)(tnpoints/nprocs))*(domain+1);
+    idEnd   = ((h5part_int64_t)(tnpoints/nprocs))*(domain+1);
   else if (domain == nprocs - 1)
-    idEnd   = tnpoints;
+    idEnd   = (h5part_int64_t)tnpoints;
 
   H5PartSetView(file,idStart,idEnd);
-	npoints= (int) H5PartGetNumParticles(file);
+	npoints= H5PartGetNumParticles(file);
 	cout << "GetVar: npoints for domain " << domain << ": " << npoints << "\n"; 
 
-  for (int j=0; j < pointvarnames.size(); j++){
+  for (size_t j=0; j < (size_t)(pointvarnames.size()); j++){
     status = H5PartGetDatasetName(file,j, name,64);
     if (pointvarnames[j] == name) {
       if (strstr(name, "id") != NULL){
-        idvar = (long long *) malloc(sizeof(long long)*npoints);
+        idvar = (h5part_int64_t *) malloc(sizeof(h5part_int64_t)*npoints);
         status = H5PartReadDataInt64(file, name, idvar);
-        if (status != 1)
+        if (status != H5PART_SUCCESS)
           EXCEPTION1(VisItException, "Could not read dataset");
         pointvars[j].resize(npoints);
-        for (long int i=0; i < npoints; i++){
+        for (size_t i=0; i < (size_t) npoints; i++){
           pointvars[j][i] = (float) idvar[i];
         }
         if (idvar != NULL)
           free(idvar);
       } else {
-        data = (double *) malloc(sizeof(double)*npoints);
+        data = (h5part_float64_t *) malloc(sizeof(h5part_float64_t)*npoints);
         status = H5PartReadDataFloat64(file, name, data);
-        if (status != 1)
+        if (status != H5PART_SUCCESS)
           EXCEPTION1(VisItException, "Could not read dataset");
         pointvars[j].resize(npoints);
-        for (long int i=0; i < npoints; i++){
+        for (size_t i=0; i < (size_t)(npoints); i++){
           pointvars[j][i] = (float) data[i];
         }
         if (data != NULL)

visit_plugins/databases/H5Part/avth5partFileFormat.h

@@ -6,7 +6,7 @@
 #define AVT_h5part_FILE_FORMAT_H
 
 #include <avtMTMDFileFormat.h>
-#include <H5Part.hh>
+#include <H5Part.h>
 
 #include <vector>
 #include <string>