23 files changed, 1681 insertions, 109 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 $LSB_JOBID
+
+cd @HDF5_BINARY_DIR@
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ctestP.sl.in.cmake b/bin/batch/ctestP.sl.in.cmake
new file mode 100644
index 0000000..6399de7
--- /dev/null
+++ b/bin/batch/ctestP.sl.in.cmake
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestP
+
+cd @HDF5_BINARY_DIR@
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running ctestP.sl" 
+
diff --git a/bin/batch/ctestS.lsf.in.cmake b/bin/batch/ctestS.lsf.in.cmake
new file mode 100644
index 0000000..a01d39b
--- /dev/null
+++ b/bin/batch/ctestS.lsf.in.cmake
@@ -0,0 +1,18 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -nnodes 1                  #number of nodes
+#BSUB -W 29                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestSerrors.txt        #stderr
+#BSUB -o ctestSoutput.txt        #stdout
+#BSUB -J hdf5_ctestS             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+cd @HDF5_BINARY_DIR@
+echo "Run command. Test output will be in build/ctestS.out"
+ctest . -E MPI_TEST_ -C Release -j 32 -T test >& ctestS.out
+
+##$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 < $1
diff --git a/bin/checkposix b/bin/checkposix
index 821d78c..233d15c 100755
--- a/bin/checkposix
+++ b/bin/checkposix
@@ -14,101 +14,165 @@ use warnings;
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
-# Robb Matzke, matzke@llnl.gov
-# 30 Aug 1997
+# Dana Robinson
+# Spring 2019
+# (Original by Robb Matzke)
 #
-# Purpose: Given the names of C source files this script will print the
-#	   file name, line number, and function name of any function that
-#	   doesn't begin with the letter `h' or `H' as stipulated by the
-#	   HDF5 programming style guide.
+# Purpose:  Given the names of C source files this script will print the
+#           file name, line number, and function name of any function that
+#           doesn't begin with the letter 'h' or 'H' as stipulated by the
+#           HDF5 programming style guide.
 #
-#	   Emacs users can run this script as the compile command and
-#	   use `next-error' (usually bound to M-`) to find each name
-#	   violation.
-
-if(<>) {
-    if($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/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..9c4e3ca
--- /dev/null
+++ b/bin/h5cc.in
@@ -0,0 +1,399 @@
+#! /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]"
+  # 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 $EXIT_SUCCESS
diff --git a/bin/h5vers b/bin/h5vers
index a00beb7..4200141 100755
--- a/bin/h5vers
+++ b/bin/h5vers
@@ -377,7 +377,7 @@ if ($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, $data);
 }
@@ -394,7 +394,7 @@ if ($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 libversion\[\] = \{ .* \};/        int libversion\[\] = \{ $version_string1 \};/;
   $data =~ s/        int majnum = \d*, minnum = \d*, relnum = \d*;/        $version_string2;/;
 
   write_file($TESTH5_JAVA, $data);
@@ -405,7 +405,7 @@ if ($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);
 }
diff --git a/bin/make_vers b/bin/make_vers
index 8316393..c6d2c04 100755
--- a/bin/make_vers
+++ b/bin/make_vers
@@ -8,8 +8,8 @@ use warnings;
 #       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, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, etc)
-$max_idx = 6;
+# Max. library "index" (0 = v1.0, 1 = 1.2, 2 = 1.4, 3 = 1.6, 4 = 1.8, 5 = 1.10, 6 = 1.12, 7 = 1.14, etc)
+$max_idx = 7;
 
 # Min. supported previous library version "index" (0 = v1.0, 1 = 1.2, etc)
 $min_sup_idx = 3;
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 afdbb51..a9cf3f0 100755
--- a/bin/release
+++ b/bin/release
@@ -55,13 +55,21 @@ for compressing the resulting tar archive (if none are given then
 
     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. 
+    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.
@@ -225,7 +233,7 @@ tar2cmakezip()
     # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
     cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmziptmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmziptmpsubdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.8-Source.tar.gz $cmziptmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.0-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
@@ -256,7 +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
@@ -320,7 +328,7 @@ tar2cmaketgz()
     # step 3: add SZIP.tar.gz, ZLib.tar.gz and cmake files
     cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpsubdir
     cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
-    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.10.8-Source.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.0-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
@@ -330,6 +338,93 @@ tar2cmaketgz()
     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 SZIP.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
+#        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, SZIP.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$$
+    cmgztmpsubdir=$cmgztmpdir/HPC-CMake-$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 SZIP.tar.gz, ZLib.tar.gz and cmake files
+    cp /mnt/scr1/pre-release/hdf5/CMake/SZip.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/ZLib.tar.gz $cmgztmpsubdir
+    cp /mnt/scr1/pre-release/hdf5/CMake/HDF5Examples-1.14.0-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
+}
+
 # This command must be run at the top level of the hdf5 source directory.
 # Verify this requirement.
 if [ ! \( -f configure.ac -a -f bin/release \) ]; then
@@ -514,6 +609,11 @@ for comp in $methods; do
 	    tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
 	    (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file) 
             ;;
+        hpc-cmake-tgz)
+	    test "$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
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 f196b85..c1413b8 100755
--- a/bin/trace
+++ b/bin/trace
@@ -47,6 +47,7 @@ $Source = "";
                "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",
@@ -68,6 +69,7 @@ $Source = "";
                "unsigned"                   => "Iu",
                "unsigned int"               => "Iu",
                "uint32_t"                   => "Iu",
+               "uint64_t"                   => "UL",
                "H5I_type_t"                 => "It",
                "H5G_link_t"                 => "Ll", #Same as H5L_type_t now
                "H5L_type_t"                 => "Ll",
@@ -77,7 +79,9 @@ $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",
@@ -96,6 +100,24 @@ $Source = "";
                "H5T_str_t"                  => "Tz",
                "unsigned long"              => "Ul",
                "unsigned long long"         => "UL",
+               "H5VL_attr_get_t"            => "Va",
+               "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_datatype_get_t"        => "Ve",
+               "H5VL_datatype_specific_t"   => "Vf",
+               "H5VL_file_get_t"            => "Vg",
+               "H5VL_file_specific_t"       => "Vh",
+               "H5VL_group_get_t"           => "Vi",
+               "H5VL_group_specific_t"      => "Vj",
+               "H5VL_link_create_type_t"    => "Vk",
+               "H5VL_link_get_t"            => "Vl",
+               "H5VL_link_specific_t"       => "Vm",
+               "H5VL_object_get_t"          => "Vn",
+               "H5VL_object_specific_t"     => "Vo",
+               "H5VL_request_specific_t"    => "Vr",
                "void"                       => "x",
                "FILE"                       => "x",
                "H5A_operator_t"             => "x",
@@ -122,14 +144,18 @@ $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",
                "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",
+               "H5M_iterate_t"              => 'x',
                "H5MM_allocate_t"            => "x",
                "H5MM_free_t"                => "x",
                "H5O_info_t"                 => "x",
@@ -149,6 +175,10 @@ $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",
@@ -297,7 +327,7 @@ 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..7e56246
--- /dev/null
+++ b/bin/warnhist
@@ -0,0 +1,511 @@
+#!/usr/bin/perl -w
+require 5.003;
+
+#
+# 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 /\:/, $_;
+    }
+
+    # 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:'", $warning, "'\n";
+    } else {
+        # Check for 'character offset' field appended to file & line #
+	# (This is probably specific to GCC)
+        if($_ =~ /^.*[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;
+
+#
+# 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";
+    }
+}
+