Preparing tag 1.4

- fix links to software
	- HDF5 build instructions removed

.gitattributes

@@ -28,6 +28,7 @@ doc/H5PartVisIt/cloud_visit_2D.png -text
 doc/H5PartVisIt/cloud_visit_2D.s.png -text
 doc/H5PartVisIt/visit_query1.png -text
 doc/H5PartVisIt/visit_query1.s.png -text
+doc/H5X_File_Format.txt -text
 doc/H5tools/H5tools.html -text
 doc/H5tools/H5tools_files/snapshot1.jpg -text
 doc/InternalLayout.html -text

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], [1.3.3], [h5part@lists.psi.ch], 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/BuildingHDF5.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">
 
 
@@ -15,7 +13,7 @@
     <title>Building HDF5</title>
   </head>
 
-  <body bgcolor="#F0F0F0">
+  <body>
     <font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
     <UL>
       <LI><a href="#ConfigOptions">Configure Options</a>
@@ -64,5 +62,3 @@ source .tcshr (.cshrc, .bashrc) in the one that you are using.
 
 You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
 </div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/Downloading.html

@@ -6,14 +6,12 @@
 <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>
 
   </head>
-   <body bgcolor="#F0F0F0">
+   <body>
     <font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
     <UL>
       <LI><a href="#hdf5">Downloading HDF5</a>
@@ -23,28 +21,17 @@
     <hr>
     <a name="hdf5">
     <h2>Downloading HDF5</h2></a>
-	You will need to download and install the hdf5 library and link H5Part with it.
+	You will need to download and install the HDF5 library and link H5Part with it.
-	<pre>
+	<UL>
-	ftp ftp.ncsa.uiuc.edu
+	  <LI><a href="ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz">ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz</a></LI>
-	username: anonymous
+	  <LI><a href="http://www.zlib.net/zlib-1.2.3.tar.gz">http://www.zlib.net/zlib-1.2.3.tar.gz</a></LI>
-	password: your email
+	  <LI><a href="ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szip-2.0.tar.gz">ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szib-2.0.tar.gz</a></LI>
-	cd HDF/HDF5/current/src
+	</UL>
-	ls
+         <P>
-	get hdf5-1.6.5.tar.gz (get the current version, this as the one on April 20th, 2006)
+	  Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
-	cd szip/src
+         </P>
-	ls
-	get szip-2.0.tar.gz (get the current version, this as the one on April 20th, 2006)
-	cd ../../
-	cd zlib/1.2/src
-	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">
+    <h2 id="h5part">Downloading H5Part</h2>
-    <h2>Downloading H5Part</h2></a>
+        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>.
-	Please contact <address><a href="mailto:andreas.adelmann@psi.ch">Andreas Adelmann</a></address>.
  
 </div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.3.1
+PROJECT_NUMBER         = 1.3.3
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English

doc/H5PartTools.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">
 
 
@@ -15,7 +13,7 @@
 	<title>H5Part Utility Tools</title>
 </head>
 
-  <body bgcolor="#F0F0F0">
+  <body>
     <font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
     <UL>
       <LI><a href="h5pAttrib">h5pAttrib</a>
@@ -94,6 +92,3 @@ usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTION
 
 </div>
 
-<!--#include virtual="/include/dateFooter.html"-->
-
-

doc/H5X_File_Format.txt

@@ -0,0 +1,151 @@
+Proposal for a more general file format used by H5Part/H5Block
+
+                                                 Authors: Achim Gsell
+                                                 Status:  Draft
+
+1. Introduction
+
+H5X is the file format used by H5Part and H5Block.  H5X is designed on
+top of HDF5: A H5X file is a very special HDF5 file.
+
+	+--------------------+
+	|   Application      |
+	+--------------------+
+	| H5Part/H5Block API |
+	+--------------------+
+	|      H5X API       |
+	+--------------------+
+	|     HDF5 API       |
+	+--------------------+
+	|  Filesystem of OS  |
+	+--------------------+
+
+
+2. H5X file format specification
+
+2.1 The root group
+
+2.1.1 File attributes
+
+Attributes of the HDF5 root group are called "file attributes". There
+are no restrictions on file attribute names. Supported values are
+scalars and arrays of 64bit integer and 64bit floating point number as
+well as string values,  but not arrays of strings.
+
+2.1.1.1 Predefined file attributes
+
+__stepname__ (optional)
+	See below.
+
+__stepnumwidth__ (optional)
+	See below.
+
+2.1.2 Members of the root group
+
+Members of the root group are special formated HDF5 groups called
+"step groups".  The name of a step group is "<name>#<number>". 
+Whereby <name> is either defined by the optional file attribute
+__stepname__ or set to "Step" by default. <number> is an 
+unsigned integer less than 2^63. 
+
+/
++- Step#0
++- Step#1
+...
++- Step#n
++- StepProperties [NEW]
++- Mesh [NEW]
+
+The optional file attribute __stepnumwidth__ defines the minimum width
+of <number> in the name of the step group. The number is padded with
+'0'. The minimum width defaults to zero, so that no paddings occurs. 
+Example: With __stepnumwidth__ := 5 the name of the step group with
+number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
+"Step#42". 
+
+Step groups may be unsorted in the HDF5 file und may not be number
+consecutively. 
+
+
+2.2    Format of a step group
+
+2.2.1  Step attributes
+
+Step attributes are HDF5 attributes asigned to a step group.  There
+are no restrictions on file attribute names. Supported values are
+scalars and arrays of 64bit integer and 64bit floating point number as
+well as string values,  but not arrays of strings.
+
+2.2.2  Predefined step attributes
+
+No predefined step attributes exists.
+
+
+2.2.3  Members of a step group
+
+Members of a step group are HDF5 datasets and optional one HDF5 group
+with the name "Block". HDF5 datasets in a step group are called "step
+datasets". The optional block group is called "block data". 
+
+Mesh?!
+
+2.2.4  Step datasets
+
+Step datasets are arrays of rank 1.  The dataset size must be the same
+for all datasets inside a step.  The size of the dataset may vary
+from step to step.  Array values are 64bit integer or 64bit floating
+point numbers. No limitations (other than given by HDF5) are given on
+step dataset names.
+
+
+2.2.5  Block Data
+
+The block data group is a container for an arbitrary number of field
+data. A field is a data structure to store arrays of rank m with
+n-dimensional vector values. Fields are represented within HDF5
+groups. The HDF5 group name is the unique identifier for a field in
+the current step.
+
+2.2.5.1 m-rank fields with n-dimensional-vector values
+
+Values are stored per dimension in separate datasets. Thus we have n
+datasets for a field with n-dimensional vector values.  Each dataset
+corresponse to one dimension. The datasets are numbered from '0' to
+'n-1'. Arrays are stored in column major order (Fortran indexing
+scheme).
+
+/				# HDF5 root group
+...
++- Step#<i>			# HDF5 group
+   |
+   +- Block			# HDF5 group
+      |
+      +- <field name>		# HDF5 group
+         |
+         +- 0			# HDF5 dataset, first dim of vector
+	 +- 1			# HDF5 dataset, second dim of vector
+         ...
+        +- n-1			# HDF5 dataset, last dim of vector
+...
+
+2.2.5.2 m-rank fields with scalar values
+
+Fields with scalar values are stored as special case of fields with
+n-dimensional vector values with n := 1.
+
+/				# HDF5 root group
+...
++- Step#<i>			# HDF5 group
+   |
+   +- Block			# HDF5 group
+      |
+      +- <field name>		# HDF5 group
+         |
+         +- 0			# HDF5 dataset, scalar value
+...
+
+
+2.3    Step properties [NEW]
+
+
+

doc/UsingC.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">
 
 <h1>The C/C++ Application Programming Interface (API)</h1>
@@ -603,4 +601,3 @@ if (H5PartReadStepAttrib(file, "filename", &name[0]) == 1){
 
 </div>
 
-<!--#include virtual="/include/dateFooter.html"-->

doc/UsingF.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">
 
 
@@ -500,5 +498,3 @@ err=h5pt_readstepattrib(file,"RealTime",data)
 
 
 </div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/h5part.html

@@ -9,7 +9,7 @@
 
 <div id="maincenter">
 <font face="arial,helvetica"><h1>H5Part: a Portable High Performance Parallel Data Interface to HDF5</h1></font>
-<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, September 2006</h2></font>
+<!--<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, September 2006</h2></font>-->
 <font face="arial,helvetica" color="#555588"><h2>Motivation</h2></font>
 <P>
 <TABLE>
@@ -105,17 +105,17 @@ of datasets that contain multiple fields.
 <LI><a href="UsingF.html">Using the F77/F90 interface</a>
 <LI><a href="InternalLayout.html">Logical Internal HDF5 File</a>
 <LI><a href="H5PartTools.html">H5Part Utility Tools</a>
-<LI><a href="ReferencePages/index.html">Reference Manual</a>
+<LI><a href="ReferencePages/index.html">Reference Manual</a> (Note: Requires doxygen
+to be run in the directory /doc)
 </UL>
 
 <font face="arial,helvetica" color="#555588"><h2>H5Part Visualization Tools</h2></font>
 <UL>
-<LI><a href="H5PartExpress.html">H5Part Express Reader</a>
+<!--<LI><a href="H5PartExpress.html">H5Part Express Reader</a>-->
 <LI><a href="H5PartVisIt.html">H5Part VisIt Reader</a>
-<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>
+<!--<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>-->
 <LI><a href="http://www.cscs.ch/a-display.php?id=170">H5Part sparticles Reader: developed at CSCS, Switzerland</a>
-
+<LI><a href="http://vis.lbl.gov/Vignettes/PartView/index.html">PartView Visualization Application</a>
-<LI><a href="H5PartPartView.html">PartView Visualization Application</a>
 </UL>
 </div>
 

src/H5Part.c

@@ -7,19 +7,40 @@ analysis needs to be preserved, reading and writing such enormous
 restart files on massively parallel supercomputing systems remains
 challenging. 
 
-H5Part consists of Particles, Block structured Fields and unstructured
+H5Part consists of Particles and Block structured Fields.
-data (Topo).
 
-Developed by  .
+Developed by:
 
-For further information contact: <a href="mailto:xxxxx">xxxxxx</a> - 
+<UL>
-xxxx xxxxx, (xxx) xxx.
+<LI> Andreas Adelmann (PSI) </LI>
+<LI> Achim Gsell (PSI) </LI>
+<LI> Benedikt Oswald (PSI) </LI>
+
+<LI> Wes Bethel (NERSC/LBNL)</LI>
+<LI> John Shalf (NERSC/LBNL)</LI>
+<LI> Cristina Siegerist (NERSC/LBNL)</LI>
+</UL>
 
-Last modified on xxx xx, 2006.
 
 Papers: 
 
-<a href="http://www-vis.lbl.gov/Research/AcceleratorSAPP/index.html">LBNL Vis Group </a><br>
+<UL>
+<LI> A. Adelmann, R.D. Ryne, C. Siegerist, J. Shalf,"From Visualization to Data Mining with Large Data Sets," <i>
+<a href="http://www.sns.gov/pac05">Particle Accelerator Conference (PAC05)</a></i>, Knoxville TN., May 16-20, 2005. (LBNL-57603)
+<a href="http://vis.lbl.gov/Publications/2005/FPAT082.pdf">FPAT082.pdf</a>
+</LI>
+
+
+<LI> A. Adelmann, R.D. Ryne, J. Shalf, C. Siegerist,"H5Part: A Portable High Performance Parallel Data Interface for Particle Simulations," <i>
+<a href="http://www.sns.gov/pac05">Particle Accelerator Conference (PAC05)</a></i>, Knoxville TN., May 16-20, 2005.
+<a href="http://vis.lbl.gov/Publications/2005/FPAT083.pdf">FPAT083.pdf</a>
+</LI>
+</UL>
+
+For further information contact: <a href="mailto:h5part@lists.psi.ch">h5part</a>
+
+Last modified on April 19, 2007.
+
 */
 
 
@@ -93,36 +114,13 @@ _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 +134,71 @@ 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->access_prop = H5Pcreate (H5P_FILE_ACCESS);
+	f->xfer_prop = f->create_prop = f->access_prop = H5P_DEFAULT;
-	if (f->access_prop < 0) {
+
-		HANDLE_H5P_CREATE_ERR;
+#ifdef PARALLEL_IO
-		goto error_cleanup;
+	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);
+		if (f->access_prop < 0) {
+			HANDLE_H5P_CREATE_ERR;
+			goto error_cleanup;
+		}
+
+		if (H5Pset_fapl_mpio (f->access_prop, comm, info) < 0) {
+			HANDLE_H5P_SET_FAPL_MPIO_ERR;
+			goto error_cleanup;
+		}
+		
+		/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
+		f->create_prop = H5P_DEFAULT;
+
+		/* currently create_prop is empty */
+		/* xfer_prop:  also used for parallel I/O, during actual writes
+		   rather than the access_prop which is for file creation. */
+		f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
+		if (f->xfer_prop < 0) {
+			HANDLE_H5P_CREATE_ERR;
+			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_fapl_mpio (f->access_prop, comm, info) < 0) {
-		HANDLE_H5P_SET_FAPL_MPIO_ERR;
-		goto error_cleanup;
-	}
-		
-	/* create_prop: tunable parameters like blocksize and btree sizes */
-	/* f->create_prop = H5Pcreate(H5P_FILE_CREATE); */
-	f->create_prop = H5P_DEFAULT;
-
-	/* currently create_prop is empty */
-	/* xfer_prop:  also used for parallel I/O, during actual writes
-	   rather than the access_prop which is for file creation. */
-	f->xfer_prop = H5Pcreate (H5P_DATASET_XFER);
-	if (f->xfer_prop < 0) {
-		HANDLE_H5P_CREATE_ERR;
-		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;
 #endif
 	if ( flags == H5PART_READ ) {
 		f->file = H5Fopen (filename, H5F_ACC_RDONLY, f->access_prop);
@@ -194,12 +206,14 @@ 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 +224,7 @@ 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 +255,9 @@ H5PartOpenFileParallel (
 
  error_cleanup:
 	if (f != NULL ) {
+		if (f->groupname_step) {
+			free (f->groupname_step);
+		}
 		if (f->pnparticles != NULL) {
 			free (f->pnparticles);
 		}
@@ -249,6 +266,39 @@ 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 +327,11 @@ 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 +411,9 @@ 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 +424,21 @@ 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 +621,8 @@ _write_data (
 	herr = H5Dclose ( dataset_id );
 	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
 
+	f->empty = 0;
+
 	return H5PART_SUCCESS;
 }
 
@@ -861,16 +855,16 @@ _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 +874,14 @@ _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 +1297,10 @@ _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 +1384,13 @@ _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 +1515,8 @@ H5PartGetNumSteps (
 	return _H5Part_get_num_objects_matching_pattern (
 		f->file,
 		"/",
-		H5G_GROUP,
+		H5G_UNKNOWN,
-		H5PART_GROUPNAME_STEP );
+		f->groupname_step );
 }
 
 /*!
@@ -1539,8 +1538,10 @@ 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 +1571,10 @@ 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,
@@ -1613,11 +1616,14 @@ 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,
+					//f->timegroup,
+		f->file,
 		step_name,
 		H5G_DATASET,
 		idx,
@@ -1734,8 +1740,10 @@ _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 +1911,7 @@ _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/Bench.c

@@ -22,13 +22,14 @@
 
 /*
 
-  bench <nParticles>
+bench <nParticles>
 
 
 */
 
 
 int main(int argc,char *argv[]){
+  printf("Start benchmarks...\n");
   MPI_Info info;
   int nprocs,rank;
   int trial;
@@ -48,6 +49,7 @@ int main(int argc,char *argv[]){
   H5PartFile *f;
 #endif
   char newfilename[128];
+  char lastfilename[128];
   FILE *fd;
   MPI_File file;
   MPI_Offset foffset;
@@ -74,7 +76,7 @@ int main(int argc,char *argv[]){
 
   
   /* printf("about to call create subarray with nparticles=%u localnp=%u offset=%u\n",
-	nparticles,localnp,offset); */
+     nparticles,localnp,offset); */
   MPI_Type_create_subarray(1, /* rank */
 			   &nparticles, /* size of the global array */
 			   &localnp, /* size of my local chunk */
@@ -86,148 +88,157 @@ int main(int argc,char *argv[]){
   MPI_Info_create(&info);
 
   if(rank==0) printf("Nprocs=%u Particles=%u*6attribs*sizeof(double) Particles/proc=%u Nsteps=%u Ntrials=%u\n",
-	nprocs,nparticles,localnp,NSTEPS,NTRIALS);
+		     nprocs,nparticles,localnp,NSTEPS,NTRIALS);
 	
 
   for(trial=0;trial<NTRIALS;trial++){
-  if(rank==0) printf("---------------------- Trial %u of %u ---------------------\n",trial+1,NTRIALS);
+    if(rank==0) printf("---------------------- Trial %u of %u ---------------------\n",trial+1,NTRIALS);
 
 
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  sprintf(filename,"%s.%u.mpio.dat",FILENAME,nprocs);
+    sprintf(filename,"%s.%u.mpio.dat",FILENAME,nprocs);
+    sprintf(lastfilename,"%s.%u.mpio.dat",FILENAME,nprocs);
 
-  if(rank==0) unlink(filename);
+    if(rank==0) unlink(filename);
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
 
-  MPI_File_open(MPI_COMM_WORLD,filename,
+    MPI_File_open(MPI_COMM_WORLD,filename,
-	MPI_MODE_CREATE | MPI_MODE_RDWR,
+		  MPI_MODE_CREATE | MPI_MODE_RDWR,
-	info,&file);
+		  info,&file);
 	
-  MPI_File_set_view(file,0,MPI_DOUBLE,chunktype,"native",info);
+    MPI_File_set_view(file,0,MPI_DOUBLE,chunktype,"native",info);
-  /* now a barrier to get the start timers roughly synced*/
+    /* now a barrier to get the start timers roughly synced*/
-  MPI_Barrier(MPI_COMM_WORLD);
+    MPI_Barrier(MPI_COMM_WORLD);
-  curtime = starttime = MPI_Wtime();
+    curtime = starttime = MPI_Wtime();
-  endtime = starttime+5.0*60.0; /* end in 5 minutes */
+    endtime = starttime+5.0*60.0; /* end in 5 minutes */
-  MPI_Bcast(&endtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    MPI_Bcast(&endtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  /* must touch the entire array after each write */
+    /* must touch the entire array after each write */
-  /* ensures cache-invalidation */
+    /* ensures cache-invalidation */
-  foffset=0;
+    foffset=0;
-  i=0;
+    i=0;
-  curtime=starttime;
+    curtime=starttime;
-  for(i=0;i<NSTEPS;i++){
+    for(i=0;i<NSTEPS;i++){
-    int n;
+      int n;
-    MPI_Status status;
+      MPI_Status status;
-    for(j=0;j<6;j++){
+      for(j=0;j<6;j++){
-      /* touch data */
+	/* touch data */
-      for(n=0;n<localnp;n++)
+	for(n=0;n<localnp;n++)
-	(data[j])[n]=(double)rank;
+	  (data[j])[n]=(double)rank;
-      /* write to that file */
+	/* write to that file */
-      /*  MPI_File_set_view(file,foffset,MPI_DOUBLE,chunktype,"native",info);*/
+	/*  MPI_File_set_view(file,foffset,MPI_DOUBLE,chunktype,"native",info);*/
-      MPI_File_write_at_all(file,
+	MPI_File_write_at_all(file,
-			    foffset,
+			      foffset,
-			    data[j],
+			      data[j],
-			    localnp,
+			      localnp,
-			    MPI_DOUBLE,&status);
+			      MPI_DOUBLE,&status);
-      foffset+=nparticles/nprocs;
+	foffset+=nparticles/nprocs;
+      }
+      curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
+      MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
     }
-    curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
+    MPI_File_close(&file);
-    MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    MPI_Barrier(MPI_COMM_WORLD);
-  }
+    endtime=MPI_Wtime();
-  MPI_File_close(&file);
+    sprintf(filename,"%s.%u.h5.dat",FILENAME,nprocs);
-  MPI_Barrier(MPI_COMM_WORLD);
+    /* foffset*=nprocs; if we want total megabytes written */
-  endtime=MPI_Wtime();
+    if(rank==0){
-  sprintf(filename,"%s.%u.h5.dat",FILENAME,nprocs);
+      puts("*");
-  /* foffset*=nprocs; if we want total megabytes written */
+      unlink(filename);
-  if(rank==0){
+      puts("======================================================");
-    puts("*");
+      printf("Raw MPI-IO Total Duration %lf seconds, iterations=%u %lf Megabytes written per processor Nprocs= %u \n",
-    unlink(filename);
+	     (endtime-starttime),i,((double)foffset)/(1024.0*1024.0),nprocs);
-    puts("======================================================");
+      printf("Raw MPI-IO Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
-    printf("Raw MPI-IO Total Duration %lf seconds, iterations=%u %lf Megabytes written per processor Nprocs= %u \n",
+	     (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
-	   (endtime-starttime),i,((double)foffset)/(1024.0*1024.0),nprocs);
+	     (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
-    printf("Raw MPI-IO Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
+      puts("======================================================");
-	   (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
+    }
-	   (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
+
-    puts("======================================================");
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  }
+    /* OK, now we do this using H5Part */
-
+    sprintf(newfilename,"testio%u.%u.dat",rank,nprocs);
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    unlink(newfilename);
-  /* OK, now we do this using H5Part */
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  sprintf(newfilename,"testio%u.%u.dat",rank,nprocs);
+    fd = fopen(newfilename,"w");
-  unlink(newfilename);
+    /* start the timer */
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    starttime=endtime=MPI_Wtime();
-  fd = fopen(newfilename,"w");
+    for(i=0;i<NSTEPS;i++){
-  /* start the timer */
+      for(j=0;j<6;j++){
-  starttime=endtime=MPI_Wtime();
+	/* touch data */
-  for(i=0;i<NSTEPS;i++){
+	for(n=0;n<localnp;n++)
-    for(j=0;j<6;j++){
+	  (data[j])[n]=(double)rank;
-      /* touch data */
+	fwrite(data[j],sizeof(double),localnp,fd);
-      for(n=0;n<localnp;n++)
+      }
-	(data[j])[n]=(double)rank;
+      curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
-      fwrite(data[j],sizeof(double),localnp,fd);
+      MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+    }
+    fclose(fd);
+    MPI_Barrier(MPI_COMM_WORLD);
+    endtime=MPI_Wtime();
+    if(rank==0) puts("*");
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    unlink(newfilename);
+    MPI_Barrier(MPI_COMM_WORLD);
+    if(rank==0){
+      puts("======================================================");
+      printf("Raw 1-file-per-proc Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
+	     (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
+      printf("Raw 1-file-per-proc Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
+	     (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
+	     (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
+      puts("======================================================");
     }
-    curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
-    MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  }
-  fclose(fd);
-  MPI_Barrier(MPI_COMM_WORLD);
-  endtime=MPI_Wtime();
-  if(rank==0) puts("*");
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  unlink(newfilename);
-  MPI_Barrier(MPI_COMM_WORLD);
-  if(rank==0){
-    puts("======================================================");
-    printf("Raw 1-file-per-proc Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
-	   (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
-    printf("Raw 1-file-per-proc Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
-	   (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
-	   (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
-    puts("======================================================");
-  }
 
 #ifndef DISABLE_H5PART
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    //printf("H5Part benchmark...");
-  /* OK, now we do this using H5Part */
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  f = H5PartOpenFileParallel(filename,H5PART_WRITE,MPI_COMM_WORLD);
+    /* OK, now we do this using H5Part */
-  MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
+    f = H5PartOpenFileParallel(filename,H5PART_WRITE,MPI_COMM_WORLD);
-  /* start the timer */
+    MPI_Barrier(MPI_COMM_WORLD); /* to prevent unlink from interfering with file open */
-  starttime=endtime=MPI_Wtime();
+    /* start the timer */
-  H5PartSetNumParticles(f,localnp);
+    starttime=endtime=MPI_Wtime();
-  for(i=0;i<NSTEPS;i++){
+    H5PartSetNumParticles(f,localnp);
-    for(j=0;j<6;j++){
+    for(i=0;i<NSTEPS;i++){
-      /* touch data */
+      for(j=0;j<6;j++){
-      for(n=0;n<localnp;n++)
+	/* touch data */
-	(data[j])[n]=(double)rank;
+	for(n=0;n<localnp;n++)
-    }
+	  (data[j])[n]=(double)rank;
-    H5PartSetStep(f,i);
+      }
-    H5PartWriteDataFloat64(f,"x",x);
+      H5PartSetStep(f,i);
-    H5PartWriteDataFloat64(f,"y",y);
+      H5PartWriteDataFloat64(f,"x",x);
-    H5PartWriteDataFloat64(f,"z",z);
+      H5PartWriteDataFloat64(f,"y",y);
-    H5PartWriteDataFloat64(f,"px",px);
+      H5PartWriteDataFloat64(f,"z",z);
-    H5PartWriteDataFloat64(f,"py",py);
+      H5PartWriteDataFloat64(f,"px",px);
-    H5PartWriteDataFloat64(f,"pz",pz);
+      H5PartWriteDataFloat64(f,"py",py);
+      H5PartWriteDataFloat64(f,"pz",pz);
 
-    curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
+      curtime=MPI_Wtime(); /* ensure no race condition by broadcasting time */
-    MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
+      MPI_Bcast(&curtime,1,MPI_DOUBLE,0,MPI_COMM_WORLD);
-  }
+    }
-  H5PartCloseFile(f);
+    H5PartCloseFile(f);
-  MPI_Barrier(MPI_COMM_WORLD);
+    MPI_Barrier(MPI_COMM_WORLD);
-  endtime=MPI_Wtime();
+    endtime=MPI_Wtime();
-  if(rank==0){
+    if(rank==0){
-    puts("*");
+      puts("*");
-    unlink(filename);
+      unlink(filename);
-    puts("======================================================");
+      puts("======================================================");
-    printf("H5Part Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
+      printf("H5Part Total Duration %lf seconds, iterations=%u %lf Megabytes written Nprocs= %u \n",
-	   (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
+	     (endtime-starttime),NSTEPS,((double)foffset)/(1024.0*1024.0),nprocs);
-    printf("H5Part Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
+      printf("H5Part Effective Data Rate = %lf Megabytes/sec global and %lf Megabytes/sec per task Nprocs= %u \n",
-	   (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
+	     (double)(nprocs*localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),
-	   (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
+	     (double)(localnp*sizeof(double))*((double)NSTEPS)*6.0/((endtime-starttime)*1024.0*1024.0),nprocs);
-    puts("======================================================");
+      puts("======================================================");
-  }
+    }
-  MPI_Barrier(MPI_COMM_WORLD);
+    MPI_Barrier(MPI_COMM_WORLD);
 #endif
   } /* trials */
+
+  if (rank==0) {
+    printf("lastfilename: %s \n", lastfilename);
+    unlink(lastfilename);
+  }
+
   MPI_Finalize();
 
+
   return 0;
 }

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");
 
@@ -76,14 +77,96 @@ int main(int argc,char *argv[]){
 
   H5PartWriteFileAttribString(file,"File Description", "This file contains HOMDYN HBUNCH.OUT data");
 
-  for (int c=0;c<nCol;c++)	
+  H5PartWriteFileAttribString(file,"tUnit","s");
-   int rc = H5PartWriteFileAttribString(file,(headers[c]+string("Unit")).c_str(), " ");	;
+  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");
+  
+/*
+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>