[svn-r28636] merge from trunk.

6 files changed, 452 insertions, 130 deletions

diff --git a/bin/bbrelease b/bin/bbrelease
index 119dc7a..cb79528 100755
--- a/bin/bbrelease
+++ b/bin/bbrelease
@@ -304,7 +304,6 @@ fi
 # Create a manifest that contains only files for distribution.
 MANIFEST=$tmpdir/H5_MANIFEST
 grep '^\.' MANIFEST | grep -v _DO_NOT_DISTRIBUTE_ >$MANIFEST
-echo "./autogen.sh" >>$MANIFEST
 
 # Prepare the source tree for a release.
 #ln -s `pwd` $tmpdir/$HDF5_VERS || exit 1
diff --git a/bin/chkmanifest b/bin/chkmanifest
index 646f815..701b6c4 100755
--- a/bin/chkmanifest
+++ b/bin/chkmanifest
@@ -17,9 +17,12 @@
 # Check that all the files in MANIFEST exist and that (if this is a
 # SVN checkout) that all the SVN-managed files appear in the
 # MANIFEST.
+# 
 
 verbose=yes
 MANIFEST=/tmp/HD_MANIFEST.$$
+AUTOGEN=./autogen.sh
+AUTOGEN_LOG=/tmp/autogen.log.$$
 
 # Main
 test "$verbose" && echo "   Checking MANIFEST..." 1>&2
@@ -49,6 +52,19 @@ else
     fi
 fi
 
+# Do an autogen if generated files (e.g., configure) is not present
+if [ ! -f configure ]; then
+    echo "   running $AUTOGEN -p"
+    $AUTOGEN -p > $AUTOGEN_LOG 2>&1
+    if [ $? -ne 0 ]; then
+	echo $AUTOGEN encountered error. Abort.
+	echo output from $AUTOGEN:
+	cat $AUTOGEN_LOG
+	exit 1
+    fi
+    rm $AUTOGEN_LOG
+fi
+
 # Check for duplicate entries.  This can be done at any time, but it may as 
 # well be sooner so that if something else fails the presence of duplicates
 # will already be known.
diff --git a/bin/cmakehdf5 b/bin/cmakehdf5
index afd4604..772e54c 100755
--- a/bin/cmakehdf5
+++ b/bin/cmakehdf5
@@ -23,6 +23,7 @@ makelog="#${progname}_2build.log"
 testlog="#${progname}_3test.log"
 packlog="#${progname}_4pack.log"
 installlog="#${progname}_5install.log"
+vflag=1		# verbose flag default to on.
 config_summary=libhdf5.settings
 exit_code=0
 
@@ -53,7 +54,10 @@ with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT=ON	# enable zlib filter default on
 with_szlib=-DHDF5_ENABLE_SZIP_SUPPORT=OFF	# enables szip filter default off
 szlib_path=""					# szip lib path default off
 shared_lib=-DBUILD_SHARED_LIBS:BOOL=ON		# enables shared lib; default on
-
+njobs=""					# number of jobs (commands) to
+						# run simultaneously; default is
+						# value from $MAKE if defined,
+						# otherwise none (1)
 
 #=============
 # Function definitions
@@ -90,6 +94,11 @@ Usage: $progname [<options>]
     Use zlib library for external deflate I/O filter. Default is on.
   --with-szlib | --with-szlib=<libpath> | --without-szlib:
     Use szlib library for external deflate I/O filter. Default is on.
+  --njobs=<-j N>:
+    number of jobs (commands) to run simultaneously; default is value from
+    $MAKE if defined, otherwise none
+  --enable-verbose | --disable-verbose:
+    enable or disable verbose output. Default is on.
   --help: shows details help page
 
   <libpath>: the file path to the library, expect <libpath>/lib and <libpath>/include.
@@ -117,12 +126,12 @@ STEP()
 
     echo "$banner" with output saved in $logfile
     (TIMESTAMP; nerror=0 ;
-	echo "eval $command"
-	eval $command || nerror=1 ;
-	TIMESTAMP; exit $nerror) < /dev/null > "$logfile" 2>&1
+  echo "eval $command"
+  eval $command || nerror=1 ;
+  TIMESTAMP; exit $nerror) < /dev/null > "$logfile" 2>&1
     if [ $? -ne 0 ]; then
-	echo "error in '$banner'.  $progname aborted."
-	exit 1
+  echo "error in '$banner'.  $progname aborted."
+  exit 1
     fi
 }
 
@@ -136,28 +145,44 @@ INSTALL_HDF5()
 {
     myos="`uname -s`"
     case "$myos" in
-	Linux)
-	    install_file=./HDF5-${version}-Linux.sh
-	    $install_file  --skip-license $*
-	    ;;
-	Darwin)		# Mac OSX DMG file
-	    install_file=HDF5-${version}-Darwin.dmg
-	    test -d hdf5 || mkdir hdf5
-	    basename=`basename $install_file .dmg`
-	    # mount the DMG file as /Volumes/$basename
-	    # echo 'Y' as yes for license.
-	    echo Y | hdiutil mount $install_file
-	    # copy the contents to the install location
-	    cp -R "/Volumes/$basename/HDF_Group" hdf5
-	    # unmount the DMG file
-	    hdiutil unmount /Volumes/$basename
-	    ;;
-	*) 		# unknown/unsupported OS.
-	    echo "INSTALL_HDF5: Error--unknown/unsupported OS($myos)"
-	    return 1
-	    ;;
+  Linux)
+      install_file=./HDF5-${version}-Linux.sh
+      $install_file  --skip-license $*
+      ;;
+  Darwin)		# Mac OSX DMG file
+      install_file=HDF5-${version}-Darwin.dmg
+      test -d hdf5 || mkdir hdf5
+      basename=`basename $install_file .dmg`
+      # mount the DMG file as /Volumes/$basename
+      # echo 'Y' as yes for license.
+      echo Y | hdiutil mount $install_file
+      # copy the contents to the install location
+      cp -R "/Volumes/$basename/HDF_Group" hdf5
+      # unmount the DMG file
+      hdiutil unmount /Volumes/$basename
+      ;;
+  *) 		# unknown/unsupported OS.
+      echo "INSTALL_HDF5: Error--unknown/unsupported OS($myos)"
+      return 1
+      ;;
     esac
-    return 0
+}
+
+
+# Print logfiles.
+# $*: logfiles
+DUMP_LOGFILE()
+{
+    for x in $*; do
+  if [ -f $x ]; then
+      echo "=================================="
+      echo "Dumping $x"
+      echo "=================================="
+      cat $x
+      echo "==== END $x ====="
+      echo
+  fi
+    done
 }
 
 
@@ -168,6 +193,12 @@ INSTALL_HDF5()
 # Show a start time stamp
 TIMESTAMP
 
+# Initialize njobs if $AMKE is defined
+if [ -n "$MAKE" ]; then
+    # assume all arguments are for --jobs
+    njobs=`echo $MAKE | cut -s -d' ' -f2-`
+fi
+
 # Parse Cmake configure options
 # --enable-XXX or --disable-XXX will enable or disable feature XXX.
 # XXX can be:
@@ -178,78 +209,88 @@ TIMESTAMP
 # tools		Build tools
 while [ $# -gt 0 ]; do
     case "$1" in
-	--enable-fortran)
-	    build_fortran=-DHDF5_BUILD_FORTRAN:BOOL=ON
-	    ;;
-	--disable-fortran)
-	    build_fortran=-DHDF5_BUILD_FORTRAN:BOOL=OFF
-	    ;;
-	--enable-cxx)
-	    build_cpp_lib=-DHDF5_BUILD_CPP_LIB:BOOL=ON
-	    ;;
-	--disable-cxx)
-	    build_cpp_lib=-DHDF5_BUILD_CPP_LIB:BOOL=OFF
-	    ;;
-	--enable-hl)
-	    build_hl_lib=-DHDF5_BUILD_HL_LIB:BOOL=ON
-	    ;;
-	--disable-hl)
-	    build_hl_lib=-DHDF5_BUILD_HL_LIB:BOOL=OFF
-	    ;;
-	--enable-shared)
-	    shared_lib=-DBUILD_SHARED_LIBS:BOOL=ON
-	    ;;
-	--disable-shared)
-	    shared_lib=-DBUILD_SHARED_LIBS:BOOL=OFF
-	    ;;
-	--enable-tools)
-	    build_tools=-DHDF5_BUILD_TOOLS:BOOL=ON
-	    ;;
-	--disable-tools)
-	    build_tools=-DHDF5_BUILD_TOOLS:BOOL=OFF
-	    ;;
-	--enable-testing)
-	    build_testing=-DBUILD_TESTING:BOOL=ON
-	    ;;
-	--disable-testing)
-	    build_testing=-DBUILD_TESTING:BOOL=OFF
-	    ;;
-	--with-zlib)
-	    with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON
-	    ;;
-	--with-zlib=*)
-	    xarg=`echo $1 | cut -d= -f2-`
-	    with_zlib="-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON -DZLIB_ROOT=$xarg"
-	    ;;
-	--without-zlib)
-	    with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF
-	    ;;
-	--with-szlib)
-	    with_szlib=-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON
-	    szlib_path=""	# szlib is in default paths
-	    ;;
-	--with-szlib=*)
-	    xarg=`echo $1 | cut -d= -f2-`
-	    with_szlib="-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON"
-	    szlib_path="SZIP_INSTALL=$xarg"
-	    ;;
-	--without-szlib)
-	    with_szlib=-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF
-	    szlib_path=""	# reset the path
-	    ;;
-	--help)
-	    # print the detail help page and exit
-	    HELP
-	    exit 0
-	    ;;
-	*)
-	    echo "Unknown options: $1"
-	    HELP
-	    exit 1
-	    ;;
+  --enable-fortran)
+      build_fortran=-DHDF5_BUILD_FORTRAN:BOOL=ON
+      ;;
+  --disable-fortran)
+      build_fortran=-DHDF5_BUILD_FORTRAN:BOOL=OFF
+      ;;
+  --enable-cxx)
+      build_cpp_lib=-DHDF5_BUILD_CPP_LIB:BOOL=ON
+      ;;
+  --disable-cxx)
+      build_cpp_lib=-DHDF5_BUILD_CPP_LIB:BOOL=OFF
+      ;;
+  --enable-hl)
+      build_hl_lib=-DHDF5_BUILD_HL_LIB:BOOL=ON
+      ;;
+  --disable-hl)
+      build_hl_lib=-DHDF5_BUILD_HL_LIB:BOOL=OFF
+      ;;
+  --enable-shared)
+      shared_lib=-DBUILD_SHARED_LIBS:BOOL=ON
+      ;;
+  --disable-shared)
+      shared_lib=-DBUILD_SHARED_LIBS:BOOL=OFF
+      ;;
+  --enable-tools)
+      build_tools=-DHDF5_BUILD_TOOLS:BOOL=ON
+      ;;
+  --disable-tools)
+      build_tools=-DHDF5_BUILD_TOOLS:BOOL=OFF
+      ;;
+  --enable-testing)
+      build_testing=-DBUILD_TESTING:BOOL=ON
+      ;;
+  --disable-testing)
+      build_testing=-DBUILD_TESTING:BOOL=OFF
+      ;;
+  --with-zlib)
+      with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON
+      ;;
+  --with-zlib=*)
+      xarg=`echo $1 | cut -d= -f2-`
+      with_zlib="-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON -DZLIB_ROOT=$xarg"
+      ;;
+  --without-zlib)
+      with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF
+      ;;
+  --with-szlib)
+      with_szlib=-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON
+      szlib_path=""	# szlib is in default paths
+      ;;
+  --with-szlib=*)
+      xarg=`echo $1 | cut -d= -f2-`
+      with_szlib="-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON"
+      szlib_path="SZIP_INSTALL=$xarg"
+      ;;
+  --without-szlib)
+      with_szlib=-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF
+      szlib_path=""	# reset the path
+      ;;
+  --njobs=*)
+      njobs=`echo $1 | cut -d= -f2-`
+      ;;
+  --enable-verbose)
+      vflag=1
+      ;;
+  --disable-verbose)
+      vflag=0
+      ;;
+  --help)
+      # print the detail help page and exit
+      HELP
+      exit 0
+      ;;
+  *)
+      echo "Unknown options: $1"
+      HELP
+      exit 1
+      ;;
     esac
     shift
 done
+$DPRINT after option parsing vflag=$vflag
 
 # Always display the brief help page
 HELP_BRIEF
@@ -271,7 +312,13 @@ if [ $? != 0 ]; then
     echo $vers failed. Aborted.
     exit 1
 fi
-echo Running Cmake for HDF5-${version} ...  
+
+# setup output of all the log files if verbose is on upon exit
+trap \
+"if [ $vflag -ne 0 ]; then DUMP_LOGFILE \$configlog \$makelog \$testlog \$packlog \$installlog; fi" \
+0
+
+echo Running Cmake for HDF5-${version} ...
 #      4. Configure the C library, tools and tests with this command:
 #         If successful, append the configure summary to the configure logfile.
 STEP "Configure..." \
@@ -288,18 +335,17 @@ STEP "Configure..." \
     $with_szlib \
     $srcdir" $configlog &&\
     cat $config_summary >> $configlog
-      
+
 #      5. Build the C library, tools and tests with this command:
-STEP "Build the library, tools and tests, ..." "cmake --build . --config Release" $makelog
-      
+STEP "Build the library, tools and tests, ..." "cmake --build . --config Release -- $njobs" $makelog
+
 #      6. Test the C library and tools with this command:
-STEP "Test the library and tools..." "ctest . -C Release" $testlog
-      
+STEP "Test the library and tools..." "ctest . -C Release $njobs" $testlog
+
 #      7. Create an install image with this command:
 STEP "Create an install image..." "cpack -C Release CPackConfig.cmake" $packlog
-      
+
 #      8. Install with this command:
-#STEP "Install..." "./HDF5-${version}-Linux.sh --skip-license" $installlog
 STEP "Install..." "INSTALL_HDF5" $installlog
 # save the last exit code
 exit_code=$?
@@ -387,7 +433,7 @@ set (SITE_BUILDNAME_SUFFIX "cmakehdf5")
 # -- URL set for internal check, default is to not update
 set (LOCAL_SKIP_UPDATE TRUE)
 set (REPOSITORY_URL "http://svn.${hdfgroup_url}/hdf5/branches/hdf5_1_8")
-# -- Standard build options  
+# -- Standard build options
 set (ADD_BUILD_OPTIONS "-DCMAKE_INSTALL_PREFIX:PATH=${CTEST_BINARY_DIRECTORY} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=\"SVN\" -DHDF5_PACKAGE_EXTLIBS:BOOL=ON")
 
 # Use multiple CPU cores to build
@@ -401,9 +447,9 @@ if(NOT N EQUAL 0)
   set(ctest_test_args ${ctest_test_args} PARALLEL_LEVEL ${N})
 endif()
 
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 # -- Get environment
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
   ## -- set hostname
   ## --------------------------
   find_program (HOSTNAME_CMD NAMES hostname)
@@ -423,10 +469,10 @@ endif()
   else (SITE_BUILDNAME_SUFFIX)
     set (CTEST_BUILD_NAME  "${osname}-${osrel}-${cpu}")
   endif (SITE_BUILDNAME_SUFFIX)
-# -----------------------------------------------------------  
-  
+# -----------------------------------------------------------
+
 set (BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDNAME:STRING=${CTEST_BUILD_NAME}")
- 
+
 #-----------------------------------------------------------------------------
 # MAC machines need special option
 #-----------------------------------------------------------------------------
@@ -434,21 +480,25 @@ if (APPLE)
   # Compiler choice
   execute_process(COMMAND xcrun --find cc OUTPUT_VARIABLE XCODE_CC OUTPUT_STRIP_TRAILING_WHITESPACE)
   execute_process(COMMAND xcrun --find c++ OUTPUT_VARIABLE XCODE_CXX OUTPUT_STRIP_TRAILING_WHITESPACE)
-  SET(ENV{CC} "${XCODE_CC}")
-  SET(ENV{CXX} "${XCODE_CXX}")
-  # Shared fortran is not supported, build static 
+  set(ENV{CC} "${XCODE_CC}")
+  set(ENV{CXX} "${XCODE_CXX}")
+  # Shared fortran is not supported, build static
   set (BUILD_OPTIONS "${BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_ANSI_CFLAGS:STRING=-fPIC")
   set (BUILD_OPTIONS "${BUILD_OPTIONS} -DCTEST_USE_LAUNCHERS:BOOL=ON -DCMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=OFF")
 endif (APPLE)
 
 
-# -----------------------------------------------------------  
+# -----------------------------------------------------------
 find_package (Subversion)
 set (CTEST_UPDATE_COMMAND "${Subversion_SVN_EXECUTABLE}")
-# -- Only clean build folder if LOCAL_CLEAR_BUILD is set  
+# -- Only clean build folder if LOCAL_CLEAR_BUILD is set
 if (LOCAL_CLEAR_BUILD)
   set (CTEST_START_WITH_EMPTY_BINARY_DIRECTORY TRUE)
-  ctest_empty_binary_directory (${CTEST_BINARY_DIRECTORY})
+  if(NOT EXISTS "${CTEST_BINARY_DIRECTORY}")
+    file(MAKE_DIRECTORY "${CTEST_BINARY_DIRECTORY}")
+  else()
+    ctest_empty_binary_directory(${CTEST_BINARY_DIRECTORY})
+  endif()
 endif (LOCAL_CLEAR_BUILD)
 
 #-----------------------------------------------------------------------------
@@ -471,7 +521,7 @@ endforeach (req)
 
 ## -- set output to english
 set($ENV{LC_MESSAGES}  "en_EN")
- 
+
 #-----------------------------------------------------------------------------
 # Initialize the CTEST commands
 #------------------------------
@@ -494,31 +544,32 @@ foreach (v
 endforeach (v)
 message ("Dashboard script configuration:\n${vars}\n")
 
-CTEST_START (${MODEL} TRACK ${MODEL})
+ctest_start (${MODEL} TRACK ${MODEL})
 if (NOT LOCAL_SKIP_UPDATE)
-  CTEST_UPDATE (SOURCE "${CTEST_SOURCE_DIRECTORY}")
+  ctest_update (SOURCE "${CTEST_SOURCE_DIRECTORY}")
 endif (NOT LOCAL_SKIP_UPDATE)
-CTEST_CONFIGURE (BUILD "${CTEST_BINARY_DIRECTORY}" RETURN_VALUE res)
 if(NOT res STREQUAL "0")
   message (FATAL_ERROR "Configure FAILED")
 endif()
 message ("Configure DONE")
-CTEST_READ_CUSTOM_FILES ("${CTEST_BINARY_DIRECTORY}")
+configure_file(${CTEST_SOURCE_DIRECTORY}/config/cmake/CTestCustom.cmake ${CTEST_BINARY_DIRECTORY}/CTestCustom.cmake)
+ctest_read_custom_files ("${CTEST_BINARY_DIRECTORY}")
+ctest_configure (BUILD "${CTEST_BINARY_DIRECTORY}" RETURN_VALUE res)
 if (NOT LOCAL_NO_SUBMIT)
-  CTEST_SUBMIT (PARTS Update Configure Notes)
+  ctest_submit (PARTS Update Configure Notes)
 endif (NOT LOCAL_NO_SUBMIT)
-CTEST_BUILD (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND RETURN_VALUE res)
+ctest_build (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND RETURN_VALUE res)
 if (NOT LOCAL_NO_SUBMIT)
-  CTEST_SUBMIT (PARTS Build)
+  ctest_submit (PARTS Build)
 endif (NOT LOCAL_NO_SUBMIT)
 if(NOT res STREQUAL "0")
   message (FATAL_ERROR "Build FAILED")
 endif()
 message ("build DONE")
 if (NOT LOCAL_SKIP_TEST)
-  CTEST_TEST (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND ${ctest_test_args} RETURN_VALUE res)
+  ctest_build (BUILD "${CTEST_BINARY_DIRECTORY}" APPEND ${ctest_test_args} RETURN_VALUE res)
   if (NOT LOCAL_NO_SUBMIT)
-    CTEST_SUBMIT (PARTS Test)
+    ctest_submit (PARTS Test)
   endif (NOT LOCAL_NO_SUBMIT)
   if(NOT res STREQUAL "0")
     message (FATAL_ERROR "Test FAILED")
diff --git a/bin/genparser b/bin/genparser
new file mode 100755
index 0000000..71a8ae2
--- /dev/null
+++ b/bin/genparser
@@ -0,0 +1,252 @@
+#! /bin/bash
+#
+# Copyright by The HDF Group.                                              
+# 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 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 script runs flex/lex and bison/yacc to generate parser code for
+# the high-level library. It used to be a part of autogen.sh, but many
+# people encountered problems with installing flex and bison on their
+# system and the parser code rarely changes, so those parts of the
+# script were moved to their own file.
+#
+# NOTE CAREFULLY!
+#
+# There is NO dependency in either the autotools or CMake to regenerate
+# the parser code. If you modify H5LT analyze.l or H5LTparse.y, you
+# will need to run this scrpit manually on a system with a suitable
+# lexer and parser generator.
+#
+# IMPORTANT OS X NOTE
+#
+# If you are using OS X, you will probably not have flex or bison
+# installed. In addtion, even if you do have bison installed, the bison
+# version you have installed may also have a bug that makes it unable to
+# process our input files.
+#
+# The easiest way to fix this is to install everything via Homebrew:
+#
+#   http://brew.sh/
+#
+# After you install the base packages, install flex/bison.
+#
+#   brew install flex
+#   brew install bison
+#
+# END IMPORTANT OS X NOTE
+#
+# If you want to use a particular version of flex or bison, the paths
+# to each tool can be overridden using the following environment
+# variables:
+#
+#   HDF5_FLEX
+#   HDF5_BISON
+#
+# This script takes two potential options:
+#
+# -p
+#
+# When this is selected, the flex/bison versions are set to the paths
+# and versions used by The HDF Group to produce the released versions
+# of the library.
+#
+# NOTE: This is probably temporary. Once we update our dev machines
+# to have recent versions of the autotools this option will probably
+# be removed.
+#
+# -v
+#
+# This emits some extra information, mainly tool versions.
+
+echo
+echo "*******************************************"
+echo "* HDF5 high-level parser generator script *"
+echo "*******************************************"
+echo
+
+# Default is not verbose output
+verbose=false
+
+optspec=":hpv-"
+while getopts "$optspec" optchar; do
+    case "${optchar}" in
+    h)
+        echo "usage: $0 [OPTIONS] /path/to/hl/src/directory"
+        echo
+        echo "      -h      Print this help message."
+        echo
+        echo "      -p      Used by THG to use hard-codes flex/bison"
+        echo "              paths on THG machines. Not for non-HDF-Group"
+        echo "              users!"
+        echo
+        echo "      -v      Show more verbose output."
+        echo
+        echo "  NOTE: Each tool can be set via an environment variable."
+        echo "        These are documented inside this script."
+        echo
+        exit 0
+        ;;
+    p)
+        echo "Setting THG production mode..."
+        echo
+        production=true
+        ;;
+    v)
+        echo "Setting verbosity: high"
+        echo
+        verbose=true
+        ;;
+    *)
+        if [ "$OPTERR" != 1 ] || [ "${optspec:0:1}" = ":" ]; then
+            echo "Non-option argument: '-${OPTARG}'" >&2
+        fi
+        ;;
+    esac
+done
+
+# Get the path to the hl src directory
+shift $(($OPTIND - 1))
+path_to_hl_src=$1
+if test -z ${path_to_hl_src}; then
+    echo "*** ERROR *** - Path to hl/src not set"
+    echo "Please add the path to the hl/src directory as a parameter"
+    echo "See $0 -h for more help."
+    echo
+    exit -1
+fi
+
+if [ "$production" = true ] ; then
+
+    # Production mode
+    #
+    # Hard-code canonical HDF Group tool locations.
+
+    # If paths to tools are not specified, assume they are
+    # located in /usr/hdf/bin/AUTOTOOLS and set paths accordingly.
+    if test -z ${HDF5_BISON}; then
+        HDF5_BISON=/usr/hdf/bin/AUTOTOOLS/bison
+    fi
+    if test -z ${HDF5_FLEX}; then
+        HDF5_FLEX=/usr/hdf/bin/AUTOTOOLS/flex
+    fi
+
+else
+
+    # Not in production mode
+    #
+    # If paths to autotools are not specified, use whatever the system
+    # has installed as the default. We use 'which <tool>' to
+    # show exactly what's being used.
+    if test -z ${HDF5_BISON}; then
+        HDF5_BISON=$(which bison)
+    fi
+    if test -z ${HDF5_FLEX}; then
+        HDF5_FLEX=$(which flex)
+    fi
+
+fi # production
+
+# Make sure that these versions of the tools are in the path
+BISON_DIR=`dirname ${HDF5_BISON}`
+FLEX_DIR=`dirname ${HDF5_FLEX}`
+PATH=${FLEX_DIR}:${BISON_DIR}:$PATH
+
+# Run flex and bison
+# automatically generates hl/src/H5LTanalyze.c and hl/src/H5LTparse.c
+# Note that, as of Xcode 6.1 (2015), the default bison version on OS X
+# is old enough to have the circular dependency bug. You'll have
+# to install a later version of bison. See the OS X note at the top
+# of this script.
+echo
+echo "Generating H5LT parser code (requires yacc/bison):"
+echo "Generate hl/src/H5LTparse.c from hl/src/H5LTparse.y"
+# HDF5_BISON is set via the environment or 'which bison', above
+if test -z ${HDF5_BISON}; then
+    echo
+    echo "*************************"
+    echo " ERROR - bison not found"
+    echo "*************************"
+    echo "bison is required to generate parser code in H5LT"
+    echo
+    exit 127
+fi
+if [ "$verbose" = true ] ; then
+    ${HDF5_BISON} --version
+fi
+${HDF5_BISON} -pH5LTyy -o ${path_to_hl_src}/H5LTparse.c -d ${path_to_hl_src}/H5LTparse.y
+
+echo
+echo "Generating H5LT lexer code (requires lex/flex):"
+echo "Generate hl/src/H5LTanalyze.c from hl/src/H5LTanalyze.l"
+# HDF5_FLEX is set via the environment or 'which flex', above
+if test -z ${HDF5_FLEX}; then
+    echo
+    echo "************************"
+    echo " ERROR - flex not found"
+    echo "************************"
+    echo "flex is required to generate lexer code in H5LT"
+    echo
+    exit 127
+fi
+if [ "$verbose" = true ] ; then
+    ${HDF5_FLEX} --version
+fi
+${HDF5_FLEX} --nounistd -PH5LTyy -o ${path_to_hl_src}/H5LTanalyze.c ${path_to_hl_src}/H5LTanalyze.l
+
+# fix H5LTparse.c to declare H5LTyyparse return type as an hid_t
+# instead of int.  Currently the generated function H5LTyyparse is
+# generated with a return value of type int, which is a mapping to the
+# flex yyparse function.  The return value in the HL library should be
+# an hid_t. 
+# I propose to not use flex to generate this function, but for now I am 
+# adding a perl command to find and replace this function declaration in
+# H5LTparse.c.
+perl -0777 -pi -e 's/int yyparse/hid_t yyparse/igs' ${path_to_hl_src}/H5LTparse.c
+perl -0777 -pi -e 's/int\nyyparse/hid_t\nyyparse/igs' ${path_to_hl_src}/H5LTparse.c
+perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5LTparse.c
+
+# Add code that disables warnings in the flex/bison-generated code.
+#
+# Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
+# will simply ignore them, but we want to avoid those warnings.
+for f in ${path_to_hl_src}/H5LTparse.c ${path_to_hl_src}/H5LTanalyze.c
+do
+    echo '#if __GNUC__ >= 4 && __GNUC_MINOR__ >=2                           ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wconversion"                     ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wimplicit-function-declaration"  ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wmissing-prototypes"             ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wnested-externs"                 ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wold-style-definition"           ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wredundant-decls"                ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wsign-compare"                   ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wsign-conversion"                ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wstrict-overflow"                ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wstrict-prototypes"              ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wsuggest-attribute=pure"         ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wswitch-default"                 ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wunused-function"                ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wunused-macros"                  ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wunused-parameter"               ' >> tmp.out
+    echo '#elif defined __SUNPRO_CC                                         ' >> tmp.out
+    echo '#pragma disable_warn                                              ' >> tmp.out
+    echo '#elif defined _MSC_VER                                            ' >> tmp.out
+    echo '#pragma warning(push, 1)                                          ' >> tmp.out
+    echo '#endif                                                            ' >> tmp.out
+
+    cat $f >> tmp.out
+    mv tmp.out $f
+done
+
+echo
+exit 0
+
diff --git a/bin/h5vers b/bin/h5vers
index 2fe9105..7e61dc8 100755
--- a/bin/h5vers
+++ b/bin/h5vers
@@ -377,12 +377,12 @@ sub gen_configure {
   $conf =~ /^(.*?)\/?configure.ac$/;
 
   if ($1) {
-    $rc = system("cd $1 && bin/reconfigure >/dev/null 2>/dev/null && rm -rf autom4te.cache");
+    $rc = system("cd $1 && ./autogen.sh -p >/dev/null 2>/dev/null && rm -rf autom4te.cache");
   } else {
-    $rc = system("bin/reconfigure >/dev/null 2>/dev/null && rm -rf autom4te.cache");
+    $rc = system("./autogen.sh -p >/dev/null 2>/dev/null && rm -rf autom4te.cache");
   }
   if ($rc) {
-    printf("bin/reconfigure failed with exit code %d. Aborted.\n", $rc);
+    printf("./autogen.sh -p failed with exit code %d. Aborted.\n", $rc);
     exit 1;
   }
 }
diff --git a/bin/trace b/bin/trace
index deed3bc..05d3186 100755
--- a/bin/trace
+++ b/bin/trace
@@ -37,6 +37,7 @@ $Source = "";
                "H5D_fill_value_t"           => "DF",
 	       "H5FD_mpio_chunk_opt_t"      => "Dh",
                "H5D_mpio_actual_io_mode_t"  => "Di",
+               "H5D_chunk_index_t"          => "Dk",
                "H5D_layout_t"               => "Dl",
                "H5D_mpio_no_collective_cause_t" => "Dn",
                "H5D_mpio_actual_chunk_opt_mode_t" => "Do",
@@ -101,6 +102,7 @@ $Source = "";
 	       "H5A_operator2_t"            => "x",
 	       "H5A_info_t"                 => "x",
                "H5AC_cache_config_t"        => "x",
+               "H5D_append_cb_t"            => "x",
                "H5D_gather_func_t"          => "x",
                "H5D_operator_t"             => "x",
                "H5D_scatter_func_t"         => "x",
@@ -110,8 +112,10 @@ $Source = "";
                "H5E_walk_t"                 => "x",
                "H5E_walk1_t"                => "x",
                "H5E_walk2_t"                => "x",
+               "H5F_flush_cb_t"             => "x",
 	       "H5F_info1_t"                => "x",
 	       "H5F_info2_t"                => "x",
+               "H5F_retry_info_t"           => "x",
                "H5FD_t"                     => "x",
                "H5FD_class_t"               => "x",
                "H5FD_stream_fapl_t"         => "x",