Merge remote-tracking branch 'origin/develop' into monotonic_timer

33 files changed, 2041 insertions, 288 deletions

diff --git a/bin/Makefile.am b/bin/Makefile.am
new file mode 100644
index 0000000..a39b695
--- /dev/null
+++ b/bin/Makefile.am
@@ -0,0 +1,57 @@
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+#
+# HDF5 Library Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+# Include src directory
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
+
+# These are our main targets
+bin_SCRIPTS=h5redeploy
+
+# Tell automake to clean h5redeploy script
+CLEANFILES=h5redeploy
+
+# These were generated by configure.  Remove them only when distclean.
+DISTCLEANFILES=h5cc
+
+# All programs rely on hdf5 library and h5tools library
+LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+
+# How to build h5redeploy script
+h5redeploy: h5redeploy.in
+	@cp $(srcdir)/$@.in $@
+
+# h5cc needs custom install and uninstall rules, since it may be
+# named h5pcc if hdf5 is being built in parallel mode.
+if BUILD_PARALLEL_CONDITIONAL
+  H5CC_NAME=h5pcc
+else
+  H5CC_NAME=h5cc
+endif
+
+$(DESTDIR)$(bindir):
+	echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
+	$(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1;
+
+install-exec-local: $(DESTDIR)$(bindir)
+	@$(INSTALL) h5cc $(DESTDIR)$(bindir)/$(H5CC_NAME)
+uninstall-local:
+	@$(RM) $(DESTDIR)$(bindir)/$(H5CC_NAME)
+
+include $(top_srcdir)/config/conclude.am
diff --git a/bin/batch/ctest.qsub.in.cmake b/bin/batch/ctest.qsub.in.cmake
new file mode 100755
index 0000000..702fca7
--- /dev/null
+++ b/bin/batch/ctest.qsub.in.cmake
@@ -0,0 +1,21 @@
+#!/bin/bash -l
+if [ $# -gt 0 ]; then
+    SUMMARY_FILE=$1
+fi
+ACCOUNT_ID=@ACCOUNT_ID@
+
+echo "Run parallel test command. Test output will be in build/${SUMMARY_FILE}"
+CTEST_CMD=`which ctest`
+
+#SKIPTESTS <<KEYWORD:script inserts list of skips tests here -- don't remove>>
+
+cd @HDF5_BINARY_DIR@
+if [[ $SUMMARY_FILE == *"ctestS"* ]]; then
+  CMD="${CTEST_CMD} . -E MPI_TEST_ -C Release -j 32 -T test"
+else
+  CMD="${CTEST_CMD} . -R MPI_TEST_ ${SKIP_TESTS} -C Release -T test"
+fi
+
+qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ctestP.lsf.in.cmake b/bin/batch/ctestP.lsf.in.cmake
new file mode 100644
index 0000000..3fdd5ce
--- /dev/null
+++ b/bin/batch/ctestP.lsf.in.cmake
@@ -0,0 +1,19 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -nnodes 1                  #number of nodes
+#BSUB -W 30                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestPerrors.txt        #stderr
+#BSUB -o ctestPoutput.txt        #stdout
+#BSUB -J hdf5_ctestP             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+##date; hostname
+##echo -n 'JobID is '; echo $LSB_JOBID
+
+cd @HDF5_BINARY_DIR@
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ctestP.sl.in.cmake b/bin/batch/ctestP.sl.in.cmake
new file mode 100644
index 0000000..1069fa9
--- /dev/null
+++ b/bin/batch/ctestP.sl.in.cmake
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestP
+
+cd @HDF5_BINARY_DIR@
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running ctestP.sl"
+
diff --git a/bin/batch/ctestS.lsf.in.cmake b/bin/batch/ctestS.lsf.in.cmake
new file mode 100644
index 0000000..a01d39b
--- /dev/null
+++ b/bin/batch/ctestS.lsf.in.cmake
@@ -0,0 +1,18 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -nnodes 1                  #number of nodes
+#BSUB -W 29                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestSerrors.txt        #stderr
+#BSUB -o ctestSoutput.txt        #stdout
+#BSUB -J hdf5_ctestS             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+cd @HDF5_BINARY_DIR@
+echo "Run command. Test output will be in build/ctestS.out"
+ctest . -E MPI_TEST_ -C Release -j 32 -T test >& ctestS.out
+
+##$CMD  >& ctestS.out
+echo "Done running command."
+
diff --git a/bin/batch/ctestS.sl.in.cmake b/bin/batch/ctestS.sl.in.cmake
new file mode 100644
index 0000000..4f96bb9
--- /dev/null
+++ b/bin/batch/ctestS.sl.in.cmake
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestS
+
+cd @HDF5_BINARY_DIR@
+CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
+
+echo "Run $CMD. Test output will be in build/ctestS.out"
+$CMD  >& ctestS.out
+echo "Done running $CMD"
diff --git a/bin/batch/knl_H5detect.sl.in.cmake b/bin/batch/knl_H5detect.sl.in.cmake
new file mode 100644
index 0000000..39a3ef3
--- /dev/null
+++ b/bin/batch/knl_H5detect.sl.in.cmake
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+#SBATCH -p knl -C quad
+#SBATCH --nodes=1
+#SBATCH -t 00:10:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+#SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=knl_h5detect
+
+
+# Inputs:  Build directory, output file name, executable file name (username/email if available).
+PROGNAME=H5detect
+OUTPUT=H5Tinit.c
+
+CMD="@HDF5_BINARY_DIR@/bin/${PROGNAME} @HDF5_GENERATED_SOURCE_DIR@/${OUTPUT}"
+echo "Run $CMD"
+srun -n 1 $CMD
+echo "Done running $CMD"
+
diff --git a/bin/batch/knl_ctestP.sl.in.cmake b/bin/batch/knl_ctestP.sl.in.cmake
new file mode 100644
index 0000000..f985fbb
--- /dev/null
+++ b/bin/batch/knl_ctestP.sl.in.cmake
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#SBATCH -p knl -C quad,cache
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestP
+
+cd @HDF5_BINARY_DIR@
+#run parallel tests except t_cache_image test
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running $CMD"
+
diff --git a/bin/batch/knl_ctestS.sl.in.cmake b/bin/batch/knl_ctestS.sl.in.cmake
new file mode 100644
index 0000000..af6353b
--- /dev/null
+++ b/bin/batch/knl_ctestS.sl.in.cmake
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+#SBATCH -p knl -C quad,cache
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestS
+
+cd @HDF5_BINARY_DIR@
+CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
+
+echo "Run $CMD. Test output will be in build/ctestS.out"
+$CMD  >& ctestS.out
+echo "Done running $CMD"
+
diff --git a/bin/batch/ray_ctestP.lsf.in.cmake b/bin/batch/ray_ctestP.lsf.in.cmake
new file mode 100644
index 0000000..7067a65
--- /dev/null
+++ b/bin/batch/ray_ctestP.lsf.in.cmake
@@ -0,0 +1,20 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -n 6                       #number of nodes
+#BSUB -R "span[ptile=6]"
+#BSUB -W 30                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestPerrors.txt        #stderr
+#BSUB -o ctestPoutput.txt        #stdout
+#BSUB -J hdf5_ctestP             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+##date; hostname
+##echo -n 'JobID is '; echo $LSB_JOBID
+
+cd @HDF5_BINARY_DIR@
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest . -R 'MPI_TEST_' -C Release -T test >& ctestP.out
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ray_ctestS.lsf.in.cmake b/bin/batch/ray_ctestS.lsf.in.cmake
new file mode 100644
index 0000000..da20438
--- /dev/null
+++ b/bin/batch/ray_ctestS.lsf.in.cmake
@@ -0,0 +1,18 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -n 1                       #number of nodes
+#BSUB -W 29                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestSerrors.txt        #stderr
+#BSUB -o ctestSoutput.txt        #stdout
+#BSUB -J hdf5_ctestS             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+cd @HDF5_BINARY_DIR@
+echo "Run command. Test output will be in build/ctestS.out"
+ctest . -E 'MPI_TEST_' -C Release -j 32 -T test >& ctestS.out
+
+##$CMD  >& ctestS.out
+echo "Done running command."
+
diff --git a/bin/batch/raybsub b/bin/batch/raybsub
new file mode 100755
index 0000000..19dceef
--- /dev/null
+++ b/bin/batch/raybsub
@@ -0,0 +1,7 @@
+#!/bin/tcsh
+
+# ray.llnl.gov requires a '<' with bsub for submitting .lsf batch jobs.
+# CMake is reluctant to pass the '<', so we put it in this script and use
+# the script to submit the bsub command on ray.
+
+bsub < $1
diff --git a/bin/checkapi b/bin/checkapi
index 6882dea..f5dcacc 100755
--- a/bin/checkapi
+++ b/bin/checkapi
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -13,6 +13,8 @@
 #
 require 5.003;
 
+use warnings;
+
 # Purpose: insures that API functions aren't called internally.
 # Usage:   checkapi H5*.c
 my $filename = "";
diff --git a/bin/checkposix b/bin/checkposix
index 7ab741c..233d15c 100755
--- a/bin/checkposix
+++ b/bin/checkposix
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 
 #
 # Copyright by The HDF Group.
@@ -13,101 +14,165 @@ require 5.003;
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
-# Robb Matzke, matzke@llnl.gov
-# 30 Aug 1997
+# Dana Robinson
+# Spring 2019
+# (Original by Robb Matzke)
 #
-# Purpose: Given the names of C source files this script will print the
-#	   file name, line number, and function name of any function that
-#	   doesn't begin with the letter `h' or `H' as stipulated by the
-#	   HDF5 programming style guide.
+# Purpose:  Given the names of C source files this script will print the
+#           file name, line number, and function name of any function that
+#           doesn't begin with the letter 'h' or 'H' as stipulated by the
+#           HDF5 programming style guide.
 #
-#	   Emacs users can run this script as the compile command and
-#	   use `next-error' (usually bound to M-`) to find each name
-#	   violation.
-
-if(<>) {
-    if($ARGV =~ /\//) {
-        ($filename) = ($ARGV =~ /^.*\/([A-Za-z0-9_]*)\.c$/);
-    } else {
-        ($filename) = ($ARGV =~ /([A-Za-z0-9_]*)\.c$/);
+#           Emacs users can run this script as the compile command and
+#           use 'next-error' (usually bound to M-`) to find each name
+#           violation.
+
+use File::Basename;
+
+# Loop over all files passed to the function
+foreach $arg (@ARGV) {
+
+    # Get the filename from the path
+    $filename = fileparse($arg);
+
+    # Skip files that don't include H5private.h
+    # H5system. has to be inspected by hand since it wraps POSIX files
+    #
+    # H5detect and H5make_libsettings are created before the library exists
+    # so calls that link to function replacements won't work. We'll ignore
+    # it here.
+    #
+    # If a user specifies one file, process it no matter what so people
+    # can inspect files we normally skip (like H5system.c).
+    if($#ARGV gt 0 and $filename =~ /H5FDmulti|H5FDstdio|H5VLpassthru|H5system|H5detect|H5make_libsettings/) {
+        print "$filename is exempt from using Standard library macro wrappers\n";
+        next;
     }
 
-    if($filename =~ /H5FDmulti|H5FDstdio/) {
-        print "$ARGV is exempt from using Standard library macro wrappers\n";
-    } else {
-        while (<>) {
-
-           # Get rid of comments by removing the inside part.
-           s|/\*.*?\*/||g;
-           if ($in_comment) {
-              if (/\*\//) {
-                 s|.*?\*/||;
-                 $in_comment = 0;
-              } else {
-                 $_="\n";
-              }
-           } elsif (m|/\*|) {
-              s|/\*.*||;
-              $in_comment = 1;
-           }
-
-           # Get rid of string constants if they begin and end on this line.
-           s/([\'\"])([^\1]|\\\1)*?\1/$1$1/g;
-
-           # Get rid of preprocessor directives
-           s/^\#.*//;
-
-           # Skip callbacks invoked as methods in a struct
-           next if $_ =~ /\b(\)?->|\.)\(?([a-z_A-Z]\w*)\s*\(/;
-
-           # Now find all function calls on this line which don't start with 'H'
-           while (($name)=/\b([a-z_A-GI-Z]\w*)\s*\(/) {
-              $_ = $';
+    # Open the file
+    open(my $fh, "<", $arg) or do {
+        warn "NOTE: Unable to open $arg: !$\n";
+        next;
+    };
+
+    # Loop over all lines in the file to find undecorated functions
+    while (<$fh>) {
+
+        # Get rid of comments by removing the inside part.
+        s|/\*.*?\*/||g;
+        if ($in_comment) {
+            if (/\*\//) {
+                s|.*?\*/||;
+                $in_comment = 0;
+            } else {
+                $_="\n";
+            }
+        } elsif (m|/\*|) {
+            s|/\*.*||;
+            $in_comment = 1;
+        }
+
+        # Get rid of string constants if they begin and end on this line.
+        s/([\'\"])([^\1]|\\\1)*?\1/$1$1/g;
+
+        # Get rid of preprocessor directives
+        s/^\#.*//;
+
+        # Skip callbacks invoked as methods in a struct
+        next if $_ =~ /\b(\)?]?->|\.)\(?([a-z_A-Z]\w*)\s*\(/;
+
+        # Now find all function calls on this line which don't start with 'H'
+        while (($name)=/\b([a-z_A-GI-Z]\w*)\s*\(/) {
+            $_ = $';
               
-              # Ignore C statements that look sort of like function
-              # calls.
-              next if $name =~ /^(if|for|offsetof|return|sizeof|switch|while|void)$/;
-
-              # Ignore things that get misdetected because of the simplified
-              # parsing that takes place here.
-              next if $name =~ /^(int|herr_t|_term_interface)$/;
-
-              # These are really HDF5 functions/macros even though they don't
-              # start with `h' or `H'.
-              next if $name =~ /^FUNC_(ENTER|LEAVE)(_(NO)?API|_PACKAGE|_STATIC)?(_NOFS|_NOCLEAR|_NOINIT)?(_NOFUNC|_TAG)?$/;
-              next if $name =~ /^(BEGIN|END)_FUNC$/;
-              next if $name =~ /^U?INT(8|16|32|64)(ENCODE|DECODE)(_VAR)?$/;
-              next if $name =~ /^CI_(PRINT_STATS|INC_SRC|INC_DST)$/;
-              next if $name =~ /^(ABS|ADDR_OVERFLOW|ALL_MEMBERS|BOUND|CONSTR|DETECT_[I|F|M]|DOWN)$/;
-              next if $name =~ /^(MIN3?|MAX3?|NELMTS|POWER_OF_TWO|REGION_OVERFLOW)$/;
-              next if $name =~ /^(UNIQUE_MEMBERS)$/;
-              next if $name =~ /^addr_defined$/;
-
-              # These functions/macros are exempt.
-              next if $name =~ /^(main|[fs]?printf|va_(start|arg|end))$/;
-
-              # These are Windows system calls. Ignore them.
-              next if $name =~ /^(_get_osfhandle|GetFileInformationByHandle|SetFilePointer|GetLastError|SetEndOfFile)$/;
-              next if $name =~ /^(FindNextFile|FindClose|_tzset|Wgettimeofday|GetSystemTimeAsFileTime|Wgetlogin|GetUserName)$/;
-
-              # These are MPI function calls. Ignore them.
-              next if $name =~ /^(MPI_|MPE_)/;
-
-              # These are POSIX threads function calls. Ignore them.
-              next if $name =~ /^pthread_/;
-
-              # These are Windows threads function calls. Ignore them.
-              next if $name =~ /^(_beginthread|(Initialize|Enter|Leave)CriticalSection|TlsAlloc)$/;
-
-              # These are zlib & szlib function calls. Ignore them.
-              next if $name =~ /^(inflate|SZ_)/;
-              next if $name =~ /^compress2$/;
-
-              print "$ARGV:$.: $name\n";
-           }
-
-        } continue {
-           close ARGV if eof;       # reset line number
+            # Ignore C statements that look sort of like function
+            # calls.
+            next if $name =~ /^(if|for|offsetof|return|sizeof|switch|while|void)$/;
+
+            # Ignore things that get misdetected because of the simplified
+            # parsing that takes place here.
+            next if $name =~ /^(int|herr_t|_term_interface|_term_package)$/;
+
+            # These are really HDF5 functions/macros even though they don't
+            # start with `h' or `H'.
+            next if $name =~ /^FUNC_(ENTER|LEAVE)(_(NO)?API|_PACKAGE|_STATIC)?(_NOFS|_NOCLEAR|_NOINIT)?(_NOFUNC|_TAG)?$/;
+            next if $name =~ /^(BEGIN|END)_FUNC$/;
+            next if $name =~ /^U?INT(8|16|32|64)(ENCODE|DECODE)(_VAR)?$/;
+            next if $name =~ /^CI_(PRINT_STATS|INC_SRC|INC_DST)$/;
+            next if $name =~ /^(ABS|ADDR_OVERFLOW|ALL_MEMBERS|BOUND|CONSTR|DETECT_[I|F|M]|DOWN)$/;
+            next if $name =~ /^(MIN3?|MAX3?|NELMTS|POWER_OF_TWO|REGION_OVERFLOW)$/;
+            next if $name =~ /^(UNIQUE_MEMBERS|S_ISDIR)$/;
+            next if $name =~ /^addr_defined$/;
+
+            # These functions/macros are exempt.
+            # op, cb, and OP are often spuriously flagged so ignore them.
+            next if $name =~ /^(main|op|cb|OP)$/;
+
+            # This often appears in preprocessor lines that span multiple lines
+            next if $name =~ /^(defined)$/;
+
+            # These are Windows system calls. Ignore them.
+            next if $name =~ /^(_get_osfhandle|GetFileInformationByHandle|SetFilePointer|GetLastError|SetEndOfFile)$/;
+            next if $name =~ /^(FindNextFile|FindClose|_tzset|Wgettimeofday|GetSystemTimeAsFileTime|Wgetlogin|GetUserName)$/;
+            next if $name =~ /^(DeleteCriticalSection|TlsFree|TlsGetValue|CreateThread)$/;
+            next if $name =~ /^(ExpandEnvironmentStringsA|LockFileEx|UnlockFileEx)$/;
+            next if $name =~ /^(DllMain|LocalAlloc|LocalFree)$/;
+            next if $name =~ /^(FindFirstFileA|FindNextFileA)$/;
+            next if $name =~ /^(_beginthread|(Initialize|Enter|Leave)CriticalSection|TlsAlloc)$/;
+
+            # These are MPI function calls. Ignore them.
+            next if $name =~ /^(MPI_|MPE_)/;
+
+            # These are POSIX threads function calls. Ignore them.
+            next if $name =~ /^pthread_/;
+
+            # These are zlib & szlib function calls. Ignore them.
+            next if $name =~ /^(inflate|SZ_)/;
+            next if $name =~ /^compress2$/;
+
+            # These is an H5Dfill function. Ignore it in this file.
+            if($filename =~ /H5Dfill/) {
+                next if $name =~ /^(alloc_func)$/;
+            }
+
+            # These are H5Zscaleoffset functions. Ignore them in this file.
+            if($filename =~ /H5Zscaleoffset/) {
+                next if $name =~ /^(pow_fun|round_fun|abs_fun|lround_fun|llround_fun)$/;
+            }
+
+            # TESTING (not comprehensive - just noise reduction)
+            
+            # Test macros and functions (testhdf5.h)
+            next if $name =~ /^(AddTest|TestErrPrintf|TestSummary|TestCleanup|TestShutdown)$/;
+            next if $name =~ /^(CHECK|CHECK_PTR|CHECK_PTR_NULL|CHECK_PTR_EQ|CHECK_I)$/;
+            next if $name =~ /^(VERIFY|VERIFY_STR|VERIFY|TYPE|MESSAGE|ERROR)$/;
+
+            # Test macros and functions (h5test.h)
+            next if $name =~ /^(TESTING|PASSED|SKIPPED|FAIL_PUTS_ERROR|FAIL_STACK_ERROR|TEST_ERROR)$/;
+            next if $name =~ /^(GetTestExpress)$/;
+
+            # Ignore functions that start with test_ or check_
+            next if $name =~ /^test_/;
+            next if $name =~ /^check_/;
+
+            # Ignore functions that start with h5_
+            next if $name =~ /^h5_/;
+
+            # Ignore usage functions
+            next if $name =~ /^usage$/;
+
+            print "$filename:$.: $name\n";
         }
+
     }
+
+    # Close the file
+    close($fh);
+}
+
+if($#ARGV gt 0) {
+    print "\n";
+    print "NOTE:\n";
+    print "If any files were skipped due to being exempt, you can inspect them manually\n";
+    print "by using this script on them one at a time, which will always process the file.\n";
 }
diff --git a/bin/cmakehdf5 b/bin/cmakehdf5
index 7f6453a..da1aef8 100755
--- a/bin/cmakehdf5
+++ b/bin/cmakehdf5
@@ -46,8 +46,9 @@ cacheinit=$srcdir/config/cmake/cacheinit.cmake
 build_cpp_lib=-DHDF5_BUILD_CPP_LIB:BOOL=OFF	# C++ interface default off
 build_fortran=-DHDF5_BUILD_FORTRAN:BOOL=OFF	# Fortran interface default off
 build_hl_lib=-DHDF5_BUILD_HL_LIB:BOOL=ON	# High Level interface default on
-build_threadsafe=-DHDF5_ENABLE_THREADSAFE:BOOL=OFF	# Threadsafe feature default off
+build_threadsafe=-DHDF5_ENABLE_THREADSAFE:BOOL=OFF  # Threadsafe feature default off
 build_testing=-DBUILD_TESTING:BOOL=ON		# Build tests default on
+build_test_shell=-DTEST_SHELL_SCRIPTS:BOOL=ON   # Run shell script tests default on
 build_tools=-DHDF5_BUILD_TOOLS:BOOL=ON		# Build tools default on
 with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT=ON	# enable zlib filter default on
 with_szlib=-DHDF5_ENABLE_SZIP_SUPPORT=OFF	# enables szip filter default off
@@ -256,6 +257,12 @@ while [ $# -gt 0 ]; do
 	--disable-testing)
 	    build_testing=-DBUILD_TESTING:BOOL=OFF
 	    ;;
+	--enable-shell-testing)
+	    build_test_shell=-DTEST_SHELL_SCRIPTS:BOOL=ON
+	    ;;
+	--disable-shell-testing)
+	    build_test_shell=-DTEST_SHELL_SCRIPTS:BOOL=OFF
+	    ;;
 	--with-zlib)
 	    with_zlib=-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON
 	    ;;
@@ -342,6 +349,7 @@ STEP "Configure..." \
     $build_threadsafe \
     $shared_lib \
     $build_testing \
+    $build_test_shell \
     $build_tools \
     $with_zlib \
     $with_szlib \
diff --git a/bin/debug-ohdr b/bin/debug-ohdr
index 5b0a4b3..1363456 100755
--- a/bin/debug-ohdr
+++ b/bin/debug-ohdr
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
diff --git a/bin/dependencies b/bin/dependencies
index 82247da..367351a 100755
--- a/bin/dependencies
+++ b/bin/dependencies
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -11,6 +11,8 @@
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
+use warnings;
+
 my $depend_file;
 my $new_depend_file;
 my $srcdir;
diff --git a/bin/distdep b/bin/distdep
index 4643700..cd310e0 100755
--- a/bin/distdep
+++ b/bin/distdep
@@ -1,4 +1,7 @@
-#!/usr/bin/perl -p
+#!/bin/sh
+#! -*-perl-*-
+eval 'exec perl -p -x -S $0 ${1+"$@"}'
+  if 0;
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
diff --git a/bin/errors b/bin/errors
index 3c99fdc..107bb9c 100755
--- a/bin/errors
+++ b/bin/errors
@@ -1,5 +1,6 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 use Text::Tabs;
 
 # NOTE: THE FORMAT OF HRETURN_ERROR AND HGOTO_ERROR MACROS HAS
diff --git a/bin/genparser b/bin/genparser
index 8cf6ec2..e6aee5b 100755
--- a/bin/genparser
+++ b/bin/genparser
@@ -218,7 +218,7 @@ perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5
 # will simply ignore them, but we want to avoid those warnings.
 for f in ${path_to_hl_src}/H5LTparse.c ${path_to_hl_src}/H5LTanalyze.c
 do
-    echo '#if __GNUC__ >= 4 && __GNUC_MINOR__ >=2                           ' >> tmp.out
+    echo '#if defined __GNUC__ && 402 <= __GNUC__ * 100 + __GNUC_MINOR__    ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wconversion"                     ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wimplicit-function-declaration"  ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
diff --git a/bin/h5cc.in b/bin/h5cc.in
new file mode 100644
index 0000000..62a0884
--- /dev/null
+++ b/bin/h5cc.in
@@ -0,0 +1,392 @@
+#! /bin/sh
+##
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+##
+
+# This tool is adapted from the mpicc command of the MPICH Software.
+
+############################################################################
+##                                                                        ##
+## Things You May Have to Modify:                                         ##
+##                                                                        ##
+## If the following paths don't point to the place were HDF5 is installed ##
+## on your system (i.e., you received a binary distribution or moved the  ##
+## files from the originally installed directory to another directory)    ##
+## then modify them accordingly to represent the new paths.               ##
+##                                                                        ##
+############################################################################
+prefix="@prefix@"
+exec_prefix="@exec_prefix@"
+libdir="@libdir@"
+includedir="@includedir@"
+HL="@HL@"
+
+############################################################################
+##                                                                        ##
+## Things You Can Modify to Override HDF5 Library Build Components:       ##
+##                                                                        ##
+## (Advanced usage - know what you're doing - you're on your own here.)   ##
+## The four variables below can be used to insert paths and flags in      ##
+## CPPFLAGS, CFLAGS, LDFLAGS, or LIBS in the h5cc compile line:           ##
+##    $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS   ##
+##    $LIBS $clibpath $link_objs $link_args $shared_link                  ##
+##                                                                        ##
+## These settings can be overriden by setting HDF5_CFLAGS,                ##
+## HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment.          ##
+##                                                                        ##
+############################################################################
+CFLAGSBASE=""
+CPPFLAGSBASE=""
+LDFLAGSBASE=""
+LIBSBASE=""
+
+############################################################################
+##                                                                        ##
+## You shouldn't have to modify anything below this line.                 ##
+##                                                                        ##
+############################################################################
+
+# Constants definitions
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+host_os="@host_os@"
+
+prog_name="`basename $0`"
+
+allargs=""
+compile_args=""
+libraries=""
+link_args=""
+link_objs=""
+clibpath=""
+
+do_link="yes"
+do_compile="no"
+dash_o="no"
+dash_c="no"
+get_output_file="no"
+
+SHOW="eval"
+CCBASE="@CC@"
+CLINKERBASE="@CC@"
+
+# CFLAGS, CPPFLAGS and LDFLAGS are reserved for use by the script user.
+# FLAGS brought from the hdf5 build are put in H5BLD_*FLAGS.
+
+# User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's
+# LDFLAGS come just before clibpath, user's LIBS come after $link_objs and
+# before the hdf5 libraries in $link_args, followed by any external library
+# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+# from the hdf5 build. The order of the flags is intended to give precedence
+# to the user's flags.
+H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@"
+H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+H5BLD_LIBS="@LIBS@"
+
+CC="${HDF5_CC:-$CCBASE}"
+CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
+CFLAGS="${HDF5_CFLAGS:-$CFLAGSBASE}"
+CPPFLAGS="${HDF5_CPPFLAGS:-$CPPFLAGSBASE}"
+LDFLAGS="${HDF5_LDFLAGS:-$LDFLAGSBASE}"
+LIBS="${HDF5_LIBS:-$LIBSBASE}"
+
+# If a static library is available, the default will be to use it.  If the only
+# available library is shared, it will be used by default.  The user can
+# override either default, although choosing an unavailable library will result
+# in link errors.
+STATIC_AVAILABLE="@enable_static@"
+if test "${STATIC_AVAILABLE}" = "yes"; then
+  USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
+else
+  USE_SHARED_LIB="${HDF5_USE_SHLIB:-yes}"
+fi
+
+
+usage() {
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS] <compile line>"
+  echo "  OPTIONS:"
+  echo "    -help        This help message."
+  echo "    -echo        Show all the shell commands executed"
+  echo "    -prefix=DIR  Prefix directory to find HDF5 lib/ and include/"
+  echo "                   subdirectories [default: $prefix]"
+  echo "    -show        Show the commands without executing them"
+  echo "    -showconfig  Show the HDF5 library configuration summary"
+  echo "    -shlib       Compile with shared HDF5 libraries [default for hdf5 built"
+  echo "                                                     without static libraries]"
+  echo "    -noshlib     Compile with static HDF5 libraries [default for hdf5 built"
+  echo "                                                     with static libraries]"
+  echo " "
+  echo "  <compile line>  - the normal compile line options for your compiler."
+  echo "                    $prog_name uses the same compiler you used to compile"
+  echo "                    HDF5. Check with your compiler's man pages for more"
+  echo "                    information on which options are needed."
+  echo " "
+  echo " You can override the compiler, linker, and whether or not to use static"
+  echo " or shared libraries to compile your program by setting the following"
+  echo " environment variables accordingly:"
+  echo " "
+  echo "   HDF5_CC                  -  use a different C compiler"
+  echo "   HDF5_CLINKER             -  use a different linker"
+  echo "   HDF5_USE_SHLIB=[yes|no]  -  use shared or static version of the HDF5 library"
+  echo "                                 [default: no except when built with only"
+  echo "                                           shared libraries]"
+  echo " "
+  echo " You can also add or change paths and flags to the compile line using"
+  echo " the following environment varibles or by assigning them to their counterparts"
+  echo " in the 'Things You Can Modify to Override...'" section of $prog_name
+  echo " "
+  echo "  Variable              Current value to be replaced"
+  echo "  HDF5_CPPFLAGS         \"$CPPFLAGSBASE\""
+  echo "  HDF5_CFLAGS           \"$CFLAGSBASE\""
+  echo "  HDF5_LDFLAGS          \"$LDFLAGSBASE\""
+  echo "  HDF5_LIBS             \"$LIBSBASE\""
+  echo " "
+  echo " Note that adding library paths to HDF5_LDFLAGS where another hdf5 version"
+  echo " is located may link your program with that other hdf5 library version."
+  echo " "
+  exit $EXIT_FAILURE
+}
+
+# Show the configuration summary of the library recorded in the
+# libhdf5.settings file reside in the lib directory.
+showconfigure()
+{
+  cat ${libdir}/libhdf5.settings
+  status=$?
+}
+
+# Main
+status=$EXIT_SUCCESS
+
+if test "$#" = "0"; then
+  # No parameters specified, issue usage statement and exit.
+  usage
+fi
+
+case "$CC" in
+  gcc)
+    kind="gcc"
+    ;;
+  mpicc|mpcc|mpicc_r)
+    # Is this gcc masquarading as an MPI compiler?
+    if test "`${CC} -v 2>&1 | sed -n 2p | cut -c1-3`" = "gcc"; then
+      kind="gcc"
+    else
+      # Nope
+      kind="$host_os"
+    fi
+    ;;
+  *)
+    kind="$host_os"
+    ;;
+esac
+
+for arg in $@ ; do
+  if test "x$get_output_file" = "xyes"; then
+    link_args="$link_args $arg"
+    output_file="$arg"
+    get_output_file="no"
+    continue
+  fi
+
+  case "$arg" in
+    -c)
+      allargs="$allargs $arg"
+      compile_args="$compile_args $arg"
+
+      if test "x$do_link" = "xyes" -a -n "$output_file"; then
+        compile_args="$compile_args -o $output_file"
+      fi
+
+      do_link="no"
+      dash_c="yes"
+      ;;
+    -o)
+      allargs="$allargs $arg"
+      dash_o="yes"
+
+      if test "x$dash_c" = "xyes"; then
+        compile_args="$compile_args $arg"
+      else
+        link_args="$link_args $arg"
+        do_link="yes"
+        get_output_file="yes"
+      fi
+      ;;
+    -E|-M|-MT)
+      allargs="$allargs $arg"
+      compile_args="$compile_args $arg"
+      dash_c="yes"
+      do_link="no"
+      ;;
+    -l*)
+      libraries=" $libraries $arg "
+      allargs="$allargs $arg"
+      ;;
+    -prefix=*)
+      prefix="`expr "$arg" : '-prefix=\(.*\)'`"
+      ;;
+    -echo)
+      set -x
+      ;;
+    -show)
+      SHOW="echo"
+      ;;
+    -showconfig)
+      showconfigure
+      exit $status
+      ;;
+    -shlib)
+      USE_SHARED_LIB="yes"
+      ;;
+    -noshlib)
+      USE_SHARED_LIB="no"
+      ;;
+    -help)
+      usage
+      ;;
+    *\"*)
+      qarg="'"$arg"'"
+      allargs="$allargs $qarg"
+      ;;
+    *\'*)
+      qarg='\"'"$arg"'\"'
+      allargs="$allargs $qarg"
+      ;;
+    *)
+      allargs="$allargs $qarg"
+
+      if test -s "$arg"; then
+        ext=`expr "$arg" : '.*\(\..*\)'`
+
+        if test "x$ext" = "x.c"; then
+          do_compile="yes"
+          compile_args="$compile_args $arg"
+          fname=`basename $arg .c`
+          link_objs="$link_objs $fname.o"
+        elif test "x$ext" = "x.o"; then
+          if test "x$dash_c" = "xyes"; then
+            compile_args="$compile_args $arg"
+          else
+            do_link="yes"
+            link_objs="$link_objs $arg"
+          fi
+        elif test "x$ext" = "x.a"; then
+          # This is an archive that we're linking in
+          libraries=" $libraries $arg "
+        else
+          compile_args="$compile_args $arg"
+          link_args="$link_args $arg"
+        fi
+      else
+        compile_args="$compile_args $arg"
+        link_args="$link_args $arg"
+      fi
+      ;;
+  esac
+done
+
+if test "$dash_c" = "yes" -a "$do_compile" = no -a "$do_link" = no ; then
+    # -c was specified.  Force do_compile on.
+    do_compile=yes
+fi
+
+if test "x$do_compile" = "xyes"; then
+  if test "x$dash_c" != "xyes"; then
+    compile_args="-c $compile_args"
+  fi
+
+  $SHOW $CC -I$includedir $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $compile_args
+  status=$?
+
+  if test "$status" != "0"; then
+    exit $status
+  fi
+fi
+
+if test "x$do_link" = "xyes"; then
+  shared_link=""
+# conditionnaly link with the hl library
+  if test "X$HL" = "Xhl"; then
+   libraries=" $libraries -lhdf5_hl -lhdf5 "
+  else
+   libraries=" $libraries  -lhdf5 "
+  fi
+  link_args="$link_args -L${libdir}"
+
+  case "$kind" in
+    gcc|linux*)
+      # MacOS X doesn't support the "-Wl,-rpath -Wl," style of linker flags.
+      # It appears to want none of them specified.
+      case "$host_os" in
+        darwin*)          flag="" ;;
+        *)                flag="-Wl,-rpath -Wl," ;;
+      esac
+      ;;
+    hpux*)                flag="-Wl,+b -Wl," ;;
+    freebsd*|solaris*)    flag="-R" ;;
+    rs6000*|aix*)         flag="-L" ;;
+    sgi)                  flag="-rpath " ;;
+    *)                    flag="" ;;
+  esac
+
+  if test -n "$flag"; then
+    shared_link="${flag}${libdir}"
+  fi
+
+  if test "x$USE_SHARED_LIB" != "xyes"; then
+    # The "-lhdf5" & "-lhdf5_hl" flags are in here already...This is a static
+    # compile though, so change it to the static version (.a) of the library.
+    new_libraries=""
+    for lib in $libraries; do
+      case "$lib" in
+        -lhdf5)
+          new_libraries="$new_libraries ${libdir}/libhdf5.a"
+          ;;
+        -lhdf5_hl)
+          new_libraries="$new_libraries ${libdir}/libhdf5_hl.a"
+          ;;
+        *)
+          new_libraries="$new_libraries $lib"
+          ;;
+      esac
+    done
+    libraries="$new_libraries"
+  fi
+
+  for lib in $libraries; do
+    if echo $link_args | grep " $lib " > /dev/null ||
+       echo $link_args | grep " $lib$" > /dev/null; then
+      :
+    else
+      link_args="$link_args $lib "
+    fi
+  done
+
+  # The LIBS are just a bunch of -l* libraries necessary for the HDF5
+  # module. It's okay if they're included twice in the compile line.
+  link_args="$link_args $H5BLD_LDFLAGS $H5BLD_LIBS"
+
+  # User's CPPFLAGS and CFLAGS come after their H5BLD counterparts.  User's
+  # LDFLAGS come just before clibpath, user's LIBS come after $link_objs and
+  # before the hdf5 libraries in $link_args, followed by any external library
+  # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+  # from the hdf5 build. The order of the flags is intended to give precedence
+  # to the user's flags.
+  $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
+  status=$?
+fi
+
+exit $status
diff --git a/bin/h5redeploy.in b/bin/h5redeploy.in
new file mode 100644
index 0000000..242459a
--- /dev/null
+++ b/bin/h5redeploy.in
@@ -0,0 +1,216 @@
+#! /bin/sh
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+
+## Update HDF5 compiler tools after the HDF5 software has been installed  ##
+## in a new location.							  ##
+## For help page, use "h5redeploy -help"				  ##
+##									  ##
+
+# Constants definitions
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+# Function definitions
+
+# show help page
+usage() {
+  # A wonderfully informative "usage" message.
+  echo "usage: $prog_name [OPTIONS]"
+  echo "  OPTIONS:"
+  echo "    -help|help        This help message"
+  echo "    -echo             Show all the shell commands executed"
+  echo "    -force            No prompt, just do it"
+  echo "    -prefix=DIR       New directory to find HDF5 lib/ and include/"
+  echo "                        subdirectories [default: current directory]"
+  echo "    -exec-prefix=DIR  New directory to find HDF5 lib/"
+  echo "                        subdirectory [default: <prefix>]"
+  echo "    -libdir=DIR       New directory for the HDF5 lib directory"
+  echo "                        [default: <exec-prefix>/lib]"
+  echo "    -includedir=DIR   New directory for the HDF5 header files"
+  echo "                        [default: <prefix>/include]"
+  echo "    -tool=TOOL        Tool to update. TOOL must be in the current"
+  echo "                        directory and writable. [default: $h5tools]"
+  echo "    -show             Show the commands without executing them"
+  echo " "
+  exit $EXIT_FAILURE
+}
+
+# display variable values
+dump_vars(){
+    echo "====Showing all variable values====="
+    echo prefix=$prefix
+    echo h5tools=$h5tools
+    echo "====End Showing====="
+}
+
+# show actions to be taken
+show_action()
+{
+    echo "Update the following tools because they are now installed at a new directory"
+    for t in $foundtools; do
+	echo "${t}:"
+	echo "   current setting=`sed -e '/^prefix=/s/prefix=//p' -e d $t`"
+	echo "   new     setting="\""$prefix"\"
+    done
+}
+
+
+# Report Error message
+ERROR()
+{
+    echo "***ERROR***"
+    echo "$1"
+}
+
+# Main
+#
+############################################################################
+## Installation directories:						  ##
+## prefix	architecture-independent files.				  ##
+## exec_prefix	architecture-dependent files, default is <prefix>.	  ##
+## libdir	libraries, default is <exec_prefix>/lib.		  ##
+## includedir	header files, default is <prefix/include>.		  ##
+## Not used here:							  ##
+## bindir	executables, <exec_prefix/bin>.				  ##
+############################################################################
+# Initialization
+h5tools="h5cc h5pcc h5fc h5pfc h5c++"	# possible hdf5 tools
+foundtools=		# tools found and will be modified
+fmode=			# force mode, default is off
+prefix=
+exec_prefix=
+libdir=
+includedir=
+
+# Parse options
+for arg in $@ ; do
+  case "$arg" in
+    -prefix=*)
+      prefix="`echo $arg | cut -f2 -d=`"
+      ;;
+    -exec-prefix=*)
+      exec_prefix="`echo $arg | cut -f2 -d=`"
+      ;;
+    -libdir=*)
+      libdir="`echo $arg | cut -f2 -d=`"
+      ;;
+    -includedir=*)
+      includedir="`echo $arg | cut -f2 -d=`"
+      ;;
+    -echo)
+      set -x
+      ;;
+    -show)
+      SHOW="echo"
+      ;;
+    -tool=*)
+      h5tools="`echo $arg | cut -f2 -d=`"
+      ;;
+    -help|help)
+      usage
+      ;;
+    -force)
+      fmode=yes
+      ;;
+    *)
+      ERROR "Unknown Option($arg)"
+      usage
+      exit $EXIT_FAILURE
+      ;;
+  esac
+done
+
+# Set to default value, one above where i am, if not given by user
+if [ -z "$prefix" ]; then
+    prefix=`(cd ..;pwd)`
+fi
+if [ -z "$exec_prefix" ]; then
+    exec_prefix='${prefix}'		# use single quotes to prevent expansion of $
+fi
+if [ -z "$libdir" ]; then
+    libdir='${exec_prefix}'/lib	# use single quotes to prevent expansion of $
+fi
+if [ -z "$includedir" ]; then
+    includedir='${prefix}'/include # use single quotes to prevent expansion of $
+fi
+
+for x in $h5tools; do
+    if [ -f $x ]; then
+	foundtools="$foundtools $x"
+	if [ ! -w $x ]; then
+	    ERROR "h5tool($x) is not writable"
+	    exit $EXIT_FAILURE
+	fi
+    fi
+done
+
+if [ -z "$foundtools" ]; then
+    ERROR "found no tools to modify"
+    exit $EXIT_FAILURE
+fi
+
+# Show actions to be taken and get consent
+show_action
+# Ask confirmation unless fmode is on
+if [ x-$fmode = x- ]; then
+    echo "Continue? (yes/no)"
+    read ansx
+    ans=`echo $ansx | tr "[A-Z]" "[a-z]"`
+    if [ x-$ans != x-yes ]; then
+	echo ABORT.  No tools changed.
+	exit $EXIT_FAILURE
+    fi
+fi
+
+
+# Create the update commands
+CMDFILE=/tmp/h5redeploy.$$
+touch $CMDFILE
+chmod 0600 $CMDFILE
+echo "/^prefix=/c"                    >> $CMDFILE
+echo prefix=\""$prefix"\"             >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^exec_prefix=/c"               >> $CMDFILE
+echo exec_prefix=\""$exec_prefix"\"   >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^libdir=/c"                    >> $CMDFILE
+echo libdir=\""$libdir"\"             >> $CMDFILE
+echo .                                >> $CMDFILE
+echo "/^includedir=/c"                >> $CMDFILE
+echo includedir=\""$includedir"\"     >> $CMDFILE
+echo .                                >> $CMDFILE
+(echo w; echo q)                      >> $CMDFILE
+
+
+# Update them
+if [ "$SHOW" = "echo" ]; then
+    echo "===Update commands are:===="
+    cat $CMDFILE
+    echo "===End Update commands====="
+fi
+
+for t in $foundtools; do
+    echo Update $t ...
+    COMMAND="ed - $t"
+    if [ "$SHOW" = "echo" ]; then
+	echo $COMMAND
+    else
+	$COMMAND < $CMDFILE
+    fi
+done
+
+
+# Cleanup
+rm -f $CMDFILE
+exit $EXIT_SUCCESS
diff --git a/bin/h5vers b/bin/h5vers
index 5228903..659a081 100755
--- a/bin/h5vers
+++ b/bin/h5vers
@@ -198,7 +198,7 @@ my $H5_JAVA = $file;
 $H5_JAVA =~ s/[^\/]*$/..\/java\/src\/hdf\/hdf5lib\/H5.java/;
 die "unable to read file: $H5_JAVA\n" unless -r $file;
 my $TESTH5_JAVA = $file;
-$TESTH5_JAVA =~ s/[^\/]*$/..\/java\/test\/TestH5.java/; 
+$TESTH5_JAVA =~ s/[^\/]*$/..\/java\/test\/TestH5.java/;
 die "unable to read file: $TESTH5_JAVA\n" unless -r $file;
 my $REPACK_LAYOUT_PLUGIN_VERSION = $file;
 $REPACK_LAYOUT_PLUGIN_VERSION =~ s/[^\/]*$/..\/tools\/test\/h5repack\/testfiles\/h5repack_layout.h5-plugin_version_test.ddl/;
@@ -213,7 +213,7 @@ my (@curver) = getvers $contents;
 # Determine the new version number.
 my @newver; #new version
 if ($set) {
-  if ($set =~ /(\d+)\.(\d+)\.(\d+)(-([a-zA-Z]\w*))?/) {
+  if ($set =~ /(\d+)\.(\d+)\.(\d+)(-([\da-zA-Z]\w*))?/) {
     @newver = ($1, $2, $3, $5);
   } elsif ($set =~ /(\d+)\D+(\d+)\D+(\d+)(\s*\(([a-zA-Z]\w*)\))?\D*$/) {
     @newver = ($1, $2, $3, $5);
@@ -354,7 +354,7 @@ if ($HDF5CONFIGCMAKE) {
   my $sub_rel_ver_str = (
      $newver[3] eq "" 
      ? sprintf("\"%s\"", "") 
-     : sprintf("\"%s\"", "-".$newver[3].", currently under development")
+     : sprintf("\"%s\"", "-".$newver[3])
      );
   my $version_string = sprintf("\"%d.%d.%d\"", @newver[0,1,2]);
 
@@ -377,7 +377,7 @@ if ($H5_JAVA) {
   my $version_string2 = sprintf("%d, %d, %d", @newver[0,1,2]);
 
   $data =~ s/\@version HDF5 .* <BR>/\@version HDF5 $version_string1 <BR>/;
-  $data =~ s/    public final static int LIB_VERSION\[\] = { \d*, \d*, \d* };/    public final static int LIB_VERSION[] = { $version_string2 };/;        
+  $data =~ s/    public final static int LIB_VERSION\[\] = \{ \d*, \d*, \d* \};/    public final static int LIB_VERSION[] = \{ $version_string2 \};/;
 
   write_file($H5_JAVA, $data);
 }
@@ -394,8 +394,8 @@ if ($TESTH5_JAVA) {
   my $version_string1 = sprintf("%d, %d, %d", @newver[0,1,2]);
   my $version_string2 = sprintf("int majnum = %d, minnum = %d, relnum = %d", @newver[0,1,2]);
 
-  $data =~ s/        int libversion\[\] = { .* };/        int libversion\[\] = { $version_string1 };/;
-  $data =~ s/        int majnum = \d*, minnum = \d*, relnum = \d*;/        $version_string2;/;        
+  $data =~ s/        int libversion\[\] = \{ .* \};/        int libversion\[\] = \{ $version_string1 \};/;
+  $data =~ s/        int majnum = \d*, minnum = \d*, relnum = \d*;/        $version_string2;/;
 
   write_file($TESTH5_JAVA, $data);
 }
@@ -405,12 +405,12 @@ if ($REPACK_LAYOUT_PLUGIN_VERSION) {
   my $data = read_file($REPACK_LAYOUT_PLUGIN_VERSION);
   my $version_string = sprintf("%d %d %d", @newver[0,1,2]);
 
-  $data =~ s/            PARAMS { 9 \d* \d* \d* }/            PARAMS { 9 $version_string }/g;
+  $data =~ s/            PARAMS \{ 9 \d* \d* \d* \}/            PARAMS \{ 9 $version_string \}/g;
 
   write_file($REPACK_LAYOUT_PLUGIN_VERSION, $data);
 }
 
-# helper function to read the file for updating c++/src/cpp_doc_config, 
+# helper function to read the file for updating c++/src/cpp_doc_config,
 # config/cmake/scripts/HDF5Config.cmake, and java files.
 # The version string in that file is not at the top, so the string replacement
 # is not for the first line, and reading/writing the entire file as one string
diff --git a/bin/iostats b/bin/iostats
index f054b9c..e389992 100755
--- a/bin/iostats
+++ b/bin/iostats
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
diff --git a/bin/make_err b/bin/make_err
index bfe8861..7f38591 100755
--- a/bin/make_err
+++ b/bin/make_err
@@ -1,6 +1,7 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
 $indent=4;
+use warnings;
 
 #
 # Copyright by The HDF Group.
@@ -244,8 +245,8 @@ sub create_init ($) {
     print HEADER   "/* Major error codes */\n";
     print HEADER   "/*********************/\n\n";
     foreach $name (keys %major) {
-        print HEADER " "x(0*$indent),"assert(${name}_g==(-1));\n";
-        print HEADER " "x(0*$indent),"if((msg = H5E_create_msg(cls, H5E_MAJOR, \"${major{$name}}\"))==NULL)\n";
+        print HEADER " "x(0*$indent),"HDassert(${name}_g==(-1));\n";
+        print HEADER " "x(0*$indent),"if((msg = H5E__create_msg(cls, H5E_MAJOR, \"${major{$name}}\"))==NULL)\n";
         print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, \"error message initialization failed\")\n";
         print HEADER " "x(0*$indent),"if((${name}_g = H5I_register(H5I_ERROR_MSG, msg, FALSE))<0)\n";
         print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, \"can't register error message\")\n";
@@ -260,8 +261,8 @@ sub create_init ($) {
 
         # Iterate over all the minor errors in each section
         for $name ( @{$section_list{$sect_name}}) {
-            print HEADER " "x(0*$indent),"assert(${name}_g==(-1));\n";
-            print HEADER " "x(0*$indent),"if((msg = H5E_create_msg(cls, H5E_MINOR, \"${minor{$name}}\"))==NULL)\n";
+            print HEADER " "x(0*$indent),"HDassert(${name}_g==(-1));\n";
+            print HEADER " "x(0*$indent),"if((msg = H5E__create_msg(cls, H5E_MINOR, \"${minor{$name}}\"))==NULL)\n";
             print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, \"error message initialization failed\")\n";
             print HEADER " "x(0*$indent),"if((${name}_g = H5I_register(H5I_ERROR_MSG, msg, FALSE))<0)\n";
             print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, \"can't register error message\")\n";
diff --git a/bin/make_overflow b/bin/make_overflow
index ccd640e..cee0126 100755
--- a/bin/make_overflow
+++ b/bin/make_overflow
@@ -1,6 +1,7 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
 use strict;
+use warnings;
 
 # Global settings
 
diff --git a/bin/make_vers b/bin/make_vers
index 7e7fba1..74b0ae2 100755
--- a/bin/make_vers
+++ b/bin/make_vers
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 require 5.003;
+use warnings;
 
 # Global settings
 # (The max_idx parameter is the only thing that needs to be changed when adding
@@ -7,8 +8,8 @@ require 5.003;
 #       is added (like support for 1.4, etc), the min_sup_idx parameter will
 #       need to be decremented. - QAK)
 
-# Max. library "index" (0 = v1.0, 1 = 1.2, etc)
-$max_idx = 5;
+# Max. library "index" (0 = v1.0, 1 = 1.2, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, 7 = 1.14, etc)
+$max_idx = 7;
 
 # Min. supported previous library version "index" (0 = v1.0, 1 = 1.2, etc)
 $min_sup_idx = 3;
@@ -89,7 +90,8 @@ sub print_checkoptions ($) {
     my $curr_idx;               # Current API version index
 
     # Print the option checking
-    print $fh "\n/* Issue error if contradicting macros have been defined. */\n";
+    print $fh "\n\n/* Issue error if contradicting macros have been defined. */\n";
+    print $fh "/* (Can't use an older (deprecated) API version if deprecated symbols have been disabled) */\n";
 
     # Print the #ifdef
     print $fh "#if (";
@@ -118,26 +120,40 @@ sub print_checkoptions ($) {
 ##############################################################################
 # Print "global" API version macro settings
 #
-sub print_globalapivers ($) {
+sub print_globalapidefvers ($) {
     my $fh = shift;             # File handle for output file
     my $curr_idx;               # Current API version index
 
     # Print the descriptive comment
-    print $fh "\n\n/* If a particular \"global\" version of the library's interfaces is chosen,\n";
-    print $fh " *      set the versions for the API symbols affected.\n";
+    print $fh "\n\n/* If a particular default \"global\" version of the library's interfaces is\n";
+    print $fh " *      chosen, set the corresponding version macro for API symbols.\n";
     print $fh " *\n";
-    print $fh " * Note: If an application has already chosen a particular version for an\n";
-    print $fh " *      API symbol, the individual API version macro takes priority.\n";
     print $fh " */\n";
 
     for $curr_idx ($min_sup_idx .. ($max_idx - 1)) {
         # Print API version ifdef
-        print $fh "#if defined(H5_USE_1", ($curr_idx * 2), "_API_DEFAULT) && !defined(H5_USE_1", ($curr_idx * 2), "_API)\n";
+        print $fh "\n#if defined(H5_USE_1", ($curr_idx * 2), "_API_DEFAULT) && !defined(H5_USE_1", ($curr_idx * 2), "_API)\n";
         # Print API version definition
         print $fh " " x $indent, "#define H5_USE_1", ($curr_idx * 2), "_API 1\n";
         # Print API version endif
-        print $fh "#endif /* H5_USE_1", ($curr_idx * 2), "_API_DEFAULT && !H5_USE_1", ($curr_idx * 2), "_API */\n\n";
+        print $fh "#endif /* H5_USE_1", ($curr_idx * 2), "_API_DEFAULT && !H5_USE_1", ($curr_idx * 2), "_API */\n";
     }
+}
+
+##############################################################################
+# Print "global" API symbol version macro settings
+#
+sub print_globalapisymbolvers ($) {
+    my $fh = shift;             # File handle for output file
+    my $curr_idx;               # Current API version index
+
+    # Print the descriptive comment
+    print $fh "\n\n/* If a particular \"global\" version of the library's interfaces is chosen,\n";
+    print $fh " *      set the versions for the API symbols affected.\n";
+    print $fh " *\n";
+    print $fh " * Note: If an application has already chosen a particular version for an\n";
+    print $fh " *      API symbol, the individual API version macro takes priority.\n";
+    print $fh " */\n";
 
     # Loop over supported older library APIs and define the appropriate macros
     for $curr_idx ($min_sup_idx .. ($max_idx - 1)) {
@@ -338,7 +354,18 @@ sub parse_line ($) {
             my $vers_idx;       # Index of version in array
 
             # Do some validation on the input
-            if(!( $_ =~ /v1[02468]/ || $_ =~ /v11[02468]/ )) {
+            # Note:  v111 is allowed because H5O functions were prematurely versioned
+            #        in HDF5 1.10.  Because users were affected by this, the versioning
+            #        was rescinded but the H5O version 2 functions were kept to be 
+            #        called directly.  Now that the version macros are added in 1.12,
+            #        along with a 3rd version of the H5O functions, the H5O function
+            #        version for default api=v110 should be version 1 to work correctly
+            #        with 1.10 applications that were using unversioned H5O functions,
+            #        and the H5O function version should be version 3 for default api=v112 
+            #        (the default api version for 1.12).  Allowing a v111 entry and 
+            #        incrementing its index 13 lines below allows a version 2 that is
+            #        never accessed via the H5O function macros.
+            if(!( $_ =~ /v1[02468]/ || $_ =~ /v11[02468]/ ||  $_ =~ /v111/ )) {
                 die "bad version information: $name";
             }
             if(exists($sym_versions{$_})) {
@@ -351,6 +378,9 @@ sub parse_line ($) {
 #print "parse_line: _=$_\n";
             # Get the index of the version
             ($vers_idx) = ($_ =~ /v1(\d+)/);
+            if($vers_idx == 11) {
+                $vers_idx++;
+            }
             $vers_idx /= 2;
 #print "parse_line: vers_idx='$vers_idx'\n";
             push(@vers_nums, $vers_idx);
@@ -443,8 +473,9 @@ sub create_public ($) {
     print_copyright(*HEADER);
     print_warning(*HEADER);
     print_startprotect(*HEADER, $file);
+    print_globalapidefvers(*HEADER);
     print_checkoptions(*HEADER);
-    print_globalapivers(*HEADER);
+    print_globalapisymbolvers(*HEADER);
     print_defaultapivers(*HEADER);
     print_endprotect(*HEADER, $file);
 
@@ -478,7 +509,7 @@ for $file (@ARGV) {
         }
     }
     close SOURCE;
-  
+
     # Create header files
     print "Generating '", $prefix, "H5version.h'\n";
     create_public($prefix);
diff --git a/bin/makehelp b/bin/makehelp
index d6fbda2..4707397 100755
--- a/bin/makehelp
+++ b/bin/makehelp
@@ -40,6 +40,7 @@ make distclean:         remove all files generated by make, make check, or
 make check-p:           Only run parallel tests
 make check-s:           Only run serial tests
 make check-vfd:         Run tests with each virtual file driver
+make check-vol:         Run tests with each virtual object layer connector
 
 HDF5 uses Automake, so any standard Automake targets not listed here
 should also work.
diff --git a/bin/release b/bin/release
index 6358b0d..a34191e 100755
--- a/bin/release
+++ b/bin/release
@@ -39,29 +39,37 @@ USAGE()
 {
 cat << EOF
 Usage: $0 -d <dir> [--docver BRANCHNAME] [-h] [--nocheck] [--private] <methods> ...
-   -d DIR	The name of the directory where the releas(es) should be
+   -d DIR    The name of the directory where the releas(es) should be
                 placed.
    --docver BRANCHNAME  This is added for 1.8 and beyond to get the correct
                         version of documentation files from the hdf5docs
                         repository.  BRANCHNAME for v1.8 should be hdf5_1_8.
    -h           print the help page.
-   --nocheck	Ignore errors in MANIFEST file.
-   --private	Make a private release with today's date in version information.
-         
+   --nocheck    Ignore errors in MANIFEST file.
+   --private    Make a private release with today's date in version information.
+
 This must be run at the top level of the source directory.
 The other command-line options are the names of the programs to use
 for compressing the resulting tar archive (if none are given then
 "tar" is assumed):
 
-    tar		-- use tar and don't do any compressing.
-    gzip	-- use gzip with "-9" and append ".gz" to the output name.
-    cmake-tgz   -- create a tar file using the gzip default level with a build-unix.sh 
+    tar        -- use tar and don't do any compressing.
+    gzip    -- use gzip with "-9" and append ".gz" to the output name.
+    bzip2       -- use bzip2 with "-9" and append ".bz2" to the output name.
+    zip        -- convert all text files to DOS style and form a zip file for Windows use.
+    cmake-tgz   -- create a tar file using the gzip default level with a build-unix.sh
                    command file and all other CMake files needed to build HDF5 source
                    using CMake on unix machines.
-    bzip2       -- use bzip2 with "-9" and append ".bz2" to the output name.
-    zip		-- convert all text files to DOS style and form a zip file for Windows use.
     cmake-zip   -- convert all text files to DOS style and create a zip file inluding cmake
-                   scripts and .bat files to build HDF5 source using CMake on Windows. 
+                   scripts and .bat files to build HDF5 source using CMake on Windows.
+    hpc-cmake-tgz
+                -- create a tar file using the gzip default level with a build-unix.sh
+                   command file and all other CMake files needed to build HDF5 source
+                   using CMake on unix machines, with HDF5options.cmake files for serial
+                   and parallel builds on machines requiring batch jobs to run tests.
+                   The default is for parallel build, with serial only build by changing
+                   the HDF5options.cmake symlink to ser-HDF5options.cmake.  More
+                   information is available in the README_HPC file.
     doc         -- produce the latest doc tree in addition to the archive.
 
 An md5 checksum is produced for each archive created and stored in the md5 file.
@@ -114,8 +122,8 @@ EOF
 tar2zip()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2zip <tarfilename> <zipfilename>"
-	return 1
+    echo "usage: tar2zip <tarfilename> <zipfilename>"
+    return 1
     fi
     ztmpdir=/tmp/ztmpdir$$
     mkdir -p $ztmpdir
@@ -127,23 +135,23 @@ tar2zip()
     (cd $ztmpdir; tar xf -) < $tarfile
     # sanity check
     if [ ! -d $ztmpdir/$version ]; then
-	echo "untar did not create $ztmpdir/$version source dir"
-	# cleanup
-	rm -rf $ztmpdir
-	return 1
+    echo "untar did not create $ztmpdir/$version source dir"
+    # cleanup
+    rm -rf $ztmpdir
+    return 1
     fi
     # step 2: convert text files
     # There maybe a simpler way to do this.
     # options used in unix2dos:
-    # -k   Keep the date stamp 
+    # -k   Keep the date stamp
     # -q   quiet mode
     # grep redirect output to /dev/null because -q or -s are not portable.
     find $ztmpdir/$version | \
-	while read inf; do \
-	    if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
-		unix2dos -q -k $inf; \
-	    fi\
-	done
+    while read inf; do \
+        if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
+        unix2dos -q -k $inf; \
+        fi\
+    done
     # step 3: make zipball
     # -9 maximum compression
     # -y Store symbolic links as such in the zip archive
@@ -169,14 +177,14 @@ tar2zip()
 #    Note: do this in a temporary directory to avoid changing
 #    the original source directory which may be around.
 # 2. add build-unix.sh script.
-# 3. add SZIP.tar.gz, ZLib.tar.gz and cmake files to top level directory.
+# 3. add LIBAEC.tar.gz, ZLib.tar.gz and cmake files to top level directory.
 # 4. create gzipped tar file with these contents:
 #        build-unix.sh          script
 #        hdf5-<version>         source code directory extracted from tar file
 #        CTestScript.cmake      cmake file copied from <hdf5 source code>/config/cmake/scripts
 #        HDF5config.cmake       cmake file copied from <hdf5 source code>/config/cmake/scripts
 #        HDF5options.cmake      cmake file copied from <hdf5 source code>/config/cmake/scripts
-#        SZip.tar.gz            copied from /mnt/scr1/pre-release/hdf5/CMake
+#        LIBAEC.tar.gz          copied from /mnt/scr1/pre-release/hdf5/CMake
 #        ZLib.tar.gz            copied from /mnt/scr1/pre-release/hdf5/CMake
 
 
@@ -188,58 +196,61 @@ tar2zip()
 # Returns 0 if successful; 1 otherwise
 #
  # need function to create another temporary directory, extract the
-            # $tmpdir/$HDF5_VERS.tar into it, add (create) build-unix.sh,
-            # CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz and ZLib.tar.gz,
-             # and then tar.gz it.
+            # $tmpdir/$HDF5_VERS.tar into it, create build-VS*.bat files,
+            # add CTestScript.cmake, HDF5config.cmake, LIBAEC.tar.gz
+            # ZLib.tar.gz, HDF5 examples, and then zip it.
 tar2cmakezip()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2cmakezip <tarfilename> <tgzfilename>"
-	return 1
+    echo "usage: tar2cmakezip <tarfilename> <zipfilename>"
+    return 1
     fi
     cmziptmpdir=/tmp/cmziptmpdir$$
-    mkdir -p $cmziptmpdir
+    cmziptmpsubdir=$cmziptmpdir/CMake-$HDF5_VERS
+    mkdir -p $cmziptmpsubdir
     version=$1
     tarfile=$2
     zipfile=$3
 
     # step 1: untar tarball in cmgztmpdir
-    (cd $cmziptmpdir; tar xf -) < $tarfile
+    (cd $cmziptmpsubdir; tar xf -) < $tarfile
     # sanity check
-    if [ ! -d $cmziptmpdir/$version ]; then
-	echo "untar did not create $cmziptmpdir/$version source dir"
-	# cleanup
-	rm -rf $cmziptmpdir
-	return 1
+    if [ ! -d $cmziptmpsubdir/$version ]; then
+    echo "untar did not create $cmziptmpsubdir/$version source dir"
+    # cleanup
+    rm -rf $cmziptmpdir
+    return 1
     fi
 
     # step 2: add batch file for building CMake on window
-    cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2013-32.bat $cmziptmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2013-64.bat $cmziptmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2015-32.bat $cmziptmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2015-64.bat $cmziptmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2017-32.bat $cmziptmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/build-VS2017-64.bat $cmziptmpdir
-
-    # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
-    cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmziptmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpdir
-    cp $cmziptmpdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpdir
-    cp $cmziptmpdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpdir
-    cp $cmziptmpdir/$version/config/cmake/scripts/HDF5options.cmake $cmziptmpdir
+    (cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2013 -C Release -V -O hdf5.log" > build-VS2013-32.bat; chmod 755 build-VS2013-32.bat)
+    (cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201364 -C Release -V -O hdf5.log" > build-VS2013-64.bat; chmod 755 build-VS2013-64.bat)
+    (cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2015 -C Release -V -O hdf5.log" > build-VS2015-32.bat; chmod 755 build-VS2015-32.bat)
+    (cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201564 -C Release -V -O hdf5.log" > build-VS2015-64.bat; chmod 755 build-VS2015-64.bat)
+    (cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS2017 -C Release -V -O hdf5.log" > build-VS2017-32.bat; chmod 755 build-VS2017-32.bat)
+    (cd $cmziptmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201764 -C Release -V -O hdf5.log" > build-VS2017-64.bat; chmod 755 build-VS2017-64.bat)
+
+    # step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
+    cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmziptmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.1-Source.zip $cmziptmpsubdir
+    cp $cmziptmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmziptmpsubdir
+    cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmziptmpsubdir
+    cp $cmziptmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmziptmpsubdir
 
     # step 4: convert text files
     # There maybe a simpler way to do this.
     # options used in unix2dos:
-    # -k   Keep the date stamp 
+    # -k   Keep the date stamp
     # -q   quiet mode
     # grep redirect output to /dev/null because -q or -s are not portable.
-    find $cmziptmpdir/$version | \
-	while read inf; do \
-	    if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
-		unix2dos -q -k $inf; \
-	    fi\
-	done
+    find $cmziptmpsubdir/$version | \
+    while read inf; do \
+        if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
+        unix2dos -q -k $inf; \
+        fi\
+    done
+
     # step 3: make zipball
     # -9 maximum compression
     # -y Store symbolic links as such in the zip archive
@@ -253,7 +264,7 @@ tar2cmakezip()
 }
 
 # Function name: tar2cmaketgz
-# Convert the release tarball to a Windows zipball with files to run CMake build.
+# Convert the release tarball to a gzipped tar file with files to run CMake build.
 #
 # Programmer: Larry Knox
 # Creation date: 2017-02-20
@@ -265,14 +276,14 @@ tar2cmakezip()
 #    Note: do this in a temporary directory to avoid changing
 #    the original source directory which may be around.
 # 2. add build-unix.sh script.
-# 3. add SZIP.tar.gz, ZLib.tar.gz and cmake files to top level directory.
+# 3. add LIBAEC.tar.gz, ZLib.tar.gz and cmake files to top level directory.
 # 4. create gzipped tar file with these contents:
 #        build-unix.sh          script
 #        hdf5-<version>         source code directory extracted from tar file
 #        CTestScript.cmake      cmake file copied from <hdf5 source code>/config/cmake/scripts
 #        HDF5config.cmake       cmake file copied from <hdf5 source code>/config/cmake/scripts
 #        HDF5options.cmake      cmake file copied from <hdf5 source code>/config/cmake/scripts
-#        SZip.tar.gz            copied from /mnt/scr1/pre-release/hdf5/CMake
+#        LIBAEC.tar.gz          copied from /mnt/scr1/pre-release/hdf5/CMake
 #        ZLib.tar.gz            copied from /mnt/scr1/pre-release/hdf5/CMake
 
 
@@ -284,43 +295,132 @@ tar2cmakezip()
 # Returns 0 if successful; 1 otherwise
 #
  # need function to create another temporary directory, extract the
-            # $tmpdir/$HDF5_VERS.tar into it, add (create) build-unix.sh,
-            # CTestScript.cmake, HDF5config.cmake, SZIP.tar.gz and ZLib.tar.gz,
-             # and then tar.gz it.
+            # $tmpdir/$HDF5_VERS.tar into it, create build-unix.sh,
+            # add CTestScript.cmake, HDF5config.cmake, LIBAEC.tar.gz
+            # ZLib.tar.gz, HDF5 examples, and then tar.gz it.
 tar2cmaketgz()
 {
     if [ $# -ne 3 ]; then
-	echo "usage: tar2cmaketgz <tarfilename> <tgzfilename>"
-	return 1
+    echo "usage: tar2cmaketgz <tarfilename> <tgzfilename>"
+    return 1
+    fi
+    cmgztmpdir=/tmp/cmgztmpdir$$
+    cmgztmpsubdir=$cmgztmpdir/CMake-$HDF5_VERS
+    mkdir -p $cmgztmpsubdir
+    version=$1
+    tarfile=$2
+    tgzfile=$3
+
+    # step 1: untar tarball in cmgztmpdir
+    (cd $cmgztmpsubdir; tar xf -) < $tarfile
+    # sanity check
+    if [ ! -d $cmgztmpsubdir/$version ]; then
+    echo "untar did not create $cmgztmpsubdir/$version source dir"
+    # cleanup
+    rm -rf $cmgztmpdir
+    return 1
+    fi
+
+
+    # step 2: add build-unix.sh script
+    (cd $cmgztmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log" > build-unix.sh; chmod 755 build-unix.sh)
+
+    # step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
+    cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.1-Source.tar.gz $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpsubdir
+    tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1
+
+    # cleanup
+    rm -rf $cmgztmpdir
+}
+
+# Function name: tar2hpccmaketgz
+# Convert the release tarball to a gzipped tarfile with files to run CMake build
+# and HDF5options.cmake files for parallel or serial only builds where build
+# tests are run on compute nodes using batch scripts.
+#
+# Programmer: Larry Knox
+# Creation date: 2019-01-28
+#
+# Modifications
+#
+# Steps:
+# 1. untar the tarball in a temporary directory;
+#    Note: do this in a temporary directory to avoid changing
+#    the original source directory which may be around.
+# 2. add build-unix.sh script.
+# 3. add LIBAEC.tar.gz, ZLib.tar.gz and cmake files to top level directory.
+# 4. create gzipped tar file with these contents:
+#        build-unix.sh          script
+#        hdf5-<version>         source code directory extracted from tar file
+#        CTestScript.cmake      cmake file copied from <hdf5 source code>/config/cmake/scripts
+#        HDF5config.cmake       cmake file copied from <hdf5 source code>/config/cmake/scripts
+#        HDF5options.cmake      cmake file copied from <hdf5 source code>/config/cmake/scripts
+#        LIBAEC.tar.gz          copied from /mnt/scr1/pre-release/hdf5/CMake
+#        ZLib.tar.gz            copied from /mnt/scr1/pre-release/hdf5/CMake
+#
+# 5. For HPC-CMake tgz file the following are also needed in the top-level directory:
+#        README_HPC                 copied from release_docs
+#        ser-HDF5options.cmake      copied from <hdf5 source code>/config/cmake/scripts/HPC
+#        par-HDF5options.cmake      copied from <hdf5 source code>/config/cmake/scripts/HPC
+#        HDF5options.cmake          symlink to par-HDF5options.cmake
+#
+
+# Parameters:
+# $1 version
+# $2 release tarball
+# $3 output zipball file name
+#
+# Returns 0 if successful; 1 otherwise
+#
+ # need function to create another temporary directory, extract the
+            # $tmpdir/$HDF5_VERS.tar into it, create build-unix.sh,
+            # add CTestScript.cmake, HDF5config.cmake, LIBAEC.tar.gz
+            # ZLib.tar.gz, HDF5 examples, and then tar.gz it.
+tar2hpccmaketgz()
+{
+    if [ $# -ne 3 ]; then
+    echo "usage: tar2hpccmaketgz <tarfilename> <tgzfilename>"
+    return 1
     fi
     cmgztmpdir=/tmp/cmgztmpdir$$
-    mkdir -p $cmgztmpdir
+    cmgztmpsubdir=$cmgztmpdir/HPC-CMake-$HDF5_VERS
+    mkdir -p $cmgztmpsubdir
     version=$1
     tarfile=$2
     tgzfile=$3
 
     # step 1: untar tarball in cmgztmpdir
-    (cd $cmgztmpdir; tar xf -) < $tarfile
+    (cd $cmgztmpsubdir; tar xf -) < $tarfile
     # sanity check
-    if [ ! -d $cmgztmpdir/$version ]; then
-	echo "untar did not create $cmgztmpdir/$version source dir"
-	# cleanup
-	rm -rf $cmgztmpdir
-	return 1
+    if [ ! -d $cmgztmpsubdir/$version ]; then
+    echo "untar did not create $cmgztmpsubdir/$version source dir"
+    # cleanup
+    rm -rf $cmgztmpdir
+    return 1
     fi
 
 
     # step 2: add build-unix.sh script
-    (cd $cmgztmpdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log" > build-unix.sh; chmod 755 build-unix.sh)
-
-    # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
-    cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpdir
-    cp $cmgztmpdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpdir
-    cp $cmgztmpdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpdir
-    cp $cmgztmpdir/$version/config/cmake/scripts/HDF5options.cmake $cmgztmpdir
-    tar czf $DEST/CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1 
-                 
+    (cd $cmgztmpsubdir; echo "ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log" > build-unix.sh; chmod 755 build-unix.sh)
+
+    # step 3: add LIBAEC.tar.gz, ZLib.tar.gz and cmake files
+    cp /mnt/scr1/pre-release/hdf5/CMake/LIBAEC.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.1-Source.tar.gz $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/CTestScript.cmake $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/HDF5config.cmake $cmgztmpsubdir
+
+    cp $cmgztmpsubdir/$version/release_docs/README_HPC $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/HPC/ser-HDF5options.cmake $cmgztmpsubdir
+    cp $cmgztmpsubdir/$version/config/cmake/scripts/HPC/par-HDF5options.cmake $cmgztmpsubdir
+    (cd $cmgztmpsubdir; ln -s par-HDF5options.cmake HDF5options.cmake)
+    tar czf $DEST/HPC-CMake-$HDF5_VERS.tar.gz -C $cmgztmpdir . || exit 1
+
     # cleanup
     rm -rf $cmgztmpdir
 }
@@ -342,7 +442,7 @@ check=yes
 release_date=`date +%F`
 today=`date +%Y%m%d`
 pmode='no'
-tmpdir="../#release_tmp.$$"	# tmp work directory
+tmpdir="../#release_tmp.$$"    # tmp work directory
 DOC_URL=https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
 CPPLUS_RM_NAME=cpplus_RM
 MAINT_MODE_ENABLED=""
@@ -359,11 +459,11 @@ fi
 RESTORE_VERSION()
 {
     if [ X-${VERS_OLD} != X- ]; then
-	echo restoring version information back to $VERS_OLD
-	rm -f config/lt_vers.am
-	cp $tmpdir/lt_vers.am config/lt_vers.am
-	bin/h5vers -s $VERS_OLD
-	VERS_OLD=
+    echo restoring version information back to $VERS_OLD
+    rm -f config/lt_vers.am
+    cp $tmpdir/lt_vers.am config/lt_vers.am
+    bin/h5vers -s $VERS_OLD
+    VERS_OLD=
     fi
 }
 
@@ -373,32 +473,32 @@ while [ -n "$1" ]; do
     arg=$1
     shift
     case "$arg" in
-	-d)
-	    DEST=$1
-	    shift
-	    ;;
-	--nocheck)
-	    check=no
-	    ;;
-	-h)
-	    USAGE
-	    exit 0
-	    ;;
-	--private)
-	    pmode=yes
-	    ;;
+    -d)
+        DEST=$1
+        shift
+        ;;
+    --nocheck)
+        check=no
+        ;;
+    -h)
+        USAGE
+        exit 0
+        ;;
+    --private)
+        pmode=yes
+        ;;
         --docver)
             DOCVERSION=$1
             shift
             ;;
-	-*)
-	    echo "Unknown switch: $arg" 1>&2
-	    USAGE
-	    exit 1
-	    ;;
-	*)
-	    methods="$methods $arg"
-	    ;;
+    -*)
+        echo "Unknown switch: $arg" 1>&2
+        USAGE
+        exit 1
+        ;;
+    *)
+        methods="$methods $arg"
+        ;;
     esac
 done
 
@@ -445,9 +545,15 @@ fi
 bin/chkmanifest || fail=yes
 if [ "X$fail" = "Xyes" ]; then
     if [ $check = yes ]; then
+        echo ""
+        echo "Note!  If you are running bin/release in a development branch"
+        echo "later than v 1.8 the MANIFEST check is expected to fail when"
+        echo "autogen.sh has not been run successfully. Either run autogen.sh "
+        echo "with /usr/hdf/bin/AUTOTOOLS at the beginning of PATH or add the"
+        echo "--nocheck argument to the bin/release command."
         exit 1
     else
-	echo "Continuing anyway..."
+    echo "Continuing anyway..."
     fi
 fi
 
@@ -481,7 +587,7 @@ test "$verbose" && echo "   Running tar..." 1>&2
 ( \
     cd $tmpdir; \
     tar cf $HDF5_VERS.tar $HDF5_VERS/Makefile \
-	`sed 's/^\.\//hdf5-'$VERS'\//' $MANIFEST` || exit 1 \
+    `sed 's/^\.\//hdf5-'$VERS'\//' $MANIFEST` || exit 1 \
 )
 
 # Compress
@@ -489,56 +595,61 @@ MD5file=$HDF5_VERS.md5
 cp /dev/null $DEST/$MD5file
 for comp in $methods; do
     case $comp in
-	tar)
-	    cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
-	    (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file) 
-	    ;;
-	gzip)
-	    test "$verbose" && echo "   Running gzip..." 1>&2
-	    gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
-	    (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file) 
-	    ;;
+    tar)
+        cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
+        (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file)
+        ;;
+    gzip)
+        test "$verbose" && echo "   Running gzip..." 1>&2
+        gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
+        (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file)
+        ;;
         cmake-tgz)
-	    test "$verbose" && echo "   Creating CMake tar.gz file..." 1>&2
-	    tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
-	    (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file) 
+        test "$verbose" && echo "   Creating CMake tar.gz file..." 1>&2
+        tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
+        (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file)
             ;;
-	bzip2)
-	    test "$verbose" && echo "   Running bzip2..." 1>&2
-	    bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
-	    (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file) 
-	    ;;
-	zip)
-	    test "$verbose" && echo "   Creating zip ball..." 1>&2
-	    tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
-	    (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file) 
-	    ;;
+        hpc-cmake-tgz)
+        test "$verbose" && echo "   Creating HPC-CMake tar.gz file..." 1>&2
+        tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
+        (cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file)
+            ;;
+    bzip2)
+        test "$verbose" && echo "   Running bzip2..." 1>&2
+        bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
+        (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file)
+        ;;
+    zip)
+        test "$verbose" && echo "   Creating zip ball..." 1>&2
+        tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
+        (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file)
+        ;;
         cmake-zip)
             test "$verbose" && echo "   Creating CMake-zip ball..." 1>&2
             tar2cmakezip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.zip 1>&2
             (cd $DEST; md5sum CMake-$HDF5_VERS.zip >> $MD5file)
             ;;
-	doc)
+    doc)
             if [ "${DOCVERSION}" = "" ]; then
                 DOCVERSION=master
             fi
-	    test "$verbose" && echo "   Creating docs..." 1>&2
-	    # Check out docs from git repo
-	    (cd $tmpdir; git clone -q $DOC_URL ${DOCVERSION} > /dev/null) || exit 1
+        test "$verbose" && echo "   Creating docs..." 1>&2
+        # Check out docs from git repo
+        (cd $tmpdir; git clone -q $DOC_URL ${DOCVERSION} > /dev/null) || exit 1
             # Create doxygen C++ RM
-	    (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1
-	    # Replace version of C++ RM with just-created version
-	    rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
-	    mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
+        (cd c++/src && doxygen cpp_doc_config > /dev/null ) || exit 1
+        # Replace version of C++ RM with just-created version
+        rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
+        mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME || exit 1
             # Compress the docs and move them to the release area
-	    mv $tmpdir/${DOCVERSION} $tmpdir/${HDF5_VERS}_docs || exit 1
-	    (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs) || exit 1
-	    mv $tmpdir/${HDF5_VERS}_docs.tar $DEST || exit 1
-	    ;;
-	*)
-	    echo "***Error*** Unknown method $comp"
-	    exit 1
-	    ;;
+        mv $tmpdir/${DOCVERSION} $tmpdir/${HDF5_VERS}_docs || exit 1
+        (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs) || exit 1
+        mv $tmpdir/${HDF5_VERS}_docs.tar $DEST || exit 1
+        ;;
+    *)
+        echo "***Error*** Unknown method $comp"
+        exit 1
+        ;;
     esac
 done
 
diff --git a/bin/runbkgprog b/bin/runbkgprog
new file mode 100755
index 0000000..f04ea89
--- /dev/null
+++ b/bin/runbkgprog
@@ -0,0 +1,88 @@
+#!/usr/bin/env perl
+require 5.003;
+use warnings;
+$indent=4;
+
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+
+# Run program in background
+#
+use warnings;
+use strict;
+
+use Carp;
+use Time::HiRes;
+use POSIX 'setsid';
+
+my $child_pid;
+my $child_proc;
+my $cmd = $ARGV[0];
+my $debug = 1;
+
+print "\nStart child process\n";
+start_child();
+print "\nStarted child process\n";
+
+sub start_child {
+    die "cannot execute cmd: $cmd" unless -x $cmd;
+    if ($^O eq 'MSWin32') { # Windows
+        require Win32::Process;
+        Win32::Process::Create($child_proc, $cmd, $cmd, 0, 0, ".") || confess "Could not spawn child: $!";
+        $child_pid = $child_proc->GetProcessID();
+    }
+    else { # Unix
+        $SIG{CHLD} = 'IGNORE';
+        $child_pid = fork();
+        unless (defined $child_pid) {
+            confess "Could not spawn child (Unix): $!";
+        }
+        if ($child_pid == 0) { # child
+            unless ($debug) {
+                open STDIN, "<", "/dev/null"   or die "Can't read /dev/null: $!";
+                open STDOUT, ">", "/dev/null"  or die "Can't write /dev/null: $!";
+            }
+            setsid or warn "setsid cannot start a new session: $!";
+            unless ($debug) {
+                open STDERR, '>&STDOUT'  or die "Can't dup stdout: $!";
+            }
+            local $| = 1;
+            unless (exec($cmd)) {
+                confess "Could not start child: $cmd: $!";
+                CORE::exit(0);
+            }
+        }
+        # parent
+        $SIG{CHLD} = 'DEFAULT';
+    }
+    # catch early child exit, e.g. if program path is incorrect
+    sleep(1.0);
+    POSIX::waitpid(-1, POSIX::WNOHANG()); # clean up any defunct child process
+    if (kill(0,$child_pid)) {
+        print "\nStarted child process id $child_pid\n";
+    }
+    else {
+        warn "Child process exited quickly: $cmd: process $child_pid";
+    }
+}
+
+sub stop_child
+{
+    if ($^O eq 'MSWin32') { # Windows
+        Win32::Process::KillProcess($child_pid,0);
+    }
+    else { # Unix
+        kill 9, $child_pid || warn "could not kill process $child_pid: $!";
+    }
+    print "Stopped child process id $child_pid\n";
+}
diff --git a/bin/snapshot b/bin/snapshot
index 5c78fc8..1218caa 100755
--- a/bin/snapshot
+++ b/bin/snapshot
@@ -130,9 +130,10 @@ DISPLAYUSAGE()
     set -
     cat <<EOF
 Usage: $PROGNAME [all] [checkout] [ftp <URL> [diff] [test] [srcdir] [release] [help]
-	[clean] [distclean] [echo] [deploy <dir>] [deploydir <dir>]
-	[zlib <zlib_path>] [releasedir <dir>] [srcdirname <dir>] [check-vfd]
-	[exec <command>] [module-load <module-list>] [op-configure <option>] 
+        [clean] [distclean] [echo] [deploy <dir>] [deploydir <dir>]
+        [zlib <zlib_path>] [releasedir <dir>] [srcdirname <dir>] [check-vfd]
+        [check-passthrough-vol]
+        [exec <command>] [module-load <module-list>] [op-configure <option>]
         [--<option>]
     all:      Run all commands (checkout, test & release)
               [Default is all]
@@ -149,8 +150,8 @@ Usage: $PROGNAME [all] [checkout] [ftp <URL> [diff] [test] [srcdir] [release] [h
     setenv <name> <value>:
               Set environment variable <name> to <value>.
     setenvN <N> <name> <value> ...:
-	      Set environment variable with <N> values.
-	      E.g., setenvN 3 x a b c is same as setenv x="a b c".
+              Set environment variable with <N> values.
+              E.g., setenvN 3 x a b c is same as setenv x="a b c".
     srcdir:   Use srcdir option (does not imply other commands)
               "snapshot srcdir" is equivalent to "snapshot srcdir all"
               "snapshot srcdir checkout" is equivalent to "snapshot checkout"
@@ -168,7 +169,12 @@ Usage: $PROGNAME [all] [checkout] [ftp <URL> [diff] [test] [srcdir] [release] [h
               Use <dir> as the release directory
               [Default is $ReleaseDir_default]
     check-vfd:
-	      Run make check-vfd instead of just make check.
+              Run make check-vfd instead of just make check.
+    check-passthrough-vol:
+              Run make check-passthrough-vol instead of just make check.
+              NOTE: Will only succeed with passthrough VOL connectors
+              that use the native VOL connector as the terminal
+              connector.
     exttest <testscript>;
               Run testscript;
     exec <command>:
@@ -422,6 +428,9 @@ while [ $# -gt 0 ] ; do
 	check-vfd)
 	    CHECKVAL=check-vfd
 	    ;;
+	check-passthrough-vol)
+	    CHECKVAL=check-passthrough-vol
+	    ;;
         module-load)
             shift
             if [ $# -lt 1 ]; then
diff --git a/bin/trace b/bin/trace
index cf41238..fd0248e 100755
--- a/bin/trace
+++ b/bin/trace
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ##
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -12,6 +12,7 @@
 # help@hdfgroup.org.
 ##
 require 5.003;
+use warnings;
 $Source = "";
 
 ##############################################################################
@@ -42,10 +43,12 @@ $Source = "";
                "H5D_space_status_t"         => "Ds",
                "H5D_vds_view_t"             => "Dv",
                "H5FD_mpio_xfer_t"           => "Dt",
+               "H5FD_splitter_vfd_config_t" => "Dr",
                "herr_t"                     => "e",
                "H5E_direction_t"            => "Ed",
                "H5E_error_t"                => "Ee",
                "H5E_type_t"                 => "Et",
+               "H5ES_status_t"              => "Es",
                "H5F_close_degree_t"         => "Fd",
                "H5F_fspace_strategy_t"      => "Ff",
                "H5F_file_space_type_t"      => "Ff",
@@ -67,7 +70,9 @@ $Source = "";
                "unsigned"                   => "Iu",
                "unsigned int"               => "Iu",
                "uint32_t"                   => "Iu",
+               "uint64_t"                   => "UL",
                "H5I_type_t"                 => "It",
+               "H5O_token_t"                => "k",
                "H5G_link_t"                 => "Ll", #Same as H5L_type_t now
                "H5L_type_t"                 => "Ll",
                "MPI_Comm"                   => "Mc",
@@ -76,7 +81,9 @@ $Source = "";
                "off_t"                      => "o",
                "H5O_type_t"                 => "Ot",
                "H5P_class_t"                => "p",
-               "hobj_ref_t"                 => "r",
+               "hobj_ref_t"                 => "Ro",
+               "hdset_reg_ref_t"            => "Rd",
+               "H5R_ref_t"                  => "Rr",
                "H5R_type_t"                 => "Rt",
                "char"                       => "s",
                "unsigned char"              => "s",
@@ -95,8 +102,38 @@ $Source = "";
                "H5T_str_t"                  => "Tz",
                "unsigned long"              => "Ul",
                "unsigned long long"         => "UL",
+               "H5VL_subclass_t"            => "VS",
+               "H5VL_get_conn_lvl_t"        => "VL",
+               "H5VL_attr_get_t"            => "Va",
+               "H5VL_attr_optional_t"       => "Vs",
+               "H5VL_attr_specific_t"       => "Vb",
+               "H5VL_blob_specific_t"       => "VB",
+               "H5VL_class_value_t"         => "VC",
+               "H5VL_dataset_get_t"         => "Vc",
+               "H5VL_dataset_specific_t"    => "Vd",
+               "H5VL_dataset_optional_t"    => "Vt",
+               "H5VL_datatype_get_t"        => "Ve",
+               "H5VL_datatype_specific_t"   => "Vf",
+               "H5VL_datatype_optional_t"   => "Vu",
+               "H5VL_file_get_t"            => "Vg",
+               "H5VL_file_specific_t"       => "Vh",
+               "H5VL_file_optional_t"       => "Vv",
+               "H5VL_group_get_t"           => "Vi",
+               "H5VL_group_specific_t"      => "Vj",
+               "H5VL_group_optional_t"      => "Vw",
+               "H5VL_link_create_type_t"    => "Vk",
+               "H5VL_link_get_t"            => "Vl",
+               "H5VL_link_specific_t"       => "Vm",
+               "H5VL_link_optional_t"       => "Vx",
+               "H5VL_object_get_t"          => "Vn",
+               "H5VL_object_specific_t"     => "Vo",
+               "H5VL_object_optional_t"     => "Vy",
+               "H5VL_request_specific_t"    => "Vr",
+               "H5VL_request_optional_t"    => "Vz",
+               "H5VL_blob_optional_t"       => "VA",
                "void"                       => "x",
                "FILE"                       => "x",
+               "H5_alloc_stats_t"           => "x",
                "H5A_operator_t"             => "x",
                "H5A_operator1_t"            => "x",
                "H5A_operator2_t"            => "x",
@@ -120,18 +157,29 @@ $Source = "";
                "H5FD_t"                     => "x",
                "H5FD_class_t"               => "x",
                "H5FD_stream_fapl_t"         => "x",
+               "H5FD_ros3_fapl_t"           => "x",
+               "H5FD_hdfs_fapl_t"           => "x",
                "H5FD_file_image_callbacks_t" => "x",
+               "H5FD_mirror_fapl_t"         => "x",
                "H5G_iterate_t"              => "x",
                "H5G_info_t"                 => "x",
                "H5I_free_t"                 => "x",
+               "H5I_iterate_func_t"         => "x",
                "H5I_search_func_t"          => "x",
                "H5L_class_t"                => "x",
                "H5L_elink_traverse_t"       => "x",
-               "H5L_iterate_t"              => "x",
+               "H5L_info1_t"                => "x",
+               "H5L_info2_t"                => "x",
+               "H5L_iterate1_t"             => "x",
+               "H5L_iterate2_t"             => "x",
+               "H5M_iterate_t"              => 'x',
                "H5MM_allocate_t"            => "x",
                "H5MM_free_t"                => "x",
-               "H5O_info_t"                 => "x",
-               "H5O_iterate_t"              => "x",
+               "H5O_info1_t"                => "x",
+               "H5O_info2_t"                => "x",
+               "H5O_native_info_t"          => "x",
+               "H5O_iterate1_t"             => "x",
+               "H5O_iterate2_t"             => "x",
                "H5O_mcdt_search_cb_t"       => "x",
                "H5P_cls_create_func_t"      => "x",
                "H5P_cls_copy_func_t"        => "x",
@@ -147,6 +195,10 @@ $Source = "";
                "H5T_cdata_t"                => "x",
                "H5T_conv_t"                 => "x",
                "H5T_conv_except_func_t"     => "x",
+               "H5VL_t"                     => "x",
+               "H5VL_class_t"               => "x",
+               "H5VL_loc_params_t"          => "x",
+               "H5VL_request_notify_t"      => "x",
                "H5Z_func_t"                 => "x",
                "H5Z_filter_func_t"          => "x",
                "va_list"                    => "x",
@@ -190,6 +242,11 @@ sub argstring ($$$) {
   # certain type qualifiers, and indirection.
   $atype =~ s/^\bconst\b//;
   $atype =~ s/\bH5_ATTR_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_DEPRECATED_USED\b//g;
+  $atype =~ s/\bH5_ATTR_NDEBUG_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_DEBUG_API_USED\b//g;
+  $atype =~ s/\bH5_ATTR_PARALLEL_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_PARALLEL_USED\b//g;
   $atype =~ s/\s+/ /g;
   $ptr = length $1 if  $atype =~ s/(\*+)//;
   $atype =~ s/^\s+//;
@@ -295,7 +352,7 @@ sub rewrite_func ($$$$$) {
     # Ignored due to NO TRACE comment.
   } elsif ($body =~ s/((\n[ \t]*)H5TRACE\d+\s*\(.*?\);)\n/"$2$trace"/es) {
     # Replaced an H5TRACE macro.
-  } elsif ($body=~s/((\n[ \t]*)FUNC_ENTER\w*\s*(\(.*?\))?;??)\n/"$1$2$trace"/es) {
+  } elsif ($body=~s/((\n[ \t]*)FUNC_ENTER\w*[ \t]*(\(.*?\))?;??)\n/"$1$2$trace"/es) {
     # Added an H5TRACE macro after a FUNC_ENTER macro.
   } else {
     errmesg $file, $name, "unable to insert tracing information";
diff --git a/bin/warnhist b/bin/warnhist
new file mode 100755
index 0000000..a88474b
--- /dev/null
+++ b/bin/warnhist
@@ -0,0 +1,523 @@
+#!/usr/bin/env perl
+require 5.003;
+use warnings;
+
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+#
+# Quincey Koziol, koziol@hdfgroup.org
+#  9 Aug 2013
+#
+# Purpose: Given an input file containing the output from a build of the
+#	   library, gather the file names and line numbers, alias
+#          identical types of warnings together into a single bin and
+#          report the number of warnings for each type of warning, each file
+#          and the total count of warnings
+
+# Perl modules/settings
+use strict;
+use Getopt::Std;
+
+# Global variables, for accumulating information
+my $totalcount = 0;
+my %warn_count = ();
+my $warncount;
+my %warn_file = ();
+my %warn_file_line = ();
+my %file_count = ();
+my $filecount;
+my $ignorecount = 0;
+my @ignorenames;
+my %ignored_files = ();
+my %warn_file_indices = ();
+my %file_warn_indices = ();
+my @warn_match_strings;
+my @file_match_strings;
+my %file_warn = ();
+my %file_warn_line = ();
+my $current_warning = 0;
+my $current_file = 0;
+my $warn_index;
+my $last_c_name;
+my $last_fort_name;
+my $last_fort_line;
+my $genericize = 1;
+
+# Display usage
+sub do_help {
+    print "Usage: 'warnhist [-h, --help] [-t <prefix>] [-w <n>] [-W] [-f <n>] [-F] [-s <warning string list>] [-S <file string list] [-l] [-u] [-i <name list>] [file]'\n";
+    print "\t-h, --help\tDisplay this usage\n";
+    print "\t-t <prefix>\tTrim pathname prefix from filenames, <prefix>\n";
+    print "\t-w <n>\tDisplay files for a given warning index list, <n>\n";
+    print "\t\t<n> can be a single value, a range, or a comma separated list\n";
+    print "\t\tFor example: '0' or '0,4' or '8-10' or '0,2-4,8-10,13'\n";
+    print "\t-W\tDisplay files for all warnings\n";
+    print "\t-f <n>\tDisplay warnings for a given file index list, <n>\n";
+    print "\t\t<n> can be a single value, a range, or a comma separated list\n";
+    print "\t\tFor example: '0' or '0,4' or '8-10' or '0,2-4,8-10,13'\n";
+    print "\t-F\tDisplay warnings for all files\n";
+    print "\t-s <warning string list>\tDisplay files for warnings which contain a string, <warning string list>\n";
+    print "\t\t<warning string list> is a comma separated list, with no spaces\n";
+    print "\t\tFor example: 'Wunused-dummy-argument' or 'Wunused-dummy-argument,Wunused-variable'\n";
+    print "\t-S <file string list>\tDisplay warnings for files which contain a string, <file string list>\n";
+    print "\t\t<file string list> is a comma separated list, with no spaces\n";
+    print "\t\tFor example: 'H5Fint' or 'H5Fint,H5Gnode'\n";
+    print "\t-l\tDisplay line nunbers for file/warning\n";
+    print "\t-u\tLeave 'unique' types in warnings, instead of genericizing them\n";
+    print "\t-i <name list>\tIgnore named files, <name list>\n";
+    print "\t\t<name list> is a comma separated list, with no spaces\n";
+    print "\t\tFor example: 'H5LTparse' or 'H5LTparse,H5LTanalyze'\n";
+    print "\tfile\tFilename containing build output\n";
+    print "\t\tIf no file is given, standard input is used.\n";
+    exit;
+}
+
+sub main::HELP_MESSAGE {
+    do_help();
+}
+
+# declare the Perl command line flags/options we want to allow
+my %options=();
+getopts("FWhut:w:f:s:S:i:l", \%options);
+
+# Display usage, if requested
+if($options{h}) {
+    do_help();
+}
+
+# Parse list of file names to ignore
+if(exists $options{i}) {
+    @ignorenames = split /,/, $options{i};
+#print @ignorenames;
+}
+
+# Parse list of warning indices to expand file names
+if(exists $options{w}) {
+    my @tmp_indices;
+
+    @tmp_indices = split /,/, $options{w};
+#print @tmp_indices;
+    for my $x (@tmp_indices) {
+#print "x = '$x'\n";
+        if($x =~ /\-/) {
+            my $start_index;
+            my $end_index;
+
+#print "matched = '$x'\n";
+            ($start_index, $end_index) = split /\-/, $x;
+#print "start_index = '$start_index', end_index = '$end_index'\n";
+            for my $y ($start_index..$end_index) {
+#print "y = '$y'\n";
+                if(!exists $warn_file_indices{$y}) {
+                    $warn_file_indices{$y} = $y;
+                }
+            }
+        }
+        else {
+            if(!exists $warn_file_indices{$x}) {
+                $warn_file_indices{$x} = $x;
+            }
+        }
+    }
+#foreach (sort keys %warn_file_indices) {
+#    print "$_ : $warn_file_indices{$_}\n";
+#}
+}
+
+# Parse list of warning strings to expand file names
+if(exists $options{s}) {
+    @warn_match_strings = split /,/, $options{s};
+# print @warn_match_strings;
+}
+
+# Parse list of file indices to expand warnings
+if(exists $options{f}) {
+    my @tmp_indices;
+
+    @tmp_indices = split /,/, $options{f};
+#print @tmp_indices;
+    for my $x (@tmp_indices) {
+#print "x = '$x'\n";
+        if($x =~ /\-/) {
+            my $start_index;
+            my $end_index;
+
+#print "matched = '$x'\n";
+            ($start_index, $end_index) = split /\-/, $x;
+#print "start_index = '$start_index', end_index = '$end_index'\n";
+            for my $y ($start_index..$end_index) {
+#print "y = '$y'\n";
+                if(!exists $file_warn_indices{$y}) {
+                    $file_warn_indices{$y} = $y;
+                }
+            }
+        }
+        else {
+            if(!exists $file_warn_indices{$x}) {
+                $file_warn_indices{$x} = $x;
+            }
+        }
+    }
+#foreach (sort keys %warn_file_indices) {
+#    print "$_ : $warn_file_indices{$_}\n";
+#}
+}
+
+# Parse list of warning strings for files to expand warnings
+if(exists $options{S}) {
+    @file_match_strings = split /,/, $options{S};
+# print @file_match_strings;
+}
+
+# Check if warnings should stay unique and not be "genericized"
+if($options{u}) {
+    $genericize = 0;
+}
+
+PARSE_LINES:
+while (<>) {
+    my $name;
+    my $line;
+    my $prev_line;
+    my $toss;
+    my $offset;
+    my $warning;
+    my $extra;
+    my $extra2;
+
+    # Retain last FORTRAN compile line, which comes a few lines before warning
+    if($_ =~ /.*\.[fF]90:.*/) {
+        ($last_fort_name, $last_fort_line, $toss) = split /\:/, $_;
+        ($last_fort_line, $toss) = split /\./, $last_fort_line;
+    }
+
+    # Retain last C/C++ compile line, which possibly comes a few lines before warning
+    if($_ =~ /.*[A-Za-z0-9_]\.[cC]:.*/) {
+        ($last_c_name, $toss) = split /\:/, $_;
+    }
+
+    # Retain C/C++ compile line, which comes with the line of warning
+    if($_ =~ /.*[A-Za-z0-9_]\.[chC]\(.*[0-9]\):.*#.*/) {
+        $last_c_name = $_;
+    }
+
+    # Skip lines that don't have the word "warning"
+    next if $_ !~ /[Ww]arning/;
+
+    # Skip warnings from linker
+    next if $_ =~ /ld: warning:/;
+
+    # Skip warnings from build_py and install_lib 
+    next if $_ =~ /warning: (build_py|install_lib)/;
+
+    # "Hide" the C++ '::' symbol until we've parsed out the parts of the line
+    while($_ =~ /\:\:/) {
+	$_ =~ s/\:\:/@@@@/g;
+    }
+
+    # Check for weird formatting of warning message
+    if($_ =~ /^cc1: warning:.*/) {
+        $name = $last_c_name;
+        $line = "??";
+        ($toss, $toss, $warning, $extra, $extra2) = split /\:/, $_;
+    # Check for CMAKE build with warning on first line and no filename
+    } elsif($_ =~ /^\s*[Ww]arning:.*/) {
+        $name = $last_c_name;
+        $line = "??";
+        ($toss, $warning, $extra, $extra2) = split /\:/, $_;
+    # Check for FORTRAN warning output
+    } elsif($_ =~ /^Warning:.*/) {
+        $name = $last_fort_name;
+        $line = $last_fort_line;
+        ($toss, $warning, $extra, $extra2) = split /\:/, $_;
+#print "1:",$.,":",$_;
+#        $_ = <>;
+#print "2:",$.,":",$_;
+#        if($_ =~ /^\sFC.*/) {
+#            $_ = <>;
+#print "3:",$.,":",$_;
+#        }
+#        ($name, $line, $toss) = split /\:/, $_;
+#print "4:","'",$name,"'","-","'",$line,"'","\n";
+        # Check for improperly parsed filename or line
+        if($name =~ /^$/) {
+            print "Filename is a null string! Input line #$. is: '$_'";
+            next
+        }
+        if($line =~ /^$/) {
+            print "Line is a null string! Input line #$. is: '$_'";
+            next
+        }
+    # Check for non-GCC warning (Solaris/Oracle?)
+    } elsif($_ =~ /^\".*, line [0-9]+: *[Ww]arning:.*/) {
+        ($name, $toss, $warning, $extra, $extra2) = split /\:/, $_;
+        ($name, $line) = split /\,/, $name;
+	    $name =~ s/^\"//g;
+	    $name =~ s/\"$//g;
+	    $line =~ s/^\s*line\s*//g;
+# print "name:'", $name, "'-'", $line, "'\n";
+# print "warning:'", $warning, "'\n";
+    # Check for Intel icc warning
+    } elsif($_ =~ /.*[A-Za-z0-9_]\.[chC]\(.*[0-9]\):.*#.*/) {
+        ($last_c_name, $toss, $warning) = split /\:/, $last_c_name;
+        ($name, $line) = split /\(/, $last_c_name;
+        $line =~ s/\)//g;
+    } else {
+        # Check for 'character offset' field appended to file & line #
+	# (This is probably specific to GCC)
+        if($_ =~ /^.*[0-9]+\:[0-9]+\:/) {
+            ($name, $line, $offset, $toss, $warning, $extra, $extra2) = split /\:/, $_;
+        } else {
+            ($name, $line, $toss, $warning, $extra, $extra2) = split /\:/, $_;
+        }
+    }
+
+    # Check for extra ':' followed by more text in original warning string,
+    #  and append the ':' and text back onto the parsed warning
+    #  (Use 'length $extra' idiom to avoid warning when $extra is undefined)
+    if(length $extra ) {
+        $warning = join ':', $warning, $extra;
+    }
+    if(length $extra2 ) {
+        $warning = join ':', $warning, $extra2;
+    }
+
+    # Restore the C++ '::' symbol now that we've parsed out the parts of the line
+    while($warning =~ /@@@@/) {
+        $warning =~ s/@@@@/\:\:/g;
+    }
+
+    # Trim leading '..' paths from filename
+    while($name =~ /^\.\.\//) {
+        $name =~ s/^\.\.\///g;
+    }
+
+    # Check for trimming prefix
+    if((exists $options{t}) && ($name =~ /$options{t}/)) {
+        $name =~ s/^$options{t}\///g;
+    }
+
+    # Check for ignored file
+    if(exists $options{i}) {
+        for my $x (@ignorenames) {
+#print "x = '$x'\n";
+            if($name =~ /$x/) {
+# print "matched name = '$name'\n";
+                $ignorecount++;
+                if(!(exists $ignored_files{$name})) {
+                    $ignored_files{$name} = $name;
+                }
+                next PARSE_LINES;
+            }
+        }
+    }
+
+    # Check for improperly parsed warning (usually an undefined warning string)
+    if(!defined $warning) {
+        print "Warning Undefined! Input line is: '$_'";
+        next
+    }
+
+    # Get rid of leading & trailing whitespace
+    $warning =~ s/^\s//g;
+    $warning =~ s/\s$//g;
+
+    # Check for improperly parsed warning
+    if($warning =~ /^$/) {
+        print "Warning is a null string! Input line is: '$_'";
+        next
+    }
+
+    # Convert all quotes to '
+    $warning =~ s/‘/'/g;
+    $warning =~ s/’/'/g;
+    $warning =~ s/"/'/g;
+
+#
+# These skipped messages & "genericizations" may be specific to GCC
+
+    # Skip supplemental warning message
+    next if $warning =~ /near initialization for/;
+
+    # Skip C++ supplemental warning message
+    next if $warning =~ /in call to/;
+
+    # Skip GCC warning that should be a note
+    next if $_ =~ /\(this will be reported only once per input file\)/;
+
+    if($genericize) {
+	# Eliminate C/C++ "{aka <some type>}" and "{aka '<some type>'}" info
+	if($warning =~ /\s(\{|\()aka '?[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#]+[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#\ ]*'?(\}|\))/) {
+	    $warning =~ s/\s(\{|\()aka '?[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#]+[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#\ ]*'?(\}|\))//g;
+	}
+
+	# Genericize C/C++ '<some type>', printf format '%<some format>', and
+	# "unknown warning group" into '-'
+	if($warning =~ /'[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#\-\=]+[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#\-\=\ ]*'/) {
+	    $warning =~ s/'[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#\-\=]+[A-Za-z_0-9\(\)\*\,\[\]\.\<\>\&\:\+\#\-\=\ ]*'/'-'/g;
+	}
+	if($warning =~ /'%[\#0\-\ \+]*[,;\:_]?[0-9\*]*\.?[0-9\*]*[hjltzL]*[aAcdeEfFgGinosuxX]'/) {
+	    $warning =~ s/'%[\#0\-\ \+]*[,;\:_]?[0-9\*]*\.?[0-9\*]*[hjltzL]*[aAcdeEfFgGinosuxX]'/'-'/g;
+	}
+
+	# Genericize C/C++ "<macro>" warnings into "-"
+	if($warning =~ /"[A-Za-z_0-9]*"/) {
+	    $warning =~ s/"[A-Za-z_0-9]*"/"-"/g;
+	}
+
+	# Genericize [GCC?] C/C++ warning text about suggessted attribute
+	if($warning =~ /attribute=[A-Za-z_0-9]*\]/) {
+	    $warning =~ s/=[A-Za-z_0-9]*\]/=-\]/g;
+	}
+
+	# Genericize FORTRAN "at (<n>)" into "at (-)", "REAL(<n>)" into "REAL(-)",
+	# 	and "INTEGER(<n>)" into "INTEGER(-)"
+	if($warning =~ /.*at\s\([0-9]+\).*/) {
+	    $warning =~ s/at\s\([0-9]+\)/at \(-\)/g;
+	}
+	if($warning =~ /.*REAL\([0-9]+\).*/) {
+	    $warning =~ s/REAL\([0-9]+\)/REAL\(-\)/g;
+	}
+	if($warning =~ /.*INTEGER\([0-9]+\).*/) {
+	    $warning =~ s/INTEGER\([0-9]+\)/INTEGER\(-\)/g;
+	}
+
+	# Genericize standalone numbers in warnings
+	if($warning =~ /(\s|')-?[0-9]+(\s|')/) {
+	    $warning =~ s/-?[0-9]+/-/g;
+	}
+
+	# Genericize unusual GCC/G++/GFORTRAN warnings that aren't handled above
+	if($warning =~ /\[deprecation\] [A-Za-z_0-9]*\([A-Za-z_,0-9]*\) in [A-Za-z_0-9]* has been deprecated.*/) {
+	    $warning =~ s/[A-Za-z_0-9]*\([A-Za-z_,0-9]*\) in [A-Za-z_0-9]*/-\(-\) in -/g;
+	}
+    }
+# print "warning = $warning\n";
+# <end possible GCC-specific code>
+
+    # Check if we've already seen this warning on this line in this file
+    # (Can happen for warnings from inside header files)
+    if( !exists $warn_file_line{$warning}{$name}{$line} ) {
+	# Increment count for [generic] warning
+	$warn_count{$warning}++;
+	$warn_file{$warning}{$name}++;
+	$warn_file_line{$warning}{$name}{$line}++;
+
+	# Increment count for filename
+	$file_count{$name}++;
+	$file_warn{$name}{$warning}++;
+	$file_warn_line{$name}{$warning}{$line}++;
+
+	# Increment total count of warnings
+	$totalcount++;
+    }
+
+#    print "name = $name\n";
+#    print "line = $line\n";
+#    print "offset = $offset\n";
+#    print "warning = \"$warning\"\n";
+}
+
+print "Total unique [non-ignored] warnings: $totalcount\n";
+print "Total ignored warnings: $ignorecount\n";
+$warncount = keys %warn_count;
+print "Total unique kinds of warnings: $warncount\n";
+$filecount = keys %file_count;
+print "Total files with warnings: $filecount\n\n";
+
+# Print warnings in decreasing frequency
+print "# of Warnings by frequency (file count)\n";
+print "=======================================\n";
+for my $x (sort {$warn_count{$b} <=> $warn_count{$a}} keys(%warn_count)) {
+    printf ("[%2d] %4d (%2d) - %s\n", $current_warning++, $warn_count{$x}, scalar(keys %{$warn_file_line{$x}}), $x);
+    if((exists $options{W}) || (exists $options{w}) || (exists $options{s})) {
+        my $curr_index = $current_warning - 1;
+	my $match = 0;
+
+	# Check for string from list in current warning
+	if(exists $options{s}) {
+	    for my $y (@warn_match_strings) {
+# print "y = '$y'\n";
+		if($x =~ /$y/) {
+# print "matched warning = '$x'\n";
+		    $match = 1;
+		    last;
+		}
+	    }
+	}
+
+	# Check if current warning index matches
+        if((exists $warn_file_indices{$curr_index}) && $curr_index == $warn_file_indices{$curr_index}) {
+	    $match = 1;
+	}
+
+        if($match) {
+            for my $y (sort {$warn_file{$x}{$b} <=> $warn_file{$x}{$a}} keys(%{$warn_file{$x}})) {
+                printf ("\t%4d - %s\n", $warn_file{$x}{$y}, $y);
+                if(exists $options{l}) {
+		    my $lines = join ", ", sort {$a <=> $b} keys %{$warn_file_line{$x}{$y}};
+                    printf("\t\tLines: $lines \n");
+                }
+            }
+        }
+    }
+}
+
+# Print warnings in decreasing frequency, by filename
+print "\n# of Warnings by filename (warning type)\n";
+print   "========================================\n";
+for my $x (sort {$file_count{$b} <=> $file_count{$a}} keys(%file_count)) {
+    printf ("[%3d] %4d (%2d) - %s\n", $current_file++, $file_count{$x}, scalar(keys %{$file_warn_line{$x}}), $x);
+    if((exists $options{F}) || (exists $options{f}) || (exists $options{S})) {
+        my $curr_index = $current_file - 1;
+	my $match = 0;
+
+	# Check for string from list in current file
+	if(exists $options{S}) {
+	    for my $y (@file_match_strings) {
+# print "y = '$y'\n";
+		if($x =~ /$y/) {
+# print "matched warning = '$x'\n";
+		    $match = 1;
+		    last;
+		}
+	    }
+	}
+
+	# Check if current file index matches
+        if((exists $file_warn_indices{$curr_index}) && $curr_index == $file_warn_indices{$curr_index}) {
+	    $match = 1;
+	}
+
+        if($match) {
+            for my $y (sort {$file_warn{$x}{$b} <=> $file_warn{$x}{$a}} keys(%{$file_warn{$x}})) {
+                printf ("\t%4d - %s\n", $file_warn{$x}{$y}, $y);
+                if(exists $options{l}) {
+		    my $lines = join ", ", sort {$a <=> $b} keys %{$file_warn_line{$x}{$y}};
+                    printf("\t\tLines: $lines \n");
+                }
+            }
+        }
+    }
+}
+
+# Print names of files that were ignored
+# Check for ignored file
+if(exists $options{i}) {
+    print "\nIgnored filenames\n";
+    print   "=================\n";
+    for my $x (sort keys(%ignored_files)) {
+	print "$x\n";
+    }
+}
+