[svn-r23577] Bring revisions 22708:22730 from trunk to revise_chunks.

h5committested.
author: Vailin Choi <vchoi@hdfgroup.org> 2013-04-11 22:12:12 (GMT)
committer: Vailin Choi <vchoi@hdfgroup.org> 2013-04-11 22:12:12 (GMT)
commit: 4ce17c9aa6515c32551104516b32caf8b0ce9f02 (patch)
tree: ca2237566b5b729f4d6a4545ffb2909d9d31309f
parent: 5185d3a76aff8288d8eaceff31b483cbf897619e (diff)
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110 files changed, 1029 insertions, 1020 deletions
diff --git a/MANIFEST b/MANIFEST
index 9fed176..e2f0f0b 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -37,7 +37,7 @@
 ./aclocal.m4
 ./acsite.m4
 ./configure
-./configure.in
+./configure.ac
 
 ./bin/COPYING
 ./bin/buildhdf5
@@ -1154,7 +1154,7 @@
 ./tools/h5import/h5import.h
 ./tools/h5import/h5import.c
 ./tools/h5import/h5importtest.c
-./tools/h5import/h5importtestutil.sh
+./tools/h5import/h5importtestutil.sh.in
 
 # testfiles for h5import
 ./tools/h5import/testfiles/binfp64.conf
@@ -1215,8 +1215,8 @@
 ./tools/h5diff/h5diff_main.c
 ./tools/h5diff/ph5diff_main.c
 ./tools/h5diff/h5diffgentest.c
-./tools/h5diff/testh5diff.sh
-./tools/h5diff/testph5diff.sh
+./tools/h5diff/testh5diff.sh.in
+./tools/h5diff/testph5diff.sh.in
 
 # h5repack sources
 ./tools/h5repack/Makefile.am
@@ -1241,7 +1241,7 @@
 ./tools/h5ls/testh5ls.sh.in
 
 # h5copy sources
-./tools/h5copy/testh5copy.sh
+./tools/h5copy/testh5copy.sh.in
 ./tools/h5copy/Makefile.in
 ./tools/h5copy/h5copy.c
 ./tools/h5copy/h5copygentest.c
@@ -1282,7 +1282,7 @@
 ./tools/misc/h5repart.c
 ./tools/misc/h5repart_gentest.c
 ./tools/misc/repart_test.c
-./tools/misc/testh5mkgrp.sh
+./tools/misc/testh5mkgrp.sh.in
 ./tools/misc/testh5repart.sh.in
 ./tools/misc/talign.c
 ./tools/misc/testfiles/h5mkgrp_help.txt
@@ -2227,7 +2227,7 @@
 ./hl/tools/gif2h5/hdfgifwr.c
 ./hl/tools/gif2h5/writehdf.c
 ./hl/tools/gif2h5/h52gifgentst.c
-./hl/tools/gif2h5/h52giftest.sh
+./hl/tools/gif2h5/h52giftest.sh.in
 ./hl/tools/gif2h5/testfiles/image1.gif
 ./hl/tools/gif2h5/testfiles/h52giftst.h5
 #
diff --git a/Makefile.in b/Makefile.in
index d0e53f1..1472be5 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -93,7 +93,7 @@ DIST_COMMON = $(am__configure_deps) $(srcdir)/Makefile.am \
 	bin/missing bin/mkinstalldirs
 subdir = .
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
@@ -178,7 +178,7 @@ distuninstallcheck_listfiles = find . -type f -print
 am__distuninstallcheck_listfiles = $(distuninstallcheck_listfiles) \
   | sed 's|^\./|$(prefix)/|' | grep -v '$(infodir)/dir$$'
 distcleancheck_listfiles = find . -type f -print
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -196,12 +196,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
diff --git a/bin/chkconfigure b/bin/chkconfigure
index f66619e..abafae8 100755
--- a/bin/chkconfigure
+++ b/bin/chkconfigure
@@ -18,8 +18,8 @@
 # Created Date: 2004/12/07
 
 #
-# Configure: should be generated by autoconf version 2.68.
-# autoconf:  should be of version 2.68.
+# Configure: should be generated by autoconf version 2.69.
+# autoconf:  should be of version 2.69.
 
 # variable initialization
 nerrors=0
diff --git a/bin/chkcopyright b/bin/chkcopyright
index f5ad67a54..fe9fe49 100755
--- a/bin/chkcopyright
+++ b/bin/chkcopyright
@@ -57,7 +57,7 @@ SH_COPYRIGHT=/tmp/h5chkright_SH.$$	# SHELL style copyright
 SH_COPYRIGHT2=/tmp/h5chkright_SH2.$$	# SHELL style copyright, 2nd style.
 WINBAT_COPYRIGHT=/tmp/h5chkright_WINBAT.$$	# Windows Batch file Copyright notice
 VMSCMD_COPYRIGHT=/tmp/h5chkright_VMSCMD.$$	# VMS command file Copyright notice
-CONFIGURE_IN_COPYRIGHT=/tmp/h5chkright_CONFIGURE_IN.$$	# configure.in file Copyright notice
+CONFIGURE_AC_COPYRIGHT=/tmp/h5chkright_CONFIGURE_AC.$$	# configure.ac file Copyright notice
 
 tmpfixfile=/tmp/h5chkright_fix.$$	# Temporary fixed copy of file
 
@@ -207,8 +207,8 @@ EOF
 @REM access to either file, you may request a copy from help@hdfgroup.org.
 EOF
 
-    # configure.in file Copyright notice
-    cat > ${CONFIGURE_IN_COPYRIGHT} << \EOF
+    # configure.ac file Copyright notice
+    cat > ${CONFIGURE_AC_COPYRIGHT} << \EOF
 dnl Copyright by The HDF Group.
 dnl Copyright by the Board of Trustees of the University of Illinois.
 dnl All rights reserved.
@@ -635,10 +635,10 @@ VMSCMD_FILE()
 
 # Check Configure.in type files
 #
-CONFIGURE_IN_FILE()
+CONFIGURE_AC_FILE()
 {
     f=$1
-    case `MATCH_COPYRIGHT $CONFIGURE_IN_COPYRIGHT $f` in
+    case `MATCH_COPYRIGHT $CONFIGURE_AC_COPYRIGHT $f` in
     PASSED)
 	PASSED $f
 	return
@@ -646,9 +646,9 @@ CONFIGURE_IN_FILE()
     FAILED)
 	# show the difference
 	FAILED $f
-	$DIFF ${EXTRACTEDFILE} ${CONFIGURE_IN_COPYRIGHT}
+	$DIFF ${EXTRACTEDFILE} ${CONFIGURE_AC_COPYRIGHT}
 	if [ -n "$FIXIT" ]; then
-	    FIX_COPYRIGHT $CONFIGURE_IN_COPYRIGHT $f
+	    FIX_COPYRIGHT $CONFIGURE_AC_COPYRIGHT $f
 	fi
 	;;
     esac
@@ -681,8 +681,8 @@ GUESS_File_Type()
 	# Put this after C_SOURCE which may have #define and such lines.
 	echo SHELL_FILE
     elif grep '^dnl' < $tmpfile > /dev/null; then
-	# Some lines start with a "dnl".  It may be a configure.in type file.
-	echo CONFIGURE_IN_FILE
+	# Some lines start with a "dnl".  It may be a configure.ac type file.
+	echo CONFIGURE_AC_FILE
     elif grep -i '^<html>' < $tmpfile > /dev/null || \
 	 grep '^<!--' < $tmpfile > /dev/null ; then
 	# Some lines start with a "<html>" or having an html comment tag.
@@ -827,8 +827,8 @@ while read file; do
 	*Makefile | *Makefile.in | *Makefile.am | Makefile.dist )
 	    MAKE_FILE ${file}
 	    ;;
-	configure.in )
-	    CONFIGURE_IN_FILE ${file}
+	configure.ac )
+	    CONFIGURE_AC_FILE ${file}
 	    ;;
 	*.bat | *.BAT )
 	    # Windows Batch files
diff --git a/bin/h5vers b/bin/h5vers
index a216577..138a8e9 100755
--- a/bin/h5vers
+++ b/bin/h5vers
@@ -71,7 +71,7 @@ use strict;
 # the command line) then the first line of the README.txt and RELEASE.txt files
 # one directory above the H5public.h file is also modified so it looks
 # something like: This is hdf5-1.2.3-pre1 currently under development.
-# The AC_INIT macro in configure.in will also change in this case to be
+# The AC_INIT macro in configure.ac will also change in this case to be
 # something like: AC_INIT([HDF5], [hdf5-1.2.3-pre1], [help@hdfgroup.org])
 # Version changes are also reflected in the Windows-maintained H5pubconf.h
 # file.
@@ -159,10 +159,10 @@ while ($_ = shift) {
 die "mutually exclusive options given\n" if $set && $inc;
 
 # Determine file to use as H5public.h, README.txt,
-# release_docs/RELEASE.txt, configure.in, windows/src/H5pubconf.h,
-# vms/src/h5pubcof.h and config/lt_vers.am. 
-# The README.txt, release_docs/RELEASE.txt, configure.in, 
-# windows/src/H5pubconf.h, vms/src/h5pubconf.h and config/lt_vers.am 
+# release_docs/RELEASE.txt, configure.ac, windows/src/H5pubconf.h,
+# vms/src/h5pubconf.h and config/lt_vers.am. 
+# The README.txt, release_docs/RELEASE.txt, configure.ac, 
+# vms/src/h5pubconf.h, windows/src/H5pubconf.h, and config/lt_vers.am 
 # files are always in the directory above H5public.h
 unless ($file) {
   for (@files) {
@@ -183,9 +183,9 @@ die "unable to read file: $README\n" unless -r $file;
 my $RELEASE = $file;
 $RELEASE =~ s/[^\/]*$/..\/release_docs\/RELEASE.txt/;
 die "unable to read file: $RELEASE\n" unless -r $file;
-# configure.in
+# configure.ac
 my $CONFIGURE = $file;
-$CONFIGURE =~ s/[^\/]*$/..\/configure.in/;
+$CONFIGURE =~ s/[^\/]*$/..\/configure.ac/;
 die "unable to read file: $CONFIGURE\n" unless -r $file;
 # windows/src/H5pubconf.h
 my $H5PUBCONF = $file;
@@ -339,7 +339,7 @@ sub gen_configure {
   print FILE @contents;
   close FILE;
 
-  $conf =~ /^(.*?)\/?configure.in$/;
+  $conf =~ /^(.*?)\/?configure.ac$/;
 
   if ($1) {
     $rc = system("cd $1 && bin/reconfigure >/dev/null 2>/dev/null && rm -rf autom4te.cache");
@@ -352,7 +352,7 @@ sub gen_configure {
   }
 }
 
-# Update the configure.in files and regenerate them
+# Update the configure.ac files and regenerate them
 gen_configure("HDF5", $CONFIGURE) if $CONFIGURE;
 
 sub gen_h5pubconf {
diff --git a/bin/reconfigure b/bin/reconfigure
index e176cfa..dba5a67 100755
--- a/bin/reconfigure
+++ b/bin/reconfigure
@@ -33,6 +33,8 @@ AUTOMAKE_VERSION="automake (GNU automake) 1.12.3"
 AUTOHEADER_VERSION="autoheader (GNU Autoconf) 2.69"
 ACLOCAL_VERSION="aclocal (GNU automake) 1.12.3"
 LIBTOOL_VERSION="(GNU libtool) 2.4.2"
+M4_VERSION="m4 (GNU M4) 1.4.16"
+
 #
 # When upgrading automake's version, don't forget to also update its
 # helper utilities, especially depcomp.
@@ -55,6 +57,9 @@ fi
 if test -z ${LIBTOOL}; then
   LIBTOOL=/mnt/hdf/packages/libtool/libtool-2.4.2/bin/libtool
 fi
+if test -z ${M4}; then
+  M4=/mnt/hdf/packages/m4/m4-1.4.16/bin/m4
+fi
 
 # Check version numbers of all autotools against the "correct" versions
 AC_VERS=`${AUTOCONF} --version 2>&1 | grep "^${AUTOCONF_VERSION}"`
@@ -82,14 +87,17 @@ if test -z "${LT_VERS}"; then
    echo "${LIBTOOL} version is not ${LIBTOOL_VERSION}"
    exit 1
 fi
-
-# Use the latest version of M4
-PATH=/mnt/hdf/packages/m4/m4-1.4.16/bin:/mnt/hdf/packages/m4/m4-1.4.16/share:$PATH
+M4_VERS=`${M4} --version 2>&1 | grep "${M4_VERSION}"`
+if test -z "${M4_VERS}"; then
+   echo "${M4} version is not ${M4_VERSION}"
+   exit 1
+fi
 
 # Make sure that the tools are in the path.
 AUTOCONF_DIR=`dirname ${AUTOCONF}`
 LIBTOOL_DIR=`dirname ${LIBTOOL}`
-PATH=${AUTOCONF_DIR}:$PATH
+M4_DIR=`dirname ${M4}`
+PATH=${AUTOCONF_DIR}:${M4_DIR}:$PATH
 
 # Run autoconf/automake commands in order
   echo ${ACLOCAL} -I ${LIBTOOL_DIR}/../share/aclocal
diff --git a/c++/Makefile.in b/c++/Makefile.in
index 290d66e..8c82ca9 100644
--- a/c++/Makefile.in
+++ b/c++/Makefile.in
@@ -73,7 +73,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = c++
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -143,7 +143,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -161,12 +161,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -438,6 +435,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -818,7 +819,7 @@ check-clean ::
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -844,7 +845,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -868,7 +869,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -878,7 +879,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -968,7 +969,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -998,7 +999,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/c++/examples/Makefile.am b/c++/examples/Makefile.am
index dc2bc7c..cd9a9f6 100644
--- a/c++/examples/Makefile.am
+++ b/c++/examples/Makefile.am
@@ -23,7 +23,7 @@ include $(top_srcdir)/config/commence.am
 
 # These are the programs that 'make all' or 'make prog' will build and
 # which 'make check' will run.  List them in the order they should be run.
-TEST_PROG=create readdata writedata compound extend_ds chunks h5group
+EXAMPLE_PROG=create readdata writedata compound extend_ds chunks h5group
 TEST_SCRIPT=testh5c++.sh
 
 # These are the example files to be installed
diff --git a/c++/examples/Makefile.in b/c++/examples/Makefile.in
index a599c1e..e9bbf47 100644
--- a/c++/examples/Makefile.in
+++ b/c++/examples/Makefile.in
@@ -76,10 +76,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am \
 	$(top_srcdir)/config/examples.am
-TESTS =
+TESTS = $(TEST_SCRIPT)
 subdir = c++/examples
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -110,7 +110,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -128,12 +128,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -394,7 +391,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5
 
 # These are the programs that 'make all' or 'make prog' will build and
 # which 'make check' will run.  List them in the order they should be run.
-TEST_PROG = create readdata writedata compound extend_ds chunks h5group
+EXAMPLE_PROG = create readdata writedata compound extend_ds chunks h5group
 TEST_SCRIPT = testh5c++.sh
 
 # These are the example files to be installed
@@ -412,12 +409,11 @@ EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/c++
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES = *.raw *.meta *.o
-CLEANFILES = $(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -430,6 +426,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -734,7 +734,7 @@ installcheck-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -760,7 +760,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -784,7 +784,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -794,7 +794,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -884,7 +884,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -914,7 +914,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/c++/examples/testh5c++.sh.in b/c++/examples/testh5c++.sh.in
index 4281e3c..40d503f 100644
--- a/c++/examples/testh5c++.sh.in
+++ b/c++/examples/testh5c++.sh.in
@@ -19,6 +19,8 @@
 # Modification:
 #
 
+srcdir=@srcdir@
+
 # Initializations
 TESTNAME=h5c++
 EXIT_SUCCESS=0
@@ -41,11 +43,6 @@ verbose=yes
 myos=`uname -s`
 myhostnama=`uname -n`
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # Generate some source files and library for tests.
 suffix=cpp		# source file suffix
 hdf5main=${H5TOOL}_hdf5main.$suffix
diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in
index e73417e..42c33a6 100644
--- a/c++/src/Makefile.in
+++ b/c++/src/Makefile.in
@@ -81,7 +81,7 @@ DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
 TESTS =
 subdir = c++/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -185,7 +185,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -203,12 +203,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -523,6 +520,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -980,7 +981,7 @@ mostlyclean-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -1006,7 +1007,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -1030,7 +1031,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -1040,7 +1041,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1130,7 +1131,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1160,7 +1161,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/c++/test/Makefile.in b/c++/test/Makefile.in
index 2eccbc5..00a8056 100644
--- a/c++/test/Makefile.in
+++ b/c++/test/Makefile.in
@@ -75,10 +75,10 @@ DIST_COMMON = $(srcdir)/H5srcdir_str.h.in $(srcdir)/Makefile.am \
 # Shared C++ libraries aren't universally supported.
 @CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_1)
 subdir = c++/test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -146,7 +146,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -164,12 +164,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -456,6 +453,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -799,7 +800,7 @@ mostlyclean-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -825,7 +826,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -849,7 +850,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -859,7 +860,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -949,7 +950,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -979,7 +980,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/config/Makefile.am.blank b/config/Makefile.am.blank
index a091c60..05799fc 100644
--- a/config/Makefile.am.blank
+++ b/config/Makefile.am.blank
@@ -20,7 +20,7 @@
 #
 
 ## Makefile.am template
-## When automake is run, it scans configure.in to find all Makefiles used by
+## When automake is run, it scans configure.ac to find all Makefiles used by
 ## the build that come from Makefile.in files.  If there are Makefile.am's 
 ## in any of those locations, it parses the Makefile.am's to produce
 ## Makefile.in's, which configure uses to create Makefiles.
diff --git a/config/cmake/HDFMacros.cmake b/config/cmake/HDFMacros.cmake
index 568b3ff..099b97f 100644
--- a/config/cmake/HDFMacros.cmake
+++ b/config/cmake/HDFMacros.cmake
@@ -34,18 +34,18 @@ MACRO (IDE_SOURCE_PROPERTIES SOURCE_PATH HEADERS SOURCES)
 ENDMACRO (IDE_SOURCE_PROPERTIES)
 
 #-------------------------------------------------------------------------------
-MACRO (TARGET_NAMING target libtype)
+MACRO (TARGET_NAMING libtarget libtype)
   IF (WIN32)
     IF (${libtype} MATCHES "SHARED")
-      SET_TARGET_PROPERTIES (${target} PROPERTIES OUTPUT_NAME "${target}dll")
+      SET_TARGET_PROPERTIES (${libtarget} PROPERTIES OUTPUT_NAME "${libtarget}dll")
     ENDIF (${libtype} MATCHES "SHARED")
   ENDIF (WIN32)
 ENDMACRO (TARGET_NAMING)
 
 #-------------------------------------------------------------------------------
-MACRO (INSTALL_TARGET_PDB target targetdestination targetcomponent)
+MACRO (INSTALL_TARGET_PDB libtarget targetdestination targetcomponent)
   IF (WIN32 AND MSVC)
-    GET_TARGET_PROPERTY (target_name ${target} RELWITHDEBINFO_OUTPUT_NAME)
+    GET_TARGET_PROPERTY (target_name ${libtarget} RELWITHDEBINFO_OUTPUT_NAME)
     INSTALL (
       FILES
           ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_BUILD_TYPE}/${CMAKE_IMPORT_LIBRARY_PREFIX}${target_name}.pdb
@@ -58,10 +58,10 @@ MACRO (INSTALL_TARGET_PDB target targetdestination targetcomponent)
 ENDMACRO (INSTALL_TARGET_PDB)
 
 #-------------------------------------------------------------------------------
-MACRO (INSTALL_PROGRAM_PDB target targetdestination targetcomponent)
+MACRO (INSTALL_PROGRAM_PDB progtarget targetdestination targetcomponent)
   IF (WIN32 AND MSVC)
-    GET_TARGET_PROPERTY (target_name ${target} RELWITHDEBINFO_OUTPUT_NAME)
-    GET_TARGET_PROPERTY (target_prefix h5dump PREFIX)
+    GET_TARGET_PROPERTY (target_name ${progtarget} RELWITHDEBINFO_OUTPUT_NAME)
+    GET_TARGET_PROPERTY (target_prefix ${progtarget} PREFIX)
     INSTALL (
       FILES
           ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_BUILD_TYPE}/${target_prefix}${target_name}.pdb
@@ -121,16 +121,16 @@ MACRO (HDF_SET_LIB_OPTIONS libtarget libname libtype)
 ENDMACRO (HDF_SET_LIB_OPTIONS)
 
 #-------------------------------------------------------------------------------
-MACRO (TARGET_FORTRAN_WIN_PROPERTIES target addlinkflags)
+MACRO (TARGET_FORTRAN_WIN_PROPERTIES forttarget addlinkflags)
   IF (WIN32 AND MSVC)
     IF (BUILD_SHARED_LIBS)
-      SET_TARGET_PROPERTIES (${target}
+      SET_TARGET_PROPERTIES (${forttarget}
           PROPERTIES
               COMPILE_FLAGS "/dll"
               LINK_FLAGS "/SUBSYSTEM:CONSOLE ${addlinkflags}"
       ) 
     ELSE (BUILD_SHARED_LIBS)
-      SET_TARGET_PROPERTIES (${target}
+      SET_TARGET_PROPERTIES (${forttarget}
           PROPERTIES
               COMPILE_FLAGS "/MD"
               LINK_FLAGS "/SUBSYSTEM:CONSOLE ${addlinkflags}"
diff --git a/config/commence.am b/config/commence.am
index 3d098d9..4bc005e 100644
--- a/config/commence.am
+++ b/config/commence.am
@@ -87,13 +87,6 @@ TRACE=perl $(top_srcdir)/bin/trace
 F9XMODEXT=@F9XMODEXT@
 F9XMODFLAG=@F9XMODFLAG@
 
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF=/home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOMAKE=/home1/packages/automake/automake-1.9.6/bin/automake-1.9
-AUTOHEADER=/home1/packages/autoconf/autoconf-2.60/bin/autoheader
-ACLOCAL=/home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
-
 # .chkexe files are used to mark tests that have run successfully.
 # .chklog files are output from those tests.
 # *.clog are from the MPE option.
diff --git a/config/conclude.am b/config/conclude.am
index 830b60c..1ba56fb 100644
--- a/config/conclude.am
+++ b/config/conclude.am
@@ -27,13 +27,18 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
       $(noinst_LTLIBRARIES) $(check_LIBRARIES) $(check_LTLIBRARIES) $(EXTRA_LIB)
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TESTS = $(TEST_PROG) $(TEST_SCRIPT) $(EXTRA_TEST) 
+
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS =
 
 # lib/progs/tests targets recurse into subdirectories. build-* targets
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -59,7 +64,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -83,7 +88,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -93,7 +98,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -188,7 +193,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -218,7 +223,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/config/examples.am b/config/examples.am
index 9acd719..bf0708c 100644
--- a/config/examples.am
+++ b/config/examples.am
@@ -44,13 +44,12 @@
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES=*.raw *.meta *.o
 CHECK_CLEANFILES+=*.h5
-CLEANFILES=$(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES=$(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # How to create EXAMPLEDIR if it doesn't already exist
 $(EXAMPLEDIR):
diff --git a/configure b/configure
index 715153d..ed8d70e 100755
--- a/configure
+++ b/configure
@@ -1,5 +1,5 @@
 #! /bin/sh
-# From configure.in Id: configure.in 23568 2013-04-09 23:18:29Z vchoi .
+# From configure.ac Id: configure.ac 22697 2012-08-19 14:35:47Z hdftest .
 # Guess values for system-dependent variables and create Makefiles.
 # Generated by GNU Autoconf 2.69 for HDF5 1.9.127-FA_a5.
 #
@@ -30259,7 +30259,7 @@ if test -n "$TESTPARALLEL"; then
   fi
 fi
 
-ac_config_files="$ac_config_files src/libhdf5.settings Makefile src/Makefile test/Makefile test/testcheck_version.sh test/testerror.sh test/testflushrefresh.sh test/H5srcdir_str.h test/testlibinfo.sh test/testlinks_env.sh testpar/Makefile testpar/testph5.sh perform/Makefile tools/Makefile tools/h5dump/Makefile tools/h5dump/testh5dump.sh tools/h5dump/testh5dumppbits.sh tools/h5dump/testh5dumpxml.sh tools/h5ls/testh5ls.sh tools/h5import/Makefile tools/h5diff/Makefile tools/h5jam/Makefile tools/h5jam/testh5jam.sh tools/h5repack/Makefile tools/h5repack/h5repack.sh tools/h5ls/Makefile tools/h5copy/Makefile tools/lib/Makefile tools/misc/Makefile tools/misc/h5cc tools/misc/testh5repart.sh tools/h5stat/testh5stat.sh tools/h5stat/Makefile examples/Makefile examples/run-c-ex.sh examples/testh5cc.sh c++/Makefile c++/src/Makefile c++/src/h5c++ c++/test/Makefile c++/test/H5srcdir_str.h c++/examples/Makefile c++/examples/run-c++-ex.sh c++/examples/testh5c++.sh fortran/Makefile fortran/src/h5fc fortran/src/Makefile fortran/test/Makefile fortran/testpar/Makefile fortran/examples/Makefile fortran/examples/run-fortran-ex.sh fortran/examples/testh5fc.sh hl/Makefile hl/src/Makefile hl/test/Makefile hl/test/H5srcdir_str.h hl/test/test_ld.sh hl/tools/Makefile hl/tools/gif2h5/Makefile hl/tools/h5watch/Makefile hl/tools/h5watch/testh5watch.sh hl/examples/Makefile hl/examples/run-hlc-ex.sh hl/c++/Makefile hl/c++/src/Makefile hl/c++/test/Makefile hl/c++/examples/Makefile hl/c++/examples/run-hlc++-ex.sh hl/fortran/Makefile hl/fortran/src/Makefile hl/fortran/test/Makefile hl/fortran/examples/Makefile hl/fortran/examples/run-hlfortran-ex.sh"
+ac_config_files="$ac_config_files src/libhdf5.settings Makefile src/Makefile test/Makefile test/testcheck_version.sh test/testerror.sh test/testflushrefresh.sh test/H5srcdir_str.h test/testlibinfo.sh test/testlinks_env.sh testpar/Makefile testpar/testph5.sh perform/Makefile tools/Makefile tools/h5dump/Makefile tools/h5dump/testh5dump.sh tools/h5dump/testh5dumppbits.sh tools/h5dump/testh5dumpxml.sh tools/h5ls/testh5ls.sh tools/h5import/Makefile tools/h5import/h5importtestutil.sh tools/h5diff/Makefile tools/h5diff/testh5diff.sh tools/h5diff/testph5diff.sh tools/h5jam/Makefile tools/h5jam/testh5jam.sh tools/h5repack/Makefile tools/h5repack/h5repack.sh tools/h5ls/Makefile tools/h5copy/Makefile tools/h5copy/testh5copy.sh tools/lib/Makefile tools/misc/Makefile tools/misc/h5cc tools/misc/testh5mkgrp.sh tools/misc/testh5repart.sh tools/h5stat/testh5stat.sh tools/h5stat/Makefile examples/Makefile examples/run-c-ex.sh examples/testh5cc.sh c++/Makefile c++/src/Makefile c++/src/h5c++ c++/test/Makefile c++/test/H5srcdir_str.h c++/examples/Makefile c++/examples/run-c++-ex.sh c++/examples/testh5c++.sh fortran/Makefile fortran/src/h5fc fortran/src/Makefile fortran/test/Makefile fortran/testpar/Makefile fortran/examples/Makefile fortran/examples/run-fortran-ex.sh fortran/examples/testh5fc.sh hl/Makefile hl/src/Makefile hl/test/Makefile hl/test/H5srcdir_str.h hl/test/test_ld.sh hl/tools/Makefile hl/tools/gif2h5/Makefile hl/tools/gif2h5/h52giftest.sh hl/tools/h5watch/Makefile hl/tools/h5watch/testh5watch.sh hl/examples/Makefile hl/examples/run-hlc-ex.sh hl/c++/Makefile hl/c++/src/Makefile hl/c++/test/Makefile hl/c++/examples/Makefile hl/c++/examples/run-hlc++-ex.sh hl/fortran/Makefile hl/fortran/src/Makefile hl/fortran/test/Makefile hl/fortran/examples/Makefile hl/fortran/examples/run-hlfortran-ex.sh"
 
 
 cat >confcache <<\_ACEOF
@@ -31532,16 +31532,21 @@ do
     "tools/h5dump/testh5dumpxml.sh") CONFIG_FILES="$CONFIG_FILES tools/h5dump/testh5dumpxml.sh" ;;
     "tools/h5ls/testh5ls.sh") CONFIG_FILES="$CONFIG_FILES tools/h5ls/testh5ls.sh" ;;
     "tools/h5import/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5import/Makefile" ;;
+    "tools/h5import/h5importtestutil.sh") CONFIG_FILES="$CONFIG_FILES tools/h5import/h5importtestutil.sh" ;;
     "tools/h5diff/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5diff/Makefile" ;;
+    "tools/h5diff/testh5diff.sh") CONFIG_FILES="$CONFIG_FILES tools/h5diff/testh5diff.sh" ;;
+    "tools/h5diff/testph5diff.sh") CONFIG_FILES="$CONFIG_FILES tools/h5diff/testph5diff.sh" ;;
     "tools/h5jam/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5jam/Makefile" ;;
     "tools/h5jam/testh5jam.sh") CONFIG_FILES="$CONFIG_FILES tools/h5jam/testh5jam.sh" ;;
     "tools/h5repack/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5repack/Makefile" ;;
     "tools/h5repack/h5repack.sh") CONFIG_FILES="$CONFIG_FILES tools/h5repack/h5repack.sh" ;;
     "tools/h5ls/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5ls/Makefile" ;;
     "tools/h5copy/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5copy/Makefile" ;;
+    "tools/h5copy/testh5copy.sh") CONFIG_FILES="$CONFIG_FILES tools/h5copy/testh5copy.sh" ;;
     "tools/lib/Makefile") CONFIG_FILES="$CONFIG_FILES tools/lib/Makefile" ;;
     "tools/misc/Makefile") CONFIG_FILES="$CONFIG_FILES tools/misc/Makefile" ;;
     "tools/misc/h5cc") CONFIG_FILES="$CONFIG_FILES tools/misc/h5cc" ;;
+    "tools/misc/testh5mkgrp.sh") CONFIG_FILES="$CONFIG_FILES tools/misc/testh5mkgrp.sh" ;;
     "tools/misc/testh5repart.sh") CONFIG_FILES="$CONFIG_FILES tools/misc/testh5repart.sh" ;;
     "tools/h5stat/testh5stat.sh") CONFIG_FILES="$CONFIG_FILES tools/h5stat/testh5stat.sh" ;;
     "tools/h5stat/Makefile") CONFIG_FILES="$CONFIG_FILES tools/h5stat/Makefile" ;;
@@ -31571,6 +31576,7 @@ do
     "hl/test/test_ld.sh") CONFIG_FILES="$CONFIG_FILES hl/test/test_ld.sh" ;;
     "hl/tools/Makefile") CONFIG_FILES="$CONFIG_FILES hl/tools/Makefile" ;;
     "hl/tools/gif2h5/Makefile") CONFIG_FILES="$CONFIG_FILES hl/tools/gif2h5/Makefile" ;;
+    "hl/tools/gif2h5/h52giftest.sh") CONFIG_FILES="$CONFIG_FILES hl/tools/gif2h5/h52giftest.sh" ;;
     "hl/tools/h5watch/Makefile") CONFIG_FILES="$CONFIG_FILES hl/tools/h5watch/Makefile" ;;
     "hl/tools/h5watch/testh5watch.sh") CONFIG_FILES="$CONFIG_FILES hl/tools/h5watch/testh5watch.sh" ;;
     "hl/examples/Makefile") CONFIG_FILES="$CONFIG_FILES hl/examples/Makefile" ;;
diff --git a/configure.in b/configure.ac
index 7e4c9e9..31e223e 100644
--- a/configure.in
+++ b/configure.ac
@@ -16,7 +16,7 @@ dnl access to either file, you may request a copy from help@hdfgroup.org.
 dnl ----------------------------------------------------------------------
 dnl Initialize configure.
 dnl
-AC_REVISION($Id$)
+AC_REVISION($Id: configure.ac 22697 2012-08-19 14:35:47Z hdftest $)
 AC_PREREQ([2.53])
 
 dnl AC_INIT takes the name of the package, the version number, and an
@@ -922,7 +922,7 @@ fi
 
 dnl ----------------------------------------------------------------------
 dnl Fortran libraries are not currently supported on Mac. Disable them.
-dnl this is overridable with '--enable-unsupported'.
+dnl (this is overridable with --enable-unsupported).
 dnl
 AC_SUBST([H5_FORTRAN_SHARED])
 H5_FORTRAN_SHARED="no"
@@ -4393,7 +4393,7 @@ AC_CONFIG_FILES([src/libhdf5.settings
                  test/Makefile
                  test/testcheck_version.sh
                  test/testerror.sh
-                 test/testflushrefresh.sh
+		 test/testflushrefresh.sh
                  test/H5srcdir_str.h
                  test/testlibinfo.sh
                  test/testlinks_env.sh
@@ -4407,16 +4407,21 @@ AC_CONFIG_FILES([src/libhdf5.settings
                  tools/h5dump/testh5dumpxml.sh
                  tools/h5ls/testh5ls.sh
                  tools/h5import/Makefile
+                 tools/h5import/h5importtestutil.sh
                  tools/h5diff/Makefile
+                 tools/h5diff/testh5diff.sh
+                 tools/h5diff/testph5diff.sh
                  tools/h5jam/Makefile
                  tools/h5jam/testh5jam.sh
                  tools/h5repack/Makefile
                  tools/h5repack/h5repack.sh
                  tools/h5ls/Makefile
                  tools/h5copy/Makefile
+                 tools/h5copy/testh5copy.sh
                  tools/lib/Makefile
                  tools/misc/Makefile
                  tools/misc/h5cc
+                 tools/misc/testh5mkgrp.sh
                  tools/misc/testh5repart.sh
                  tools/h5stat/testh5stat.sh
                  tools/h5stat/Makefile
@@ -4443,11 +4448,12 @@ AC_CONFIG_FILES([src/libhdf5.settings
                  hl/src/Makefile
                  hl/test/Makefile
                  hl/test/H5srcdir_str.h
-                 hl/test/test_ld.sh
+		 hl/test/test_ld.sh
                  hl/tools/Makefile
                  hl/tools/gif2h5/Makefile
+                 hl/tools/gif2h5/h52giftest.sh
 		 hl/tools/h5watch/Makefile
-               	 hl/tools/h5watch/testh5watch.sh
+                 hl/tools/h5watch/testh5watch.sh
                  hl/examples/Makefile
                  hl/examples/run-hlc-ex.sh
                  hl/c++/Makefile
diff --git a/examples/Makefile.am b/examples/Makefile.am
index a35d8ca..58f50e7 100644
--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -22,14 +22,14 @@
 include $(top_srcdir)/config/commence.am
 
 if BUILD_PARALLEL_CONDITIONAL
-  TEST_PROG_PARA = ph5example
+  EXAMPLE_PROG_PARA = ph5example
 endif
 
 # Example programs.
 # Don't tell automake about them, because if it knew they were programs,
 # it would try to compile them instead of using the h5cc script.
 # Use the boilerplate in config/examples.am instead.
-TEST_PROG = h5_write h5_read h5_extend_write h5_chunk_read h5_compound   \
+EXAMPLE_PROG = h5_write h5_read h5_extend_write h5_chunk_read h5_compound   \
            h5_group h5_select h5_attribute h5_mount h5_reference h5_drivers \
            h5_ref2reg h5_extlink h5_elink_unix2win h5_shared_mesg
 TEST_SCRIPT=testh5cc.sh
diff --git a/examples/Makefile.in b/examples/Makefile.in
index 2e17ae6..04c010d 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -76,10 +76,10 @@ DIST_COMMON = README $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am \
 	$(top_srcdir)/config/examples.am
-TESTS =
+TESTS = $(TEST_SCRIPT)
 subdir = examples
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -110,7 +110,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -128,12 +128,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -391,13 +388,13 @@ TRACE = perl $(top_srcdir)/bin/trace
 # .chklog files are output from those tests.
 # *.clog are from the MPE option.
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog $(EXTLINK_DIRS) *.h5
-@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_PROG_PARA = ph5example
+@BUILD_PARALLEL_CONDITIONAL_TRUE@EXAMPLE_PROG_PARA = ph5example
 
 # Example programs.
 # Don't tell automake about them, because if it knew they were programs,
 # it would try to compile them instead of using the h5cc script.
 # Use the boilerplate in config/examples.am instead.
-TEST_PROG = h5_write h5_read h5_extend_write h5_chunk_read h5_compound   \
+EXAMPLE_PROG = h5_write h5_read h5_extend_write h5_chunk_read h5_compound   \
            h5_group h5_select h5_attribute h5_mount h5_reference h5_drivers \
            h5_ref2reg h5_extlink h5_elink_unix2win h5_shared_mesg
 
@@ -426,12 +423,11 @@ EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES = *.raw *.meta *.o
-CLEANFILES = $(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -444,6 +440,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -766,7 +766,7 @@ installcheck-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -792,7 +792,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -816,7 +816,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -826,7 +826,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -916,7 +916,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -946,7 +946,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/examples/testh5cc.sh.in b/examples/testh5cc.sh.in
index 0e2b851..d3f1cfc 100644
--- a/examples/testh5cc.sh.in
+++ b/examples/testh5cc.sh.in
@@ -23,6 +23,8 @@
 #	Added version compatibility tests.
 #
 
+srcdir=@srcdir@
+
 # Initializations
 TESTNAME=h5cc
 EXIT_SUCCESS=0
@@ -53,11 +55,6 @@ H5_USE_16_API_DEFAULT=`grep '#define H5_USE_16_API_DEFAULT ' ../src/H5pubconf.h`
 myos=`uname -s`
 myhostnama=`uname -n`
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # Generate some source files and library for tests.
 suffix=c		# source file suffix
 hdf5main=${H5TOOL}_hdf5main.$suffix
diff --git a/fortran/Makefile.in b/fortran/Makefile.in
index ff54d6a..806eb30 100644
--- a/fortran/Makefile.in
+++ b/fortran/Makefile.in
@@ -77,7 +77,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = fortran
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -147,7 +147,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -165,12 +165,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -447,6 +444,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -827,7 +828,7 @@ check-clean ::
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -853,7 +854,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -877,7 +878,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -887,7 +888,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -977,7 +978,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1007,7 +1008,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/fortran/examples/Makefile.am b/fortran/examples/Makefile.am
index 7465b98..4fb4180 100644
--- a/fortran/examples/Makefile.am
+++ b/fortran/examples/Makefile.am
@@ -23,7 +23,7 @@ include $(top_srcdir)/config/commence.am
 
 # Compile parallel fortran examples only if parallel is enabled
 if BUILD_PARALLEL_CONDITIONAL
-   TEST_PROG_PARA=ph5example
+   EXAMPLE_PROG_PARA=ph5example
 endif
 
 # These are the programs that 'make all' or 'make tests' will build and
@@ -32,7 +32,7 @@ endif
 # We don't tell automake about these programs so that it doesn't try to
 # compile them with the regular fortran compiler.
 
-TEST_PROG=dsetexample fileexample rwdsetexample attrexample groupexample \
+EXAMPLE_PROG=dsetexample fileexample rwdsetexample attrexample groupexample \
      grpsexample grpdsetexample hyperslab selectele grpit refobjexample  \
      refregexample mountexample compound
 
@@ -46,7 +46,7 @@ INSTALL_SCRIPT_FILES = run-fortran-ex.sh
 
 # Add attention tests for Fortran 2003 features
 if FORTRAN_2003_CONDITIONAL_F
-  TEST_PROG +=  rwdset_fortran2003 nested_derived_type \
+  EXAMPLE_PROG +=  rwdset_fortran2003 nested_derived_type \
       compound_fortran2003 compound_complex_fortran2003
   INSTALL_FILES +=  rwdset_fortran2003.f90 nested_derived_type.f90 \
       compound_fortran2003.f90 compound_complex_fortran2003.f90
diff --git a/fortran/examples/Makefile.in b/fortran/examples/Makefile.in
index 2db7861..06c2632 100644
--- a/fortran/examples/Makefile.in
+++ b/fortran/examples/Makefile.in
@@ -84,10 +84,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 @FORTRAN_2003_CONDITIONAL_F_TRUE@am__append_2 = rwdset_fortran2003.f90 nested_derived_type.f90 \
 @FORTRAN_2003_CONDITIONAL_F_TRUE@      compound_fortran2003.f90 compound_complex_fortran2003.f90
 
-TESTS =
+TESTS = $(TEST_SCRIPT)
 subdir = fortran/examples
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -118,7 +118,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -136,12 +136,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -401,14 +398,14 @@ TRACE = perl $(top_srcdir)/bin/trace
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5
 
 # Compile parallel fortran examples only if parallel is enabled
-@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_PROG_PARA = ph5example
+@BUILD_PARALLEL_CONDITIONAL_TRUE@EXAMPLE_PROG_PARA = ph5example
 
 # These are the programs that 'make all' or 'make tests' will build and
 # that 'make check' will run.  List them in the order in which they should
 # be run.
 # We don't tell automake about these programs so that it doesn't try to
 # compile them with the regular fortran compiler.
-TEST_PROG = dsetexample fileexample rwdsetexample attrexample \
+EXAMPLE_PROG = dsetexample fileexample rwdsetexample attrexample \
 	groupexample grpsexample grpdsetexample hyperslab selectele \
 	grpit refobjexample refregexample mountexample compound \
 	$(am__append_1)
@@ -431,12 +428,11 @@ EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/fortran
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES = *.raw *.meta *.o
-CLEANFILES = $(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -449,6 +445,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -774,7 +774,7 @@ installcheck-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -800,7 +800,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -824,7 +824,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -834,7 +834,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -924,7 +924,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -954,7 +954,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/fortran/examples/testh5fc.sh.in b/fortran/examples/testh5fc.sh.in
index 234d4e2..cd3b86e 100644
--- a/fortran/examples/testh5fc.sh.in
+++ b/fortran/examples/testh5fc.sh.in
@@ -19,6 +19,8 @@
 # Modification:
 #
 
+srcdir=@srcdir@
+
 # Initializations
 TESTNAME=h5fc
 EXIT_SUCCESS=0
@@ -46,11 +48,6 @@ verbose=yes
 myos=`uname -s`
 myhostnama=`uname -n`
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # Generate some source files and library for tests.
 suffix=f90		# source file suffix
 hdf5main=${H5TOOL}_hdf5main.$suffix
diff --git a/fortran/src/CMakeLists.txt b/fortran/src/CMakeLists.txt
index c0fea8c..25e14ba 100644
--- a/fortran/src/CMakeLists.txt
+++ b/fortran/src/CMakeLists.txt
@@ -272,7 +272,7 @@ ENDIF (WIN32 AND NOT CYGWIN)
 IF (HDF5_EXPORTED_TARGETS)
 
   INSTALL_TARGET_PDB (${HDF5_F90_C_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} fortlibraries)
-  INSTALL_TARGET_PDB (${HDF5_F90_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} fortlibraries)
+  #INSTALL_TARGET_PDB (${HDF5_F90_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} fortlibraries)
 
   INSTALL (
       TARGETS
diff --git a/fortran/src/Makefile.in b/fortran/src/Makefile.in
index 08098c9..98c85f3 100644
--- a/fortran/src/Makefile.in
+++ b/fortran/src/Makefile.in
@@ -84,7 +84,7 @@ noinst_PROGRAMS = H5match_types$(EXEEXT) H5fortran_detect$(EXEEXT) \
 TESTS =
 subdir = fortran/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -234,7 +234,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -253,12 +253,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -610,6 +607,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -1138,7 +1139,7 @@ HDF5mpio.lo:         $(srcdir)/H5FDmpioff.f90 H5f90global.lo H5_ff$(F_STATUS).lo
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -1164,7 +1165,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -1188,7 +1189,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -1198,7 +1199,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1288,7 +1289,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1318,7 +1319,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/fortran/test/Makefile.in b/fortran/test/Makefile.in
index 4b2648d..e42b080 100644
--- a/fortran/test/Makefile.in
+++ b/fortran/test/Makefile.in
@@ -78,10 +78,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 @FORTRAN_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 @FORTRAN_2003_CONDITIONAL_F_TRUE@am__append_2 = fortranlib_test_F03
 check_PROGRAMS = $(am__EXEEXT_2)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_2)
 subdir = fortran/test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -215,7 +215,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -236,12 +236,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -552,6 +549,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -997,7 +998,7 @@ fflush2.chkexe_: fflush1.chkexe_
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -1023,7 +1024,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -1047,7 +1048,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -1057,7 +1058,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1147,7 +1148,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1177,7 +1178,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/fortran/testpar/Makefile.in b/fortran/testpar/Makefile.in
index 2002577..1cbc87e 100644
--- a/fortran/testpar/Makefile.in
+++ b/fortran/testpar/Makefile.in
@@ -78,10 +78,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 # parallel code.  But you're welcome to try...)
 @FORTRAN_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS)
+TESTS =
 subdir = fortran/testpar
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -141,7 +141,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -163,12 +163,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -452,6 +449,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -758,7 +759,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -784,7 +785,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -808,7 +809,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -818,7 +819,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -908,7 +909,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -938,7 +939,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/Makefile.in b/hl/Makefile.in
index c471eb7..dddd693 100644
--- a/hl/Makefile.in
+++ b/hl/Makefile.in
@@ -77,7 +77,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -147,7 +147,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -165,12 +165,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -444,6 +441,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -828,7 +829,7 @@ build-check-clean:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -854,7 +855,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -878,7 +879,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -888,7 +889,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -978,7 +979,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1008,7 +1009,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/c++/Makefile.in b/hl/c++/Makefile.in
index e190dfb..4a33b33 100644
--- a/hl/c++/Makefile.in
+++ b/hl/c++/Makefile.in
@@ -73,7 +73,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/c++
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -143,7 +143,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -161,12 +161,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -438,6 +435,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -818,7 +819,7 @@ check-clean ::
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -844,7 +845,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -868,7 +869,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -878,7 +879,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -968,7 +969,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -998,7 +999,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/c++/examples/Makefile.am b/hl/c++/examples/Makefile.am
index c690a12..5dd5a75 100644
--- a/hl/c++/examples/Makefile.am
+++ b/hl/c++/examples/Makefile.am
@@ -23,7 +23,7 @@ include $(top_srcdir)/config/commence.am
 
 # These are the programs that 'make all' or 'make prog' will build and
 # which 'make check' will run.  List them in the order they should be run.
-TEST_PROG=ptExampleFL ptExampleVL
+EXAMPLE_PROG=ptExampleFL ptExampleVL
 
 # These are the example files to be installed
 INSTALL_FILES=ptExampleFL.cpp ptExampleVL.cpp
diff --git a/hl/c++/examples/Makefile.in b/hl/c++/examples/Makefile.in
index 46d4a98..bd0edf0 100644
--- a/hl/c++/examples/Makefile.in
+++ b/hl/c++/examples/Makefile.in
@@ -78,7 +78,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/c++/examples
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -109,7 +109,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -127,12 +127,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -393,7 +390,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5
 
 # These are the programs that 'make all' or 'make prog' will build and
 # which 'make check' will run.  List them in the order they should be run.
-TEST_PROG = ptExampleFL ptExampleVL
+EXAMPLE_PROG = ptExampleFL ptExampleVL
 
 # These are the example files to be installed
 INSTALL_FILES = ptExampleFL.cpp ptExampleVL.cpp
@@ -408,12 +405,11 @@ EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl/c++
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES = *.raw *.meta *.o
-CLEANFILES = $(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -426,6 +422,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -719,7 +719,7 @@ installcheck-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -745,7 +745,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -769,7 +769,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -779,7 +779,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -869,7 +869,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -899,7 +899,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in
index 0923487..68c14e7 100644
--- a/hl/c++/src/Makefile.in
+++ b/hl/c++/src/Makefile.in
@@ -80,7 +80,7 @@ DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
 TESTS =
 subdir = hl/c++/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -176,7 +176,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -194,12 +194,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -494,6 +491,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -878,7 +879,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -904,7 +905,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -928,7 +929,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -938,7 +939,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1028,7 +1029,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1058,7 +1059,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/c++/test/Makefile.in b/hl/c++/test/Makefile.in
index d71f1ce..0213f38 100644
--- a/hl/c++/test/Makefile.in
+++ b/hl/c++/test/Makefile.in
@@ -74,10 +74,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 # Shared C++ libraries aren't universally supported.
 @CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_1)
 subdir = hl/c++/test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -142,7 +142,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -160,12 +160,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -449,6 +446,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -771,7 +772,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -797,7 +798,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -821,7 +822,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -831,7 +832,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -921,7 +922,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -951,7 +952,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/examples/Makefile.am b/hl/examples/Makefile.am
index ae65a3b..1c51f05 100644
--- a/hl/examples/Makefile.am
+++ b/hl/examples/Makefile.am
@@ -22,7 +22,7 @@
 include $(top_srcdir)/config/commence.am
 
 if BUILD_PARALLEL_CONDITIONAL
-  TEST_PROG_PARA =
+  EXAMPLE_PROG_PARA =
 endif
 
 # Example directory
@@ -34,7 +34,7 @@ EXAMPLETOPDIR=${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl
 # Don't tell automake about them, because if it knew they were programs,
 # it would try to compile them instead of using the h5cc script.
 # Use the boilerplate in config/examples.am instead.
-TEST_PROG = ex_lite1 ex_lite2 ex_lite3 ptExampleFL ptExampleVL \
+EXAMPLE_PROG = ex_lite1 ex_lite2 ex_lite3 ptExampleFL ptExampleVL \
             ex_image1 ex_image2 \
             ex_table_01 ex_table_02 ex_table_03 ex_table_04 \
             ex_table_05 ex_table_06 ex_table_07 ex_table_08 \
diff --git a/hl/examples/Makefile.in b/hl/examples/Makefile.in
index 7a3ef18..1794e38 100644
--- a/hl/examples/Makefile.in
+++ b/hl/examples/Makefile.in
@@ -78,7 +78,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/examples
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -109,7 +109,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -127,12 +127,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -390,7 +387,7 @@ TRACE = perl $(top_srcdir)/bin/trace
 # .chklog files are output from those tests.
 # *.clog are from the MPE option.
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5
-@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_PROG_PARA = 
+@BUILD_PARALLEL_CONDITIONAL_TRUE@EXAMPLE_PROG_PARA = 
 
 # Example directory
 # Note: no '/' after DESTDIR.  Explanation in commence.am
@@ -401,7 +398,7 @@ EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl
 # Don't tell automake about them, because if it knew they were programs,
 # it would try to compile them instead of using the h5cc script.
 # Use the boilerplate in config/examples.am instead.
-TEST_PROG = ex_lite1 ex_lite2 ex_lite3 ptExampleFL ptExampleVL \
+EXAMPLE_PROG = ex_lite1 ex_lite2 ex_lite3 ptExampleFL ptExampleVL \
             ex_image1 ex_image2 \
             ex_table_01 ex_table_02 ex_table_03 ex_table_04 \
             ex_table_05 ex_table_06 ex_table_07 ex_table_08 \
@@ -424,12 +421,11 @@ INSTALL_TOP_SCRIPT_FILES = run-hl-ex.sh
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES = *.raw *.meta *.o
-CLEANFILES = $(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -442,6 +438,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -759,7 +759,7 @@ installcheck-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -785,7 +785,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -809,7 +809,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -819,7 +819,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -909,7 +909,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -939,7 +939,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/fortran/Makefile.in b/hl/fortran/Makefile.in
index ffa3c96..6fe288c 100644
--- a/hl/fortran/Makefile.in
+++ b/hl/fortran/Makefile.in
@@ -77,7 +77,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/fortran
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -147,7 +147,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -165,12 +165,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -442,6 +439,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -822,7 +823,7 @@ check-clean ::
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -848,7 +849,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -872,7 +873,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -882,7 +883,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -972,7 +973,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1002,7 +1003,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/fortran/examples/Makefile.am b/hl/fortran/examples/Makefile.am
index 4286fe3..f94f031 100644
--- a/hl/fortran/examples/Makefile.am
+++ b/hl/fortran/examples/Makefile.am
@@ -23,7 +23,7 @@ include $(top_srcdir)/config/commence.am
 
 # Compile parallel fortran examples only if parallel is enabled
 if BUILD_PARALLEL_CONDITIONAL
-   TEST_PROG_PARA=
+   EXAMPLE_PROG_PARA=
 endif
 
 # These are the programs that 'make all' or 'make tests' will build and
@@ -31,7 +31,7 @@ endif
 # be run.
 # We don't tell automake about these programs so that it doesn't try to
 # compile them with the regular fortran compiler.
-TEST_PROG=exlite ex_ds1
+EXAMPLE_PROG=exlite ex_ds1
 
 # List files to be installed here
 INSTALL_FILES= exlite.f90 ex_ds1.f90
diff --git a/hl/fortran/examples/Makefile.in b/hl/fortran/examples/Makefile.in
index f298a91..7dd855b 100644
--- a/hl/fortran/examples/Makefile.in
+++ b/hl/fortran/examples/Makefile.in
@@ -79,7 +79,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/fortran/examples
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -110,7 +110,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -128,12 +128,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -393,14 +390,14 @@ TRACE = perl $(top_srcdir)/bin/trace
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5
 
 # Compile parallel fortran examples only if parallel is enabled
-@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_PROG_PARA = 
+@BUILD_PARALLEL_CONDITIONAL_TRUE@EXAMPLE_PROG_PARA = 
 
 # These are the programs that 'make all' or 'make tests' will build and
 # that 'make check' will run.  List them in the order in which they should
 # be run.
 # We don't tell automake about these programs so that it doesn't try to
 # compile them with the regular fortran compiler.
-TEST_PROG = exlite ex_ds1
+EXAMPLE_PROG = exlite ex_ds1
 
 # List files to be installed here
 INSTALL_FILES = exlite.f90 ex_ds1.f90
@@ -416,12 +413,11 @@ EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl/fortran
 
 # Assume that all tests in this directory are examples, and tell
 # conclude.am when to build them.
-EXAMPLE_PROG = $(TEST_PROG_PARA) $(TEST_PROG)
-EXTRA_PROG = $(EXAMPLE_PROG)
+EXTRA_PROG = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # We need to tell automake what to clean
 MOSTLYCLEANFILES = *.raw *.meta *.o
-CLEANFILES = $(TEST_PROG) $(TEST_PROG_PARA)
+CLEANFILES = $(EXAMPLE_PROG) $(EXAMPLE_PROG_PARA)
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -434,6 +430,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -722,7 +722,7 @@ installcheck-local:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -748,7 +748,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -772,7 +772,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -782,7 +782,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -872,7 +872,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -902,7 +902,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/fortran/src/CMakeLists.txt b/hl/fortran/src/CMakeLists.txt
index b6f6d08..ec54d8c 100644
--- a/hl/fortran/src/CMakeLists.txt
+++ b/hl/fortran/src/CMakeLists.txt
@@ -97,7 +97,7 @@ ENDIF (WIN32 AND NOT CYGWIN)
 IF (HDF5_EXPORTED_TARGETS)
 
   INSTALL_TARGET_PDB (${HDF5_HL_F90_C_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} hlfortlibraries)
-  INSTALL_TARGET_PDB (${HDF5_HL_F90_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} hlfortlibraries)
+  #INSTALL_TARGET_PDB (${HDF5_HL_F90_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} hlfortlibraries)
   
   INSTALL (
       TARGETS
diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in
index 42cacb6..3af3abd 100644
--- a/hl/fortran/src/Makefile.in
+++ b/hl/fortran/src/Makefile.in
@@ -80,7 +80,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/fortran/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -191,7 +191,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -210,12 +210,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -513,6 +510,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -922,7 +923,7 @@ H5TBff.lo:          $(srcdir)/H5TBff.f90
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -948,7 +949,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -972,7 +973,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -982,7 +983,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1072,7 +1073,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1102,7 +1103,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/fortran/test/Makefile.in b/hl/fortran/test/Makefile.in
index 4b10b12..7e69b79 100644
--- a/hl/fortran/test/Makefile.in
+++ b/hl/fortran/test/Makefile.in
@@ -76,10 +76,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 # of the HDF5 library.  We do this by passing the -static flag to the linker.
 @FORTRAN_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_1)
 subdir = hl/fortran/test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -152,7 +152,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -174,12 +174,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -466,6 +463,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -781,7 +782,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -807,7 +808,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -831,7 +832,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -841,7 +842,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -931,7 +932,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -961,7 +962,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in
index b86eab5..d43f2cb 100644
--- a/hl/src/Makefile.in
+++ b/hl/src/Makefile.in
@@ -77,7 +77,7 @@ DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
 TESTS =
 subdir = hl/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -173,7 +173,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -193,12 +193,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -489,6 +486,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -880,7 +881,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -906,7 +907,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -930,7 +931,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -940,7 +941,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1030,7 +1031,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1060,7 +1061,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in
index 0e6a78a..61ddff7 100644
--- a/hl/test/Makefile.in
+++ b/hl/test/Makefile.in
@@ -76,10 +76,10 @@ DIST_COMMON = $(srcdir)/H5srcdir_str.h.in $(srcdir)/Makefile.am \
 check_PROGRAMS = $(am__EXEEXT_1) ld_monitor$(EXEEXT) \
 	ld_extend$(EXEEXT)
 @BUILD_ALL_CONDITIONAL_TRUE@noinst_PROGRAMS = $(am__EXEEXT_2)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = hl/test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -191,7 +191,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -214,12 +214,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -516,6 +513,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -893,7 +894,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -919,7 +920,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -943,7 +944,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -953,7 +954,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1043,7 +1044,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1073,7 +1074,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/tools/Makefile.in b/hl/tools/Makefile.in
index 8cc50d2..08d8827 100644
--- a/hl/tools/Makefile.in
+++ b/hl/tools/Makefile.in
@@ -73,7 +73,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = hl/tools
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -144,7 +144,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -162,12 +162,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -441,6 +438,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -805,7 +806,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -831,7 +832,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -855,7 +856,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -865,7 +866,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -955,7 +956,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -985,7 +986,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/tools/gif2h5/Makefile.am b/hl/tools/gif2h5/Makefile.am
index 895c75f..d1d416a 100644
--- a/hl/tools/gif2h5/Makefile.am
+++ b/hl/tools/gif2h5/Makefile.am
@@ -25,7 +25,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib -I$(top_srcdir)/hl/src
 
 # These are our main targets, the tools
 
-TEST_SCRIPT=$(srcdir)/h52giftest.sh
+TEST_SCRIPT=h52giftest.sh
 check_SCRIPTS=$(TEST_SCRIPT)
 
 bin_PROGRAMS=gif2h5 h52gif
diff --git a/hl/tools/gif2h5/Makefile.in b/hl/tools/gif2h5/Makefile.in
index 145877f..8b98276 100644
--- a/hl/tools/gif2h5/Makefile.in
+++ b/hl/tools/gif2h5/Makefile.in
@@ -68,20 +68,21 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
+	$(srcdir)/h52giftest.sh.in $(top_srcdir)/bin/depcomp \
+	$(top_srcdir)/bin/mkinstalldirs \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = gif2h5$(EXEEXT) h52gif$(EXEEXT)
 noinst_PROGRAMS = h52gifgentst$(EXEEXT)
-TESTS = $(check_SCRIPTS)
+TESTS = $(TEST_SCRIPT)
 subdir = hl/tools/gif2h5
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_FILES = h52giftest.sh
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
@@ -157,7 +158,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -175,12 +176,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -443,7 +441,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5 *.gif
 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib -I$(top_srcdir)/hl/src
 
 # These are our main targets, the tools
-TEST_SCRIPT = $(srcdir)/h52giftest.sh
+TEST_SCRIPT = h52giftest.sh
 check_SCRIPTS = $(TEST_SCRIPT)
 
 # Add h52gif and gif2h5 specific linker flags here
@@ -468,6 +466,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -507,6 +509,8 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(am__aclocal_m4_deps):
+h52giftest.sh: $(top_builddir)/config.status $(srcdir)/h52giftest.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 install-binPROGRAMS: $(bin_PROGRAMS)
 	@$(NORMAL_INSTALL)
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -854,7 +858,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -880,7 +884,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -904,7 +908,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -914,7 +918,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1004,7 +1008,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1034,7 +1038,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/hl/tools/gif2h5/h52giftest.sh b/hl/tools/gif2h5/h52giftest.sh.in
index 186b369..186b369 100644
--- a/hl/tools/gif2h5/h52giftest.sh
+++ b/hl/tools/gif2h5/h52giftest.sh.in
diff --git a/hl/tools/h5watch/Makefile.in b/hl/tools/h5watch/Makefile.in
index f4baf01..c7a4120 100644
--- a/hl/tools/h5watch/Makefile.in
+++ b/hl/tools/h5watch/Makefile.in
@@ -74,10 +74,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = h5watch$(EXEEXT)
 noinst_PROGRAMS = h5watchgentest$(EXEEXT) extend_dset$(EXEEXT)
-TESTS = $(check_SCRIPTS)
+TESTS = $(TEST_SCRIPT)
 subdir = hl/tools/h5watch
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -155,7 +155,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -173,12 +173,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -473,6 +470,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -857,7 +858,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -883,7 +884,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -907,7 +908,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -917,7 +918,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1007,7 +1008,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1037,7 +1038,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/perform/Makefile.in b/perform/Makefile.in
index bb4eba7..13c4904 100644
--- a/perform/Makefile.in
+++ b/perform/Makefile.in
@@ -79,10 +79,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 check_PROGRAMS = iopipe$(EXEEXT) chunk$(EXEEXT) overhead$(EXEEXT) \
 	zip_perf$(EXEEXT) perf_meta$(EXEEXT) $(am__EXEEXT_2) \
 	perf$(EXEEXT)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_3)
 subdir = perform
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -191,8 +191,11 @@ am__tty_colors_dummy = \
   mgn= red= grn= lgn= blu= brg= std=; \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
+am__EXEEXT_3 = iopipe$(EXEEXT) chunk$(EXEEXT) overhead$(EXEEXT) \
+	zip_perf$(EXEEXT) perf_meta$(EXEEXT) h5perf_serial$(EXEEXT) \
+	$(am__EXEEXT_2)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -210,12 +213,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -519,6 +519,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -932,7 +936,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -958,7 +962,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -982,7 +986,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -992,7 +996,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1082,7 +1086,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1112,7 +1116,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 69923ff..f64e334 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -38,6 +38,10 @@ New Features
 
     Configuration:
     -------------
+    - Updated to latest autotools and changed all hard *.sh scripts to
+      configure managed *.sh.in files. Removed overloading of autotools
+      TESTS variable by examples and tests. Renamed configure.in to
+      configure.ac. (ADB - 2012/08/23 - HDFFV-8129)
     - Added code to display the version information of XL fortran and C++
       in the summary of configure. (AKC - 2012/02/28 - HDFFV-7793)
     - Configure now generates Makefiles that build in "silent make mode"
@@ -1056,22 +1060,14 @@ Platforms Tested
                                   Sun Fortran 95 8.4 SunOS_sparc Patch
 128231-06
                                   Sun C++ 5.10 SunOS_sparc 128228-11
- 
-    Windows XP                    Visual Studio 2008 w/ Intel Fortran 11.1
-                                  Visual Studio 2010
-                                  Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
-          
-    Windows XP x64                Visual Studio 2008 w/ Intel Fortran 11.1
-                                  Visual Studio 2010
-                                  Cygwin(1.7.7 native gcc(4.3.4) compiler and gfortran)
-
-    Windows Vista                 Visual Studio 2008 w/ Intel Fortran 11.1
-
-    Windows Vista x64             Visual Studio 2008 w/ Intel Fortran 11.1
 
-    Windows 7                     Visual Studio 2010
+    Windows 7                     Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
+                                  Visual Studio 2010 w/ Intel Fortran 12 (cmake)
+                                  Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
 
-    Windows 7 x64                 Visual Studio 2010
+    Windows 7 x64                 Visual Studio 2008 w/ Intel Fortran 11.1 (cmake)
+                                  Visual Studio 2010 w/ Intel Fortran 12 (cmake)
+                                  Cygwin(1.7.9 native gcc(4.5.3) compiler and gfortran)
 
     MAC OS  10.5 (Intel)          gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 
                                   G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
@@ -1094,10 +1090,8 @@ Platform                          C        F90    F90      C++   zlib  SZIP
                                   parallel        parallel
 SunOS5.10 64-bit                   n        y      n        y     y     y
 SunOS5.10 32-bit                   n        y      n        y     y     y
-Windows XP                         n        y(3)   n(3)     y     y     y
-Windows XP x64                     n        y(3)   n(3)     y     y     y
-Windows Vista                      n        y(3)   n(3)     y     y     y
-Windows Vista x64                  n        y(3)   n(3)     y     y     y
+Windows 7                          y        y      n        y     y     y
+Windows 7 x64                      y        y      n        y     y     y
 Mac OS X 10.5 Intel                n        y      n        y     y     y
 FreeBSD 8.2 32- and 64-bit         n        x      n        x     y     y
 RedHat EL4 2.6.9 i686 GNU        W y(2)     y(4)   y(2)     y     y     y
diff --git a/src/H5config.h.in b/src/H5config.h.in
index a2b75df..fdbcd49 100644
--- a/src/H5config.h.in
+++ b/src/H5config.h.in
@@ -1,4 +1,4 @@
-/* src/H5config.h.in.  Generated from configure.in by autoheader.  */
+/* src/H5config.h.in.  Generated from configure.ac by autoheader.  */
 
 /* Define if building universal (internal helper macro) */
 #undef AC_APPLE_UNIVERSAL_BUILD
diff --git a/src/H5private.h b/src/H5private.h
index 2d97ad3..b8b1754 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -94,13 +94,13 @@
 
 /*
  * If a program may include both `time.h' and `sys/time.h' then
- * TIME_WITH_SYS_TIME is defined (see AC_HEADER_TIME in configure.in).
+ * TIME_WITH_SYS_TIME is defined (see AC_HEADER_TIME in configure.ac).
  * On some older systems, `sys/time.h' includes `time.h' but `time.h' is not
  * protected against multiple inclusion, so programs should not explicitly
  * include both files. This macro is useful in programs that use, for example,
  * `struct timeval' or `struct timezone' as well as `struct tm'.  It is best
  * used in conjunction with `HAVE_SYS_TIME_H', whose existence is checked
- * by `AC_CHECK_HEADERS(sys/time.h)' in configure.in.
+ * by `AC_CHECK_HEADERS(sys/time.h)' in configure.ac.
  */
 #if defined(H5_TIME_WITH_SYS_TIME)
 #   include <sys/time.h>
diff --git a/src/Makefile.in b/src/Makefile.in
index 02cd243..8913399 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -81,7 +81,7 @@ noinst_PROGRAMS = H5detect$(EXEEXT) H5make_libsettings$(EXEEXT)
 TESTS =
 subdir = src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -243,7 +243,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -261,12 +261,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -642,6 +639,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -1432,7 +1433,7 @@ trace: $(libhdf5_la_SOURCES)
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -1458,7 +1459,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -1482,7 +1483,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -1492,7 +1493,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1582,7 +1583,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1612,7 +1613,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/test/Makefile.in b/test/Makefile.in
index 45bfca6..721bc87 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -83,10 +83,10 @@ check_PROGRAMS = $(am__EXEEXT_1) error_test$(EXEEXT) \
 	err_compat$(EXEEXT) tcheck_version$(EXEEXT) testmeta$(EXEEXT) \
 	links_env$(EXEEXT) flushrefresh$(EXEEXT)
 @BUILD_ALL_CONDITIONAL_TRUE@noinst_PROGRAMS = $(am__EXEEXT_2)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -547,7 +547,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -565,12 +565,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -938,6 +935,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -1711,7 +1712,7 @@ flush2.chkexe_: flush1.chkexe_
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -1737,7 +1738,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -1761,7 +1762,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -1771,7 +1772,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1861,7 +1862,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1891,7 +1892,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/test/testcheck_version.sh.in b/test/testcheck_version.sh.in
index a2c812d..ed9845e 100644
--- a/test/testcheck_version.sh.in
+++ b/test/testcheck_version.sh.in
@@ -19,6 +19,8 @@
 # Programmer: Albert Cheng
 #	      Sep 28, 2009
 
+srcdir=@srcdir@
+
 # Variables filled in by the configure process.
 # Determine the configure options of the hdf5 library and executables.
 Shared_Lib=@enable_shared@
@@ -215,11 +217,6 @@ h5libsettings=../src/libhdf5.settings
 
 PURPOSE
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # Figure out library version numbers from the header file.
 h5versmajor=`grep '#define H5_VERS_MAJOR' $srcdir/../src/H5public.h | cut -f2` 
 h5versminor=`grep '#define H5_VERS_MINOR' $srcdir/../src/H5public.h | cut -f2` 
diff --git a/test/testerror.sh.in b/test/testerror.sh.in
index 440be4f..b68fa7e 100644
--- a/test/testerror.sh.in
+++ b/test/testerror.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for test_error and err_compat 
 
+srcdir=@srcdir@
+
 # Determine backward compatibility options eneabled
 DEPRECATED_SYMBOLS="@DEPRECATED_SYMBOLS@"
 
@@ -24,11 +26,6 @@ DIFF='diff -c'
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 test -d ./testfiles || mkdir ./testfiles
 
 # Print a line-line message left justified in a field of 70 characters
diff --git a/test/testlibinfo.sh.in b/test/testlibinfo.sh.in
index 91eda16..fba1794 100644
--- a/test/testlibinfo.sh.in
+++ b/test/testlibinfo.sh.in
@@ -27,6 +27,8 @@
 # Programmer: Albert Cheng
 #	      Sep 18, 2009
 
+srcdir=@srcdir@
+
 # Determine the configure options of the hdf5 library and executables.
 
 Shared_Lib=@enable_shared@
diff --git a/test/testlinks_env.sh.in b/test/testlinks_env.sh.in
index 5a7e045..7120430 100644
--- a/test/testlinks_env.sh.in
+++ b/test/testlinks_env.sh.in
@@ -15,12 +15,9 @@
 #
 # Test for external link with environment variable: HDF5_EXT_PREFIX
 
-nerrors=0
+srcdir=@srcdir@
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
+nerrors=0
 
 ##############################################################################
 ##############################################################################
@@ -35,6 +32,7 @@ TEST_BIN=`pwd`/$TEST_NAME 	# The path of the test binary
 ENVCMD="env HDF5_EXT_PREFIX=.:tmp" 	# The environment variable & value
 #
 # Run the test
+echo "$ENVCMD $RUNSERIAL $TEST_BIN"
 $ENVCMD $RUNSERIAL $TEST_BIN
 exitcode=$?
 if [ $exitcode -eq 0 ]; then
diff --git a/testpar/Makefile.in b/testpar/Makefile.in
index 4edf2a8..5b44e6e 100644
--- a/testpar/Makefile.in
+++ b/testpar/Makefile.in
@@ -72,10 +72,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am COPYING
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS) $(am__EXEEXT_2)
+TESTS =
 subdir = testpar
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -170,9 +170,8 @@ am__tty_colors_dummy = \
   mgn= red= grn= lgn= blu= brg= std=; \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
-am__EXEEXT_2 =
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -190,12 +189,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -485,6 +481,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -843,7 +843,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -869,7 +869,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -893,7 +893,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -903,7 +903,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -993,7 +993,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1023,7 +1023,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/testpar/testph5.sh.in b/testpar/testph5.sh.in
index f78cfac..83327ca 100644
--- a/testpar/testph5.sh.in
+++ b/testpar/testph5.sh.in
@@ -25,11 +25,6 @@ TEST_APP_BIN=`pwd`/$TEST_APP    # The path of the tool binary
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # Print a line-line message left justified in a field of 70 characters
 # beginning with the word "Testing".
 #
diff --git a/tools/Makefile.in b/tools/Makefile.in
index f497875..70e11ae 100644
--- a/tools/Makefile.in
+++ b/tools/Makefile.in
@@ -73,7 +73,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 TESTS =
 subdir = tools
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -144,7 +144,7 @@ am__relativize = \
     dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
   done; \
   reldir="$$dir2"
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -162,12 +162,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -441,6 +438,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -805,7 +806,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -831,7 +832,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -855,7 +856,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -865,7 +866,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -955,7 +956,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -985,7 +986,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5copy/CMakeLists.txt b/tools/h5copy/CMakeLists.txt
index 94eb732..95341a2 100644
--- a/tools/h5copy/CMakeLists.txt
+++ b/tools/h5copy/CMakeLists.txt
@@ -375,7 +375,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5copy ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5copy ${HDF5_INSTALL_BIN_DIR} toolsapplications)
   
 INSTALL (
     TARGETS
diff --git a/tools/h5copy/Makefile.am b/tools/h5copy/Makefile.am
index dd0c5c3..47e8685 100644
--- a/tools/h5copy/Makefile.am
+++ b/tools/h5copy/Makefile.am
@@ -25,7 +25,8 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 # Test programs and scripts
 TEST_PROG=h5copygentest
-TEST_SCRIPT=$(srcdir)/testh5copy.sh
+TEST_SCRIPT=testh5copy.sh
+
 check_SCRIPTS=$(TEST_SCRIPT)
 SCRIPT_DEPEND=h5copy$(EXEEXT)
 
diff --git a/tools/h5copy/Makefile.in b/tools/h5copy/Makefile.in
index cd4b085..da9d0b7 100644
--- a/tools/h5copy/Makefile.in
+++ b/tools/h5copy/Makefile.in
@@ -68,20 +68,21 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
+	$(srcdir)/testh5copy.sh.in $(top_srcdir)/bin/depcomp \
+	$(top_srcdir)/bin/mkinstalldirs \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = h5copy$(EXEEXT)
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = tools/h5copy
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_FILES = testh5copy.sh
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 am__EXEEXT_1 = h5copygentest$(EXEEXT)
@@ -149,7 +150,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -167,12 +168,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -439,7 +437,7 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 # Test programs and scripts
 TEST_PROG = h5copygentest
-TEST_SCRIPT = $(srcdir)/testh5copy.sh
+TEST_SCRIPT = testh5copy.sh
 check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5copy$(EXEEXT)
 
@@ -463,6 +461,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -502,6 +504,8 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(am__aclocal_m4_deps):
+testh5copy.sh: $(top_builddir)/config.status $(srcdir)/testh5copy.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 install-binPROGRAMS: $(bin_PROGRAMS)
 	@$(NORMAL_INSTALL)
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -839,7 +843,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -865,7 +869,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -889,7 +893,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -899,7 +903,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -989,7 +993,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1019,7 +1023,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5copy/testh5copy.sh b/tools/h5copy/testh5copy.sh.in
index 9b4fcff..c7acd9a 100644
--- a/tools/h5copy/testh5copy.sh
+++ b/tools/h5copy/testh5copy.sh.in
@@ -19,10 +19,7 @@
 # Thursday, July 20, 2006
 #
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-    srcdir=.
-fi
+srcdir=@srcdir@
 
 # source dirs
 SRC_TOOLS="$srcdir/.."
@@ -148,7 +145,7 @@ TESTING()
 VERIFY() 
 {
     SPACES="                                                               "
-    echo "Verifying h5diff output `basename $1` `basename $2` `basename $3` `basename $4` $SPACES" | cut -c1-70 | tr -d '\012'
+    echo "Verifying h5diff output $* $SPACES" | cut -c1-70 | tr -d '\012'
 }
 
 # Print a line-line message left justified in a field of 70 characters
@@ -198,7 +195,7 @@ TOOLTEST()
       runh5diff=no
      fi
   
-    TESTING $H5COPY $5 $6 $7 $8 $9
+    TESTING $H5COPY $@
     (
     echo "#############################"
     echo " output for '$H5COPY $@'"
@@ -268,7 +265,7 @@ TOOLTEST_FAIL()
       outputfile=$4
     fi
 
-    TESTING $H5COPY $5 $6 $7 $8 $9
+    TESTING $H5COPY $@
     (
     #echo "#############################"
     #echo " output for '$H5COPY $@'"
@@ -550,8 +547,6 @@ COPY_REFERENCES
 COPY_EXT_LINKS
 TEST_MISC
 
-# Add newline for nicer formatting
-echo " "
 
 if test $nerrors -eq 0 ; then
     echo "All $TESTNAME tests passed."
diff --git a/tools/h5diff/CMakeLists.txt b/tools/h5diff/CMakeLists.txt
index 903564f..994a6f2 100644
--- a/tools/h5diff/CMakeLists.txt
+++ b/tools/h5diff/CMakeLists.txt
@@ -1436,7 +1436,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5diff ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5diff ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
@@ -1449,7 +1449,7 @@ INSTALL (
 
 IF (H5_HAVE_PARALLEL)
 
-  INSTALL_PROGRAM_PDB (ph5diff ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+  #INSTALL_PROGRAM_PDB (ph5diff ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
   INSTALL (
       TARGETS
diff --git a/tools/h5diff/Makefile.am b/tools/h5diff/Makefile.am
index 0b8816f..190c083 100644
--- a/tools/h5diff/Makefile.am
+++ b/tools/h5diff/Makefile.am
@@ -27,7 +27,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 # is enabled.
 if BUILD_PARALLEL_CONDITIONAL
   H5PDIFF=ph5diff
-  TEST_SCRIPT_PARA=$(srcdir)/testph5diff.sh
+  TEST_SCRIPT_PARA=testph5diff.sh
 endif
 
 # Our main target, h5diff
@@ -38,7 +38,7 @@ h5diff_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Test programs and scripts
 TEST_PROG=h5diffgentest
-TEST_SCRIPT=$(srcdir)/testh5diff.sh
+TEST_SCRIPT=testh5diff.sh
 
 check_PROGRAMS=$(TEST_PROG)
 check_SCRIPTS=$(TEST_SCRIPT) $(TEST_SCRIPT_PARA)
diff --git a/tools/h5diff/Makefile.in b/tools/h5diff/Makefile.in
index 66d2c90..4676341 100644
--- a/tools/h5diff/Makefile.in
+++ b/tools/h5diff/Makefile.in
@@ -68,20 +68,21 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+	$(srcdir)/testh5diff.sh.in $(srcdir)/testph5diff.sh.in \
 	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = h5diff$(EXEEXT) $(am__EXEEXT_1)
 check_PROGRAMS = $(am__EXEEXT_2)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_2) $(TEST_SCRIPT)
 subdir = tools/h5diff
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_FILES = testh5diff.sh testph5diff.sh
 CONFIG_CLEAN_VPATH_FILES =
 @BUILD_PARALLEL_CONDITIONAL_TRUE@am__EXEEXT_1 = ph5diff$(EXEEXT)
 am__installdirs = "$(DESTDIR)$(bindir)"
@@ -156,7 +157,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -174,12 +175,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -448,14 +446,14 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 # Always build and test h5diff but build and test ph5diff only if parallel
 # is enabled.
 @BUILD_PARALLEL_CONDITIONAL_TRUE@H5PDIFF = ph5diff
-@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_SCRIPT_PARA = $(srcdir)/testph5diff.sh
+@BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_SCRIPT_PARA = testph5diff.sh
 
 # Add h5diff specific linker flags here
 h5diff_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Test programs and scripts
 TEST_PROG = h5diffgentest
-TEST_SCRIPT = $(srcdir)/testh5diff.sh
+TEST_SCRIPT = testh5diff.sh
 check_SCRIPTS = $(TEST_SCRIPT) $(TEST_SCRIPT_PARA)
 # The parallel test script testph5diff.sh actually depends on testh5diff.sh.
 SCRIPT_DEPEND = h5diff$(EXEEXT) $(H5PDIFF) $(srcdir)/testh5diff.sh
@@ -479,6 +477,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -518,6 +520,10 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(am__aclocal_m4_deps):
+testh5diff.sh: $(top_builddir)/config.status $(srcdir)/testh5diff.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+testph5diff.sh: $(top_builddir)/config.status $(srcdir)/testph5diff.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 install-binPROGRAMS: $(bin_PROGRAMS)
 	@$(NORMAL_INSTALL)
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -860,7 +866,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -886,7 +892,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -910,7 +916,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -920,7 +926,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1010,7 +1016,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1040,7 +1046,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5diff/testh5diff.sh b/tools/h5diff/testh5diff.sh.in
index 02dacd8..3455287 100755..100644
--- a/tools/h5diff/testh5diff.sh
+++ b/tools/h5diff/testh5diff.sh.in
@@ -29,7 +29,7 @@
 #    Added test 400 - 425  (links with --follow-symlinks option)
 #    Added test 450 - 459  (dangling links)
 
-
+srcdir=@srcdir@
 
 TESTNAME=h5diff
 EXIT_SUCCESS=0
@@ -51,11 +51,6 @@ h5haveexitcode=yes	    # default is yes
 pmode=			    # default to run h5diff tests
 mydomainname=`domainname 2>/dev/null`
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
@@ -100,8 +95,6 @@ $SRC_H5DIFF_TESTFILES/h5diff_extlink_src.h5
 $SRC_H5DIFF_TESTFILES/h5diff_extlink_trg.h5
 $SRC_H5DIFF_TESTFILES/h5diff_ext2softlink_src.h5
 $SRC_H5DIFF_TESTFILES/h5diff_ext2softlink_trg.h5
-$SRC_H5DIFF_TESTFILES/h5diff_dset_idx1.h5
-$SRC_H5DIFF_TESTFILES/h5diff_dset_idx2.h5
 $SRC_H5DIFF_TESTFILES/h5diff_dset_zero_dim_size1.h5
 $SRC_H5DIFF_TESTFILES/h5diff_dset_zero_dim_size2.h5
 $SRC_H5DIFF_TESTFILES/h5diff_danglelinks1.h5
@@ -938,12 +931,6 @@ TOOLTEST h5diff_424.txt --follow-symlinks -v h5diff_ext2softlink_trg.h5 h5diff_e
 # extlink_to_softlink_to_dset1 vs extlink_to_softlink_to_dset2"
 TOOLTEST h5diff_425.txt --follow-symlinks -v h5diff_ext2softlink_src.h5 h5diff_ext2softlink_src.h5 /ext_link_to_slink1 /ext_link_to_slink2
 
-# ##############################################################################
-# 19.  The comparision for the two datasets between the 2 files should be the same
-#		FILE19: B-tree indexing is used for the datasets
-#		FILE20: Fixed Array indexing is used for the datasets
-# ##############################################################################
-TOOLTEST h5diff_idx.txt -v $FILE19 $FILE20 
 
 # ##############################################################################
 # # Dangling links compare (--follow-symlinks and --no-dangling-links)
diff --git a/tools/h5diff/testph5diff.sh b/tools/h5diff/testph5diff.sh.in
index c619ab5..ca212a1 100755..100644
--- a/tools/h5diff/testph5diff.sh
+++ b/tools/h5diff/testph5diff.sh.in
@@ -14,16 +14,13 @@
 # access to either file, you may request a copy from help@hdfgroup.org.
 #
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
+srcdir=@srcdir@
 
 TESTNAME=ph5diff
 EXIT_SUCCESS=0
 EXIT_FAILURE=1
 
-TOOL=${srcdir}/testh5diff.sh
+TOOL=testh5diff.sh
 
 nerrors=0
 
diff --git a/tools/h5dump/CMakeLists.txt b/tools/h5dump/CMakeLists.txt
index 302f854..16e3b53 100644
--- a/tools/h5dump/CMakeLists.txt
+++ b/tools/h5dump/CMakeLists.txt
@@ -1899,7 +1899,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5dump ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5dump ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
diff --git a/tools/h5dump/Makefile.in b/tools/h5dump/Makefile.in
index 57e30b0..6b4a6e6 100644
--- a/tools/h5dump/Makefile.in
+++ b/tools/h5dump/Makefile.in
@@ -75,10 +75,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/conclude.am
 check_PROGRAMS = $(am__EXEEXT_1) binread$(EXEEXT)
 bin_PROGRAMS = h5dump$(EXEEXT)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = tools/h5dump
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -156,7 +156,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -174,12 +174,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -471,6 +468,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -860,7 +861,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -886,7 +887,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -910,7 +911,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -920,7 +921,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1010,7 +1011,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1040,7 +1041,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index 23fd1d9..2921fb9 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -233,23 +233,23 @@ usage(const char *prog)
     HDfflush(rawoutstream);
     HDfprintf(rawoutstream, "usage: %s [OPTIONS] files\n", prog);
     HDfprintf(rawoutstream, "  OPTIONS\n");
-    HDfprintf(rawoutstream, "     -h, --help           Print a usage message and exit\n");
-    HDfprintf(rawoutstream, "     -n, --contents       Print a list of the file contents and exit\n");
+    HDfprintf(rawoutstream, "     -h,   --help         Print a usage message and exit\n");
+    HDfprintf(rawoutstream, "     -n,   --contents     Print a list of the file contents and exit\n");
     HDfprintf(rawoutstream, "                          Optional value 1 also prints attributes.\n");
-    HDfprintf(rawoutstream, "     -B, --superblock     Print the content of the super block\n");
-    HDfprintf(rawoutstream, "     -H, --header         Print the header only; no data is displayed\n");
-    HDfprintf(rawoutstream, "     -A, --onlyattr       Print the header and value of attributes\n");
-    HDfprintf(rawoutstream, "     -i, --object-ids     Print the object ids\n");
-    HDfprintf(rawoutstream, "     -r, --string         Print 1-byte integer datasets as ASCII\n");
-    HDfprintf(rawoutstream, "     -e, --escape         Escape non printing characters\n");
-    HDfprintf(rawoutstream, "     -V, --version        Print version number and exit\n");
+    HDfprintf(rawoutstream, "     -B,   --superblock   Print the content of the super block\n");
+    HDfprintf(rawoutstream, "     -H,   --header       Print the header only; no data is displayed\n");
+    HDfprintf(rawoutstream, "     -A,   --onlyattr     Print the header and value of attributes\n");
+    HDfprintf(rawoutstream, "     -i,   --object-ids   Print the object ids\n");
+    HDfprintf(rawoutstream, "     -r,   --string       Print 1-byte integer datasets as ASCII\n");
+    HDfprintf(rawoutstream, "     -e,   --escape       Escape non printing characters\n");
+    HDfprintf(rawoutstream, "     -V,   --version      Print version number and exit\n");
     HDfprintf(rawoutstream, "     -a P, --attribute=P  Print the specified attribute\n");
     HDfprintf(rawoutstream, "                          If an attribute name contains a slash (/), escape the\n");
     HDfprintf(rawoutstream, "                          slash with a preceding backslash (\\).\n");
     HDfprintf(rawoutstream, "                          (See example section below.)\n");
     HDfprintf(rawoutstream, "     -d P, --dataset=P    Print the specified dataset\n");
-    HDfprintf(rawoutstream, "     -y, --noindex        Do not print array indices with the data\n");
-    HDfprintf(rawoutstream, "     -p, --properties     Print dataset filters, storage layout and fill value\n");
+    HDfprintf(rawoutstream, "     -y,   --noindex      Do not print array indices with the data\n");
+    HDfprintf(rawoutstream, "     -p,   --properties   Print dataset filters, storage layout and fill value\n");
     HDfprintf(rawoutstream, "     -f D, --filedriver=D Specify which driver to open the file with\n");
     HDfprintf(rawoutstream, "     -g P, --group=P      Print the specified group and all members\n");
     HDfprintf(rawoutstream, "     -l P, --soft-link=P  Print the value(s) of the specified soft link\n");
@@ -270,17 +270,17 @@ usage(const char *prog)
   "                          the data value and length is the number of bits of\n"
   "                          the mask.\n"
   );
-    HDfprintf(rawoutstream, "     -R, --region         Print dataset pointed by region references\n");
-    HDfprintf(rawoutstream, "     -x, --xml            Output in XML using Schema\n");
-    HDfprintf(rawoutstream, "     -u, --use-dtd        Output in XML using DTD\n");
+    HDfprintf(rawoutstream, "     -R,   --region       Print dataset pointed by region references\n");
+    HDfprintf(rawoutstream, "     -x,   --xml          Output in XML using Schema\n");
+    HDfprintf(rawoutstream, "     -u,   --use-dtd      Output in XML using DTD\n");
     HDfprintf(rawoutstream, "     -D U, --xml-dtd=U    Use the DTD or schema at U\n");
-    HDfprintf(rawoutstream, "     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML\n");
+    HDfprintf(rawoutstream, "     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML\n");
     HDfprintf(rawoutstream, "                          \":\": no namespace, default: \"hdf5:\"\n");
     HDfprintf(rawoutstream, "                          E.g., to dump a file called `-f', use h5dump -- -f\n");
     HDfprintf(rawoutstream, "     --enable-error-stack Prints messages from the HDF5 error stack as they\n");
     HDfprintf(rawoutstream, "                          occur.\n");
     HDfprintf(rawoutstream, "     --no-compact-subset  Disable compact form of subsetting and allow the use\n");
-    HDfprintf(rawoutstream, "                          of \"[\" in datset names.\n");
+    HDfprintf(rawoutstream, "                          of \"[\" in dataset names.\n");
     HDfprintf(rawoutstream, "\n");
     HDfprintf(rawoutstream, " Subsetting is available by using the following options with a dataset\n");
     HDfprintf(rawoutstream, " attribute. Subsetting is done by selecting a hyperslab from the data.\n");
@@ -294,7 +294,8 @@ usage(const char *prog)
     HDfprintf(rawoutstream, "      -c COUNT,  --count=COUNT    Number of blocks to include in selection\n");
     HDfprintf(rawoutstream, "      -k BLOCK,  --block=BLOCK    Size of block in hyperslab\n");
     HDfprintf(rawoutstream, "  START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the\n");
-    HDfprintf(rawoutstream, "        number of dimensions in the dataspace being queried\n");
+    HDfprintf(rawoutstream, "      number of dimensions in the dataspace being queried\n");
+    HDfprintf(rawoutstream, "      (Alternate compact form of subsetting is described in the Reference Manual)\n");
     HDfprintf(rawoutstream, "\n");
     HDfprintf(rawoutstream, "  D - is the file driver to use in opening the file. Acceptable values\n");
     HDfprintf(rawoutstream, "      are \"sec2\", \"family\", \"split\", \"multi\", \"direct\", and \"stream\". Without\n");
diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in
index f969876..2373f6f 100644
--- a/tools/h5dump/testh5dump.sh.in
+++ b/tools/h5dump/testh5dump.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5dump tool
 
+srcdir=@srcdir@
+
 TESTNAME=h5dump
 EXIT_SUCCESS=0
 EXIT_FAILURE=1
@@ -39,10 +41,6 @@ AWK='awk'
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
 # source dirs
 SRC_TOOLS="$srcdir/../"
 
diff --git a/tools/h5dump/testh5dumppbits.sh.in b/tools/h5dump/testh5dumppbits.sh.in
index 3d9685c..a390766 100644
--- a/tools/h5dump/testh5dumppbits.sh.in
+++ b/tools/h5dump/testh5dumppbits.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5dump tool with packed bits type files
 
+srcdir=@srcdir@
+
 # Determine which filters are available
 USE_FILTER_SZIP="@USE_FILTER_SZIP@"
 USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
@@ -47,10 +49,6 @@ AWK='awk'
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
 # source dirs
 SRC_TOOLS="$srcdir/../"
 
@@ -80,6 +78,8 @@ test -d $TESTDIR || mkdir $TESTDIR
 # --------------------------------------------------------------------
 LIST_HDF5_TEST_FILES="
 $SRC_H5DUMP_TESTFILES/packedbits.h5
+$SRC_H5DUMP_TESTFILES/tarray1.h5
+$SRC_H5DUMP_TESTFILES/tcompound.h5
 "
 
 LIST_OTHER_TEST_FILES="
diff --git a/tools/h5dump/testh5dumpxml.sh.in b/tools/h5dump/testh5dumpxml.sh.in
index 1a6b2b1..374f504 100644
--- a/tools/h5dump/testh5dumpxml.sh.in
+++ b/tools/h5dump/testh5dumpxml.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5dump tool
 
+srcdir=@srcdir@
+
 TESTNAME=h5dumpxml
 EXIT_SUCCESS=0
 EXIT_FAILURE=1
@@ -34,10 +36,6 @@ AWK='awk'
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
 # source dirs
 SRC_TOOLS="$srcdir/../"
 
diff --git a/tools/h5import/CMakeLists.txt b/tools/h5import/CMakeLists.txt
index 4e320a1..bc47244 100644
--- a/tools/h5import/CMakeLists.txt
+++ b/tools/h5import/CMakeLists.txt
@@ -381,7 +381,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5import ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5import ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
diff --git a/tools/h5import/Makefile.am b/tools/h5import/Makefile.am
index 49f4f71..167dbc9 100644
--- a/tools/h5import/Makefile.am
+++ b/tools/h5import/Makefile.am
@@ -25,7 +25,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 # Test programs and scripts
 TEST_PROG=h5importtest
-TEST_SCRIPT=$(srcdir)/h5importtestutil.sh
+TEST_SCRIPT=h5importtestutil.sh
 
 check_PROGRAMS=$(TEST_PROG)
 check_SCRIPT=h5importtestutil.sh
diff --git a/tools/h5import/Makefile.in b/tools/h5import/Makefile.in
index 3376706..16e8901 100644
--- a/tools/h5import/Makefile.in
+++ b/tools/h5import/Makefile.in
@@ -68,20 +68,21 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
+	$(srcdir)/h5importtestutil.sh.in $(top_srcdir)/bin/depcomp \
+	$(top_srcdir)/bin/mkinstalldirs \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 check_PROGRAMS = $(am__EXEEXT_1)
 bin_PROGRAMS = h5import$(EXEEXT)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = tools/h5import
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_FILES = h5importtestutil.sh
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 am__EXEEXT_1 = h5importtest$(EXEEXT)
@@ -149,7 +150,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -167,12 +168,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -436,7 +434,7 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 # Test programs and scripts
 TEST_PROG = h5importtest
-TEST_SCRIPT = $(srcdir)/h5importtestutil.sh
+TEST_SCRIPT = h5importtestutil.sh
 check_SCRIPT = h5importtestutil.sh
 SCRIPT_DEPEND = h5import$(EXEEXT)
 
@@ -457,6 +455,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -496,6 +498,8 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(am__aclocal_m4_deps):
+h5importtestutil.sh: $(top_builddir)/config.status $(srcdir)/h5importtestutil.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 install-binPROGRAMS: $(bin_PROGRAMS)
 	@$(NORMAL_INSTALL)
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -833,7 +837,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -859,7 +863,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -883,7 +887,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -893,7 +897,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -983,7 +987,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1013,7 +1017,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5import/h5importtestutil.sh b/tools/h5import/h5importtestutil.sh.in
index 4831f71..ba0743b 100755..100644
--- a/tools/h5import/h5importtestutil.sh
+++ b/tools/h5import/h5importtestutil.sh.in
@@ -16,6 +16,8 @@
 # HDF Utilities Test script
 # Usage: h5importtestutil.sh [machine-type]
 
+srcdir=@srcdir@
+
 # Determine which filters are available
 USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
 
@@ -31,11 +33,6 @@ AWK='awk'
 # initialize errors variable
 nerrors=0
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
diff --git a/tools/h5jam/CMakeLists.txt b/tools/h5jam/CMakeLists.txt
index d0bf30f..b44e734 100644
--- a/tools/h5jam/CMakeLists.txt
+++ b/tools/h5jam/CMakeLists.txt
@@ -535,7 +535,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5jam ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5jam ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
diff --git a/tools/h5jam/Makefile.in b/tools/h5jam/Makefile.in
index aeb116d..ff8b089 100644
--- a/tools/h5jam/Makefile.in
+++ b/tools/h5jam/Makefile.in
@@ -74,10 +74,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = h5jam$(EXEEXT) h5unjam$(EXEEXT)
 check_PROGRAMS = tellub$(EXEEXT) h5jamgentest$(EXEEXT) getub$(EXEEXT)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(TEST_SCRIPT)
 subdir = tools/h5jam
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -164,7 +164,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -182,12 +182,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -474,6 +471,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -865,7 +866,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -891,7 +892,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -915,7 +916,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -925,7 +926,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1015,7 +1016,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1045,7 +1046,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5jam/testh5jam.sh.in b/tools/h5jam/testh5jam.sh.in
index 29e02bd..b2c6bec 100644
--- a/tools/h5jam/testh5jam.sh.in
+++ b/tools/h5jam/testh5jam.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5jam/h5unjam tools
 
+srcdir=@srcdir@
+
 # Determine which filters are available
 USE_FILTER_SZIP="@USE_FILTER_SZIP@"
 USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
@@ -43,11 +45,6 @@ AWK='awk'
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
diff --git a/tools/h5ls/CMakeLists.txt b/tools/h5ls/CMakeLists.txt
index 81a6787..e2b3285 100644
--- a/tools/h5ls/CMakeLists.txt
+++ b/tools/h5ls/CMakeLists.txt
@@ -434,7 +434,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5ls ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5ls ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
diff --git a/tools/h5ls/Makefile.in b/tools/h5ls/Makefile.in
index 673b625..7aa4329 100644
--- a/tools/h5ls/Makefile.in
+++ b/tools/h5ls/Makefile.in
@@ -73,10 +73,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = h5ls$(EXEEXT)
-TESTS = $(check_SCRIPTS)
+TESTS = $(TEST_SCRIPT)
 subdir = tools/h5ls
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -144,7 +144,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -162,12 +162,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -451,6 +448,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -815,7 +816,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -841,7 +842,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -865,7 +866,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -875,7 +876,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -965,7 +966,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -995,7 +996,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5ls/testh5ls.sh.in b/tools/h5ls/testh5ls.sh.in
index c0667f5..f941567 100644
--- a/tools/h5ls/testh5ls.sh.in
+++ b/tools/h5ls/testh5ls.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5ls tool
 
+srcdir=@srcdir@
+
 TESTNAME=h5ls
 EXIT_SUCCESS=0
 EXIT_FAILURE=1
@@ -35,13 +37,11 @@ WORDS_BIGENDIAN="@WORDS_BIGENDIAN@"
 nerrors=0
 verbose=yes
 h5haveexitcode=yes      # default is yes
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-    srcdir=.
-fi
+
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
+
 # testfiles source dirs for tools
 SRC_H5LS_TESTFILES="$SRC_TOOLS_TESTFILES"
 SRC_H5DUMP_TESTFILES="$SRC_TOOLS_TESTFILES"
diff --git a/tools/h5repack/CMakeLists.txt b/tools/h5repack/CMakeLists.txt
index 936559e..3ee1cba 100644
--- a/tools/h5repack/CMakeLists.txt
+++ b/tools/h5repack/CMakeLists.txt
@@ -899,7 +899,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5repack ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5repack ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index 01b6a6a..389339f 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -75,10 +75,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 noinst_PROGRAMS = testh5repack_detect_szip$(EXEEXT)
 check_PROGRAMS = $(am__EXEEXT_1)
 bin_PROGRAMS = h5repack$(EXEEXT)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = tools/h5repack
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -164,7 +164,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -182,12 +182,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -485,6 +482,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -888,7 +889,7 @@ h5repack.sh.chkexe_: h5repacktst.chkexe_
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -914,7 +915,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -938,7 +939,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -948,7 +949,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1038,7 +1039,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1068,7 +1069,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index b702152..2614dd6 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -20,6 +20,8 @@
 #  Added $FILEN variables for file names
 #   
 
+srcdir=@srcdir@
+
 USE_FILTER_SZIP="@USE_FILTER_SZIP@"
 USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
 USE_FILTER_SHUFFLE="@USE_FILTER_SHUFFLE@"
@@ -53,15 +55,10 @@ H5DETECTSZIP_BIN=`pwd`/$H5DETECTSZIP
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-#
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
+
 # testfiles source dirs for tools
 SRC_H5LS_TESTFILES="$SRC_TOOLS_TESTFILES"
 SRC_H5DUMP_TESTFILES="$SRC_TOOLS_TESTFILES"
diff --git a/tools/h5stat/CMakeLists.txt b/tools/h5stat/CMakeLists.txt
index e8d75e3..3518cfd 100644
--- a/tools/h5stat/CMakeLists.txt
+++ b/tools/h5stat/CMakeLists.txt
@@ -206,7 +206,7 @@ ENDIF (BUILD_TESTING)
 # Rules for Installation of tools using make Install target
 #-----------------------------------------------------------------------------
 
-INSTALL_PROGRAM_PDB (h5stat ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+#INSTALL_PROGRAM_PDB (h5stat ${HDF5_INSTALL_BIN_DIR} toolsapplications)
 
 INSTALL (
     TARGETS
diff --git a/tools/h5stat/Makefile.in b/tools/h5stat/Makefile.in
index 2efdf0c..389e460 100644
--- a/tools/h5stat/Makefile.in
+++ b/tools/h5stat/Makefile.in
@@ -75,10 +75,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/conclude.am
 check_PROGRAMS = $(am__EXEEXT_1)
 bin_PROGRAMS = h5stat$(EXEEXT)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = tools/h5stat
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -179,7 +179,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -197,12 +197,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -499,6 +496,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -915,7 +916,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -941,7 +942,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -965,7 +966,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -975,7 +976,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1065,7 +1066,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1095,7 +1096,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/h5stat/testh5stat.sh.in b/tools/h5stat/testh5stat.sh.in
index 8646fd3..8d294be 100644
--- a/tools/h5stat/testh5stat.sh.in
+++ b/tools/h5stat/testh5stat.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5dump tool
 
+srcdir=@srcdir@
+
 # Determine which filters are available
 USE_FILTER_SZIP="@USE_FILTER_SZIP@"
 USE_FILTER_DEFLATE="@USE_FILTER_DEFLATE@"
@@ -40,11 +42,6 @@ AWK='awk'
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 # source dirs
 SRC_TOOLS="$srcdir/.."
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
diff --git a/tools/lib/Makefile.in b/tools/lib/Makefile.in
index af3b0b5..6a76e1d 100644
--- a/tools/lib/Makefile.in
+++ b/tools/lib/Makefile.in
@@ -72,10 +72,10 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 check_PROGRAMS = $(am__EXEEXT_1)
-TESTS = $(check_PROGRAMS)
+TESTS = $(am__EXEEXT_1)
 subdir = tools/lib
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
@@ -142,7 +142,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -160,12 +160,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -452,6 +449,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -797,7 +798,7 @@ help:
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -823,7 +824,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -847,7 +848,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -857,7 +858,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -947,7 +948,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -977,7 +978,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/misc/CMakeLists.txt b/tools/misc/CMakeLists.txt
index 0687323..909b2ca 100644
--- a/tools/misc/CMakeLists.txt
+++ b/tools/misc/CMakeLists.txt
@@ -319,9 +319,9 @@ ENDIF (BUILD_TESTING)
 # 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_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
diff --git a/tools/misc/Makefile.am b/tools/misc/Makefile.am
index 11c86fa..0055f39 100644
--- a/tools/misc/Makefile.am
+++ b/tools/misc/Makefile.am
@@ -25,7 +25,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 #test script and program
 TEST_PROG=h5repart_gentest talign
-TEST_SCRIPT=testh5repart.sh $(srcdir)/testh5mkgrp.sh
+TEST_SCRIPT=testh5repart.sh testh5mkgrp.sh
 
 check_PROGRAMS=$(TEST_PROG) repart_test
 check_SCRIPTS=$(TEST_SCRIPT)
diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in
index 50f8f23..8c2e1c1 100644
--- a/tools/misc/Makefile.in
+++ b/tools/misc/Makefile.in
@@ -69,21 +69,22 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(srcdir)/h5cc.in $(srcdir)/testh5repart.sh.in \
-	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
+	$(srcdir)/h5cc.in $(srcdir)/testh5mkgrp.sh.in \
+	$(srcdir)/testh5repart.sh.in $(top_srcdir)/bin/depcomp \
+	$(top_srcdir)/bin/mkinstalldirs \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 check_PROGRAMS = $(am__EXEEXT_1) repart_test$(EXEEXT)
 bin_PROGRAMS = h5debug$(EXEEXT) h5repart$(EXEEXT) h5mkgrp$(EXEEXT)
-TESTS = $(check_PROGRAMS) $(check_SCRIPTS)
+TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
 subdir = tools/misc
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
-am__aclocal_m4_deps = $(top_srcdir)/configure.in
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES = h5cc testh5repart.sh
+CONFIG_CLEAN_FILES = h5cc testh5mkgrp.sh testh5repart.sh
 CONFIG_CLEAN_VPATH_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"
 am__EXEEXT_1 = h5repart_gentest$(EXEEXT) talign$(EXEEXT)
@@ -203,7 +204,7 @@ am__tty_colors_dummy = \
   am__color_tests=no
 am__tty_colors = $(am__tty_colors_dummy)
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
-ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
+ACLOCAL = @ACLOCAL@
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
 
@@ -221,12 +222,9 @@ AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AS = @AS@
-
-# Set the paths for AFS installs of autotools for Linux machines
-# Ideally, these tools should never be needed during the build.
-AUTOCONF = /home1/packages/autoconf/autoconf-2.60/bin/autoconf
-AUTOHEADER = /home1/packages/autoconf/autoconf-2.60/bin/autoheader
-AUTOMAKE = /home1/packages/automake/automake-1.9.6/bin/automake-1.9
+AUTOCONF = @AUTOCONF@
+AUTOHEADER = @AUTOHEADER@
+AUTOMAKE = @AUTOMAKE@
 AWK = @AWK@
 BYTESEX = @BYTESEX@
 CC = @CC@
@@ -495,7 +493,7 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 #test script and program
 TEST_PROG = h5repart_gentest talign
-TEST_SCRIPT = testh5repart.sh $(srcdir)/testh5mkgrp.sh
+TEST_SCRIPT = testh5repart.sh testh5mkgrp.sh
 check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5repart$(EXEEXT) h5mkgrp$(EXEEXT)
 bin_SCRIPTS = h5redeploy
@@ -530,6 +528,10 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+TEST_EXTENSIONS = .sh
+SH_LOG_COMPILER = $(SHELL)
+AM_SH_LOG_FLAGS = 
 TEST_PROG_CHKEXE = $(TEST_PROG:=.chkexe_)
 TEST_PROG_PARA_CHKEXE = $(TEST_PROG_PARA:=.chkexe_)
 TEST_SCRIPT_CHKSH = $(TEST_SCRIPT:=.chkexe_)
@@ -571,6 +573,8 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 $(am__aclocal_m4_deps):
 h5cc: $(top_builddir)/config.status $(srcdir)/h5cc.in
 	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+testh5mkgrp.sh: $(top_builddir)/config.status $(srcdir)/testh5mkgrp.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 testh5repart.sh: $(top_builddir)/config.status $(srcdir)/testh5repart.sh.in
 	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 install-binPROGRAMS: $(bin_PROGRAMS)
@@ -976,7 +980,7 @@ h5redeploy: h5redeploy.in
 # build files in this directory.
 build-lib: $(LIB)
 build-progs: $(LIB) $(PROGS)
-build-tests: $(LIB) $(PROGS) $(TESTS)
+build-tests: $(LIB) $(PROGS) $(chk_TESTS)
 
 # General rule for recursive building targets.
 # BUILT_SOURCES contain targets that need to be built before anything else
@@ -1002,7 +1006,7 @@ check-clean ::
 # Tell Automake to build tests when the user types `make all' (this is
 # not its default behavior).  Also build EXTRA_LIB and EXTRA_PROG since
 # Automake won't build them automatically, either.
-all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(TESTS)
+all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
 
 # make install-doc doesn't do anything outside of doc directory, but
 # Makefiles should recognize it.
@@ -1026,7 +1030,7 @@ check-install: installcheck
 # Set HDF5_Make_Ignore to a non-blank string to ignore errors inside the loop.
 # The timestamps give a rough idea how much time the tests use.
 #
-# Note that targets in TESTS (defined above) will be built when the user
+# Note that targets in chk_TESTS (defined above) will be built when the user
 # types 'make tests' or 'make check', but only programs in TEST_PROG,
 # TEST_PROG_PARA, or TEST_SCRIPT will actually be executed.
 check-TESTS: test
@@ -1036,7 +1040,7 @@ test _test:
 	@$(MAKE) build-check-p
 
 # Actual execution of check-s.
-build-check-s: $(LIB) $(PROGS) $(TESTS)
+build-check-s: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG)$(TEST_SCRIPT)"; then      \
 	   echo "===Serial tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1126,7 +1130,7 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	fi
 
 # Actual execution of check-p.
-build-check-p: $(LIB) $(PROGS) $(TESTS)
+build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	@if test -n "$(TEST_PROG_PARA)$(TEST_SCRIPT_PARA)"; then      \
 	   echo "===Parallel tests in `echo ${PWD} | sed -e s:.*/::` begin `date`==="; \
 	fi
@@ -1156,7 +1160,7 @@ build-check-p: $(LIB) $(PROGS) $(TESTS)
 	fi
 
 # Run test with different Virtual File Driver
-check-vfd: $(LIB) $(PROGS) $(TESTS)
+check-vfd: $(LIB) $(PROGS) $(chk_TESTS)
 	@for vfd in $(VFD_LIST) dummy; do                                     \
 	    if test $$vfd != dummy; then                                      \
 	        echo "============================";                          \
diff --git a/tools/misc/testh5mkgrp.sh b/tools/misc/testh5mkgrp.sh.in
index 7bb98cb..dc127e8 100644
--- a/tools/misc/testh5mkgrp.sh
+++ b/tools/misc/testh5mkgrp.sh.in
@@ -19,6 +19,8 @@
 # Tuesday, February 13, 2007
 #
 
+srcdir=@srcdir@
+
 TESTNAME=h5mkgrp
 EXIT_SUCCESS=0
 EXIT_FAILURE=1
@@ -37,10 +39,6 @@ OUTDIR=../testfiles
 CMP='cmp -s'
 DIFF='diff -c'
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-    srcdir=.
-fi
 test -d $OUTDIR || mkdir $OUTDIR
 
 # Print a line-line message left justified in a field of 70 characters
diff --git a/tools/misc/testh5repart.sh.in b/tools/misc/testh5repart.sh.in
index 7d4e020..fc33e0e 100644
--- a/tools/misc/testh5repart.sh.in
+++ b/tools/misc/testh5repart.sh.in
@@ -15,6 +15,8 @@
 #
 # Tests for the h5repart tool
 
+srcdir=@srcdir@
+
 TESTNAME=h5repart
 EXIT_SUCCESS=0
 EXIT_FAILURE=1
@@ -28,11 +30,6 @@ REPARTED_FAM_BIN=`pwd`/$REPARTED_FAM    # The path of the test binary
 nerrors=0
 verbose=yes
 
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
 test -d ../testfiles || mkdir ../testfiles
 
 actual_dir=`pwd`/../testfiles
diff --git a/tools/testfiles/h5dump-help.txt b/tools/testfiles/h5dump-help.txt
index 5e0a8f1..74fc104 100644
--- a/tools/testfiles/h5dump-help.txt
+++ b/tools/testfiles/h5dump-help.txt
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tnofilename-with-packed-bits.ddl b/tools/testfiles/tnofilename-with-packed-bits.ddl
index a82c94e..5e6f580 100644
--- a/tools/testfiles/tnofilename-with-packed-bits.ddl
+++ b/tools/testfiles/tnofilename-with-packed-bits.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tpbitsIncomplete.ddl b/tools/testfiles/tpbitsIncomplete.ddl
index 72d54fc..10b5a23 100644
--- a/tools/testfiles/tpbitsIncomplete.ddl
+++ b/tools/testfiles/tpbitsIncomplete.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tpbitsLengthExceeded.ddl b/tools/testfiles/tpbitsLengthExceeded.ddl
index d8b627c..17dd963 100644
--- a/tools/testfiles/tpbitsLengthExceeded.ddl
+++ b/tools/testfiles/tpbitsLengthExceeded.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tpbitsLengthPositive.ddl b/tools/testfiles/tpbitsLengthPositive.ddl
index 39cef23..6d05b47 100644
--- a/tools/testfiles/tpbitsLengthPositive.ddl
+++ b/tools/testfiles/tpbitsLengthPositive.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tpbitsMaxExceeded.ddl b/tools/testfiles/tpbitsMaxExceeded.ddl
index 5f35825..eca1248 100644
--- a/tools/testfiles/tpbitsMaxExceeded.ddl
+++ b/tools/testfiles/tpbitsMaxExceeded.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tpbitsOffsetExceeded.ddl b/tools/testfiles/tpbitsOffsetExceeded.ddl
index 92cc816..b0c655d 100644
--- a/tools/testfiles/tpbitsOffsetExceeded.ddl
+++ b/tools/testfiles/tpbitsOffsetExceeded.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/tools/testfiles/tpbitsOffsetNegative.ddl b/tools/testfiles/tpbitsOffsetNegative.ddl
index c318834..213641b 100644
--- a/tools/testfiles/tpbitsOffsetNegative.ddl
+++ b/tools/testfiles/tpbitsOffsetNegative.ddl
@@ -1,22 +1,22 @@
 usage: h5dump [OPTIONS] files
   OPTIONS
-     -h, --help           Print a usage message and exit
-     -n, --contents       Print a list of the file contents and exit
+     -h,   --help         Print a usage message and exit
+     -n,   --contents     Print a list of the file contents and exit
                           Optional value 1 also prints attributes.
-     -B, --superblock     Print the content of the super block
-     -H, --header         Print the header only; no data is displayed
-     -A, --onlyattr       Print the header and value of attributes
-     -i, --object-ids     Print the object ids
-     -r, --string         Print 1-byte integer datasets as ASCII
-     -e, --escape         Escape non printing characters
-     -V, --version        Print version number and exit
+     -B,   --superblock   Print the content of the super block
+     -H,   --header       Print the header only; no data is displayed
+     -A,   --onlyattr     Print the header and value of attributes
+     -i,   --object-ids   Print the object ids
+     -r,   --string       Print 1-byte integer datasets as ASCII
+     -e,   --escape       Escape non printing characters
+     -V,   --version      Print version number and exit
      -a P, --attribute=P  Print the specified attribute
                           If an attribute name contains a slash (/), escape the
                           slash with a preceding backslash (\).
                           (See example section below.)
      -d P, --dataset=P    Print the specified dataset
-     -y, --noindex        Do not print array indices with the data
-     -p, --properties     Print dataset filters, storage layout and fill value
+     -y,   --noindex      Do not print array indices with the data
+     -p,   --properties   Print dataset filters, storage layout and fill value
      -f D, --filedriver=D Specify which driver to open the file with
      -g P, --group=P      Print the specified group and all members
      -l P, --soft-link=P  Print the value(s) of the specified soft link
@@ -35,17 +35,17 @@ usage: h5dump [OPTIONS] files
                           separated by commas. Offset is the beginning bit in
                           the data value and length is the number of bits of
                           the mask.
-     -R, --region         Print dataset pointed by region references
-     -x, --xml            Output in XML using Schema
-     -u, --use-dtd        Output in XML using DTD
+     -R,   --region       Print dataset pointed by region references
+     -x,   --xml          Output in XML using Schema
+     -u,   --use-dtd      Output in XML using DTD
      -D U, --xml-dtd=U    Use the DTD or schema at U
-     -X S, --xml-ns=S      (XML Schema) Use qualified names n the XML
+     -X S, --xml-ns=S     (XML Schema) Use qualified names n the XML
                           ":": no namespace, default: "hdf5:"
                           E.g., to dump a file called `-f', use h5dump -- -f
      --enable-error-stack Prints messages from the HDF5 error stack as they
                           occur.
      --no-compact-subset  Disable compact form of subsetting and allow the use
-                          of "[" in datset names.
+                          of "[" in dataset names.
 
  Subsetting is available by using the following options with a dataset
  attribute. Subsetting is done by selecting a hyperslab from the data.
@@ -59,7 +59,8 @@ usage: h5dump [OPTIONS] files
       -c COUNT,  --count=COUNT    Number of blocks to include in selection
       -k BLOCK,  --block=BLOCK    Size of block in hyperslab
   START, COUNT, STRIDE, and BLOCK - is a list of integers the number of which are equal to the
-        number of dimensions in the dataspace being queried
+      number of dimensions in the dataspace being queried
+      (Alternate compact form of subsetting is described in the Reference Manual)
 
   D - is the file driver to use in opening the file. Acceptable values
       are "sec2", "family", "split", "multi", "direct", and "stream". Without
diff --git a/vms/src/h5pubconf.h b/vms/src/h5pubconf.h
index ee45b8e..f7c5549 100644
--- a/vms/src/h5pubconf.h
+++ b/vms/src/h5pubconf.h
@@ -13,7 +13,7 @@
  * access to either file, you may request a copy from help@hdfgroup.org.     *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 /* src/H5config.h.  Generated from H5config.h.in by configure.  */
-/* src/H5config.h.in.  Generated from configure.in by autoheader.  */
+/* src/H5config.h.in.  Generated from configure.ac by autoheader.  */
 
 /* Define if building universal (internal helper macro) */
 /* #undef H5_AC_APPLE_UNIVERSAL_BUILD */
author	Vailin Choi <vchoi@hdfgroup.org>	2013-04-11 22:12:12 (GMT)
committer	Vailin Choi <vchoi@hdfgroup.org>	2013-04-11 22:12:12 (GMT)
commit	4ce17c9aa6515c32551104516b32caf8b0ce9f02 (patch)
tree	ca2237566b5b729f4d6a4545ffb2909d9d31309f
parent	5185d3a76aff8288d8eaceff31b483cbf897619e (diff)
download	hdf5-4ce17c9aa6515c32551104516b32caf8b0ce9f02.zip hdf5-4ce17c9aa6515c32551104516b32caf8b0ce9f02.tar.gz hdf5-4ce17c9aa6515c32551104516b32caf8b0ce9f02.tar.bz2