Split tools into src and test - add folders

7 files changed, 2316 insertions, 0 deletions

diff --git a/tools/src/misc/CMakeLists.txt b/tools/src/misc/CMakeLists.txt
new file mode 100644
index 0000000..6fcff9c
--- /dev/null
+++ b/tools/src/misc/CMakeLists.txt
@@ -0,0 +1,67 @@
+cmake_minimum_required (VERSION 3.1.0)
+PROJECT (HDF5_TOOLS_SRC_MISC)
+
+#-----------------------------------------------------------------------------
+# Setup include Directories
+#-----------------------------------------------------------------------------
+INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
+
+# --------------------------------------------------------------------
+# Add the misc executables
+# --------------------------------------------------------------------
+#-- Misc Executables
+add_executable (h5debug ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c)
+TARGET_NAMING (h5debug STATIC)
+TARGET_C_PROPERTIES (h5debug STATIC " " " ")
+target_link_libraries (h5debug ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+set_target_properties (h5debug PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug")
+
+add_executable (h5repart ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c)
+TARGET_NAMING (h5repart STATIC)
+TARGET_C_PROPERTIES (h5repart STATIC " " " ")
+target_link_libraries (h5repart ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+set_target_properties (h5repart PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart")
+
+add_executable (h5mkgrp ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c)
+TARGET_NAMING (h5mkgrp STATIC)
+TARGET_C_PROPERTIES (h5mkgrp STATIC " " " ")
+target_link_libraries (h5mkgrp  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5mkgrp PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp")
+
+set (H5_DEP_EXECUTABLES
+    h5debug
+    h5repart
+    h5mkgrp
+)
+
+#-----------------------------------------------------------------------------
+# Generate the h5cc file containing settings needed to compile programs
+#-----------------------------------------------------------------------------
+#if (NOT WIN32)
+#  configure_file (${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5cc.in ${HDF5_BINARY_DIR}/h5cc @ONLY)
+#endif (NOT WIN32)
+
+##############################################################################
+##############################################################################
+###           I N S T A L L A T I O N                                      ###
+##############################################################################
+##############################################################################
+
+#-----------------------------------------------------------------------------
+# Rules for Installation of tools using make Install target
+#-----------------------------------------------------------------------------
+
+#INSTALL_PROGRAM_PDB (h5debug ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5repart ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5mkgrp ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+
+install (
+    TARGETS
+        h5debug h5repart h5mkgrp
+    EXPORT
+        ${HDF5_EXPORTED_TARGETS}
+    RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+)
diff --git a/tools/src/misc/Makefile.am b/tools/src/misc/Makefile.am
new file mode 100644
index 0000000..c069e9a
--- /dev/null
+++ b/tools/src/misc/Makefile.am
@@ -0,0 +1,61 @@
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+#
+# HDF5 Library Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+# Include src directory
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
+
+# These are our main targets, the tools
+bin_PROGRAMS=h5debug h5repart h5mkgrp
+bin_SCRIPTS=h5redeploy
+
+# Add h5debug, h5repart, and h5mkgrp specific linker flags here
+h5debug_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5repart_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+
+# Tell automake to clean h5redeploy script
+CLEANFILES=h5redeploy
+
+# These were generated by configure.  Remove them only when distclean.
+DISTCLEANFILES=h5cc
+
+# All programs rely on hdf5 library and h5tools library
+LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+
+# h5cc needs custom install and uninstall rules, since it may be
+# named h5pcc if hdf5 is being built in parallel mode.
+if BUILD_PARALLEL_CONDITIONAL
+  H5CC_NAME=h5pcc
+else
+  H5CC_NAME=h5cc
+endif
+
+install-exec-local:
+	@$(INSTALL) h5cc $(DESTDIR)$(bindir)/$(H5CC_NAME)
+uninstall-local:
+	@$(RM) $(DESTDIR)$(bindir)/$(H5CC_NAME)
+
+# How to build h5redeploy script
+h5redeploy: h5redeploy.in
+	@cp $(srcdir)/$@.in $@
+
+include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/misc/h5cc.in b/tools/src/misc/h5cc.in
new file mode 100644
index 0000000..1645855
--- /dev/null
+++ b/tools/src/misc/h5cc.in
@@ -0,0 +1,401 @@
+#! /bin/sh
+##
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+##
+
+# This tool is adapted from the mpicc command of the MPICH Software.
+
+############################################################################
+##                                                                        ##
+## Things You May Have to Modify:                                         ##
+##                                                                        ##
+## If the following paths don't point to the place were HDF5 is installed ##
+## on your system (i.e., you received a binary distribution or moved the  ##
+## files from the originally installed directory to another directory)    ##
+## then modify them accordingly to represent the new paths.               ##
+##                                                                        ##
+############################################################################
+prefix="@prefix@"
+exec_prefix="@exec_prefix@"
+libdir="@libdir@"
+includedir="@includedir@"
+HL="@HL@"
+
+############################################################################
+##                                                                        ##
+## Things You Can Modify to Override HDF5 Library Build Components:       ##
+##                                                                        ##
+## (Advanced usage - know what you're doing - you're on your own here.)   ##
+## The four variables below can be used to insert paths and flags in      ##
+## CPPFLAGS, CFLAGS, LDFLAGS, or LIBS in the h5cc compile line:           ##
+##    $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS   ##
+##    $LIBS $clibpath $link_objs $link_args $shared_link                  ##
+##                                                                        ##
+## These settings can be overriden by setting HDF5_CFLAGS,                ##
+## HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment.          ##
+##                                                                        ##
+############################################################################
+CFLAGSBASE=""
+CPPFLAGSBASE=""
+LDFLAGSBASE=""
+LIBSBASE=""
+
+############################################################################
+##                                                                        ##
+## You shouldn't have to modify anything below this line.                 ##
+##                                                                        ##
+############################################################################
+
+# Constants definitions
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+host_os="@host_os@"
+
+prog_name="`basename $0`"
+
+allargs=""
+compile_args=""
+libraries=""
+link_args=""
+link_objs=""
+clibpath=""
+
+do_link="yes"
+do_compile="no"
+dash_o="no"
+dash_c="no"
+get_output_file="no"
+
+SHOW="eval"
+CCBASE="@CC@"
+CLINKERBASE="@CC@"
+
+# CFLAGS, CPPFLAGS and LDFLAGS are reserved for use by the script user.
+# FLAGS brought from the hdf5 build are put in H5BLD_*FLAGS.
+
+# User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's 
+# LDFLAGS come just before clibpath, user's LIBS come after $link_objs and 
+# before the hdf5 libraries in $link_args, followed by any external library 
+# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in 
+# from the hdf5 build. The order of the flags is intended to give precedence
+# to the user's flags.
+H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@"
+H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+H5BLD_LIBS="@LIBS@"
+
+CC="${HDF5_CC:-$CCBASE}"
+CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
+CFLAGS="${HDF5_CFLAGS:-$CFLAGSBASE}"
+CPPFLAGS="${HDF5_CPPFLAGS:-$CPPFLAGSBASE}"
+LDFLAGS="${HDF5_LDFLAGS:-$LDFLAGSBASE}"
+LIBS="${HDF5_LIBS:-$LIBSBASE}"
+
+# If a static library is available, the default will be to use it.  If the only
+# available library is shared, it will be used by default.  The user can 
+# override either default, although choosing an unavailable library will result
+# in link errors.  
+STATIC_AVAILABLE="@enable_static@"
+if test "${STATIC_AVAILABLE}" = "yes"; then
+  USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
+else
+  USE_SHARED_LIB="${HDF5_USE_SHLIB:-yes}"
+fi
+
+
+usage() {
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS] <compile line>"
+  echo "  OPTIONS:"
+  echo "    -help        This help message."
+  echo "    -echo        Show all the shell commands executed"
+  echo "    -prefix=DIR  Prefix directory to find HDF5 lib/ and include/"
+  echo "                   subdirectories [default: $prefix]"
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS] <compile line>"
+  echo "  OPTIONS:"
+  echo "    -help        This help message."
+  echo "    -echo        Show all the shell commands executed"
+  echo "    -prefix=DIR  Prefix directory to find HDF5 lib/ and include/"
+  echo "                   subdirectories [default: $prefix]"
+  echo "    -show        Show the commands without executing them"
+  echo "    -showconfig  Show the HDF5 library configuration summary"
+  echo "    -shlib       Compile with shared HDF5 libraries [default for hdf5 built"
+  echo "                                                     without static libraries]"
+  echo "    -noshlib     Compile with static HDF5 libraries [default for hdf5 built"
+  echo "                                                     with static libraries]"
+  echo " "
+  echo "  <compile line>  - the normal compile line options for your compiler."
+  echo "                    $prog_name uses the same compiler you used to compile"
+  echo "                    HDF5. Check with your compiler's man pages for more"
+  echo "                    information on which options are needed."
+  echo " "
+  echo " You can override the compiler, linker, and whether or not to use static"
+  echo " or shared libraries to compile your program by setting the following"
+  echo " environment variables accordingly:"
+  echo " "
+  echo "   HDF5_CC                  -  use a different C compiler"
+  echo "   HDF5_CLINKER             -  use a different linker"
+  echo "   HDF5_USE_SHLIB=[yes|no]  -  use shared or static version of the HDF5 library"
+  echo "                                 [default: no except when built with only" 
+  echo "                                           shared libraries]"
+  echo " "
+  echo " You can also add or change paths and flags to the compile line using"
+  echo " the following environment varibles or by assigning them to their counterparts"
+  echo " in the 'Things You Can Modify to Override...'" section of $prog_name
+  echo " "
+  echo "  Variable              Current value to be replaced"
+  echo "  HDF5_CPPFLAGS         \"$CPPFLAGSBASE\""
+  echo "  HDF5_CFLAGS           \"$CFLAGSBASE\""
+  echo "  HDF5_LDFLAGS          \"$LDFLAGSBASE\""
+  echo "  HDF5_LIBS             \"$LIBSBASE\""
+  echo " "
+  echo " Note that adding library paths to HDF5_LDFLAGS where another hdf5 version"
+  echo " is located may link your program with that other hdf5 library version."
+  echo " "
+  exit $EXIT_FAILURE
+}
+
+# Show the configuration summary of the library recorded in the
+# libhdf5.settings file reside in the lib directory.
+showconfigure()
+{
+  cat ${libdir}/libhdf5.settings
+  status=$?
+}
+
+# Main
+status=$EXIT_SUCCESS
+
+if test "$#" = "0"; then
+  # No parameters specified, issue usage statement and exit.
+  usage
+fi
+
+case "$CC" in
+  gcc)
+    kind="gcc"
+    ;;
+  mpicc|mpcc|mpicc_r)
+    # Is this gcc masquarading as an MPI compiler?
+    if test "`${CC} -v 2>&1 | sed -n 2p | cut -c1-3`" = "gcc"; then
+      kind="gcc"
+    else
+      # Nope
+      kind="$host_os"
+    fi
+    ;;
+  *)
+    kind="$host_os"
+    ;;
+esac
+
+for arg in $@ ; do
+  if test "x$get_output_file" = "xyes"; then
+    link_args="$link_args $arg"
+    output_file="$arg"
+    get_output_file="no"
+    continue
+  fi
+
+  case "$arg" in
+    -c)
+      allargs="$allargs $arg"
+      compile_args="$compile_args $arg"
+
+      if test "x$do_link" = "xyes" -a -n "$output_file"; then
+        compile_args="$compile_args -o $output_file"
+      fi
+
+      do_link="no"
+      dash_c="yes"
+      ;;
+    -o)
+      allargs="$allargs $arg"
+      dash_o="yes"
+
+      if test "x$dash_c" = "xyes"; then
+        compile_args="$compile_args $arg"
+      else
+        link_args="$link_args $arg"
+        do_link="yes"
+        get_output_file="yes"
+      fi
+      ;;
+    -E|-M|-MT)
+      allargs="$allargs $arg"
+      compile_args="$compile_args $arg"
+      dash_c="yes"
+      do_link="no"
+      ;;
+    -l*)
+      libraries=" $libraries $arg "
+      allargs="$allargs $arg"
+      ;;
+    -prefix=*)
+      prefix="`expr "$arg" : '-prefix=\(.*\)'`"
+      ;;
+    -echo)
+      set -x
+      ;;
+    -show)
+      SHOW="echo"
+      ;;
+    -showconfig)
+      showconfigure
+      exit $status
+      ;;
+    -shlib)
+      USE_SHARED_LIB="yes"
+      ;;
+    -noshlib)
+      USE_SHARED_LIB="no"
+      ;;
+    -help)
+      usage
+      ;;
+    *\"*)
+      qarg="'"$arg"'"
+      allargs="$allargs $qarg"
+      ;;
+    *\'*)
+      qarg='\"'"$arg"'\"'
+      allargs="$allargs $qarg"
+      ;;
+    *)
+      allargs="$allargs $qarg"
+
+      if test -s "$arg"; then
+        ext=`expr "$arg" : '.*\(\..*\)'`
+
+        if test "x$ext" = "x.c"; then
+          do_compile="yes"
+          compile_args="$compile_args $arg"
+          fname=`basename $arg .c`
+          link_objs="$link_objs $fname.o"
+        elif test "x$ext" = "x.o"; then
+          if test "x$dash_c" = "xyes"; then
+            compile_args="$compile_args $arg"
+          else
+            do_link="yes"
+            link_objs="$link_objs $arg"
+          fi
+        elif test "x$ext" = "x.a"; then
+          # This is an archive that we're linking in
+          libraries=" $libraries $arg "
+        else
+          compile_args="$compile_args $arg"
+          link_args="$link_args $arg"
+        fi
+      else
+        compile_args="$compile_args $arg"
+        link_args="$link_args $arg"
+      fi
+      ;;
+  esac
+done
+
+if test "$dash_c" = "yes" -a "$do_compile" = no -a "$do_link" = no ; then
+    # -c was specified.  Force do_compile on.
+    do_compile=yes
+fi
+
+if test "x$do_compile" = "xyes"; then
+  if test "x$dash_c" != "xyes"; then
+    compile_args="-c $compile_args"
+  fi
+
+  $SHOW $CC -I$includedir $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $compile_args
+  status=$?
+
+  if test "$status" != "0"; then
+    exit $status
+  fi
+fi
+
+if test "x$do_link" = "xyes"; then
+  shared_link=""
+# conditionnaly link with the hl library  
+  if test "X$HL" = "Xhl"; then
+   libraries=" $libraries -lhdf5_hl -lhdf5 "
+  else
+   libraries=" $libraries  -lhdf5 "
+  fi
+  link_args="$link_args -L${libdir}"
+
+  case "$kind" in
+    gcc|linux*)
+      # MacOS X doesn't support the "-Wl,-rpath -Wl," style of linker flags.
+      # It appears to want none of them specified.
+      case "$host_os" in
+        darwin*)          flag="" ;;
+        *)                flag="-Wl,-rpath -Wl," ;;
+      esac
+      ;;
+    hpux*)                flag="-Wl,+b -Wl," ;;
+    freebsd*|solaris*)    flag="-R" ;;
+    rs6000*|aix*)         flag="-L" ;;
+    sgi)                  flag="-rpath " ;;
+    *)                    flag="" ;;
+  esac
+
+  if test -n "$flag"; then
+    shared_link="${flag}${libdir}"
+  fi
+
+  if test "x$USE_SHARED_LIB" != "xyes"; then
+    # The "-lhdf5" & "-lhdf5_hl" flags are in here already...This is a static
+    # compile though, so change it to the static version (.a) of the library.
+    new_libraries=""
+    for lib in $libraries; do
+      case "$lib" in
+        -lhdf5)
+          new_libraries="$new_libraries ${libdir}/libhdf5.a"
+          ;;
+        -lhdf5_hl)
+          new_libraries="$new_libraries ${libdir}/libhdf5_hl.a"
+          ;;
+        *)
+          new_libraries="$new_libraries $lib"
+          ;;
+      esac
+    done
+    libraries="$new_libraries"
+  fi
+
+  for lib in $libraries; do
+    if echo $link_args | grep " $lib " > /dev/null ||
+       echo $link_args | grep " $lib$" > /dev/null; then
+      :
+    else
+      link_args="$link_args $lib "
+    fi
+  done
+
+  # The LIBS are just a bunch of -l* libraries necessary for the HDF5
+  # module. It's okay if they're included twice in the compile line.
+  link_args="$link_args $H5BLD_LDFLAGS $H5BLD_LIBS"
+
+  # User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's 
+  # LDFLAGS come just before clibpath, user's LIBS come after $link_objs and 
+  # before the hdf5 libraries in $link_args, followed by any external library 
+  # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in 
+  # from the hdf5 build. The order of the flags is intended to give precedence
+  # to the user's flags.
+  $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
+  status=$?
+fi
+
+exit $status
diff --git a/tools/src/misc/h5debug.c b/tools/src/misc/h5debug.c
new file mode 100644
index 0000000..ae64952
--- /dev/null
+++ b/tools/src/misc/h5debug.c
@@ -0,0 +1,723 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*-------------------------------------------------------------------------
+ *
+ * Created:             debug.c
+ *                      Jul 18 1997
+ *                      Robb Matzke <matzke@llnl.gov>
+ *
+ * Purpose:             Debugs an existing HDF5 file at a low level.
+ *
+ *-------------------------------------------------------------------------
+ */
+#define H5A_FRIEND		/*suppress error about including H5Apkg  */
+#define H5B2_FRIEND		/*suppress error about including H5B2pkg */
+#define H5B2_TESTING		/*suppress warning about H5B2 testing funcs*/
+#define H5D_FRIEND		/*suppress error about including H5Dpkg  */
+#define H5EA_FRIEND		/*suppress error about including H5EApkg */
+#define H5EA_TESTING		/*suppress warning about H5EA testing funcs*/
+#define H5FA_FRIEND		/*suppress error about including H5FApkg */
+#define H5FA_TESTING		/*suppress warning about H5FA testing funcs*/
+#define H5F_FRIEND		/*suppress error about including H5Fpkg  */
+#define H5G_FRIEND		/*suppress error about including H5Gpkg  */
+#define H5HF_FRIEND		/*suppress error about including H5HFpkg */
+#define H5O_FRIEND		/*suppress error about including H5Opkg  */
+#define H5SM_FRIEND		/*suppress error about including H5SMpkg */
+
+#include "H5private.h"  /* Generic Functions    */
+#include "H5Apkg.h"     /* Attributes           */
+#include "H5B2pkg.h"    /* v2 B-trees           */
+#include "H5Dpkg.h"     /* Datasets             */
+#include "H5Eprivate.h" /* Error handling       */
+#include "H5EApkg.h"    /* Extensible Arrays    */
+#include "H5FApkg.h"    /* Fixed Arrays         */
+#include "H5Fpkg.h"     /* File access          */
+#include "H5FSprivate.h" /* Free space manager  */
+#include "H5Gpkg.h"     /* Groups               */
+#include "H5HFpkg.h"    /* Fractal heaps        */
+#include "H5HGprivate.h" /* Global Heaps        */
+#include "H5Iprivate.h" /* IDs                  */
+#include "H5Opkg.h"     /* Object headers       */
+#include "H5SMpkg.h"    /* Implicitly shared messages    */
+
+/* File drivers */
+#include "H5FDfamily.h"
+
+#define VCOL    50
+
+
+/*-------------------------------------------------------------------------
+ * Function:    get_H5B2_class
+ *
+ * Purpose:  Determine the v2 B-tree class from the buffer read in.
+ *              B-trees are debugged through the B-tree subclass.  The subclass
+ *              identifier is two bytes after the B-tree signature.
+ *
+ * Return:  Non-NULL on success/NULL on failure
+ *
+ * Programmer:  Quincey Koziol
+ *    koziol@hdfgroup.org
+ *    Sep 11 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static const H5B2_class_t *
+get_H5B2_class(const uint8_t *sig)
+{
+    H5B2_subid_t subtype = (H5B2_subid_t)sig[H5_SIZEOF_MAGIC + 1];
+    const H5B2_class_t *cls;
+
+    switch(subtype) {
+        case H5B2_TEST_ID:
+            cls = H5B2_TEST;
+            break;
+
+        case H5B2_FHEAP_HUGE_INDIR_ID:
+            cls = H5HF_HUGE_BT2_INDIR;
+            break;
+
+        case H5B2_FHEAP_HUGE_FILT_INDIR_ID:
+            cls = H5HF_HUGE_BT2_FILT_INDIR;
+            break;
+
+        case H5B2_FHEAP_HUGE_DIR_ID:
+            cls = H5HF_HUGE_BT2_DIR;
+            break;
+
+        case H5B2_FHEAP_HUGE_FILT_DIR_ID:
+            cls = H5HF_HUGE_BT2_FILT_DIR;
+            break;
+
+        case H5B2_GRP_DENSE_NAME_ID:
+            cls = H5G_BT2_NAME;
+            break;
+
+        case H5B2_GRP_DENSE_CORDER_ID:
+            cls = H5G_BT2_CORDER;
+            break;
+
+        case H5B2_SOHM_INDEX_ID:
+            cls = H5SM_INDEX;
+            break;
+
+        case H5B2_ATTR_DENSE_NAME_ID:
+            cls = H5A_BT2_NAME;
+            break;
+
+        case H5B2_ATTR_DENSE_CORDER_ID:
+            cls = H5A_BT2_CORDER;
+            break;
+
+        case H5B2_CDSET_ID:
+            cls = H5D_BT2;
+            break;
+
+        case H5B2_CDSET_FILT_ID:
+            cls = H5D_BT2_FILT;
+            break;
+
+        case H5B2_TEST2_ID:
+            cls = H5B2_TEST2;
+            break;
+
+        case H5B2_NUM_BTREE_ID:
+        default:
+            HDfprintf(stderr, "Unknown v2 B-tree subtype %u\n", (unsigned)(subtype));
+            HDexit(4);
+    } /* end switch */
+
+    return(cls);
+} /* end get_H5B2_class() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    get_H5EA_class
+ *
+ * Purpose:  Determine the extensible array class from the buffer read in.
+ *              Extensible arrays are debugged through the array subclass.
+ *              The subclass identifier is two bytes after the signature.
+ *
+ * Return:  Non-NULL on success/NULL on failure
+ *
+ * Programmer:  Quincey Koziol
+ *    koziol@hdfgroup.org
+ *    Sep 11 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static const H5EA_class_t *
+get_H5EA_class(const uint8_t *sig)
+{
+    H5EA_cls_id_t clsid = (H5EA_cls_id_t)sig[H5_SIZEOF_MAGIC + 1];
+    const H5EA_class_t *cls;
+
+    switch(clsid) {
+        case H5EA_CLS_TEST_ID:
+            cls = H5EA_CLS_TEST;
+            break;
+
+        case H5EA_CLS_CHUNK_ID:
+            cls = H5EA_CLS_CHUNK;
+            break;
+
+        case H5EA_CLS_FILT_CHUNK_ID:
+            cls = H5EA_CLS_FILT_CHUNK;
+            break;
+
+        case H5EA_NUM_CLS_ID:
+        default:
+            HDfprintf(stderr, "Unknown extensible array class %u\n", (unsigned)(clsid));
+            HDexit(4);
+    } /* end switch */
+
+    return(cls);
+} /* end get_H5EA_class() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    get_H5FA_class
+ *
+ * Purpose:  Determine the fixed array class from the buffer read in.
+ *              Extensible arrays are debugged through the array subclass.
+ *              The subclass identifier is two bytes after the signature.
+ *
+ * Return:  Non-NULL on success/NULL on failure
+ *
+ * Programmer:  Quincey Koziol
+ *    koziol@hdfgroup.org
+ *    Sep 11 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static const H5FA_class_t *
+get_H5FA_class(const uint8_t *sig)
+{
+    H5FA_cls_id_t clsid = (H5FA_cls_id_t)sig[H5_SIZEOF_MAGIC + 1];
+    const H5FA_class_t *cls;
+
+    switch(clsid) {
+        case H5FA_CLS_TEST_ID:
+            cls = H5FA_CLS_TEST;
+            break;
+
+        case H5FA_CLS_CHUNK_ID:
+            cls = H5FA_CLS_CHUNK;
+            break;
+
+        case H5FA_CLS_FILT_CHUNK_ID:
+            cls = H5FA_CLS_FILT_CHUNK;
+            break;
+
+        case H5FA_NUM_CLS_ID: 
+        default:
+            HDfprintf(stderr, "Unknown fixed array class %u\n", (unsigned)(clsid));
+            HDexit(4);
+    } /* end switch */
+
+    return(cls);
+} /* end get_H5FA_class() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    main
+ *
+ * Usage:       debug FILENAME [OFFSET]
+ *
+ * Return:      Success:        exit (0)
+ *
+ *              Failure:        exit (non-zero)
+ *
+ * Programmer:  Robb Matzke
+ *              matzke@llnl.gov
+ *              Jul 18 1997
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, char *argv[])
+{
+    hid_t  fid, fapl, dxpl;
+    H5F_t       *f;
+    haddr_t     addr = 0, extra = 0, extra2 = 0, extra3 = 0, extra4 = 0;
+    uint8_t     sig[H5F_SIGNATURE_LEN];
+    size_t      u;
+    H5E_auto2_t func;
+    void 	*edata;
+    herr_t      status = SUCCEED;
+
+    if(argc == 1) {
+  	HDfprintf(stderr, "Usage: %s filename [signature-addr [extra]]\n", argv[0]);
+  	HDexit(1);
+    } /* end if */
+
+    /* Initialize the library */
+    if(H5open() < 0) {
+        HDfprintf(stderr, "cannot initialize the library\n");
+        HDexit(1);
+    } /* end if */
+
+    /* Disable error reporting */
+    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /*
+     * Open the file and get the file descriptor.
+     */
+    dxpl = H5AC_ind_read_dxpl_id;
+    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+        HDfprintf(stderr, "cannot create file access property list\n");
+        HDexit(1);
+    } /* end if */
+    if(HDstrchr(argv[1], '%'))
+        if(H5Pset_fapl_family (fapl, (hsize_t)0, H5P_DEFAULT) < 0) {
+            fprintf(stderr, "cannot set file access property list\n");
+            HDexit(1);
+        }
+    if((fid = H5Fopen(argv[1], H5F_ACC_RDONLY, fapl)) < 0) {
+        HDfprintf(stderr, "cannot open file\n");
+        HDexit(1);
+    } /* end if */
+    if(NULL == (f = (H5F_t *)H5I_object(fid))) {
+        HDfprintf(stderr, "cannot obtain H5F_t pointer\n");
+        HDexit(2);
+    } /* end if */
+
+    /* Ignore metadata tags while using h5debug */
+    if(H5AC_ignore_tags(f) < 0) {
+        HDfprintf(stderr, "cannot ignore metadata tags\n");
+        HDexit(1);
+    }
+
+    /*
+     * Parse command arguments.
+     */
+    if(argc > 2)
+        addr = (haddr_t)HDstrtoll(argv[2], NULL, 0);
+    if(argc > 3)
+        extra = (haddr_t)HDstrtoll(argv[3], NULL, 0);
+    if(argc > 4)
+        extra2 = (haddr_t)HDstrtoll(argv[4], NULL, 0);
+    if(argc > 5)
+        extra3 = (haddr_t)HDstrtoll(argv[5], NULL, 0);
+    if(argc > 6)
+        extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0);
+
+    /*
+     * Read the signature at the specified file position.
+     */
+    HDfprintf(stdout, "Reading signature at address %a (rel)\n", addr);
+    if(H5F_block_read(f, H5FD_MEM_SUPER, addr, sizeof(sig), dxpl, sig) < 0) {
+        HDfprintf(stderr, "cannot read signature\n");
+        HDexit(3);
+    }
+    if(!HDmemcmp(sig, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN)) {
+        /*
+         * Debug the file's super block.
+         */
+        status = H5F_debug(f, stdout, 0, VCOL);
+
+    } else if(!HDmemcmp(sig, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a local heap.
+         */
+        status = H5HL_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL);
+
+    } else if(!HDmemcmp (sig, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+	/*
+	 * Debug a global heap collection.
+	 */
+	status = H5HG_debug (f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL);
+
+    } else if(!HDmemcmp(sig, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a symbol table node.
+         */
+
+        /* Check for extra parameters */
+        if(extra == 0) {
+            HDfprintf(stderr, "\nWarning: Providing the group's local heap address will give more information\n");
+            HDfprintf(stderr, "Symbol table node usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <Symbol table node address> <address of local heap>\n\n");
+        } /* end if */
+
+        status = H5G_node_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra);
+
+    } else if(!HDmemcmp(sig, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a B-tree.  B-trees are debugged through the B-tree
+         * subclass.  The subclass identifier is the byte immediately
+         * after the B-tree signature.
+         */
+        H5B_subid_t subtype = (H5B_subid_t)sig[H5_SIZEOF_MAGIC];
+        unsigned    ndims;
+        uint32_t    dim[H5O_LAYOUT_NDIMS];
+
+        switch(subtype) {
+            case H5B_SNODE_ID:
+                /* Check for extra parameters */
+                if(extra == 0) {
+                    HDfprintf(stderr, "\nWarning: Providing the group's local heap address will give more information\n");
+                    HDfprintf(stderr, "B-tree symbol table node usage:\n");
+                    HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <address of local heap>\n\n");
+                    HDexit(4);
+                } /* end if */
+
+                status = H5G_node_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra);
+                break;
+
+            case H5B_CHUNK_ID:
+                /* Check for extra parameters */
+                if(extra == 0) {
+                    HDfprintf(stderr, "ERROR: Need number of dimensions of chunk in order to dump chunk B-tree node\n");
+                    HDfprintf(stderr, "B-tree chunked storage node usage:\n");
+                    HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n");
+                    HDexit(4);
+                } /* end if */
+
+                /* Build array of chunk dimensions */
+                ndims = (unsigned)extra;
+                dim[0] = (uint32_t)extra2;
+                if(ndims > 1)
+                    dim[1] = (uint32_t)extra3;
+                if(ndims > 2)
+                    dim[2] = (uint32_t)extra4;
+
+                /* Check for dimension error */
+                if(ndims > 3) {
+                    HDfprintf(stderr, "ERROR: Only 3 dimensions support currently (fix h5debug)\n");
+                    HDfprintf(stderr, "B-tree chunked storage node usage:\n");
+                    HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n");
+                    HDexit(4);
+                } /* end for */
+                for(u = 0; u < ndims; u++)
+                    if(0 == dim[u]) {
+                        HDfprintf(stderr, "ERROR: Chunk dimensions should be >0\n");
+                        HDfprintf(stderr, "B-tree chunked storage node usage:\n");
+                        HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n");
+                        HDexit(4);
+                    } /* end if */
+
+                /* Set the last dimension (the element size) to zero */
+                dim[ndims] = 0;
+
+                status = H5D_btree_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, ndims, dim);
+                break;
+
+            case H5B_NUM_BTREE_ID:
+            default:
+                HDfprintf(stderr, "Unknown v1 B-tree subtype %u\n", (unsigned)(subtype));
+                HDexit(4);
+        }
+
+    } else if(!HDmemcmp(sig, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a v2 B-tree header.
+         */
+        const H5B2_class_t *cls = get_H5B2_class(sig);
+        HDassert(cls);
+
+	    if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && extra == 0) {
+            HDfprintf(stderr, "ERROR: Need v2 B-tree header address and object header address containing the layout message in order to dump header\n");
+            HDfprintf(stderr, "v2 B-tree hdr usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <v2 B-tree header address> <object header address>\n");
+            HDexit(4);
+	    } /* end if */
+
+        status = H5B2__hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, (haddr_t)extra);
+
+    } else if(!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a v2 B-tree internal node.
+         */
+        const H5B2_class_t *cls = get_H5B2_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+	if((cls == H5D_BT2 || cls == H5D_BT2_FILT) &&
+	   (extra == 0 || extra2 == 0 || extra3 == 0 || extra4 == 0)) {
+
+            fprintf(stderr, "ERROR: Need v2 B-tree header address, the node's number of records, depth, and object header address containing the layout message in order to dump internal node\n");
+            fprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n");
+            fprintf(stderr, "v2 B-tree internal node usage:\n");
+            fprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth> <object header address>\n");
+            HDexit(4);
+
+        } else if(extra == 0 || extra2 == 0 || extra3 == 0) {
+            HDfprintf(stderr, "ERROR: Need v2 B-tree header address and the node's number of records and depth in order to dump internal node\n");
+            HDfprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n");
+            HDfprintf(stderr, "v2 B-tree internal node usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5B2__int_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (unsigned)extra3, (haddr_t)extra4);
+
+    } else if(!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a v2 B-tree leaf node.
+         */
+        const H5B2_class_t *cls = get_H5B2_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+	if((cls == H5D_BT2 || cls == H5D_BT2_FILT) &&
+	   (extra == 0 || extra2 == 0 || extra3 == 0 )) {
+
+            fprintf(stderr, "ERROR: Need v2 B-tree header address, number of records, and object header address containing the layout message in order to dump leaf node\n");
+            fprintf(stderr, "v2 B-tree leaf node usage:\n");
+            fprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records> <object header address>\n");
+            HDexit(4);
+
+        } else if(extra == 0 || extra2 == 0) {
+            HDfprintf(stderr, "ERROR: Need v2 B-tree header address and number of records in order to dump leaf node\n");
+            HDfprintf(stderr, "v2 B-tree leaf node usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5B2__leaf_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (haddr_t)extra3);
+
+    } else if(!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a fractal heap header.
+         */
+        status = H5HF_hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL);
+
+    } else if(!HDmemcmp(sig, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a fractal heap direct block.
+         */
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0) {
+            HDfprintf(stderr, "ERROR: Need fractal heap header address and size of direct block in order to dump direct block\n");
+            HDfprintf(stderr, "Fractal heap direct block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <direct block address> <heap header address> <size of direct block>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5HF_dblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra, (size_t)extra2);
+
+    } else if(!HDmemcmp(sig, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a fractal heap indirect block.
+         */
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0) {
+            HDfprintf(stderr, "ERROR: Need fractal heap header address and number of rows in order to dump indirect block\n");
+            HDfprintf(stderr, "Fractal heap indirect block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <indirect block address> <heap header address> <number of rows>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5HF_iblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra, (unsigned)extra2);
+
+    } else if(!HDmemcmp(sig, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a free space header.
+         */
+
+        status = H5FS_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL);
+
+    } else if(!HDmemcmp(sig, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug free space serialized sections.
+         */
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0) {
+            HDfprintf(stderr, "ERROR: Need free space header address and client address in order to dump serialized sections\n");
+            HDfprintf(stderr, "Free space serialized sections usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <serialized sections address> <free space header address> <client address>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5FS_sects_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra, extra2);
+
+    } else if(!HDmemcmp(sig, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug shared message master table.
+         */
+
+        status = H5SM_table_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, (unsigned) UFAIL, (unsigned) UFAIL);
+
+    } else if(!HDmemcmp(sig, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug shared message list index.
+         */
+
+        /* Check for enough valid parameters */
+        if(extra == 0) {
+            HDfprintf(stderr, "ERROR: Need shared message header address in order to shared message list\n");
+            HDfprintf(stderr, "Shared message list usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <shared message list address> <shared message header address>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5SM_list_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, (haddr_t)extra);
+
+    } else if(!HDmemcmp(sig, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug an extensible aray header.
+         */
+        const H5EA_class_t *cls = get_H5EA_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+        if(extra == 0) {
+            HDfprintf(stderr, "ERROR: Need object header address containing the layout message in order to dump header\n");
+            HDfprintf(stderr, "Extensible array header block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <Extensible Array header address> <object header address>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5EA__hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra);
+
+    } else if(!HDmemcmp(sig, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug an extensible aray index block.
+         */
+        const H5EA_class_t *cls = get_H5EA_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0) {
+            HDfprintf(stderr, "ERROR: Need extensible array header address and object header address containing the layout message in order to dump index block\n");
+            HDfprintf(stderr, "Extensible array index block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <index block address> <array header address> <object header address\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5EA__iblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, extra2);
+
+    } else if(!HDmemcmp(sig, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug an extensible aray super block.
+         */
+        const H5EA_class_t *cls = get_H5EA_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0 || extra3 == 0) {
+            HDfprintf(stderr, "ERROR: Need extensible array header address, super block index and object header address containing the layout message in order to dump super block\n");
+            HDfprintf(stderr, "Extensible array super block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <super block address> <array header address> <super block index> <object header address>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5EA__sblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, extra3);
+
+    } else if(!HDmemcmp(sig, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug an extensible aray data block.
+         */
+        const H5EA_class_t *cls = get_H5EA_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0 || extra3 == 0) {
+            HDfprintf(stderr, "ERROR: Need extensible array header address, # of elements in data block and object header address containing the layout message in order to dump data block\n");
+            HDfprintf(stderr, "Extensible array data block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <# of elements in data block> <object header address\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5EA__dblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (size_t)extra2, extra3);
+
+    } else if(!HDmemcmp(sig, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a fixed array header.
+         */
+        const H5FA_class_t *cls = get_H5FA_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+        if(extra == 0) {
+            HDfprintf(stderr, "ERROR: Need object header address containing the layout message in order to dump header\n");
+            HDfprintf(stderr, "Fixed array header block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <Fixed Array header address> <object header address>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5FA__hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra);
+
+    } else if(!HDmemcmp(sig, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug a fixed array data block.
+         */
+        const H5FA_class_t *cls = get_H5FA_class(sig);
+        HDassert(cls);
+
+        /* Check for enough valid parameters */
+        if(extra == 0 || extra2 == 0) {
+            HDfprintf(stderr, "ERROR: Need fixed array header address and object header address containing the layout message in order to dump data block\n");
+            HDfprintf(stderr, "fixed array data block usage:\n");
+            HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <object header address>\n");
+            HDexit(4);
+        } /* end if */
+
+        status = H5FA__dblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, extra2);
+
+    } else if(!HDmemcmp(sig, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) {
+        /*
+         * Debug v2 object header (which have signatures).
+         */
+
+        status = H5O_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL);
+
+    } else if(sig[0] == H5O_VERSION_1) {
+        /*
+         * This could be a v1 object header.  Since they don't have a signature
+         * it's a somewhat "ify" detection.
+         */
+        status = H5O_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL);
+
+    } else {
+        /*
+         * Got some other unrecognized signature.
+         */
+        printf("%-*s ", VCOL, "Signature:");
+        for (u = 0; u < sizeof(sig); u++) {
+            if (sig[u] > ' ' && sig[u] <= '~' && '\\' != sig[u])
+                HDputchar(sig[u]);
+            else if ('\\' == sig[u]) {
+                HDputchar('\\');
+                HDputchar('\\');
+            } else
+                printf("\\%03o", sig[u]);
+        }
+        HDputchar('\n');
+
+        HDfprintf(stderr, "unknown signature\n");
+        HDexit(4);
+    } /* end else */
+
+    /* Check for an error when dumping information */
+    if(status < 0) {
+        HDfprintf(stderr, "An error occurred!\n");
+        H5Eprint2(H5E_DEFAULT, stderr);
+        HDexit(5);
+    } /* end if */
+
+    H5Pclose(fapl);
+    H5Fclose(fid);
+
+    H5Eset_auto2(H5E_DEFAULT, func, edata);
+
+    return 0;
+} /* main() */
+
diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c
new file mode 100644
index 0000000..ad2d306
--- /dev/null
+++ b/tools/src/misc/h5mkgrp.c
@@ -0,0 +1,336 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+#include <string.h>
+#include <stdlib.h>
+
+/* Name of tool */
+#define PROGRAMNAME "h5mkgrp"
+
+/* Exit status for tools library routines */
+int d_status = EXIT_SUCCESS;
+
+/* command-line options: short and long-named parameters */
+static const char *s_opts = "hlpvV";
+static struct long_options l_opts[] = {
+    { "help", no_arg, 'h' },
+    { "latest", no_arg, 'l' },
+    { "parents", no_arg, 'p' },
+    { "verbose", no_arg, 'v' },
+    { "version", no_arg, 'V' },
+    { NULL, 0, '\0' }
+};
+
+/* Command line parameter settings */
+typedef struct {
+    char *fname;                /* File name to operate on */
+    hbool_t latest;             /* Whether file should use latest format versions */
+    hbool_t verbose;            /* Whether output should be verbose */
+    hbool_t parents;            /* Whether to create intermediate groups */
+    size_t ngroups;             /* Number of groups to create */
+    char **groups;              /* Pointer to array of group names */
+} param_t;
+param_t params;             /* Command line parameter settings */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    leave
+ *
+ * Purpose:     Shutdown MPI and/or HDF5 and call exit()
+ *
+ * Return:      Does not return
+ *
+ * Programmer: Quincey Koziol, 2/13/2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+leave(int ret)
+{
+    size_t curr_group;
+
+    if (params.fname)
+        HDfree (params.fname);
+    if (params.ngroups) {
+        for(curr_group = 0; curr_group < params.ngroups; curr_group++)
+            HDfree (params.groups[curr_group]);
+        HDfree (params.groups);
+    }
+    h5tools_close();
+    HDexit(ret);
+} /* end leave() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: usage
+ *
+ * Purpose: Prints a usage message on stderr and then returns.
+ *
+ * Return: void
+ *
+ * Programmer: Quincey Koziol, 2/13/2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(void)
+{
+    HDfprintf(stdout, "\
+usage: h5mkgrp [OPTIONS] FILE GROUP...\n\
+   OPTIONS\n\
+      -h, --help         Print a usage message and exit\n\
+      -l, --latest       Use latest version of file format to create groups\n\
+      -p, --parents      No error if existing, make parent groups as needed\n\
+      -v, --verbose      Print information about OBJECTS and OPTIONS\n\
+      -V, --version      Print version number and exit\n");
+} /* end usage() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: parse_command_line
+ *
+ * Purpose: Parses command line and sets up global variable to control output
+ *
+ * Return:  Success: 0
+ *    Failure: -1
+ *
+ * Programmer: Quincey Koziol, 2/13/2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+parse_command_line(int argc, const char *argv[], param_t *parms)
+{
+    int opt;            /* Option from command line */
+    size_t curr_group;  /* Current group name to copy */
+
+    /* Check for empty command line */
+    if(argc == 1) {
+        usage();
+        leave(EXIT_SUCCESS);
+    } /* end if */
+
+    /* Parse command line options */
+    while((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+        switch((char)opt) {
+            /* Display 'help' */
+            case 'h':
+                usage();
+                leave(EXIT_SUCCESS);
+
+            /* Create objects with the latest version of the format */
+            case 'l':
+                parms->latest = TRUE;
+                break;
+
+            /* Create parent groups */
+            case 'p':
+                parms->parents = TRUE;
+                break;
+
+            /* Verbose output */
+            case 'v':
+                parms->verbose = TRUE;
+                break;
+
+            /* Display version */
+            case 'V':
+                print_version(h5tools_getprogname());
+                leave(EXIT_SUCCESS);
+
+            /* Bad command line argument */
+            default:
+                usage();
+                leave(EXIT_FAILURE);
+        } /* end switch */
+    } /* end while */
+
+    /* Check for file name to be processed */
+    if(argc <= opt_ind) {
+        error_msg("missing file name\n");
+        usage();
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Retrieve file name */
+    parms->fname = HDstrdup(argv[opt_ind]);
+    opt_ind++;
+
+    /* Check for group(s) to be created */
+    if(argc <= opt_ind) {
+        error_msg("missing group name(s)\n");
+        usage();
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Allocate space for the group name pointers */
+    parms->ngroups = (size_t)(argc - opt_ind);
+    parms->groups = (char **)HDmalloc(parms->ngroups * sizeof(char *));
+
+    /* Retrieve the group names */
+    curr_group = 0;
+    while(opt_ind < argc) {
+        parms->groups[curr_group] = HDstrdup(argv[opt_ind]);
+        curr_group++;
+        opt_ind++;
+    } /* end while */
+
+#ifdef QAK
+HDfprintf(stderr, "parms->parents = %t\n", parms->parents);
+HDfprintf(stderr, "parms->verbose = %t\n", parms->verbose);
+HDfprintf(stderr, "parms->fname = '%s'\n", parms->fname);
+HDfprintf(stderr, "parms->ngroups = %Zu\n", parms->ngroups);
+for(curr_group = 0; curr_group < parms->ngroups; curr_group++)
+    HDfprintf(stderr, "parms->group[%Zu] = '%s'\n", curr_group, parms->groups[curr_group]);
+#endif /* QAK */
+
+    return(0);
+} /* parse_command_line() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: Create group(s) in an HDF5 file
+ *
+ * Programmer: Quincey Koziol, 2/13/2007
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, const char *argv[])
+{
+    hid_t fid;                  /* HDF5 file ID */
+    hid_t fapl_id;              /* File access property list ID */
+    hid_t lcpl_id;              /* Link creation property list ID */
+    size_t curr_group;          /* Current group to create */
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
+    /* Disable the HDF5 library's error reporting */
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /* Initialize h5tools lib */
+    h5tools_init();
+
+    /* Parse command line */
+    HDmemset(&params, 0, sizeof(params));
+    if(parse_command_line(argc, argv, &params) < 0) {
+        error_msg("unable to parse command line arguments\n");
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Create file access property list */
+    if((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+        error_msg("Could not create file access property list\n");
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Check for creating groups with new format version */
+    if(params.latest) {
+        /* Set the "use the latest version of the format" bounds */
+        if(H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+            error_msg("Could not set property for using latest version of the format\n");
+            leave(EXIT_FAILURE);
+        } /* end if */
+
+        /* Display some output if requested */
+        if(params.verbose)
+            printf("%s: Creating groups with latest version of the format\n", h5tools_getprogname());
+    } /* end if */
+
+    /* Attempt to open an existing HDF5 file first */
+    fid = h5tools_fopen(params.fname, H5F_ACC_RDWR, fapl_id, NULL, NULL, 0);
+
+    /* If we couldn't open an existing file, try creating file */
+    /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */
+    if(fid < 0)
+        fid = H5Fcreate(params.fname, H5F_ACC_EXCL, H5P_DEFAULT, fapl_id);
+
+    /* Test for error in opening file */
+    if(fid < 0) {
+        error_msg("Could not open output file '%s'\n", params.fname);
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Create link creation property list */
+    if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
+        error_msg("Could not create link creation property list\n");
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Check for creating intermediate groups */
+    if(params.parents) {
+        /* Set the intermediate group creation property */
+        if(H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) {
+            error_msg("Could not set property for creating parent groups\n");
+            leave(EXIT_FAILURE);
+        } /* end if */
+
+        /* Display some output if requested */
+        if(params.verbose)
+            printf("%s: Creating parent groups\n", h5tools_getprogname());
+    } /* end if */
+
+    /* Loop over creating requested groups */
+    for(curr_group = 0; curr_group < params.ngroups; curr_group++) {
+        hid_t gid;              /* Group ID */
+
+        /* Attempt to create a group */
+        if((gid = H5Gcreate2(fid, params.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
+            error_msg("Could not create group '%s'\n", params.groups[curr_group]);
+            leave(EXIT_FAILURE);
+        } /* end if */
+
+        /* Close the group */
+        if(H5Gclose(gid) < 0) {
+            error_msg("Could not close group '%s'??\n", params.groups[curr_group]);
+            leave(EXIT_FAILURE);
+        } /* end if */
+
+        /* Display some output if requested */
+        if(params.verbose)
+            printf("%s: created group '%s'\n", h5tools_getprogname(), params.groups[curr_group]);
+    } /* end for */
+
+    /* Close link creation property list */
+    if(H5Pclose(lcpl_id) < 0) {
+        error_msg("Could not close link creation property list\n");
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Close file */
+    if(H5Fclose(fid) < 0) {
+        error_msg("Could not close output file '%s'??\n", params.fname);
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Close file access property list */
+    if(H5Pclose(fapl_id) < 0) {
+        error_msg("Could not close file access property list\n");
+        leave(EXIT_FAILURE);
+    } /* end if */
+
+    /* Shut down h5tools lib */
+    h5tools_close();
+
+    leave(EXIT_SUCCESS);
+} /* end main() */
+
diff --git a/tools/src/misc/h5redeploy.in b/tools/src/misc/h5redeploy.in
new file mode 100644
index 0000000..6b6ef87
--- /dev/null
+++ b/tools/src/misc/h5redeploy.in
@@ -0,0 +1,218 @@
+#! /bin/sh
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+#
+
+## Update HDF5 compiler tools after the HDF5 software has been installed  ##
+## in a new location.							  ##
+## For help page, use "h5redeploy -help"				  ##
+##									  ##
+
+# Constants definitions
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+# Function definitions
+
+# show help page
+usage() {
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS]"
+  echo "  OPTIONS:"
+  echo "    -help|help        This help message"
+  echo "    -echo             Show all the shell commands executed"
+  echo "    -force            No prompt, just do it"
+  echo "    -prefix=DIR       New directory to find HDF5 lib/ and include/"
+  echo "                        subdirectories [default: current directory]"
+  echo "    -exec-prefix=DIR  New directory to find HDF5 lib/"
+  echo "                        subdirectory [default: <prefix>]"
+  echo "    -libdir=DIR       New directory for the HDF5 lib directory"
+  echo "                        [default: <exec-prefix>/lib]"
+  echo "    -includedir=DIR   New directory for the HDF5 header files"
+  echo "                        [default: <prefix>/include]"
+  echo "    -tool=TOOL        Tool to update. TOOL must be in the current"
+  echo "                        directory and writable. [default: $h5tools]"
+  echo "    -show             Show the commands without executing them"
+  echo " "
+  exit $EXIT_FAILURE
+}
+
+# display variable values
+dump_vars(){
+    echo "====Showing all variable values====="
+    echo prefix=$prefix
+    echo h5tools=$h5tools
+    echo "====End Showing====="
+}
+
+# show actions to be taken
+show_action()
+{
+    echo "Update the following tools because they are now installed at a new directory"
+    for t in $foundtools; do
+	echo "${t}:"
+	echo "   current setting=`sed -e '/^prefix=/s/prefix=//p' -e d $t`"
+	echo "   new     setting="\""$prefix"\"
+    done
+}
+
+
+# Report Error message
+ERROR()
+{
+    echo "***ERROR***"
+    echo "$1"
+}
+
+# Main
+#
+############################################################################
+## Installation directories:						  ##
+## prefix	architecture-independent files.				  ##
+## exec_prefix	architecture-dependent files, default is <prefix>.	  ##
+## libdir	libraries, default is <exec_prefix>/lib.		  ##
+## includedir	header files, default is <prefix/include>.		  ##
+## Not used here:							  ##
+## bindir	executables, <exec_prefix/bin>.				  ##
+############################################################################
+# Initialization
+h5tools="h5cc h5pcc h5fc h5pfc h5c++"	# possible hdf5 tools
+foundtools=		# tools found and will be modified
+fmode=			# force mode, default is off
+prefix=
+exec_prefix=
+libdir=
+includedir=
+
+# Parse options
+for arg in $@ ; do
+  case "$arg" in
+    -prefix=*)
+      prefix="`echo $arg | cut -f2 -d=`"
+      ;;
+    -exec-prefix=*)
+      exec_prefix="`echo $arg | cut -f2 -d=`"
+      ;;
+    -libdir=*)
+      libdir="`echo $arg | cut -f2 -d=`"
+      ;;
+    -includedir=*)
+      includedir="`echo $arg | cut -f2 -d=`"
+      ;;
+    -echo)
+      set -x
+      ;;
+    -show)
+      SHOW="echo"
+      ;;
+    -tool=*)
+      h5tools="`echo $arg | cut -f2 -d=`"
+      ;;
+    -help|help)
+      usage
+      ;;
+    -force)
+      fmode=yes
+      ;;
+    *)
+      ERROR "Unknown Option($arg)"
+      usage
+      exit $EXIT_FAILURE
+      ;;
+  esac
+done
+
+# Set to default value, one above where i am, if not given by user
+if [ -z "$prefix" ]; then
+    prefix=`(cd ..;pwd)`
+fi
+if [ -z "$exec_prefix" ]; then
+    exec_prefix='${prefix}'		# use single quotes to prevent expansion of $
+fi
+if [ -z "$libdir" ]; then
+    libdir='${exec_prefix}'/lib	# use single quotes to prevent expansion of $
+fi
+if [ -z "$includedir" ]; then
+    includedir='${prefix}'/include # use single quotes to prevent expansion of $
+fi
+
+for x in $h5tools; do
+    if [ -f $x ]; then
+	foundtools="$foundtools $x"
+	if [ ! -w $x ]; then
+	    ERROR "h5tool($x) is not writable"
+	    exit $EXIT_FAILURE
+	fi
+    fi
+done
+
+if [ -z "$foundtools" ]; then
+    ERROR "found no tools to modify"
+    exit $EXIT_FAILURE
+fi
+
+# Show actions to be taken and get consent
+show_action
+# Ask confirmation unless fmode is on
+if [ x-$fmode = x- ]; then
+    echo "Continue? (yes/no)"
+    read ansx
+    ans=`echo $ansx | tr "[A-Z]" "[a-z]"`
+    if [ x-$ans != x-yes ]; then
+	echo ABORT.  No tools changed.
+	exit $EXIT_FAILURE
+    fi
+fi
+
+
+# Create the update commands
+CMDFILE=/tmp/h5redeploy.$$
+touch $CMDFILE
+chmod 0600 $CMDFILE
+echo "/^prefix=/c"                    >> $CMDFILE
+echo prefix=\""$prefix"\"             >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^exec_prefix=/c"               >> $CMDFILE
+echo exec_prefix=\""$exec_prefix"\"   >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^libdir=/c"                    >> $CMDFILE
+echo libdir=\""$libdir"\"             >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^includedir=/c"                >> $CMDFILE
+echo includedir=\""$includedir"\"     >> $CMDFILE
+echo .                                >> $CMDFILE
+(echo w; echo q)                      >> $CMDFILE
+
+
+# Update them
+if [ "$SHOW" = "echo" ]; then
+    echo "===Update commands are:===="
+    cat $CMDFILE
+    echo "===End Update commands====="
+fi
+
+for t in $foundtools; do
+    echo Update $t ...
+    COMMAND="ed - $t"
+    if [ "$SHOW" = "echo" ]; then
+	echo $COMMAND
+    else
+	$COMMAND < $CMDFILE
+    fi
+done
+
+
+# Cleanup
+rm -f $CMDFILE
+exit $EXIT_SUCCESS
diff --git a/tools/src/misc/h5repart.c b/tools/src/misc/h5repart.c
new file mode 100644
index 0000000..e44c957
--- /dev/null
+++ b/tools/src/misc/h5repart.c
@@ -0,0 +1,510 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Wednesday, May 13, 1998
+ *
+ * Purpose:	Repartitions a file family.  This program can be used to
+ *		split a single file into a family of files, join a family of
+ *		files into a single file, or copy one family to another while
+ *		changing the size of the family members.  It can also be used
+ *		to copy a single file to a single file with holes.
+ */
+
+/* See H5private.h for how to include system headers */
+#include "hdf5.h"
+#include "H5private.h"
+#ifdef H5_STDC_HEADERS
+#   include <ctype.h>
+#   include <errno.h>
+#   include <fcntl.h>
+#   include <stdio.h>
+#   include <stdlib.h>
+#   include <string.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#   include <sys/types.h>
+#   include <unistd.h>
+#endif
+
+#ifdef H5_HAVE_SYS_STAT_H
+#   include <sys/stat.h>
+#endif
+
+#ifndef FALSE
+#   define FALSE	0
+#endif
+#ifndef TRUE
+#   define TRUE 	1
+#endif
+#   define NAMELEN	4096
+#define GB	*1024*1024*1024
+
+#ifndef MIN
+#   define MIN(X,Y)	((X)<(Y)?(X):(Y))
+#endif
+#ifndef MIN3
+#   define MIN3(X,Y,Z)	MIN(MIN(X,Y),Z)
+#endif
+
+/*Make these 2 private properties(defined in H5Fprivate.h) available to h5repart.
+ *The first one updates the member file size in the superblock.  The second one
+ *change file driver from family to sec2. */
+#define H5F_ACS_FAMILY_NEWSIZE_NAME            "family_newsize"
+#define H5F_ACS_FAMILY_TO_SEC2_NAME            "family_to_sec2"
+
+
+/*-------------------------------------------------------------------------
+ * Function:	usage
+ *
+ * Purpose:	Prints a usage message.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, May 13, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage (const char *progname)
+{
+    fprintf(stderr, "usage: %s [-v] [-V] [-[b|m] N[g|m|k]] [-family_to_sec2] SRC DST\n",
+	    progname);
+    fprintf(stderr, "   -v     Produce verbose output\n");
+    fprintf(stderr, "   -V     Print a version number and exit\n");
+    fprintf(stderr, "   -b N   The I/O block size, defaults to 1kB\n");
+    fprintf(stderr, "   -m N   The destination member size or 1GB\n");
+    fprintf(stderr, "   -family_to_sec2   Change file driver from family to sec2\n");
+    fprintf(stderr, "   SRC    The name of the source file\n");
+    fprintf(stderr, "   DST	The name of the destination files\n");
+    fprintf(stderr, "Sizes may be suffixed with `g' for GB, `m' for MB or "
+	    "`k' for kB.\n");
+    fprintf(stderr, "File family names include an integer printf "
+	    "format such as `%%d'\n");
+    exit (EXIT_FAILURE);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	get_size
+ *
+ * Purpose:	Reads a size option of the form `-XNS' where `X' is any
+ *		letter, `N' is a multi-character positive decimal number, and
+ *		`S' is an optional suffix letter in the set [GgMmk].  The
+ *		option may also be split among two arguments as: `-X NS'.
+ *		The input value of ARGNO is the argument number for the
+ *		switch in the ARGV vector and ARGC is the number of entries
+ *		in that vector.
+ *
+ * Return:	Success:	The value N multiplied according to the
+ *				suffix S.  On return ARGNO will be the number
+ *				of the next argument to process.
+ *
+ *		Failure:	Calls usage() which exits with a non-zero
+ *				status.
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, May 13, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static off_t
+get_size (const char *progname, int *argno, int argc, char *argv[])
+{
+    off_t	retval=-1;
+    char	*suffix;
+
+    if (isdigit ((int)(argv[*argno][2]))) {
+	retval = strtol (argv[*argno]+2, &suffix, 10);
+	(*argno)++;
+    } else if (argv[*argno][2] || *argno+1>=argc) {
+	usage (progname);
+    } else {
+	retval = strtol (argv[*argno+1], &suffix, 0);
+	if (suffix==argv[*argno+1]) usage (progname);
+	*argno += 2;
+    }
+    if (suffix && suffix[0] && !suffix[1]) {
+	switch (*suffix) {
+	case 'G':
+	case 'g':
+	    retval *= 1024 * 1024 * 1024;
+	    break;
+	case 'M':
+	case 'm':
+	    retval *= 1024 * 1024;
+	    break;
+	case 'k':
+	    retval *= 1024;
+	    break;
+	default:
+	    usage (progname);
+	}
+    } else if (suffix && suffix[0]) {
+	usage (progname);
+    }
+    return retval;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	Split an hdf5 file
+ *
+ * Return:	Success:
+ *
+ *		Failure:
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, May 13, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main (int argc, char *argv[])
+{
+    const char	*prog_name;		/*program name			*/
+    size_t	blk_size=1024;		/*size of each I/O block	*/
+    char	*buf=NULL;		/*I/O block buffer		*/
+    size_t	n, i;			/*counters			*/
+    ssize_t	nio;			/*I/O return value		*/
+    int		argno=1;		/*program argument number	*/
+    int		src, dst=-1;		/*source & destination files	*/
+    int		need_seek=FALSE;	/*destination needs to seek?	*/
+    int		need_write;		/*data needs to be written?	*/
+    h5_stat_t sb;                       /*temporary file stat buffer	*/
+
+    int		verbose=FALSE;		/*display file names?		*/
+
+    const char	*src_gen_name;  /*general source name		*/
+    char	*src_name=NULL;	    /*source member name		*/
+
+    int		src_is_family;		/*is source name a family name?	*/
+    int		src_membno=0;		/*source member number		*/
+
+    const char	*dst_gen_name;	/*general destination name	*/
+    char	*dst_name=NULL;	    /*destination member name	*/
+    int		dst_is_family;		/*is dst name a family name?	*/
+    int		dst_membno=0;		/*destination member number	*/
+
+    off_t	left_overs=0;		/*amount of zeros left over	*/
+    off_t	src_offset=0;		/*offset in source member	*/
+    off_t	dst_offset=0;		/*offset in destination member	*/
+    off_t	src_size;           /*source logical member size	*/
+    off_t	src_act_size;		/*source actual member size	*/
+    off_t	dst_size=1 GB;		/*destination logical memb size	*/
+    hid_t       fapl;                   /*file access property list     */
+    hid_t       file;
+    hsize_t     hdsize;                 /*destination logical memb size */
+    hbool_t     family_to_sec2=FALSE;   /*change family to sec2 driver? */
+
+    /*
+     * Get the program name from argv[0]. Use only the last component.
+     */
+    if ((prog_name=strrchr (argv[0], '/'))) prog_name++;
+    else prog_name = argv[0];
+
+    /*
+     * Parse switches.
+     */
+    while (argno<argc && '-'==argv[argno][0]) {
+        if (!strcmp (argv[argno], "-v")) {
+            verbose = TRUE;
+            argno++;
+        } else if (!strcmp(argv[argno], "-V")) {
+            printf("This is %s version %u.%u release %u\n",
+                prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE);
+            exit(EXIT_SUCCESS);
+        } else if (!strcmp (argv[argno], "-family_to_sec2")) {
+            family_to_sec2 = TRUE;
+            argno++;
+        } else if ('b'==argv[argno][1]) {
+            blk_size = (size_t)get_size (prog_name, &argno, argc, argv);
+        } else if ('m'==argv[argno][1]) {
+            dst_size = get_size (prog_name, &argno, argc, argv);
+        } else {
+            usage (prog_name);
+        } /* end if */
+    } /* end while */
+
+    /* allocate names */
+    if(NULL == (src_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char))))
+        exit(EXIT_FAILURE);
+    if(NULL == (dst_name = (char *)HDcalloc((size_t)NAMELEN, sizeof(char))))
+        exit(EXIT_FAILURE);
+
+    /*
+     * Get the name for the source file and open the first member.  The size
+     * of the first member determines the logical size of all the members.
+     */
+    if (argno>=argc) usage (prog_name);
+    src_gen_name = argv[argno++];
+    sprintf (src_name, src_gen_name, src_membno);
+    src_is_family = strcmp (src_name, src_gen_name);
+
+    if ((src=HDopen(src_name, O_RDONLY,0))<0) {
+        perror (src_name);
+        exit (EXIT_FAILURE);
+    }
+
+    if (HDfstat(src, &sb)<0) {
+        perror ("fstat");
+        exit (EXIT_FAILURE);
+    }
+    src_size = src_act_size = sb.st_size;
+    if (verbose) fprintf (stderr, "< %s\n", src_name);
+
+    /*
+     * Get the name for the destination file and open the first member.
+     */
+    if (argno>=argc) usage (prog_name);
+    dst_gen_name = argv[argno++];
+    sprintf (dst_name, dst_gen_name, dst_membno);
+    dst_is_family = strcmp (dst_name, dst_gen_name);
+
+    if ((dst=HDopen (dst_name, O_RDWR|O_CREAT|O_TRUNC, 0666))<0) {
+	perror (dst_name);
+	exit (EXIT_FAILURE);
+    }
+    if (verbose) fprintf (stderr, "> %s\n", dst_name);
+
+    /* No more arguments */
+    if (argno<argc) usage (prog_name);
+
+    /* Now the real work, split the file */
+    buf = (char *)HDmalloc(blk_size);
+    while (src_offset<src_size) {
+
+	/* Read a block.  The amount to read is the minimum of:
+	 *    1. The I/O block size
+	 *    2. What's left to write in the destination member
+	 *    3. Left over zeros or what's left in the source member.
+	 */
+	n = blk_size;
+	if (dst_is_family) n = (size_t)MIN((off_t)n, dst_size-dst_offset);
+	if (left_overs) {
+	    n = (size_t)MIN ((off_t)n, left_overs);
+	    left_overs = left_overs - (off_t)n;
+	    need_write = FALSE;
+	} else if (src_offset<src_act_size) {
+	    n = (size_t)MIN ((off_t)n, src_act_size-src_offset);
+	    if ((nio=HDread (src, buf, n))<0) {
+		perror ("read");
+		exit (EXIT_FAILURE);
+	    } else if ((size_t)nio!=n) {
+		fprintf (stderr, "%s: short read\n", src_name);
+		exit (EXIT_FAILURE);
+	    }
+	    for (i=0; i<n; i++) {
+		if (buf[i]) break;
+	    }
+	    need_write = (i<n);
+	} else {
+	    n = 0;
+	    left_overs = src_size - src_act_size;
+	    need_write = FALSE;
+	}
+
+	/*
+	 * If the block contains non-zero data then write it to the
+	 * destination, otherwise just remember that we'll have to do a seek
+	 * later in the destination when we finally get non-zero data.
+	 */
+	if (need_write) {
+	    if (need_seek && HDlseek (dst, dst_offset, SEEK_SET)<0) {
+		perror ("HDlseek");
+		exit (EXIT_FAILURE);
+	    }
+	    if ((nio=HDwrite (dst, buf, n))<0) {
+		perror ("write");
+		exit (EXIT_FAILURE);
+	    } else if ((size_t)nio!=n) {
+		fprintf (stderr, "%s: short write\n", dst_name);
+		exit (EXIT_FAILURE);
+	    }
+	    need_seek = FALSE;
+	} else {
+	    need_seek = TRUE;
+	}
+
+	/*
+	 * Update the source offset and open the next source family member if
+	 * necessary.  The source stream ends at the first member which
+	 * cannot be opened because it doesn't exist.  At the end of the
+	 * source stream, update the destination offset and break out of the
+	 * loop.   The destination offset must be updated so we can fix
+	 * trailing holes.
+	 */
+	src_offset = src_offset + (off_t)n;
+	if (src_offset==src_act_size) {
+	    HDclose (src);
+	    if (!src_is_family) {
+                dst_offset = dst_offset + (off_t)n;
+		break;
+	    }
+	    sprintf (src_name, src_gen_name, ++src_membno);
+	    if ((src=HDopen (src_name, O_RDONLY,0))<0 && ENOENT==errno) {
+                dst_offset = dst_offset + (off_t)n;
+		break;
+	    } else if (src<0) {
+		perror (src_name);
+		exit (EXIT_FAILURE);
+	    }
+	    if (HDfstat (src, &sb)<0) {
+		perror ("fstat");
+		exit (EXIT_FAILURE);
+	    }
+	    src_act_size = sb.st_size;
+	    if (src_act_size>src_size) {
+		fprintf (stderr, "%s: member truncated to %lu bytes\n",
+			 src_name, (unsigned long)src_size);
+	    }
+	    src_offset = 0;
+	    if (verbose) fprintf (stderr, "< %s\n", src_name);
+	}
+
+	/*
+	 * Update the destination offset, opening a new member if one will be
+	 * needed. The first member is extended to the logical member size
+	 * but other members might be smaller if they end with a hole.
+	 */
+        dst_offset = dst_offset + (off_t)n;
+	if (dst_is_family && dst_offset==dst_size) {
+	    if (0==dst_membno) {
+		if (HDlseek (dst, dst_size-1, SEEK_SET)<0) {
+		    perror ("HDHDlseek");
+		    exit (EXIT_FAILURE);
+		}
+		if (HDread (dst, buf, 1)<0) {
+		    perror ("read");
+		    exit (EXIT_FAILURE);
+		}
+		if (HDlseek (dst, dst_size-1, SEEK_SET)<0) {
+		    perror ("HDlseek");
+		    exit (EXIT_FAILURE);
+		}
+		if (HDwrite (dst, buf, 1)<0) {
+		    perror ("write");
+		    exit (EXIT_FAILURE);
+		}
+	    }
+	    HDclose (dst);
+	    sprintf (dst_name, dst_gen_name, ++dst_membno);
+	    if ((dst=HDopen (dst_name, O_RDWR|O_CREAT|O_TRUNC, 0666))<0) {
+		perror (dst_name);
+		exit (EXIT_FAILURE);
+	    }
+	    dst_offset = 0;
+	    need_seek = FALSE;
+	    if (verbose) fprintf (stderr, "> %s\n", dst_name);
+	}
+    }
+
+    /*
+     * Make sure the last family member is the right size and then close it.
+     * The last member can't end with a hole or hdf5 will think that the
+     * family has been truncated.
+     */
+    if (need_seek) {
+	if (HDlseek (dst, dst_offset-1, SEEK_SET)<0) {
+	    perror ("HDlseek");
+	    exit (EXIT_FAILURE);
+	}
+	if (HDread (dst, buf, 1)<0) {
+	    perror ("read");
+	    exit (EXIT_FAILURE);
+	}
+	if (HDlseek (dst, dst_offset-1, SEEK_SET)<0) {
+	    perror ("HDlseek");
+	    exit (EXIT_FAILURE);
+	}
+	if (HDwrite (dst, buf, 1)<0) {
+	    perror ("write");
+	    exit (EXIT_FAILURE);
+	}
+    }
+    HDclose (dst);
+
+    /* Modify family driver information saved in superblock through private property.
+     * These private properties are for this tool only. */
+    if ((fapl=H5Pcreate(H5P_FILE_ACCESS))<0) {
+        perror ("H5Pcreate");
+        exit (EXIT_FAILURE);
+    }
+
+    if(family_to_sec2) {
+        /* The user wants to change file driver from family to sec2. Open the file
+         * with sec2 driver.  This property signals the library to ignore the family
+         * driver information saved in the superblock. */
+        if(H5Pset(fapl, H5F_ACS_FAMILY_TO_SEC2_NAME, &family_to_sec2) < 0) {
+            perror ("H5Pset");
+            exit (EXIT_FAILURE);
+        }
+    } else {
+        /* Modify family size saved in superblock through private property. It signals
+         * library to save the new member size(specified in command line) in superblock.
+         * This private property is for this tool only. */
+        if(H5Pset_fapl_family(fapl, H5F_FAMILY_DEFAULT, H5P_DEFAULT) < 0) {
+            perror ("H5Pset_fapl_family");
+            exit (EXIT_FAILURE);
+        }
+
+        /* Set the property of the new member size as hsize_t */
+        hdsize = (hsize_t)dst_size;
+        if(H5Pset(fapl, H5F_ACS_FAMILY_NEWSIZE_NAME, &hdsize) < 0) {
+            perror ("H5Pset");
+            exit (EXIT_FAILURE);
+        }
+    }
+
+    /* If the new file is a family file, try to open file for "read and write" to
+     * flush metadata. Flushing metadata will update the superblock to the new
+     * member size.  If the original file is a family file and the new file is a sec2
+     * file, the property FAMILY_TO_SEC2 will signal the library to switch to sec2
+     * driver when the new file is opened.  If the original file is a sec2 file and the
+     * new file can only be a sec2 file, reopen the new file should fail.  There's
+     * nothing to do in this case. */
+    H5E_BEGIN_TRY {
+        file=H5Fopen(dst_gen_name, H5F_ACC_RDWR, fapl);
+    } H5E_END_TRY;
+
+    if(file>=0) {
+        if(H5Fclose(file)<0) {
+            perror ("H5Fclose");
+            exit (EXIT_FAILURE);
+        } /* end if */
+    } /* end if */
+
+    if(H5Pclose(fapl)<0) {
+        perror ("H5Pclose");
+        exit (EXIT_FAILURE);
+    } /* end if */
+
+    /* Free resources and return */
+    HDfree(src_name);
+    HDfree(dst_name);
+    HDfree(buf);
+    return EXIT_SUCCESS;
+} /* end main */