[svn-r17865] Small bug fix: Added gfortran information to the list of the compilers used

for testing. Recreated release tar ball to reflect the change.

COPYING

@@ -4,18 +4,13 @@ HDF5 (Hierarchical Data Format 5) Software Library and Utilities
 -----------------------------------------------------------------------------
 
 HDF5 (Hierarchical Data Format 5) Software Library and Utilities
-Copyright 2006-2008 by The HDF Group (THG).
+Copyright 2006-2009 by The HDF Group.
 
 NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities
 Copyright 1998-2006 by the Board of Trustees of the University of Illinois.
 
 All rights reserved.
 
-Contributors:   National Center for Supercomputing Applications  (NCSA) at 
-the University of Illinois, Fortner Software, Unidata Program Center (netCDF), 
-The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), 
-and Digital Equipment Corporation (DEC).
-
 Redistribution and use in source and binary forms, with or without 
 modification, are permitted for any purpose (including commercial purposes) 
 provided that the following conditions are met:
@@ -39,17 +34,26 @@ provided that the following conditions are met:
 
 5. Neither the name of The HDF Group, the name of the University, nor the 
    name of any Contributor may be used to endorse or promote products derived 
-   from this software without specific prior written permission from the 
-   University, THG, or the Contributor, respectively.
+   from this software without specific prior written permission from 
+   The HDF Group, the University, or the Contributor, respectively.
 
 DISCLAIMER: 
-THIS SOFTWARE IS PROVIDED BY THE HDF GROUP (THG) AND THE CONTRIBUTORS 
+THIS SOFTWARE IS PROVIDED BY THE HDF GROUP AND THE CONTRIBUTORS 
 "AS IS" WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no 
-event shall THG or the Contributors be liable for any damages suffered by 
-the users arising out of the use of this software, even if advised of the 
-possibility of such damage. 
+event shall The HDF Group or the Contributors be liable for any damages 
+suffered by the users arising out of the use of this software, even if 
+advised of the possibility of such damage. 
 
 -----------------------------------------------------------------------------
+-----------------------------------------------------------------------------
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at 
+the University of Illinois, Fortner Software, Unidata Program Center (netCDF), 
+The Independent JPEG Group (JPEG), Jean-loup Gailly and Mark Adler (gzip), 
+and Digital Equipment Corporation (DEC).
+
+-----------------------------------------------------------------------------
+
 Portions of HDF5 were developed with support from the University of 
 California, Lawrence Livermore National Laboratory (UC LLNL).  
 The following statement applies to those portions of the product and must 

Makefile.am

@@ -73,12 +73,15 @@ else
 endif
 
 SUBDIRS = src test $(TESTPARALLEL_DIR) tools . $(CXX_DIR) $(FORTRAN_DIR) \
-          $(HDF5_HL_DIR)
+          $(HDF5_HL_DIR) perform
 DIST_SUBDIRS = src test testpar tools . c++ fortran hl perform examples
 
 # Some files generated during configure that should be cleaned
 DISTCLEANFILES=config/stamp1 config/stamp2
 
+# Some files/directories generated during check that should be cleaned
+CHECK_CLEANFILES+=*-tmp
+
 # Define rules for lib, progs, check, and tests.
 # These simply involve recursing into subdirectories.
 test _test: check
@@ -113,6 +116,7 @@ check-clean:
 	   (cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;            \
 	  fi;                                                           \
 	done
+	$(RM) -rf prefix-tmp destdir-tmp
 
 # Some C++ compilers/linkers will create a directory named ii_files in
 # the root directory, which should be cleaned.
@@ -150,6 +154,23 @@ installcheck-local:
 # check-install is just a synonym for installcheck
 check-install: installcheck
 
+# check-all-install tests all installation methods.
+# Install via different mechanism and then compare against the default.
+# Fine if only libXXX.a files are different since they may have been ranlib'ed.
+check-all-install:
+	@echo Installing to default location
+	$(MAKE) install
+	@echo Installing to different prefix location
+	$(MAKE) prefix=${ROOT}/prefix-tmp install
+	@echo Compare against the default installation.
+	@echo Fine if only libXXX.a files are different.
+	-diff -r prefix-tmp ${prefix}
+	@echo Installing to different $$\DESTDIR location
+	env DESTDIR=${ROOT}/destdir-tmp $(MAKE) install
+	@echo Compare against the default installation.
+	@echo Fine if only libXXX.a files are different.
+	-diff -r destdir-tmp${prefix} ${prefix}
+
 # Only source files in the src directory include tracing information,
 # so 'make trace' only needs to recurse into that directory.
 trace:

Makefile.in

@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006  Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -48,8 +49,9 @@
 
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
 install_sh_DATA = $(install_sh) -c -m 644
 install_sh_PROGRAM = $(install_sh) -c
@@ -79,6 +81,7 @@ am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
 CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
 SOURCES =
 DIST_SOURCES =
 RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
@@ -90,15 +93,43 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
 	ps-recursive uninstall-recursive
 RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
   distclean-recursive maintainer-clean-recursive
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+	distdir dist dist-all distcheck
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 top_distdir = $(distdir)
 am__remove_distdir = \
-  { test ! -d $(distdir) \
-    || { find $(distdir) -type d ! -perm -200 -exec chmod u+w {} ';' \
-         && rm -fr $(distdir); }; }
+  { test ! -d "$(distdir)" \
+    || { find "$(distdir)" -type d ! -perm -200 -exec chmod u+w {} ';' \
+         && rm -fr "$(distdir)"; }; }
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
 DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
 distuninstallcheck_listfiles = find . -type f -print
@@ -106,6 +137,16 @@ distcleancheck_listfiles = find . -type f -print
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -119,46 +160,47 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
+CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
+DIRECT_VFD = @DIRECT_VFD@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
 DYNAMIC_DIRS = @DYNAMIC_DIRS@
-ECHO = @ECHO@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
 EXEEXT = @EXEEXT@
-F77 = @F77@
+EXTERNAL_FILTERS = @EXTERNAL_FILTERS@
 
 # Make sure that these variables are exported to the Makefiles
 F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FGREP = @FGREP@
 FILTERS = @FILTERS@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+GPFS = @GPFS@
 GREP = @GREP@
 H5_CFLAGS = @H5_CFLAGS@
 H5_CPPFLAGS = @H5_CPPFLAGS@
@@ -167,11 +209,14 @@ H5_FCFLAGS = @H5_FCFLAGS@
 H5_LONE_COLON = @H5_LONE_COLON@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
+HAVE_DMALLOC = @HAVE_DMALLOC@
+HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
+HDF_CXX = @HDF_CXX@
+HDF_FORTRAN = @HDF_FORTRAN@
 HID_T = @HID_T@
 HL = @HL@
 HL_FOR = @HL_FOR@
-HSIZET = @HSIZET@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
 INSTALL = @INSTALL@
@@ -179,11 +224,16 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+INSTRUMENT = @INSTRUMENT@
 INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@
+LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
+LINUX_LFS = @LINUX_LFS@
+LIPO = @LIPO@
+LL_PATH = @LL_PATH@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 LT_STATIC_EXEC = @LT_STATIC_EXEC@
@@ -192,13 +242,19 @@ MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 MPI_GET_SIZE = @MPI_GET_SIZE@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
 OBJECT_NAMELEN_DEFAULT_F = @OBJECT_NAMELEN_DEFAULT_F@
 OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PARALLEL = @PARALLEL@
 PATH_SEPARATOR = @PATH_SEPARATOR@
@@ -211,22 +267,21 @@ RUNSERIAL = @RUNSERIAL@
 R_INTEGER = @R_INTEGER@
 R_LARGE = @R_LARGE@
 SEARCH = @SEARCH@
+SED = @SED@
 SETX = @SETX@
 SET_MAKE = @SET_MAKE@
-
-# Hardcode SHELL to be /bin/sh.  Most machines have this shell, and
-# on at least one machine configure fails to detect its existence (janus).
-# Also, when HDF5 is configured on one machine but run on another,
-# configure's automatic SHELL detection may not work on the build machine.
-SHELL = /bin/sh
+SHELL = @SHELL@
 SIZE_T = @SIZE_T@
+STATIC_EXEC = @STATIC_EXEC@
 STATIC_SHARED = @STATIC_SHARED@
 STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@
 STRIP = @STRIP@
 TESTPARALLEL = @TESTPARALLEL@
+THREADSAFE = @THREADSAFE@
 TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
+UNAME_INFO = @UNAME_INFO@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_FLETCHER32 = @USE_FILTER_FLETCHER32@
 USE_FILTER_NBIT = @USE_FILTER_NBIT@
@@ -235,13 +290,14 @@ USE_FILTER_SHUFFLE = @USE_FILTER_SHUFFLE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
 VERSION = @VERSION@
+WORDS_BIGENDIAN = @WORDS_BIGENDIAN@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_CXX = @ac_ct_CXX@
-ac_ct_F77 = @ac_ct_F77@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 ac_ct_FC = @ac_ct_FC@
 am__include = @am__include@
 am__leading_dot = @am__leading_dot@
@@ -257,8 +313,12 @@ build_vendor = @build_vendor@
 builddir = @builddir@
 datadir = @datadir@
 datarootdir = @datarootdir@
+
+# Install directories that automake doesn't know about
 docdir = $(exec_prefix)/doc
 dvidir = @dvidir@
+enable_shared = @enable_shared@
+enable_static = @enable_static@
 exec_prefix = @exec_prefix@
 host = @host@
 host_alias = @host_alias@
@@ -266,15 +326,14 @@ host_cpu = @host_cpu@
 host_os = @host_os@
 host_vendor = @host_vendor@
 htmldir = @htmldir@
-
-# Install directories that automake doesn't know about
-includedir = $(exec_prefix)/include
+includedir = @includedir@
 infodir = @infodir@
 install_sh = @install_sh@
 libdir = @libdir@
 libexecdir = @libexecdir@
 localedir = @localedir@
 localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
 mandir = @mandir@
 mkdir_p = @mkdir_p@
 oldincludedir = @oldincludedir@
@@ -287,6 +346,7 @@ sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 
@@ -330,7 +390,9 @@ TRACE = perl $(top_srcdir)/bin/trace
 # .chkexe files are used to mark tests that have run successfully.
 # .chklog files are output from those tests.
 # *.clog are from the MPE option.
-CHECK_CLEANFILES = *.chkexe *.chklog *.clog
+
+# Some files/directories generated during check that should be cleaned
+CHECK_CLEANFILES = *.chkexe *.chklog *.clog *-tmp
 @BUILD_PARALLEL_CONDITIONAL_FALSE@TESTPARALLEL_DIR = 
 
 # Define subdirectories to build.
@@ -351,7 +413,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog
 @BUILD_HDF5_HL_CONDITIONAL_FALSE@HDF5_HL_DIR = 
 @BUILD_HDF5_HL_CONDITIONAL_TRUE@HDF5_HL_DIR = hl
 SUBDIRS = src test $(TESTPARALLEL_DIR) tools . $(CXX_DIR) $(FORTRAN_DIR) \
-          $(HDF5_HL_DIR)
+          $(HDF5_HL_DIR) perform
 
 DIST_SUBDIRS = src test testpar tools . c++ fortran hl perform examples
 
@@ -366,15 +428,15 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
-	      echo ' cd $(srcdir) && $(AUTOMAKE) --foreign '; \
-	      cd $(srcdir) && $(AUTOMAKE) --foreign  \
+	      echo ' cd $(srcdir) && $(AUTOMAKE) --foreign'; \
+	      $(am__cd) $(srcdir) && $(AUTOMAKE) --foreign \
 		&& exit 0; \
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  Makefile'; \
-	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign  Makefile
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
@@ -387,9 +449,10 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	esac;
 
 $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
-	cd $(srcdir) && $(AUTOCONF)
+	$(am__cd) $(srcdir) && $(AUTOCONF)
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
-	cd $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
+	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
+$(am__aclocal_m4_deps):
 
 mostlyclean-libtool:
 	-rm -f *.lo
@@ -398,7 +461,7 @@ clean-libtool:
 	-rm -rf .libs _libs
 
 distclean-libtool:
-	-rm -f libtool
+	-rm -f libtool config.lt
 
 # This directory's subdirectories are mostly independent; you can cd
 # into them and run `make' without going through this Makefile.
@@ -424,7 +487,7 @@ $(RECURSIVE_TARGETS):
 	  else \
 	    local_target="$$target"; \
 	  fi; \
-	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
 	  || eval $$failcom; \
 	done; \
 	if test "$$dot_seen" = "no"; then \
@@ -458,16 +521,16 @@ $(RECURSIVE_CLEAN_TARGETS):
 	  else \
 	    local_target="$$target"; \
 	  fi; \
-	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
 	  || eval $$failcom; \
 	done && test -z "$$fail"
 tags-recursive:
 	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
 	done
 ctags-recursive:
 	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
 	done
 
 ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
@@ -475,14 +538,14 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
 	mkid -fID $$unique
 tags: TAGS
 
 TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
+	set x; \
 	here=`pwd`; \
 	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
 	  include_option=--etags-include; \
@@ -494,46 +557,50 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 	list='$(SUBDIRS)'; for subdir in $$list; do \
 	  if test "$$subdir" = .; then :; else \
 	    test ! -f $$subdir/TAGS || \
-	      tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
 	  fi; \
 	done; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
 	  test -n "$$unique" || unique=$$empty_fix; \
-	  $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	    $$tags $$unique; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
 	fi
 ctags: CTAGS
 CTAGS: ctags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
-	here=`pwd`; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	test -z "$(CTAGS_ARGS)$$tags$$unique" \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
 	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$tags $$unique
+	     $$unique
 
 GTAGS:
 	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && cd $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) $$here
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
 
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
 
 distdir: $(DISTFILES)
 	$(am__remove_distdir)
-	test -d $(distdir) || mkdir $(distdir)
+	test -d "$(distdir)" || mkdir "$(distdir)"
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
 	list='$(DISTFILES)'; \
@@ -549,38 +616,54 @@ distdir: $(DISTFILES)
 	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
 	  if test -d $$d/$$file; then \
 	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
 	    fi; \
-	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
 	  else \
-	    test -f $(distdir)/$$file \
-	    || cp -p $$d/$$file $(distdir)/$$file \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
 	    || exit 1; \
 	  fi; \
 	done
-	list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
 	  if test "$$subdir" = .; then :; else \
 	    test -d "$(distdir)/$$subdir" \
 	    || $(MKDIR_P) "$(distdir)/$$subdir" \
 	    || exit 1; \
-	    distdir=`$(am__cd) $(distdir) && pwd`; \
-	    top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
-	    (cd $$subdir && \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
 	      $(MAKE) $(AM_MAKEFLAGS) \
-	        top_distdir="$$top_distdir" \
-	        distdir="$$distdir/$$subdir" \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
 		am__remove_distdir=: \
 		am__skip_length_check=: \
+		am__skip_mode_fix=: \
 	        distdir) \
 	      || exit 1; \
 	  fi; \
 	done
-	-find $(distdir) -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
+	-test -n "$(am__skip_mode_fix)" \
+	|| find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \
 	  ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -400 -exec chmod a+r {} \; -o \
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
-	|| chmod -R a+r $(distdir)
+	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
 	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
 	$(am__remove_distdir)
@@ -589,6 +672,14 @@ dist-bzip2: distdir
 	tardir=$(distdir) && $(am__tar) | bzip2 -9 -c >$(distdir).tar.bz2
 	$(am__remove_distdir)
 
+dist-lzma: distdir
+	tardir=$(distdir) && $(am__tar) | lzma -9 -c >$(distdir).tar.lzma
+	$(am__remove_distdir)
+
+dist-xz: distdir
+	tardir=$(distdir) && $(am__tar) | xz -c >$(distdir).tar.xz
+	$(am__remove_distdir)
+
 dist-tarZ: distdir
 	tardir=$(distdir) && $(am__tar) | compress -c >$(distdir).tar.Z
 	$(am__remove_distdir)
@@ -615,6 +706,10 @@ distcheck: dist
 	  GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\
+	*.tar.lzma*) \
+	  unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\
+	*.tar.xz*) \
+	  xz -dc $(distdir).tar.xz | $(am__untar) ;;\
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
@@ -626,9 +721,11 @@ distcheck: dist
 	mkdir $(distdir)/_build
 	mkdir $(distdir)/_inst
 	chmod a-w $(distdir)
+	test -d $(distdir)/_build || exit 0; \
 	dc_install_base=`$(am__cd) $(distdir)/_inst && pwd | sed -e 's,^[^:\\/]:[\\/],/,'` \
 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
-	  && cd $(distdir)/_build \
+	  && am__cwd=`pwd` \
+	  && $(am__cd) $(distdir)/_build \
 	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
 	    $(DISTCHECK_CONFIGURE_FLAGS) \
 	  && $(MAKE) $(AM_MAKEFLAGS) \
@@ -650,13 +747,15 @@ distcheck: dist
 	  && rm -rf "$$dc_destdir" \
 	  && $(MAKE) $(AM_MAKEFLAGS) dist \
 	  && rm -rf $(DIST_ARCHIVES) \
-	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck
+	  && $(MAKE) $(AM_MAKEFLAGS) distcleancheck \
+	  && cd "$$am__cwd" \
+	  || exit 1
 	$(am__remove_distdir)
 	@(echo "$(distdir) archives ready for distribution: "; \
 	  list='$(DIST_ARCHIVES)'; for i in $$list; do echo $$i; done) | \
 	  sed -e 1h -e 1s/./=/g -e 1p -e 1x -e '$$p' -e '$$x'
 distuninstallcheck:
-	@cd $(distuninstallcheck_dir) \
+	@$(am__cd) '$(distuninstallcheck_dir)' \
 	&& test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
 	   || { echo "ERROR: files left after uninstall:" ; \
 	        if test -n "$(DESTDIR)"; then \
@@ -698,6 +797,7 @@ clean-generic:
 
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
 	-test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
 
 maintainer-clean-generic:
@@ -719,6 +819,8 @@ dvi-am:
 
 html: html-recursive
 
+html-am:
+
 info: info-recursive
 
 info-am:
@@ -727,18 +829,28 @@ install-data-am:
 
 install-dvi: install-dvi-recursive
 
+install-dvi-am:
+
 install-exec-am: install-exec-local
 
 install-html: install-html-recursive
 
+install-html-am:
+
 install-info: install-info-recursive
 
+install-info-am:
+
 install-man:
 
 install-pdf: install-pdf-recursive
 
+install-pdf-am:
+
 install-ps: install-ps-recursive
 
+install-ps-am:
+
 installcheck-am: installcheck-local
 
 maintainer-clean: maintainer-clean-recursive
@@ -762,22 +874,22 @@ ps-am:
 
 uninstall-am: uninstall-local
 
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
-	install-strip
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) ctags-recursive \
+	install-am install-strip tags-recursive
 
 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
 	all all-am all-local am--refresh check check-am clean \
 	clean-generic clean-libtool ctags ctags-recursive dist \
-	dist-all dist-bzip2 dist-gzip dist-shar dist-tarZ dist-zip \
-	distcheck distclean distclean-generic distclean-libtool \
-	distclean-tags distcleancheck distdir distuninstallcheck dvi \
-	dvi-am html html-am info info-am install install-am \
-	install-data install-data-am install-dvi install-dvi-am \
-	install-exec install-exec-am install-exec-local install-html \
-	install-html-am install-info install-info-am install-man \
-	install-pdf install-pdf-am install-ps install-ps-am \
-	install-strip installcheck installcheck-am installcheck-local \
-	installdirs installdirs-am maintainer-clean \
+	dist-all dist-bzip2 dist-gzip dist-lzma dist-shar dist-tarZ \
+	dist-xz dist-zip distcheck distclean distclean-generic \
+	distclean-libtool distclean-tags distcleancheck distdir \
+	distuninstallcheck dvi dvi-am html html-am info info-am \
+	install install-am install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am install-exec-local \
+	install-html install-html-am install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installcheck-local installdirs installdirs-am maintainer-clean \
 	maintainer-clean-generic mostlyclean mostlyclean-generic \
 	mostlyclean-libtool mostlyclean-local pdf pdf-am ps ps-am tags \
 	tags-recursive uninstall uninstall-am uninstall-local
@@ -828,6 +940,7 @@ check-clean:
 	   (cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;            \
 	  fi;                                                           \
 	done
+	$(RM) -rf prefix-tmp destdir-tmp
 
 # Some C++ compilers/linkers will create a directory named ii_files in
 # the root directory, which should be cleaned.
@@ -865,6 +978,23 @@ installcheck-local:
 # check-install is just a synonym for installcheck
 check-install: installcheck
 
+# check-all-install tests all installation methods.
+# Install via different mechanism and then compare against the default.
+# Fine if only libXXX.a files are different since they may have been ranlib'ed.
+check-all-install:
+	@echo Installing to default location
+	$(MAKE) install
+	@echo Installing to different prefix location
+	$(MAKE) prefix=${ROOT}/prefix-tmp install
+	@echo Compare against the default installation.
+	@echo Fine if only libXXX.a files are different.
+	-diff -r prefix-tmp ${prefix}
+	@echo Installing to different $$\DESTDIR location
+	env DESTDIR=${ROOT}/destdir-tmp $(MAKE) install
+	@echo Compare against the default installation.
+	@echo Fine if only libXXX.a files are different.
+	-diff -r destdir-tmp${prefix} ${prefix}
+
 # Only source files in the src directory include tracing information,
 # so 'make trace' only needs to recurse into that directory.
 trace:
@@ -890,6 +1020,7 @@ $(top_builddir)/config.status:
 
 # Don't include conclude.am in root Makefile; tests target needs to
 # recurse into perform directory as well as reguar subdirs.
+
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:

README.txt

@@ -1,39 +1,40 @@
-HDF5 version 1.8.0 currently under development
+HDF5 version 1.8.4 released on Tue Nov 10 15:18:57 CST 2009
 Please refer to the release_docs/INSTALL file for installation instructions.
 ------------------------------------------------------------------------------
 
-This release is almost fully functional for the entire API defined in the
-documentation, see the RELEASE.txt file in the release_docs directory for information
-specific to this release of the library.  The INSTALL file contains
-instructions on compiling and installing the library.  The INSTALL_parallel
-file contains instructions on installing the parallel version of the
-library.  The INSTALL* files can be found in the release_docs/ directory.
+This release is fully functional for the API described in the documentation. 
+See the RELEASE.txt file in the release_docs/ directory for information 
+specific to this release of the library.  Several INSTALL* files can also be 
+found in the release_docs/ directory:  INSTALL contains instructions for 
+compiling and installing the library;  INSTALL_parallel contains instructions 
+for installing the parallel version of the library;  similarly-named files
+contain instructions for VMS and several environments on MS Windows systems. 
 
 Documentation for this release can be found at the following URL:
-http://www.hdfgroup.uiuc.edu/HDF5/release/beta/obtain518.html
+    http://www.hdfgroup.org/HDF5/doc/.
 
-Four mailing lists are currently set up for use with the HDF5
-library.
+The following  mailing lists are currently set up for HDF5 Library users:
 
-   news         - For announcements of HDF5 related developments,
-		  not a discussion list.
+    news        - For announcements of HDF5 related developments,
+                  not a discussion list.
 
-   hdf-forum    - For general discussion of the HDF5 library with
-		  other users.
+    hdf-forum   - For general discussion of the HDF5 library with
+                  other users.
 
-   hdf5dev      - For discussion of the HDF5 library development
-		  with developers and other interested parties.
+    hdf5dev     - For discussion of the HDF5 library development
+                  with developers and other interested parties.
 
 To subscribe to a list, send mail to "<list>-subscribe@hdfgroup.org".
-where <list> is the name of the list.
-E.g., mail hdf5-subscribe@hdfgroup.org
+where <list> is the name of the list.  For example, send a request 
+to subscribe to the 'news' mail list to the following address:
+    news-subscribe@hdfgroup.org
 
-Messages to be sent to the list should be sent to "<list>@hdfgroup.org".
+Messages sent to the list should be addressed to "<list>@hdfgroup.org".
 
 Periodic code snapshots are provided at the following URL:
     ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots
-Please read the README.txt file in that directory before working with a library
-snapshot.
+Please read the README.txt file in that directory before working with a 
+library snapshot.
 
 The HDF5 website is located at http://hdfgroup.org/HDF5/
 

bin/COPYING

@@ -1,5 +1,5 @@
 
-  Copyright by  The HDF Group (THG) and 
+  Copyright by  The HDF Group and 
                 The Board of Trustees of the University of Illinois. 
   All rights reserved. 
 

bin/chkconfigure

@@ -23,7 +23,7 @@
 
 # variable initialization
 nerrors=0
-AUTOCONFVERSION=2.61
+AUTOCONFVERSION=2.64
 AUTOCONFVERSIONLEAD='Generated by GNU Autoconf'
 CONFIGUREFILES="configure"
 

bin/chkmanifest

@@ -107,6 +107,21 @@ else
     fi
 fi
 
+# Check for duplicate entries.  This can be done at any time, but it may as 
+# well be sooner so that if something else fails the presence of duplicates
+# will already be known.
+errcode=0
+DUPLICATES=`perl -ne 's/#.*//; next if /^\s*$/; if ($uniq{$_}++) { print $_; }' MANIFEST`
+if [ "$DUPLICATES" ]; then
+   cat 1>&2 <<EOF
+These entries appear more than once in the MANIFEST:  
+$DUPLICATES
+Please remove the duplicate lines and try again.
+
+EOF
+errcode=1 
+fi
+
 # Copy the manifest file to get a list of file names.
 grep '^\.' MANIFEST | expand | cut -f1 -d' ' >$MANIFEST
 
@@ -117,6 +132,7 @@ for file in `cat $MANIFEST`; do
     fi
 done
 
+
 # Inspect the .svn/entries to figure out what version of svn file entry is
 # used.
 # The following algorithm is formed via reverse engineering.
@@ -130,7 +146,7 @@ if head -1 $svn_entry_file | grep 'xml version="1.0"' > /dev/null 2>&1;then
 elif grep '^file$' $svn_entry_file > /dev/null 2>&1; then
     getsvnentries=GETSVNENTRIES_14
 else
-    echo "Unknow svn entries format. Aborted"
+    echo "Unknown svn entries format. Aborted"
     exit 1
 fi
 
@@ -155,5 +171,9 @@ EOF
     exit 1
 fi
 
+if [ $errcode -ne 0 ]; then
+    exit 1
+fi 
+
 test "$verbose" && echo "   The MANIFEST is up to date." 1>&2
 exit 0

bin/gcov_script

@@ -17,36 +17,37 @@
 # Configures, builds, and runs tests in-place; the output files will be placed
 # in a directory called gcov_logs.
 # Must be invoked from the root hdf5 directory.
-# This script has only been tested on heping.
+# This script has been tested on kagiso.
 
 CFLAGS="$CFLAGS -ftest-coverage -fprofile-arcs"
 export CFLAGS
-./configure --enable-debug=all
+LDFLAGS="$LDFLAGS -lgcov"
+export LDFLAGS
+CC=gcc
+export CC
+./configure
 make
 make check
 mkdir gcov_logs
 cd src
-for j in *.c
+for j in *.h *.c
+  do
+  ln -s ../$j .libs/$j
+  done 
+cd .libs
+for j in *.gcda
   do
   gcov -b $j >> gcov.log 2>&1
   done
 for j in *.gcov
+   do
+   mv $j ../../gcov_logs
+   done
+mv gcov.log ../../gcov_logs
+for j in *.c *.h
   do
-  mv $j ../gcov_logs
+  rm $j
   done
-mv gcov.log ../gcov_logs
-cd ..
-
-
-
-
-
-
-
-
-
-
-
-
+cd ../..
 
 

bin/h5vers

@@ -73,6 +73,8 @@ use strict;
 # something like: This is hdf5-1.2.3-pre1 currently under development.
 # The AC_INIT macro in configure.in will also change in this case to be
 # something like: AC_INIT([HDF5], [hdf5-1.2.3-pre1], [help@hdfgroup.org])
+# Version changes are also reflected in the Windows-maintained H5pubconf.h
+# file.
 #
 # Whenever the version changes, this script will increment the revision
 # field in HDF5's libtool shared library version in config/lt_vers.am,
@@ -157,9 +159,11 @@ while ($_ = shift) {
 die "mutually exclusive options given\n" if $set && $inc;
 
 # Determine file to use as H5public.h, README.txt,
-# release_docs/RELEASE.txt, configure.in, and config/lt_vers.am. The
-# README.txt, release_docs/RELEASE.txt, configure.in, and
-# config/lt_vers.am files are always in the directory above H5public.h
+# release_docs/RELEASE.txt, configure.in, windows/src/H5pubconf.h,
+# vms/src/h5pubconf.h and config/lt_vers.am. 
+# The README.txt, release_docs/RELEASE.txt, configure.in, 
+# vms/src/h5pubconf.h, windows/src/H5pubconf.h, and config/lt_vers.am 
+# files are always in the directory above H5public.h
 unless ($file) {
   for (@files) {
     ($file=$_,last) if -f $_;
@@ -183,6 +187,14 @@ die "unable to read file: $RELEASE\n" unless -r $file;
 my $CONFIGURE = $file;
 $CONFIGURE =~ s/[^\/]*$/..\/configure.in/;
 die "unable to read file: $CONFIGURE\n" unless -r $file;
+# windows/src/H5pubconf.h
+my $H5PUBCONF = $file;
+$H5PUBCONF =~ s/[^\/]*$/..\/windows\/src\/H5pubconf.h/;
+die "unable to read file: $H5PUBCONF\n" unless -r $file;
+# vms/src/h5pubconf.h
+my $H5VMSPUBCONF = $file;
+$H5VMSPUBCONF =~ s/[^\/]*$/..\/vms\/src\/h5pubconf.h/;
+die "unable to read file: $H5VMSPUBCONF\n" unless -r $file;
 
 # Get the current version number.
 open FILE, $file or die "unable to open $file: $!\n";
@@ -230,6 +242,8 @@ if ($set) {
   $README = "";
   $RELEASE = "";
   $CONFIGURE = "";
+  $H5PUBCONF = "";
+  $H5VMSPUBCONF = "";
   $LT_VERS = "";
   @newver = @curver;
 }
@@ -341,6 +355,49 @@ sub gen_configure {
 # Update the configure.in files and regenerate them
 gen_configure("HDF5", $CONFIGURE) if $CONFIGURE;
 
+sub gen_h5pubconf {
+    my ($name, $pubconf, @vers) = @_;
+
+    my $namelc = lc($name);
+    my $nameuc = uc($name);
+
+    open FILE, $pubconf or die "$pubconf: $!\n";
+    my @contents = <FILE>;
+    close FILE;
+
+    for (my $i = 0; $i < $#contents; ++$i) {
+	if ($contents[$i] =~ /\#\s*define\s+H5_PACKAGE\s+/) {
+	    $contents[$i] = "\#define H5_PACKAGE \"$namelc\"\n";
+	} elsif ($contents[$i] =~ /\#\s*define\s+H5_PACKAGE_NAME\s+/) {
+	    $contents[$i] = "\#define H5_PACKAGE_NAME \"$nameuc\"\n";
+	} elsif ($contents[$i] =~ /\#\s*define\s+H5_PACKAGE_STRING\s+/) {
+	    $contents[$i] = sprintf("\#define H5_PACKAGE_STRING \"$nameuc %d.%d.%d%s\"\n",
+				    @vers[0,1,2],
+				    $newver[3] eq "" ? "" : "-".$newver[3]);
+	} elsif ($contents[$i] =~ /\#\s*define\s+H5_PACKAGE_TARNAME\s+/) {
+	    $contents[$i] = "\#define H5_PACKAGE_TARNAME \"$namelc\"\n";
+	} elsif ($contents[$i] =~ /\#\s*define\s+H5_PACKAGE_VERSION\s+/) {
+	    $contents[$i] = sprintf("\#define H5_PACKAGE_VERSION \"%d.%d.%d%s\"\n",
+				    @vers[0,1,2],
+				    $newver[3] eq "" ? "" : "-".$newver[3]);
+	} elsif ($contents[$i] =~ /\#\s*define\s+H5_VERSION\s+/) {
+	    $contents[$i] = sprintf("\#define H5_VERSION \"%d.%d.%d%s\"\n",
+				    @vers[0,1,2],
+				    $newver[3] eq "" ? "" : "-".$newver[3]);
+	}
+    }
+
+    open FILE, ">$pubconf" or die "$pubconf: $!\n";
+    print FILE @contents;
+    close FILE;
+}
+
+# Update the Windows-maintained H5pubconf.h file
+gen_h5pubconf("HDF5", $H5PUBCONF, @newver) if $H5PUBCONF;
+    
+# Update the VMS-maintained h5pubconf.h file
+gen_h5pubconf("HDF5", $H5VMSPUBCONF, @newver) if $H5VMSPUBCONF;
+    
 # Print the new version number
 if ($verbose) {
   printf("version %d.%d release %d%s\n", @newver[0,1,2],

bin/install-sh

@@ -1,251 +1,520 @@
 #!/bin/sh
-#
 # install - install a program, script, or datafile
-# This comes from X11R5 (mit/util/scripts/install.sh).
+
+scriptversion=2009-04-28.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
 #
-# Copyright 1991 by the Massachusetts Institute of Technology
+# Copyright (C) 1994 X Consortium
 #
-# Permission to use, copy, modify, distribute, and sell this software and its
-# documentation for any purpose is hereby granted without fee, provided that
-# the above copyright notice appear in all copies and that both that
-# copyright notice and this permission notice appear in supporting
-# documentation, and that the name of M.I.T. not be used in advertising or
-# publicity pertaining to distribution of the software without specific,
-# written prior permission.  M.I.T. makes no representations about the
-# suitability of this software for any purpose.  It is provided "as is"
-# without express or implied warranty.
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
 #
 # Calling this script install-sh is preferred over install.sh, to prevent
 # `make' implicit rules from creating a file called install from it
 # when there is no Makefile.
 #
 # This script is compatible with the BSD install script, but was written
-# from scratch.  It can only install one file at a time, a restriction
-# shared with many OS's install programs.
+# from scratch.
 
+nl='
+'
+IFS=" ""	$nl"
 
 # set DOITPROG to echo to test this script
 
 # Don't use :- since 4.3BSD and earlier shells don't like it.
-doit="${DOITPROG-}"
+doit=${DOITPROG-}
+if test -z "$doit"; then
+  doit_exec=exec
+else
+  doit_exec=$doit
+fi
 
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
 
-# put in absolute paths if you don't have them in your path; or use env. vars.
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
 
-mvprog="${MVPROG-mv}"
-cpprog="${CPPROG-cp}"
-chmodprog="${CHMODPROG-chmod}"
-chownprog="${CHOWNPROG-chown}"
-chgrpprog="${CHGRPPROG-chgrp}"
-stripprog="${STRIPPROG-strip}"
-rmprog="${RMPROG-rm}"
-mkdirprog="${MKDIRPROG-mkdir}"
+posix_glob='?'
+initialize_posix_glob='
+  test "$posix_glob" != "?" || {
+    if (set -f) 2>/dev/null; then
+      posix_glob=
+    else
+      posix_glob=:
+    fi
+  }
+'
 
-transformbasename=""
-transform_arg=""
-instcmd="$mvprog"
-chmodcmd="$chmodprog 0755"
-chowncmd=""
-chgrpcmd=""
-stripcmd=""
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
 rmcmd="$rmprog -f"
-mvcmd="$mvprog"
-src=""
-dst=""
-dir_arg=""
+stripcmd=
 
-while [ x"$1" != x ]; do
-    case $1 in
-	-c) instcmd="$cpprog"
-	    shift
-	    continue;;
+src=
+dst=
+dir_arg=
+dst_arg=
 
-	-d) dir_arg=true
-	    shift
-	    continue;;
+copy_on_change=false
+no_target_directory=
 
-	-m) chmodcmd="$chmodprog $2"
-	    shift
-	    shift
-	    continue;;
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+   or: $0 [OPTION]... SRCFILES... DIRECTORY
+   or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+   or: $0 [OPTION]... -d DIRECTORIES...
 
-	-o) chowncmd="$chownprog $2"
-	    shift
-	    shift
-	    continue;;
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
 
-	-g) chgrpcmd="$chgrpprog $2"
-	    shift
-	    shift
-	    continue;;
+Options:
+     --help     display this help and exit.
+     --version  display version info and exit.
 
-	-s) stripcmd="$stripprog"
-	    shift
-	    continue;;
+  -c            (ignored)
+  -C            install only if different (preserve the last data modification time)
+  -d            create directories instead of installing files.
+  -g GROUP      $chgrpprog installed files to GROUP.
+  -m MODE       $chmodprog installed files to MODE.
+  -o USER       $chownprog installed files to USER.
+  -s            $stripprog installed files.
+  -t DIRECTORY  install into DIRECTORY.
+  -T            report an error if DSTFILE is a directory.
 
-	-t=*) transformarg=`echo $1 | sed 's/-t=//'`
-	    shift
-	    continue;;
+Environment variables override the default commands:
+  CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+  RMPROG STRIPPROG
+"
 
-	-b=*) transformbasename=`echo $1 | sed 's/-b=//'`
-	    shift
-	    continue;;
+while test $# -ne 0; do
+  case $1 in
+    -c) ;;
 
-	*)  if [ x"$src" = x ]
-	    then
-		src=$1
-	    else
-		# this colon is to work around a 386BSD /bin/sh bug
-		:
-		dst=$1
-	    fi
-	    shift
-	    continue;;
+    -C) copy_on_change=true;;
+
+    -d) dir_arg=true;;
+
+    -g) chgrpcmd="$chgrpprog $2"
+	shift;;
+
+    --help) echo "$usage"; exit $?;;
+
+    -m) mode=$2
+	case $mode in
+	  *' '* | *'	'* | *'
+'*	  | *'*'* | *'?'* | *'['*)
+	    echo "$0: invalid mode: $mode" >&2
+	    exit 1;;
+	esac
+	shift;;
+
+    -o) chowncmd="$chownprog $2"
+	shift;;
+
+    -s) stripcmd=$stripprog;;
+
+    -t) dst_arg=$2
+	shift;;
+
+    -T) no_target_directory=true;;
+
+    --version) echo "$0 $scriptversion"; exit $?;;
+
+    --)	shift
+	break;;
+
+    -*)	echo "$0: invalid option: $1" >&2
+	exit 1;;
+
+    *)  break;;
+  esac
+  shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+  # When -d is used, all remaining arguments are directories to create.
+  # When -t is used, the destination is already specified.
+  # Otherwise, the last argument is the destination.  Remove it from $@.
+  for arg
+  do
+    if test -n "$dst_arg"; then
+      # $@ is not empty: it contains at least $arg.
+      set fnord "$@" "$dst_arg"
+      shift # fnord
+    fi
+    shift # arg
+    dst_arg=$arg
+  done
+fi
+
+if test $# -eq 0; then
+  if test -z "$dir_arg"; then
+    echo "$0: no input file specified." >&2
+    exit 1
+  fi
+  # It's OK to call `install-sh -d' without argument.
+  # This can happen when creating conditional directories.
+  exit 0
+fi
+
+if test -z "$dir_arg"; then
+  trap '(exit $?); exit' 1 2 13 15
+
+  # Set umask so as not to create temps with too-generous modes.
+  # However, 'strip' requires both read and write access to temps.
+  case $mode in
+    # Optimize common cases.
+    *644) cp_umask=133;;
+    *755) cp_umask=22;;
+
+    *[0-7])
+      if test -z "$stripcmd"; then
+	u_plus_rw=
+      else
+	u_plus_rw='% 200'
+      fi
+      cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+    *)
+      if test -z "$stripcmd"; then
+	u_plus_rw=
+      else
+	u_plus_rw=,u+rw
+      fi
+      cp_umask=$mode$u_plus_rw;;
+  esac
+fi
+
+for src
+do
+  # Protect names starting with `-'.
+  case $src in
+    -*) src=./$src;;
+  esac
+
+  if test -n "$dir_arg"; then
+    dst=$src
+    dstdir=$dst
+    test -d "$dstdir"
+    dstdir_status=$?
+  else
+
+    # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+    # might cause directories to be created, which would be especially bad
+    # if $src (and thus $dsttmp) contains '*'.
+    if test ! -f "$src" && test ! -d "$src"; then
+      echo "$0: $src does not exist." >&2
+      exit 1
+    fi
+
+    if test -z "$dst_arg"; then
+      echo "$0: no destination specified." >&2
+      exit 1
+    fi
+
+    dst=$dst_arg
+    # Protect names starting with `-'.
+    case $dst in
+      -*) dst=./$dst;;
     esac
-done
 
-if [ x"$src" = x ]
-then
-	echo "install:	no input file specified"
+    # If destination is a directory, append the input filename; won't work
+    # if double slashes aren't ignored.
+    if test -d "$dst"; then
+      if test -n "$no_target_directory"; then
+	echo "$0: $dst_arg: Is a directory" >&2
 	exit 1
-else
-	true
-fi
+      fi
+      dstdir=$dst
+      dst=$dstdir/`basename "$src"`
+      dstdir_status=0
+    else
+      # Prefer dirname, but fall back on a substitute if dirname fails.
+      dstdir=`
+	(dirname "$dst") 2>/dev/null ||
+	expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+	     X"$dst" : 'X\(//\)[^/]' \| \
+	     X"$dst" : 'X\(//\)$' \| \
+	     X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+	echo X"$dst" |
+	    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\/\)[^/].*/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\/\)$/{
+		   s//\1/
+		   q
+		 }
+		 /^X\(\/\).*/{
+		   s//\1/
+		   q
+		 }
+		 s/.*/./; q'
+      `
 
-if [ x"$dir_arg" != x ]; then
-	dst=$src
-	src=""
-	
-	if [ -d $dst ]; then
-		instcmd=:
-		chmodcmd=""
-	else
-		instcmd=$mkdirprog
-	fi
-else
+      test -d "$dstdir"
+      dstdir_status=$?
+    fi
+  fi
 
-# Waiting for this to be detected by the "$instcmd $src $dsttmp" command
-# might cause directories to be created, which would be especially bad 
-# if $src (and thus $dsttmp) contains '*'.
+  obsolete_mkdir_used=false
 
-	if [ -f $src -o -d $src ]
-	then
-		true
+  if test $dstdir_status != 0; then
+    case $posix_mkdir in
+      '')
+	# Create intermediate dirs using mode 755 as modified by the umask.
+	# This is like FreeBSD 'install' as of 1997-10-28.
+	umask=`umask`
+	case $stripcmd.$umask in
+	  # Optimize common cases.
+	  *[2367][2367]) mkdir_umask=$umask;;
+	  .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+	  *[0-7])
+	    mkdir_umask=`expr $umask + 22 \
+	      - $umask % 100 % 40 + $umask % 20 \
+	      - $umask % 10 % 4 + $umask % 2
+	    `;;
+	  *) mkdir_umask=$umask,go-w;;
+	esac
+
+	# With -d, create the new directory with the user-specified mode.
+	# Otherwise, rely on $mkdir_umask.
+	if test -n "$dir_arg"; then
+	  mkdir_mode=-m$mode
 	else
-		echo "install:  $src does not exist"
-		exit 1
-	fi
-	
-	if [ x"$dst" = x ]
-	then
-		echo "install:	no destination specified"
-		exit 1
-	else
-		true
+	  mkdir_mode=
 	fi
 
-# If destination is a directory, append the input filename; if your system
-# does not like double slashes in filenames, you may need to add some logic
+	posix_mkdir=false
+	case $umask in
+	  *[123567][0-7][0-7])
+	    # POSIX mkdir -p sets u+wx bits regardless of umask, which
+	    # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+	    ;;
+	  *)
+	    tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+	    trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
 
-	if [ -d $dst ]
-	then
-		dst="$dst"/`basename $src`
+	    if (umask $mkdir_umask &&
+		exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+	    then
+	      if test -z "$dir_arg" || {
+		   # Check for POSIX incompatibilities with -m.
+		   # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+		   # other-writeable bit of parent directory when it shouldn't.
+		   # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+		   ls_ld_tmpdir=`ls -ld "$tmpdir"`
+		   case $ls_ld_tmpdir in
+		     d????-?r-*) different_mode=700;;
+		     d????-?--*) different_mode=755;;
+		     *) false;;
+		   esac &&
+		   $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+		     ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+		     test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+		   }
+		 }
+	      then posix_mkdir=:
+	      fi
+	      rmdir "$tmpdir/d" "$tmpdir"
+	    else
+	      # Remove any dirs left behind by ancient mkdir implementations.
+	      rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+	    fi
+	    trap '' 0;;
+	esac;;
+    esac
+
+    if
+      $posix_mkdir && (
+	umask $mkdir_umask &&
+	$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+      )
+    then :
+    else
+
+      # The umask is ridiculous, or mkdir does not conform to POSIX,
+      # or it failed possibly due to a race condition.  Create the
+      # directory the slow way, step by step, checking for races as we go.
+
+      case $dstdir in
+	/*) prefix='/';;
+	-*) prefix='./';;
+	*)  prefix='';;
+      esac
+
+      eval "$initialize_posix_glob"
+
+      oIFS=$IFS
+      IFS=/
+      $posix_glob set -f
+      set fnord $dstdir
+      shift
+      $posix_glob set +f
+      IFS=$oIFS
+
+      prefixes=
+
+      for d
+      do
+	test -z "$d" && continue
+
+	prefix=$prefix$d
+	if test -d "$prefix"; then
+	  prefixes=
 	else
-		true
+	  if $posix_mkdir; then
+	    (umask=$mkdir_umask &&
+	     $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+	    # Don't fail if two instances are running concurrently.
+	    test -d "$prefix" || exit 1
+	  else
+	    case $prefix in
+	      *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+	      *) qprefix=$prefix;;
+	    esac
+	    prefixes="$prefixes '$qprefix'"
+	  fi
 	fi
-fi
+	prefix=$prefix/
+      done
 
-## this sed command emulates the dirname command
-dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
+      if test -n "$prefixes"; then
+	# Don't fail if two instances are running concurrently.
+	(umask $mkdir_umask &&
+	 eval "\$doit_exec \$mkdirprog $prefixes") ||
+	  test -d "$dstdir" || exit 1
+	obsolete_mkdir_used=true
+      fi
+    fi
+  fi
 
-# Make sure that the destination directory exists.
-#  this part is taken from Noah Friedman's mkinstalldirs script
+  if test -n "$dir_arg"; then
+    { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+    { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+      test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+  else
 
-# Skip lots of stat calls in the usual case.
-if [ ! -d "$dstdir" ]; then
-defaultIFS='
-	'
-IFS="${IFS-${defaultIFS}}"
+    # Make a couple of temp file names in the proper directory.
+    dsttmp=$dstdir/_inst.$$_
+    rmtmp=$dstdir/_rm.$$_
 
-oIFS="${IFS}"
-# Some sh's can't handle IFS=/ for some reason.
-IFS='%'
-set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'`
-IFS="${oIFS}"
+    # Trap to clean up those temp files at exit.
+    trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
 
-pathcomp=''
+    # Copy the file name to the temp name.
+    (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
 
-while [ $# -ne 0 ] ; do
-	pathcomp="${pathcomp}${1}"
-	shift
+    # and set any options; do chmod last to preserve setuid bits.
+    #
+    # If any of these fail, we abort the whole thing.  If we want to
+    # ignore errors from any of these, just make sure not to ignore
+    # errors from the above "$doit $cpprog $src $dsttmp" command.
+    #
+    { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+    { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+    { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+    { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
 
-	if [ ! -d "${pathcomp}" ] ;
-        then
-		$mkdirprog "${pathcomp}"
-	else
-		true
-	fi
+    # If -C, don't bother to copy if it wouldn't change the file.
+    if $copy_on_change &&
+       old=`LC_ALL=C ls -dlL "$dst"	2>/dev/null` &&
+       new=`LC_ALL=C ls -dlL "$dsttmp"	2>/dev/null` &&
 
-	pathcomp="${pathcomp}/"
+       eval "$initialize_posix_glob" &&
+       $posix_glob set -f &&
+       set X $old && old=:$2:$4:$5:$6 &&
+       set X $new && new=:$2:$4:$5:$6 &&
+       $posix_glob set +f &&
+
+       test "$old" = "$new" &&
+       $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+    then
+      rm -f "$dsttmp"
+    else
+      # Rename the file to the real destination.
+      $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+      # The rename failed, perhaps because mv can't rename something else
+      # to itself, or perhaps because mv is so ancient that it does not
+      # support -f.
+      {
+	# Now remove or move aside any old file at destination location.
+	# We try this two ways since rm can't unlink itself on some
+	# systems and the destination file might be busy for other
+	# reasons.  In this case, the final cleanup might fail but the new
+	# file should still install successfully.
+	{
+	  test ! -f "$dst" ||
+	  $doit $rmcmd -f "$dst" 2>/dev/null ||
+	  { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+	    { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+	  } ||
+	  { echo "$0: cannot unlink or rename $dst" >&2
+	    (exit 1); exit 1
+	  }
+	} &&
+
+	# Now rename the file to the real destination.
+	$doit $mvcmd "$dsttmp" "$dst"
+      }
+    fi || exit 1
+
+    trap '' 0
+  fi
 done
-fi
 
-if [ x"$dir_arg" != x ]
-then
-	$doit $instcmd $dst &&
-
-	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi &&
-	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi &&
-	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi &&
-	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi
-else
-
-# If we're going to rename the final executable, determine the name now.
-
-	if [ x"$transformarg" = x ] 
-	then
-		dstfile=`basename $dst`
-	else
-		dstfile=`basename $dst $transformbasename | 
-			sed $transformarg`$transformbasename
-	fi
-
-# don't allow the sed command to completely eliminate the filename
-
-	if [ x"$dstfile" = x ] 
-	then
-		dstfile=`basename $dst`
-	else
-		true
-	fi
-
-# Make a temp file name in the proper directory.
-
-	dsttmp=$dstdir/#inst.$$#
-
-# Move or copy the file name to the temp name
-
-	$doit $instcmd $src $dsttmp &&
-
-	trap "rm -f ${dsttmp}" 0 &&
-
-# and set any options; do chmod last to preserve setuid bits
-
-# If any of these fail, we abort the whole thing.  If we want to
-# ignore errors from any of these, just make sure not to ignore
-# errors from the above "$doit $instcmd $src $dsttmp" command.
-
-	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi &&
-	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi &&
-	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi &&
-	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi &&
-
-# Now rename the file to the real destination.
-
-	$doit $rmcmd -f $dstdir/$dstfile &&
-	$doit $mvcmd $dsttmp $dstdir/$dstfile 
-
-fi &&
-
-
-exit 0
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

bin/make_err

@@ -239,7 +239,7 @@ sub create_init ($) {
         print HEADER " "x(0*$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(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, \"error message initialization failed\")\n";
-        print HEADER " "x(0*$indent),"if((${name}_g = H5I_register(H5I_ERROR_MSG, msg))<0)\n";
+        print HEADER " "x(0*$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";
     }
 
@@ -255,7 +255,7 @@ sub create_init ($) {
             print HEADER " "x(0*$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(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, \"error message initialization failed\")\n";
-            print HEADER " "x(0*$indent),"if((${name}_g = H5I_register(H5I_ERROR_MSG, msg))<0)\n";
+            print HEADER " "x(0*$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";
         }
     }

bin/make_overflow

@@ -0,0 +1,219 @@
+#!/usr/bin/perl -w
+require 5.003;
+use strict;
+
+# Global settings
+
+# List of supported C types to generate overflow assignment code for
+my @ctypes = ( () );
+
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+#
+
+# Create assignment overflow #ifdefs
+#
+# Programmer: Quincey Koziol
+# Creation Date: 2009/04/09
+
+##############################################################################
+# Parse a meaningful line (not a comment or blank line) into the appropriate
+# data structure
+#
+sub parse_line ($) {
+    my $line = shift;   # Get the line to parse
+
+    # Parse get the type name and whether it's signed or unsigned
+#print "line=$line\n";
+    if($line =~ /.*SIGNED\s*;\s*$/ || $line =~ /.*UNSIGNED\s*;\s*$/) {
+        my $name;           # The name of the type
+        my $signed;         # Whether the type is signed or not
+
+        # Get the type's name & signed status
+        ($name, $signed) = ($line =~ /^\s*(\w*)\s*,\s*(\w*)\s*;\s*$/);
+#print "name = '$name', signed = '$signed'\n";
+
+        # Append the type to the list of C types already parsed
+        push @ctypes, [$name, $signed];
+
+    }
+    # Unknown keyword
+    else {
+        die "unknown keyword: $line";
+    }
+}
+
+##############################################################################
+# Print the copyright into an open file
+#
+sub print_copyright ($) {
+    my $fh = shift;
+
+    print $fh "/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\n";
+    print $fh " * Copyright by The HDF Group.                                               *\n";
+    print $fh " * Copyright by the Board of Trustees of the University of Illinois.         *\n";
+    print $fh " * All rights reserved.                                                      *\n";
+    print $fh " *                                                                           *\n";
+    print $fh " * This file is part of HDF5.  The full HDF5 copyright notice, including     *\n";
+    print $fh " * terms governing use, modification, and redistribution, is contained in    *\n";
+    print $fh " * the files COPYING and Copyright.html.  COPYING can be found at the root   *\n";
+    print $fh " * of the source code distribution tree; Copyright.html can be found at the  *\n";
+    print $fh " * root level of an installed copy of the electronic HDF5 document set and   *\n";
+    print $fh " * is linked from the top-level documents page.  It can also be found at     *\n";
+    print $fh " * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *\n";
+    print $fh " * access to either file, you may request a copy from help\@hdfgroup.org.     *\n";
+    print $fh " * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */\n";
+}
+
+##############################################################################
+# Print the "do not change this file" warning
+#
+sub print_warning ($) {
+    my $fh = shift;
+
+    print $fh "\n/* Generated automatically by bin/make_overflow -- do not edit */\n";
+    print $fh "/* Add new types to H5overflow.txt file */\n\n";
+}
+
+##############################################################################
+# Print start of ifdef's to prevent a file from being re-included
+#
+sub print_startprotect ($$) {
+    my ($fh, $file) = @_;
+
+    # Clip off the ".h" part of the name
+    $file =~ s/(\w*)\.h/$1/;
+
+    # Print the ifdef info
+    print $fh "\n#ifndef _${file}_H\n";
+    print $fh "#define _${file}_H\n";
+}
+
+##############################################################################
+# Print assignment overflow macros for each type
+#
+sub print_typemacros ($) {
+    my $fh = shift;             # File handle for output file
+    my ($src_aref, $dst_aref);  # References for each type's information
+
+    # Print the descriptive comment
+    print $fh "\n\n/* Each type in this file is tested for assignment to the other types,\n";
+    print $fh " *      and range checks are defined for bad assignments at run-time.\n";
+    print $fh " */\n";
+
+    for $src_aref (@ctypes) {
+        # Print a descriptive comment
+        print $fh "\n/* Assignment checks for @$src_aref[0] */\n\n";
+
+        for $dst_aref (@ctypes) {
+            if (@$src_aref[0] ne @$dst_aref[0]) {
+                # Print a descriptive comment
+                print $fh "/* src: @$src_aref[0], dst: @$dst_aref[0] */\n";
+
+                # Print actual type size checks & macro definitions
+                print $fh "#if H5_SIZEOF_", uc @$src_aref[0], " < H5_SIZEOF_", uc @$dst_aref[0], "\n";
+                print $fh "    #define ASSIGN_", @$src_aref[0], "_TO_", @$dst_aref[0], "(dst, dsttype, src, srctype) \\\n";
+                if ( @$src_aref[1] eq @$dst_aref[1]) {
+                    print $fh "        ASSIGN_TO_LARGER_SIZE_SAME_SIGNED(dst, dsttype, src, srctype)\n";
+                } elsif ( @$src_aref[1] eq "SIGNED") {
+                    print $fh "        ASSIGN_TO_LARGER_SIZE_SIGNED_TO_UNSIGNED(dst, dsttype, src, srctype)\n";
+                } else {
+                    print $fh "        ASSIGN_TO_LARGER_SIZE_UNSIGNED_TO_SIGNED(dst, dsttype, src, srctype)\n";
+                }
+                print $fh "#elif H5_SIZEOF_", uc @$src_aref[0], " > H5_SIZEOF_", uc @$dst_aref[0], "\n";
+                print $fh "    #define ASSIGN_", @$src_aref[0], "_TO_", @$dst_aref[0], "(dst, dsttype, src, srctype) \\\n";
+                print $fh "        ASSIGN_TO_SMALLER_SIZE(dst, dsttype, src, srctype)\n";
+                print $fh "#else /* H5_SIZEOF_", uc @$src_aref[0], " == H5_SIZEOF_", uc @$dst_aref[0], " */\n";
+                print $fh "    #define ASSIGN_", @$src_aref[0], "_TO_", @$dst_aref[0], "(dst, dsttype, src, srctype) \\\n";
+                if ( @$src_aref[1] eq @$dst_aref[1]) {
+                    print $fh "        ASSIGN_TO_SAME_SIZE_SAME_SIGNED(dst, dsttype, src, srctype)\n";
+                } elsif ( @$src_aref[1] eq "SIGNED") {
+                    print $fh "        ASSIGN_TO_SAME_SIZE_SIGNED_TO_UNSIGNED(dst, dsttype, src, srctype)\n";
+                } else {
+                    print $fh "        ASSIGN_TO_SAME_SIZE_UNSIGNED_TO_SIGNED(dst, dsttype, src, srctype)\n";
+                }
+                print $fh "#endif /* src: @$src_aref[0] dst: @$dst_aref[0] */\n\n";
+            }
+        }
+    }
+
+}
+
+##############################################################################
+# Print end of ifdef's to prevent a file from being re-included
+#
+sub print_endprotect ($$) {
+    my ($fh, $file) = @_;
+
+    # Clip off the ".h" part of the name
+    $file =~ s/(\w*)\.h/$1/;
+
+    # Print the endif info
+    print $fh "#endif /* ${file}_H */\n\n";
+}
+
+##############################################################################
+# Create the generated portion of the public header file
+#
+sub create_public ($) {
+    my $prefix = shift;         # Get the prefix for the generated file
+    my $file = "H5overflow.h";   # Name of file to generate
+    my $name;                   # Name of function
+
+    # Rename previous file
+#    rename "${prefix}${file}", "${prefix}${file}~" or die "unable to make backup";
+
+    # Open new header file
+    open HEADER, ">${prefix}${file}" or die "unable to modify source";
+
+    # Create file contents
+    print_copyright(*HEADER);
+    print_warning(*HEADER);
+    print_startprotect(*HEADER, $file);
+    print_typemacros(*HEADER);
+    print_endprotect(*HEADER, $file);
+
+    # Close header file
+    close HEADER;
+}
+
+##############################################################################
+# Read symbol version file (given as command-line argument) in and process it
+# into internal data structures, then create header files.
+#
+my $file;       # Filename of input file
+
+for $file (@ARGV) {
+    my $prefix;         # Local prefix for generated files
+    my $line;           # Line from input file
+
+#print "file = '$file'\n";
+    ($prefix) = ($file =~ /(^.*\/)/);
+#print "prefix = '$prefix'\n";
+    # Read in the entire file
+    open SOURCE, $file or die "$file: $!\n";
+    while ( defined ($line=<SOURCE>) ) {
+        # Skip blank lines and those lines whose first character is a '#'
+        if(!($line =~ /(^\s*#.*$)|(^\s*$)/)) {
+            # Construct data structures for later printing
+            parse_line($line);
+        }
+    }
+    close SOURCE;
+  
+    # Create header files
+    print "Generating 'H5overflow.h'\n";
+    create_public($prefix);
+}
+

bin/make_vers

@@ -106,6 +106,15 @@ sub print_globalapivers ($) {
     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 API version definition
+        print $fh "#define H5_USE_1", ($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";
+    }
+
     # Loop over supported older library APIs and define the appropriate macros
     for $curr_idx ($min_sup_idx .. ($max_idx - 1)) {
         # Print API version ifdef

bin/reconfigure

@@ -28,11 +28,11 @@
 # of versions that can get confused (not even counting the m4 utility)!
 
 # HDF5 currently uses the following versions of the autotools:
-AUTOCONF_VERSION="autoconf (GNU Autoconf) 2.61"
-AUTOMAKE_VERSION="automake (GNU automake) 1.10"
-AUTOHEADER_VERSION="autoheader (GNU Autoconf) 2.61"
-ACLOCAL_VERSION="aclocal (GNU automake) 1.10"
-LIBTOOL_VERSION="(GNU libtool) 1.5.22"
+AUTOCONF_VERSION="autoconf (GNU Autoconf) 2.64"
+AUTOMAKE_VERSION="automake (GNU automake) 1.11"
+AUTOHEADER_VERSION="autoheader (GNU Autoconf) 2.64"
+ACLOCAL_VERSION="aclocal (GNU automake) 1.11"
+LIBTOOL_VERSION="(GNU libtool) 2.2.6"
 #
 # When upgrading automake's version, don't forget to also update its
 # helper utilities, especially depcomp.
@@ -41,19 +41,19 @@ LIBTOOL_VERSION="(GNU libtool) 1.5.22"
 # If paths to autotools are not specified by the user, assume tools are
 # running on kagiso and set paths accordingly.
 if test -z ${AUTOCONF}; then
-  AUTOCONF=/home1/packages/autoconf/autoconf-2.61/bin/autoconf
+  AUTOCONF=/mnt/hdf/packages/autoconf/autoconf-2.64/bin/autoconf
 fi
 if test -z ${AUTOMAKE}; then
-  AUTOMAKE=/home1/packages/automake/automake-1.10.0/bin/automake-1.10
+  AUTOMAKE=/mnt/hdf/packages/automake/automake-1.11/bin/automake-1.11
 fi
 if test -z ${AUTOHEADER}; then
-  AUTOHEADER=/home1/packages/autoconf/autoconf-2.61/bin/autoheader
+  AUTOHEADER=/mnt/hdf/packages/autoconf/autoconf-2.64/bin/autoheader
 fi
 if test -z ${ACLOCAL}; then
-  ACLOCAL=/home1/packages/automake/automake-1.10.0/bin/aclocal-1.10
+  ACLOCAL=/mnt/hdf/packages/automake/automake-1.11/bin/aclocal-1.11
 fi
 if test -z ${LIBTOOL}; then
-  LIBTOOL=/home1/packages/libtool/libtool-1.5.22/bin/libtool
+  LIBTOOL=/mnt/hdf/packages/libtool/libtool-2.2.6a/bin/libtool
 fi
 
 # Check version numbers of all autotools against the "correct" versions
@@ -84,7 +84,7 @@ if test -z "${LT_VERS}"; then
 fi
 
 # Use the latest version of M4
-PATH=/home1/packages/m4/m4-1.4.7/bin:/home1/packages/m4/m4-1.4.7/share:$PATH
+PATH=/mnt/hdf/packages/m4/m4-1.4.7/bin:/mnt/hdf/packages/m4/m4-1.4.7/share:$PATH
 
 # Make sure that the tools are in the path.
 AUTOCONF_DIR=`dirname ${AUTOCONF}`

bin/release

@@ -14,42 +14,10 @@
 # access to either file, you may request a copy from help@hdfgroup.org.
 #
 
-# Make a release of hdf5.  The command-line switches are:
+# Make a release of hdf5.
 #
-#  -d DIR	The name of the directory where the releas(es) should be
-#               placed.  By default, the directory is ./releases
-#
-#  --nocheck	Ignore errors in MANIFEST file.
-#          
-#  --private	Make a private release with today's date in version information.
-#          
-# 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 md5' is assumed):
-#
-#   tar		-- use tar and don't do any compressing.
-#   compress	-- use compress and append `.Z' to the output name.
-#   gzip	-- use gzip with `-9' and append `.gz' to the output name.
-#   bzip2       -- use bzip2 with `-9' and append `.bz2' to the output name.
-#   md5         -- produce a md5 checksum in addition to the archive.
-#   doc         -- produce the latest doc tree in addition to the archive.
-#
-# Examples:
-#
-#   $ release
-#   releases/hdf5-1.0.38.tar
-#   releases/hdf5-1.0.38.tar.md5
-#
-#   $ release gzip
-#   releases/hdf5-1.0.38.tar.gz
-#
-#   $ release -d /tmp tar compress gzip bzip2 md5 doc
-#   /tmp/hdf5-1.0.38.tar
-#   /tmp/hdf5-1.0.38.tar.Z
-#   /tmp/hdf5-1.0.38.tar.gz
-#   /tmp/hdf5-1.0.38.tar.bz2
-#   /tmp/hdf5-1.0.38.tar.md5
-#   /tmp/hdf5-1.0.38_doc.tar
+# Programmer: Robb Matzke
+# Creation date: on or before 1998-01-29.
 #
 # Modifications
 #   Robb Matzke, 1999-07-16
@@ -59,6 +27,12 @@
 #   Albert Cheng, 1999-10-26
 #   Moved the MANIFEST checking to a separate command file so that
 #   it can be invoked individually.
+#
+#   Albert Cheng, 2004-08-14
+#   Added the --private option.
+#
+#   James Laird, 2005-09-07
+#   Added the md5 method.
 
 # Function definitions
 #
@@ -70,6 +44,10 @@ Usage: $0 [--nocheck] [-d <dir>] [-h] <methods> ...
    -d DIR	The name of the directory where the releas(es) should be
                 placed.  By default, the directory is ./releases
 
+   --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.
+
    --nocheck	Ignore errors in MANIFEST file.
          
    --private	Make a private release with today's date in version information.
@@ -157,6 +135,10 @@ while [ -n "$1" ]; do
 	--private)
 	    pmode=yes
 	    ;;
+        --docver)
+            DOCVERSION=$1
+            shift
+            ;;
 	-*)
 	    echo "Unknown switch: $arg" 1>&2
 	    USAGE
@@ -222,18 +204,25 @@ grep '^\.' MANIFEST | grep -v _DO_NOT_DISTRIBUTE_ >$MANIFEST
 
 # Prepare the source tree for a release.
 ln -s `pwd` $tmpdir/$HDF5_VERS || exit 1
-mv Makefile $tmpdir/Makefile.x 2>/dev/null #might fail
+# Save a backup copy of Makefile if exists.
+test -f Makefile && mv Makefile $tmpdir/Makefile.x
 cp -p Makefile.dist Makefile
 
-# Update README.txt and release_docs/RELEASE.txt with release information.
+# Update README.txt and release_docs/RELEASE.txt with release information in
+# line 1.
 for f in README.txt release_docs/RELEASE.txt; do
     echo "HDF5 version $VERS released on `date`" >$f.x
-    tail +2l $f >>$f.x
+    sed -e 1d $f >>$f.x
     mv $f.x $f
     # Make sure new files are of the right access mode
     chmod 644 $f
 done
 
+# trunk is different than branches.
+if [ "${DOCVERSION}" ]; then
+    DOC_URL=http://svn.hdfgroup.uiuc.edu/hdf5doc/branches/${DOCVERSION}
+fi
+
 # Create the tar file
 test "$verbose" && echo "   Running tar..." 1>&2
 ( \
@@ -265,16 +254,19 @@ for comp in $methods; do
 	    (cd $tmpdir; md5sum $HDF5_VERS.tar ) > $DEST/$HDF5_VERS.tar.md5
 	    ;;
 	doc)
+            if [ "${DOCVERSION}" = "" ]; then
+                DOCVERSION=trunk
+            fi
 	    test "$verbose" && echo "   Creating docs..." 1>&2
 	    # Check out docs from svn repo
 	    (cd $tmpdir; svn co $DOC_URL > /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 $tmpdir/trunk/html/$CPPLUS_RM_NAME
-	    mv c++/src/$CPPLUS_RM_NAME $tmpdir/trunk/html/$CPPLUS_RM_NAME
-	    # Compress the docs and move them to the release area
-	    mv $tmpdir/trunk $tmpdir/${HDF5_VERS}_docs
+            rm -rf $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME
+            mv c++/src/$CPPLUS_RM_NAME $tmpdir/${DOCVERSION}/html/$CPPLUS_RM_NAME
+            # Compress the docs and move them to the release area
+            mv $tmpdir/$DOCVERSION $tmpdir/${HDF5_VERS}_docs
 	    (cd $tmpdir && tar cf ${HDF5_VERS}_docs.tar ${HDF5_VERS}_docs)
 	    mv $tmpdir/${HDF5_VERS}_docs.tar $DEST
 	    ;;
@@ -284,7 +276,8 @@ done
 # Copy the RELEASE.txt to the release area.
 cp release_docs/RELEASE.txt $DEST/$HDF5_VERS-RELEASE.txt
 
-# Restore previous Makefile if existed.
+# Remove distributed Makefile and restore previous Makefile if existed.
+rm -f Makefile
 test -f $tmpdir/Makefile.x && mv $tmpdir/Makefile.x Makefile
 
 # Restore OLD version information, then no need for trap.

bin/snapshot

@@ -412,7 +412,7 @@ if [ "$cmd" = "all" -o -n "$cmdtest" -o -n "$cmddiff" ]; then
 	    TIMESTAMP "check-install" && \
 	    ${MAKE} check-install && DISKUSAGE \
 	    TIMESTAMP "uninstall" && \
-	    ${MAKE} uninstall-all) && DISKUSAGE ; then
+	    ${MAKE} uninstall-all && DISKUSAGE); then
 	    :
 	else
 	    errcode=$?

bin/snapshot_version

@@ -18,4 +18,6 @@
 # latest revision of that branch.  If set to "hdf5", it uses the main
 # version.
 # H5VER tells runtest which version to run
-H5VERSION=hdf5
+H5VERSION=hdf5_1_8
+H5VER="-r1.8"
+

bin/trace

@@ -104,7 +104,9 @@ $Source = "";
                "H5FD_stream_fapl_t"         => "x",
                "H5G_iterate_t"              => "x",
 	       "H5G_info_t"                 => "x",
+	       "H5I_free_t"                 => "x",
                "H5L_class_t"                => "x",
+               "H5L_elink_traverse_t"       => "x",
                "H5L_iterate_t"              => "x",
                "H5MM_allocate_t"            => "x",
                "H5MM_free_t"                => "x",

c++/COPYING

@@ -1,5 +1,5 @@
 
-  Copyright by  The HDF Group (THG) and 
+  Copyright by  The HDF Group and 
                 The Board of Trustees of the University of Illinois. 
   All rights reserved. 
 

c++/Makefile.in

@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006  Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -32,8 +33,9 @@
 # 
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
 install_sh_DATA = $(install_sh) -c -m 644
 install_sh_PROGRAM = $(install_sh) -c
@@ -60,6 +62,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
 CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
 SOURCES =
 DIST_SOURCES =
 RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
@@ -71,12 +74,52 @@ RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
 	ps-recursive uninstall-recursive
 RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
   distclean-recursive maintainer-clean-recursive
+AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \
+	$(RECURSIVE_CLEAN_TARGETS:-recursive=) tags TAGS ctags CTAGS \
+	distdir
 ETAGS = etags
 CTAGS = ctags
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -90,46 +133,47 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
+CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
+DIRECT_VFD = @DIRECT_VFD@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
 DYNAMIC_DIRS = @DYNAMIC_DIRS@
-ECHO = @ECHO@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
 EXEEXT = @EXEEXT@
-F77 = @F77@
+EXTERNAL_FILTERS = @EXTERNAL_FILTERS@
 
 # Make sure that these variables are exported to the Makefiles
 F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FGREP = @FGREP@
 FILTERS = @FILTERS@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+GPFS = @GPFS@
 GREP = @GREP@
 H5_CFLAGS = @H5_CFLAGS@
 H5_CPPFLAGS = @H5_CPPFLAGS@
@@ -138,11 +182,14 @@ H5_FCFLAGS = @H5_FCFLAGS@
 H5_LONE_COLON = @H5_LONE_COLON@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
+HAVE_DMALLOC = @HAVE_DMALLOC@
+HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
+HDF_CXX = @HDF_CXX@
+HDF_FORTRAN = @HDF_FORTRAN@
 HID_T = @HID_T@
 HL = @HL@
 HL_FOR = @HL_FOR@
-HSIZET = @HSIZET@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
 INSTALL = @INSTALL@
@@ -150,11 +197,16 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+INSTRUMENT = @INSTRUMENT@
 INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@
+LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
+LINUX_LFS = @LINUX_LFS@
+LIPO = @LIPO@
+LL_PATH = @LL_PATH@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 LT_STATIC_EXEC = @LT_STATIC_EXEC@
@@ -163,13 +215,19 @@ MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 MPI_GET_SIZE = @MPI_GET_SIZE@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
 OBJECT_NAMELEN_DEFAULT_F = @OBJECT_NAMELEN_DEFAULT_F@
 OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PARALLEL = @PARALLEL@
 PATH_SEPARATOR = @PATH_SEPARATOR@
@@ -182,22 +240,21 @@ RUNSERIAL = @RUNSERIAL@
 R_INTEGER = @R_INTEGER@
 R_LARGE = @R_LARGE@
 SEARCH = @SEARCH@
+SED = @SED@
 SETX = @SETX@
 SET_MAKE = @SET_MAKE@
-
-# Hardcode SHELL to be /bin/sh.  Most machines have this shell, and
-# on at least one machine configure fails to detect its existence (janus).
-# Also, when HDF5 is configured on one machine but run on another,
-# configure's automatic SHELL detection may not work on the build machine.
-SHELL = /bin/sh
+SHELL = @SHELL@
 SIZE_T = @SIZE_T@
+STATIC_EXEC = @STATIC_EXEC@
 STATIC_SHARED = @STATIC_SHARED@
 STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@
 STRIP = @STRIP@
 TESTPARALLEL = @TESTPARALLEL@
+THREADSAFE = @THREADSAFE@
 TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
+UNAME_INFO = @UNAME_INFO@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_FLETCHER32 = @USE_FILTER_FLETCHER32@
 USE_FILTER_NBIT = @USE_FILTER_NBIT@
@@ -206,13 +263,14 @@ USE_FILTER_SHUFFLE = @USE_FILTER_SHUFFLE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
 VERSION = @VERSION@
+WORDS_BIGENDIAN = @WORDS_BIGENDIAN@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_CXX = @ac_ct_CXX@
-ac_ct_F77 = @ac_ct_F77@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 ac_ct_FC = @ac_ct_FC@
 am__include = @am__include@
 am__leading_dot = @am__leading_dot@
@@ -228,8 +286,12 @@ build_vendor = @build_vendor@
 builddir = @builddir@
 datadir = @datadir@
 datarootdir = @datarootdir@
+
+# Install directories that automake doesn't know about
 docdir = $(exec_prefix)/doc
 dvidir = @dvidir@
+enable_shared = @enable_shared@
+enable_static = @enable_static@
 exec_prefix = @exec_prefix@
 host = @host@
 host_alias = @host_alias@
@@ -237,15 +299,14 @@ host_cpu = @host_cpu@
 host_os = @host_os@
 host_vendor = @host_vendor@
 htmldir = @htmldir@
-
-# Install directories that automake doesn't know about
-includedir = $(exec_prefix)/include
+includedir = @includedir@
 infodir = @infodir@
 install_sh = @install_sh@
 libdir = @libdir@
 libexecdir = @libexecdir@
 localedir = @localedir@
 localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
 mandir = @mandir@
 mkdir_p = @mkdir_p@
 oldincludedir = @oldincludedir@
@@ -258,6 +319,7 @@ sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 
@@ -327,14 +389,14 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
-	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
-		&& exit 0; \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  c++/Makefile'; \
-	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign  c++/Makefile
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign c++/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign c++/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
@@ -352,6 +414,7 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
 
 mostlyclean-libtool:
 	-rm -f *.lo
@@ -383,7 +446,7 @@ $(RECURSIVE_TARGETS):
 	  else \
 	    local_target="$$target"; \
 	  fi; \
-	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
 	  || eval $$failcom; \
 	done; \
 	if test "$$dot_seen" = "no"; then \
@@ -417,16 +480,16 @@ $(RECURSIVE_CLEAN_TARGETS):
 	  else \
 	    local_target="$$target"; \
 	  fi; \
-	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
 	  || eval $$failcom; \
 	done && test -z "$$fail"
 tags-recursive:
 	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
 	done
 ctags-recursive:
 	list='$(SUBDIRS)'; for subdir in $$list; do \
-	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
+	  test "$$subdir" = . || ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) ctags); \
 	done
 
 ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
@@ -434,14 +497,14 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
 	mkid -fID $$unique
 tags: TAGS
 
 TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
+	set x; \
 	here=`pwd`; \
 	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
 	  include_option=--etags-include; \
@@ -453,39 +516,43 @@ TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 	list='$(SUBDIRS)'; for subdir in $$list; do \
 	  if test "$$subdir" = .; then :; else \
 	    test ! -f $$subdir/TAGS || \
-	      tags="$$tags $$include_option=$$here/$$subdir/TAGS"; \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
 	  fi; \
 	done; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
 	  test -n "$$unique" || unique=$$empty_fix; \
-	  $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	    $$tags $$unique; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
 	fi
 ctags: CTAGS
 CTAGS: ctags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
-	here=`pwd`; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	test -z "$(CTAGS_ARGS)$$tags$$unique" \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
 	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$tags $$unique
+	     $$unique
 
 GTAGS:
 	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && cd $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) $$here
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
 
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
@@ -506,29 +573,44 @@ distdir: $(DISTFILES)
 	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
 	  if test -d $$d/$$file; then \
 	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
 	    fi; \
-	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
 	  else \
-	    test -f $(distdir)/$$file \
-	    || cp -p $$d/$$file $(distdir)/$$file \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
 	    || exit 1; \
 	  fi; \
 	done
-	list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
 	  if test "$$subdir" = .; then :; else \
 	    test -d "$(distdir)/$$subdir" \
 	    || $(MKDIR_P) "$(distdir)/$$subdir" \
 	    || exit 1; \
-	    distdir=`$(am__cd) $(distdir) && pwd`; \
-	    top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
-	    (cd $$subdir && \
+	  fi; \
+	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
 	      $(MAKE) $(AM_MAKEFLAGS) \
-	        top_distdir="$$top_distdir" \
-	        distdir="$$distdir/$$subdir" \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
 		am__remove_distdir=: \
 		am__skip_length_check=: \
+		am__skip_mode_fix=: \
 	        distdir) \
 	      || exit 1; \
 	  fi; \
@@ -559,6 +641,7 @@ clean-generic:
 
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
 
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
@@ -577,6 +660,8 @@ dvi-am:
 
 html: html-recursive
 
+html-am:
+
 info: info-recursive
 
 info-am:
@@ -585,18 +670,28 @@ install-data-am:
 
 install-dvi: install-dvi-recursive
 
+install-dvi-am:
+
 install-exec-am:
 
 install-html: install-html-recursive
 
+install-html-am:
+
 install-info: install-info-recursive
 
+install-info-am:
+
 install-man:
 
 install-pdf: install-pdf-recursive
 
+install-pdf-am:
+
 install-ps: install-ps-recursive
 
+install-ps-am:
+
 installcheck-am: installcheck-local
 
 maintainer-clean: maintainer-clean-recursive
@@ -618,8 +713,8 @@ ps-am:
 
 uninstall-am:
 
-.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
-	install-strip
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) check-am \
+	ctags-recursive install-am install-strip tags-recursive
 
 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
 	all all-am all-local check check-TESTS check-am clean \
@@ -752,10 +847,10 @@ $(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
 	      else \
@@ -791,10 +886,10 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
 	      else \
@@ -858,6 +953,7 @@ check-vfd: $(LIB) $(PROGS) $(TESTS)
 	        HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1;    \
 	    fi;                                                               \
 	done
+
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:

c++/examples/Makefile.am

@@ -35,7 +35,7 @@ readdata.chkexe_: create.chkexe_
 chunks.chkexe_: extend_ds.chkexe_
 
 # Tell conclude.am that these are C++ tests.
-HDF_CXX=yes
+CXX_API=yes
 
 # Where to install examples
 EXAMPLEDIR=$(docdir)/hdf5/examples/c++

c++/examples/Makefile.in

@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006  Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -36,8 +37,9 @@
 # This creates some extra work for us.
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
 install_sh_DATA = $(install_sh) -c -m 644
 install_sh_PROGRAM = $(install_sh) -c
@@ -65,12 +67,25 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
 CONFIG_CLEAN_FILES = testh5c++.sh
+CONFIG_CLEAN_VPATH_FILES =
 SOURCES =
 DIST_SOURCES =
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -84,46 +99,47 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
+CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
+DIRECT_VFD = @DIRECT_VFD@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
 DYNAMIC_DIRS = @DYNAMIC_DIRS@
-ECHO = @ECHO@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
 EXEEXT = @EXEEXT@
-F77 = @F77@
+EXTERNAL_FILTERS = @EXTERNAL_FILTERS@
 
 # Make sure that these variables are exported to the Makefiles
 F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FGREP = @FGREP@
 FILTERS = @FILTERS@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+GPFS = @GPFS@
 GREP = @GREP@
 H5_CFLAGS = @H5_CFLAGS@
 H5_CPPFLAGS = @H5_CPPFLAGS@
@@ -132,11 +148,14 @@ H5_FCFLAGS = @H5_FCFLAGS@
 H5_LONE_COLON = @H5_LONE_COLON@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
+HAVE_DMALLOC = @HAVE_DMALLOC@
+HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
+HDF_CXX = @HDF_CXX@
+HDF_FORTRAN = @HDF_FORTRAN@
 HID_T = @HID_T@
 HL = @HL@
 HL_FOR = @HL_FOR@
-HSIZET = @HSIZET@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
 INSTALL = @INSTALL@
@@ -144,11 +163,16 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+INSTRUMENT = @INSTRUMENT@
 INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@
+LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
+LINUX_LFS = @LINUX_LFS@
+LIPO = @LIPO@
+LL_PATH = @LL_PATH@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 LT_STATIC_EXEC = @LT_STATIC_EXEC@
@@ -157,13 +181,19 @@ MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 MPI_GET_SIZE = @MPI_GET_SIZE@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
 OBJECT_NAMELEN_DEFAULT_F = @OBJECT_NAMELEN_DEFAULT_F@
 OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PARALLEL = @PARALLEL@
 PATH_SEPARATOR = @PATH_SEPARATOR@
@@ -176,22 +206,21 @@ RUNSERIAL = @RUNSERIAL@
 R_INTEGER = @R_INTEGER@
 R_LARGE = @R_LARGE@
 SEARCH = @SEARCH@
+SED = @SED@
 SETX = @SETX@
 SET_MAKE = @SET_MAKE@
-
-# Hardcode SHELL to be /bin/sh.  Most machines have this shell, and
-# on at least one machine configure fails to detect its existence (janus).
-# Also, when HDF5 is configured on one machine but run on another,
-# configure's automatic SHELL detection may not work on the build machine.
-SHELL = /bin/sh
+SHELL = @SHELL@
 SIZE_T = @SIZE_T@
+STATIC_EXEC = @STATIC_EXEC@
 STATIC_SHARED = @STATIC_SHARED@
 STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@
 STRIP = @STRIP@
 TESTPARALLEL = @TESTPARALLEL@
+THREADSAFE = @THREADSAFE@
 TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
+UNAME_INFO = @UNAME_INFO@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_FLETCHER32 = @USE_FILTER_FLETCHER32@
 USE_FILTER_NBIT = @USE_FILTER_NBIT@
@@ -200,13 +229,14 @@ USE_FILTER_SHUFFLE = @USE_FILTER_SHUFFLE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
 VERSION = @VERSION@
+WORDS_BIGENDIAN = @WORDS_BIGENDIAN@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_CXX = @ac_ct_CXX@
-ac_ct_F77 = @ac_ct_F77@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 ac_ct_FC = @ac_ct_FC@
 am__include = @am__include@
 am__leading_dot = @am__leading_dot@
@@ -222,8 +252,12 @@ build_vendor = @build_vendor@
 builddir = @builddir@
 datadir = @datadir@
 datarootdir = @datarootdir@
+
+# Install directories that automake doesn't know about
 docdir = $(exec_prefix)/doc
 dvidir = @dvidir@
+enable_shared = @enable_shared@
+enable_static = @enable_static@
 exec_prefix = @exec_prefix@
 host = @host@
 host_alias = @host_alias@
@@ -231,15 +265,14 @@ host_cpu = @host_cpu@
 host_os = @host_os@
 host_vendor = @host_vendor@
 htmldir = @htmldir@
-
-# Install directories that automake doesn't know about
-includedir = $(exec_prefix)/include
+includedir = @includedir@
 infodir = @infodir@
 install_sh = @install_sh@
 libdir = @libdir@
 libexecdir = @libexecdir@
 localedir = @localedir@
 localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
 mandir = @mandir@
 mkdir_p = @mkdir_p@
 oldincludedir = @oldincludedir@
@@ -252,6 +285,7 @@ sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 
@@ -308,7 +342,7 @@ INSTALL_FILES = create.cpp readdata.cpp writedata.cpp compound.cpp         \
 
 
 # Tell conclude.am that these are C++ tests.
-HDF_CXX = yes
+CXX_API = yes
 
 # Where to install examples
 EXAMPLEDIR = $(docdir)/hdf5/examples/c++
@@ -344,14 +378,14 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
-	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
-		&& exit 0; \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  c++/examples/Makefile'; \
-	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign  c++/examples/Makefile
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign c++/examples/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign c++/examples/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
@@ -369,6 +403,7 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
 testh5c++.sh: $(top_builddir)/config.status $(srcdir)/testh5c++.sh.in
 	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 
@@ -400,13 +435,17 @@ distdir: $(DISTFILES)
 	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
 	  if test -d $$d/$$file; then \
 	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
 	    fi; \
-	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
 	  else \
-	    test -f $(distdir)/$$file \
-	    || cp -p $$d/$$file $(distdir)/$$file \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
 	    || exit 1; \
 	  fi; \
 	done
@@ -437,6 +476,7 @@ clean-generic:
 
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
 
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
@@ -455,6 +495,8 @@ dvi-am:
 
 html: html-am
 
+html-am:
+
 info: info-am
 
 info-am:
@@ -463,18 +505,28 @@ install-data-am: install-data-local
 
 install-dvi: install-dvi-am
 
+install-dvi-am:
+
 install-exec-am:
 
 install-html: install-html-am
 
+install-html-am:
+
 install-info: install-info-am
 
+install-info-am:
+
 install-man:
 
 install-pdf: install-pdf-am
 
+install-pdf-am:
+
 install-ps: install-ps-am
 
+install-ps-am:
+
 installcheck-am: installcheck-local
 
 maintainer-clean: maintainer-clean-am
@@ -496,7 +548,7 @@ ps-am:
 
 uninstall-am: uninstall-local
 
-.MAKE: install-am install-strip
+.MAKE: check-am install-am install-strip
 
 .PHONY: all all-am all-local check check-TESTS check-am clean \
 	clean-generic clean-libtool distclean distclean-generic \
@@ -665,10 +717,10 @@ $(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
 	      else \
@@ -704,10 +756,10 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
 	      else \
@@ -771,6 +823,7 @@ check-vfd: $(LIB) $(PROGS) $(TESTS)
 	        HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1;    \
 	    fi;                                                               \
 	done
+
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:

c++/examples/chunks.cpp

@@ -80,7 +80,7 @@ int main (void)
 	hsize_t dims[2]; 	// dataset dimensions
 	rank = filespace.getSimpleExtentDims( dims );
 	cout << "dataset rank = " << rank << ", dimensions "
-	     << (unsigned long)(dims[0]) << " x " 
+	     << (unsigned long)(dims[0]) << " x "
 	     << (unsigned long)(dims[1]) << endl;
 
 	/*

c++/examples/h5group.cpp

@@ -94,7 +94,7 @@ int main(void)
 	 * Create the first dataset.
 	 */
 	DataSet* dataset = new DataSet(file->createDataSet(
-		"/Data/Compressed_Data", PredType::NATIVE_INT, 
+		"/Data/Compressed_Data", PredType::NATIVE_INT,
 		*dataspace, ds_creatplist ));
 
 	/*
@@ -109,7 +109,7 @@ int main(void)
 	dims[0] = 500;
 	dims[1] = 20;
 	dataspace = new DataSpace(RANK, dims); // create second dspace
-	dataset = new DataSet(file->createDataSet("/Data/Float_Data", 
+	dataset = new DataSet(file->createDataSet("/Data/Float_Data",
 			PredType::NATIVE_FLOAT, *dataspace));
 
 	delete dataset;

c++/examples/testexamples.sh

@@ -1,68 +0,0 @@
-#!/bin/sh
-#
-# Copyright by The HDF Group.
-# Copyright by the Board of Trustees of the University of Illinois.
-# All rights reserved.
-#
-# This file is part of HDF5.  The full HDF5 copyright notice, including
-# terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
-
-CMP='cmp -s'
-DIFF='diff -c'
-
-nerrors=0
-verbose=yes
-
-# The build (current) directory might be different than the source directory.
-if test -z "$srcdir"; then
-   srcdir=.
-fi
-
-actual=sample.out
-expect=$srcdir/expected.out
-
-# Print a line-line message left justified in a field of 70 characters
-# beginning with the word "Testing".
-TESTING()
-{
-    SPACES="                                                               "
-    echo "Testing $* $SPACES" |cut -c1-70 |tr -d '\012'
-}
-
-TESTING C++ Examples
-
-(
-   ./create
-   ./readdata
-   ./writedata
-   ./compound
-   ./extend_ds
-   ./chunks
-   ./h5group
-) > $actual
-
-if $CMP $expect $actual; then
-   echo " PASSED"
-else
-   echo "*FAILED*"
-   echo "    Expected result differs from actual result"
-   nerrors="`expr $nerrors + 1`"
-   test yes = "$verbose" && $DIFF $expect $actual | sed 's/^/    /'
-fi
-
-# Clean up output file
-if test -z "$HDF5_NOCLEANUP"; then
-   rm -f $actual
-fi
-
-if test $nerrors -eq 0 ; then
-   echo "All tests passed."
-fi
-
-exit $nerrors

c++/examples/testh5c++.sh.in

@@ -22,8 +22,8 @@
 # Initializations
 # Where the tool is installed.
 prefix="${prefix:-@prefix@}"
-AR=@AR@
-RANLIB=@RANLIB@
+AR="@AR@"
+RANLIB="@RANLIB@"
 H5TOOL="h5c++"           	# The tool name
 H5TOOL_BIN="${prefix}/bin/${H5TOOL}"   # The path of the tool binary
 

c++/src/H5AbstractDs.cpp

@@ -25,6 +25,11 @@
 #include "H5CommonFG.h"
 #include "H5Alltypes.h"
 
+#include <iostream> // remove when done
+
+    using std::cerr;
+    using std::endl;
+
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
 #endif
@@ -34,21 +39,21 @@ namespace H5 {
 ///\brief	Default constructor
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-AbstractDs::AbstractDs() : H5Object() {}
+AbstractDs::AbstractDs(){}
 
 //--------------------------------------------------------------------------
 // Function:	AbstractDs default constructor
 ///\brief	Creates an AbstractDs instance using an existing id.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-AbstractDs::AbstractDs( const hid_t ds_id ) : H5Object( ds_id ) {}
+AbstractDs::AbstractDs(const hid_t ds_id){}
 
 //--------------------------------------------------------------------------
 // Function:	AbstractDs copy constructor
 ///\brief	Copy constructor: makes a copy of the original AbstractDs object.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-AbstractDs::AbstractDs( const AbstractDs& original ) : H5Object( original ) {}
+AbstractDs::AbstractDs(const AbstractDs& original){}
 
 //--------------------------------------------------------------------------
 // Function:	AbstractDs::getTypeClass
@@ -80,8 +85,10 @@ H5T_class_t AbstractDs::getTypeClass() const
       return( type_class );
    else
    {
-      throw DataTypeIException(inMemFunc("getTypeClass"),
-		"H5Tget_class returns H5T_NO_CLASS");
+      if (fromClass() == "DataSet")
+	 throw DataTypeIException("DataSet::getTypeClass", "H5Tget_class returns H5T_NO_CLASS");
+      else if (fromClass() == "Attribute")
+	 throw DataTypeIException("Attribute::getTypeClass", "H5Tget_class returns H5T_NO_CLASS");
    }
 }
 

c++/src/H5AbstractDs.h

@@ -33,7 +33,7 @@ class FloatType;
 class IntType;
 class StrType;
 class VarLenType;
-class H5_DLLCPP AbstractDs : public H5Object {
+class H5_DLLCPP AbstractDs {
    public:
 	// Gets a copy the datatype of that this abstract dataset uses.
 	// Note that this datatype is a generic one and can only be accessed
@@ -51,6 +51,9 @@ class H5_DLLCPP AbstractDs : public H5Object {
 	StrType getStrType() const;
 	VarLenType getVarLenType() const;
 
+	// Gets the size in memory of this abstract dataset.
+	virtual size_t getInMemDataSize() const = 0;
+
 	// Gets the dataspace of this abstract dataset - pure virtual.
 	virtual DataSpace getSpace() const = 0;
 
@@ -62,6 +65,9 @@ class H5_DLLCPP AbstractDs : public H5Object {
 	// dataset - pure virtual.
 	virtual hsize_t getStorageSize() const = 0;
 
+	// Returns this class name
+	virtual H5std_string fromClass() const = 0;
+
 	// Copy constructor
 	AbstractDs( const AbstractDs& original );
 

c++/src/H5ArrayType.h

@@ -36,7 +36,7 @@ class H5_DLLCPP ArrayType : public DataType {
 	// Returns the sizes of dimensions of this array datatype.
 	int getArrayDims(hsize_t* dims);
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("ArrayType"); }
 
 	// Copy constructor: makes copy of the original object.

c++/src/H5AtomType.cpp

@@ -98,7 +98,7 @@ H5T_order_t AtomType::getOrder() const
 //--------------------------------------------------------------------------
 // Function:	AtomType::getOrder
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It takes a reference to a \c std::string for the buffer that
+///		It takes a reference to a \c H5std_string for the buffer that
 ///		provide the text description of the returned byte order.
 ///		The text description can be either of the following:
 ///		"Little endian byte ordering (0)";
@@ -178,7 +178,7 @@ size_t AtomType::getPrecision() const
 ///\exception	H5::DataTypeIException
 ///\par Description
 ///		For information, please see C layer Reference Manuat at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5T.html#Datatype-SetPrecision
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-SetPrecision
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void AtomType::setPrecision( size_t precision ) const
@@ -198,7 +198,7 @@ void AtomType::setPrecision( size_t precision ) const
 ///\exception	H5::DataTypeIException
 ///\par Description
 ///		For information, please see C layer Reference Manuat at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5T.html#Datatype-GetOffset
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetOffset
 // Programmer	Binh-Minh Ribler - 2000
 // Modification
 //		12/05/00: due to C API change
@@ -225,7 +225,7 @@ int AtomType::getOffset() const
 ///\exception	H5::DataTypeIException
 ///\par Description
 ///		For information, please see C layer Reference Manuat at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5T.html#Datatype-SetOffset
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-SetOffset
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void AtomType::setOffset( size_t offset ) const

c++/src/H5AtomType.h

@@ -57,7 +57,7 @@ class H5_DLLCPP AtomType : public DataType {
 	// Sets the total size for an atomic datatype.
 	void setSize( size_t size ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("AtomType"); }
 
 	// Copy constructor - makes copy of the original object

c++/src/H5Attribute.cpp

@@ -26,12 +26,15 @@
 #include "H5PropList.h"
 #include "H5Object.h"
 #include "H5AbstractDs.h"
-#include "H5Attribute.h"
+#include "H5FaccProp.h"
+#include "H5FcreatProp.h"
 #include "H5DcreatProp.h"
 #include "H5CommonFG.h"
 #include "H5DataType.h"
 #include "H5DataSpace.h"
-#include "H5private.h"
+#include "H5File.h"
+#include "H5Attribute.h"
+#include "H5private.h"		// for HDfree
 
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
@@ -46,7 +49,7 @@ namespace H5 {
 ///\brief	Default constructor: Creates a stub attribute
 // Programmer	Binh-Minh Ribler - May, 2004
 //--------------------------------------------------------------------------
-Attribute::Attribute() : AbstractDs() {}
+Attribute::Attribute() : AbstractDs(), IdComponent(), id(0) {}
 
 //--------------------------------------------------------------------------
 // Function:	Attribute copy constructor
@@ -54,7 +57,11 @@ Attribute::Attribute() : AbstractDs() {}
 ///\param	original  - IN: Original Attribute object to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-Attribute::Attribute( const Attribute& original ) : AbstractDs( original ) {}
+Attribute::Attribute(const Attribute& original) : AbstractDs(), IdComponent()
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	Attribute overloaded constructor
@@ -64,7 +71,10 @@ Attribute::Attribute( const Attribute& original ) : AbstractDs( original ) {}
 ///\exception	H5::AttributeIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-Attribute::Attribute(const hid_t existing_id) : AbstractDs(existing_id) {}
+Attribute::Attribute(const hid_t existing_id) : AbstractDs(), IdComponent()
+{
+   id = existing_id;
+}
 
 //--------------------------------------------------------------------------
 // Function:	Attribute::write
@@ -86,23 +96,40 @@ void Attribute::write( const DataType& mem_type, const void *buf ) const
 //--------------------------------------------------------------------------
 // Function:	Attribute::write
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It writes a \a std::string to this attribute.
+///		It writes a \a H5std_string to this attribute.
 ///\param	mem_type  - IN: Attribute datatype (in memory)
 ///\param	strg      - IN: Data to be written
 ///\exception	H5::AttributeIException
 // Programmer	Binh-Minh Ribler - Apr, 2003
 //--------------------------------------------------------------------------
-void Attribute::write( const DataType& mem_type, const H5std_string& strg ) const
+void Attribute::write(const DataType& mem_type, const H5std_string& strg) const
 {
-   // Convert string to C-string
-   const char* strg_C;
-   strg_C = strg.c_str();  // strg_C refers to the contents of strg as a C-str
+    // Check if this attribute has variable-len string or fixed-len string and
+    // proceed appropriately.
+    htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
+    if (is_variable_len < 0)
+    {
+	throw AttributeIException("Attribute::write", "H5Tis_variable_str failed");
+    }
+    // Convert string to C-string
+    const char* strg_C;
+    strg_C = strg.c_str();  // strg_C refers to the contents of strg as a C-str
+    herr_t ret_value = 0;
 
-   herr_t ret_value = H5Awrite( id, mem_type.getId(), &strg_C );
-   if( ret_value < 0 )
-   {
-      throw AttributeIException("Attribute::write", "H5Awrite failed");
-   }
+    // Pass string in differently depends on variable or fixed length
+    if (!is_variable_len)
+    {
+	ret_value = H5Awrite(id, mem_type.getId(), strg_C);
+    }
+    else
+    {
+	// passing third argument by address
+	ret_value = H5Awrite(id, mem_type.getId(), &strg_C);
+    }
+    if (ret_value < 0)
+    {
+	throw AttributeIException("Attribute::write", "H5Awrite failed");
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -118,35 +145,95 @@ void Attribute::read( const DataType& mem_type, void *buf ) const
    herr_t ret_value = H5Aread( id, mem_type.getId(), buf );
    if( ret_value < 0 )
    {
-      throw AttributeIException("Attribute::read", "H5Aread  failed");
+      throw AttributeIException("Attribute::read", "H5Aread failed");
    }
 }
 
 //--------------------------------------------------------------------------
 // Function:	Attribute::read
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It reads a \a std::string from this attribute.
+///		It reads a \a H5std_string from this attribute.
 ///\param	mem_type  - IN: Attribute datatype (in memory)
 ///\param	strg      - IN: Buffer for read string
 ///\exception	H5::AttributeIException
 // Programmer	Binh-Minh Ribler - Apr, 2003
 // Modification
-//		2006/12/9 - H5Aread allocates memory for character string
-//			    buffer with malloc, therefore, no allocation here,
-//			    but HDfree is needed. - BMR
+//	Mar 2008
+//		Corrected a misunderstanding that H5Aread would allocate
+//		space for the buffer.  Obtained the attribute size and
+//		allocated memory properly. - BMR
+//	Apr 2009
+//		Used getInMemDataSize to get attribute data size. - BMR
+//	Jul 2009
+//		Divided into specific private functions for fixed- and
+//		variable-len string data: p_read_fixed_len and 
+//		p_read_variable_len.  This should improve readability.
 //--------------------------------------------------------------------------
-void Attribute::read( const DataType& mem_type, H5std_string& strg ) const
+void Attribute::read(const DataType& mem_type, H5std_string& strg) const
 {
-   char* strg_C;  // temporary C-string for C API
+    // Check if this attribute has variable-len string or fixed-len string and
+    // proceed appropriately.
+    htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
+    if (is_variable_len < 0)
+    {
+        throw AttributeIException("Attribute::read", "H5Tis_variable_str failed");
+    }
 
-   // call C API to get the attribute string of chars
-   herr_t ret_value = H5Aread( id, mem_type.getId(), &strg_C);
-   if( ret_value < 0 )
-   {
-      throw AttributeIException("Attribute::read", "H5Aread failed");
-   }
-   strg = strg_C;	// get 'string' from the C char*
-   HDfree(strg_C);
+    if (!is_variable_len)	// string is fixed length
+    {
+        p_read_fixed_len(mem_type, strg);
+    }
+    else
+    {
+        p_read_variable_len(mem_type, strg);
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	Attribute::getInMemDataSize
+///\brief	Gets the size in memory of the attribute's data.
+///\return	Size of data (in memory)
+///\exception	H5::AttributeIException
+// Programmer	Binh-Minh Ribler - Apr 2009
+//--------------------------------------------------------------------------
+size_t Attribute::getInMemDataSize() const
+{
+    char *func = "Attribute::getInMemDataSize";
+
+    // Get the data type of this attribute
+    hid_t mem_type_id = H5Aget_type(id);
+    if( mem_type_id < 0 )
+    {
+	throw AttributeIException(func, "H5Aget_type failed");
+    }
+
+    // Get the data type's size
+    hid_t native_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT);
+    if (native_type < 0)
+    {
+	throw AttributeIException(func, "H5Tget_native_type failed");
+    }
+    size_t type_size = H5Tget_size(native_type);
+    if (type_size == 0)
+    {
+	throw AttributeIException(func, "H5Tget_size failed");
+    }
+
+    // Get number of elements of the attribute
+    hid_t space_id = H5Aget_space(id);
+    if (space_id < 0)
+    {
+	throw AttributeIException(func, "H5Aget_space failed");
+    }
+    hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
+    if (num_elements < 0)
+    {
+	throw AttributeIException(func, "H5Sget_simple_extent_npoints failed");
+    }
+
+    // Calculate and return the size of the data
+    size_t data_size = type_size * num_elements;
+    return(data_size);
 }
 
 //--------------------------------------------------------------------------
@@ -174,22 +261,19 @@ DataSpace Attribute::getSpace() const
 }
 
 //--------------------------------------------------------------------------
-// Function:	Attribute::p_get_type (private)
-// Purpose	Gets the datatype of this attribute.
-// Return	Id of the datatype
-// Exception	H5::AttributeIException
-// Description
-// 		This private function is used in AbstractDs.
-// Programmer	Binh-Minh Ribler - 2000
+// Function:	Attribute::getFileName
+///\brief	Gets the name of the file, in which this attribute belongs.
+///\return	File name
+///\exception	H5::IdComponentException
+// Programmer	Binh-Minh Ribler - Jul, 2004
 //--------------------------------------------------------------------------
-hid_t Attribute::p_get_type() const
+H5std_string Attribute::getFileName() const
 {
-   hid_t type_id = H5Aget_type( id );
-   if( type_id > 0 )
-      return( type_id );
-   else
-   {
-      throw AttributeIException("", "H5Aget_type failed");
+   try {
+      return(p_get_file_name());
+   }
+   catch (IdComponentException E) {
+      throw FileIException("Attribute::getFileName", E.getDetailMsg());
    }
 }
 
@@ -282,6 +366,135 @@ hsize_t Attribute::getStorageSize() const
    return (storage_size);
 }
 
+//--------------------------------------------------------------------------
+// Function:    Attribute::getId
+// Purpose:     Get the id of this attribute
+// Description:
+//		Class hierarchy is revised to address bugzilla 1068.  Class
+//		AbstractDS and Attribute are moved out of H5Object.  In
+//		addition, member IdComponent::id is moved into subclasses, and
+//		IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t Attribute::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:	Attribute::p_get_type (private)
+// Purpose	Gets the datatype of this attribute.
+// Return	Id of the datatype
+// Exception	H5::AttributeIException
+// Description
+// 		This private function is used in AbstractDs.
+// Programmer	Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+hid_t Attribute::p_get_type() const
+{
+   hid_t type_id = H5Aget_type( id );
+   if( type_id > 0 )
+      return( type_id );
+   else
+   {
+      throw AttributeIException("", "H5Aget_type failed");
+   }
+}
+
+//--------------------------------------------------------------------------
+// Function:	Attribute::p_read_fixed_len (private)
+// brief	Reads a fixed length \a H5std_string from an attribute.
+// param	mem_type  - IN: Attribute datatype (in memory)
+// param	strg      - IN: Buffer for read string
+// exception	H5::AttributeIException
+// Programmer	Binh-Minh Ribler - Jul, 2009
+// Modification
+//	Jul 2009
+//		Separated the fixed length case from the original
+//		Attribute::read
+//--------------------------------------------------------------------------
+void Attribute::p_read_fixed_len(const DataType& mem_type, H5std_string& strg) const
+{
+    // Only allocate for fixed-len string.
+
+    // Get the size of the attribute's data
+    size_t attr_size = getInMemDataSize();
+
+    // If there is data, allocate buffer and read it.
+    if (attr_size > 0)
+    {
+	char *strg_C = NULL;
+
+	strg_C = new char [(size_t)attr_size+1];
+	herr_t ret_value = H5Aread(id, mem_type.getId(), strg_C);
+
+	if( ret_value < 0 )
+	{
+	    delete []strg_C;	// de-allocate for fixed-len string
+	    throw AttributeIException("Attribute::read", "H5Aread failed");
+	}
+
+	// Get string from the C char* and release resource allocated locally
+	strg = strg_C;
+	delete []strg_C;
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	Attribute::p_read_variable_len (private)
+// brief	Reads a variable length \a H5std_string from an attribute.
+// param	mem_type  - IN: Attribute datatype (in memory)
+// param	strg      - IN: Buffer for read string
+// exception	H5::AttributeIException
+// Programmer	Binh-Minh Ribler - Jul, 2009
+// Modification
+//	Jul 2009
+//		Separated the variable length case from the original
+//		Attribute::read
+//--------------------------------------------------------------------------
+void Attribute::p_read_variable_len(const DataType& mem_type, H5std_string& strg) const
+{
+    // Prepare and call C API to read attribute.
+    char *strg_C;
+
+    // Read attribute, no allocation for variable-len string; C library will
+    herr_t ret_value = H5Aread(id, mem_type.getId(), &strg_C);
+
+    if( ret_value < 0 )
+    {
+	throw AttributeIException("Attribute::read", "H5Aread failed");
+    }
+
+    // Get string from the C char* and release resource allocated by C API
+    strg = strg_C;
+    HDfree(strg_C);
+}
+
+//--------------------------------------------------------------------------
+// Function:    Attribute::p_setId
+///\brief       Sets the identifier of this object to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///		object fails
+// Description:
+//		The underlaying reference counting in the C library ensures
+//		that the current valid id of this object is properly closed.
+//		Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void Attribute::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+	close();
+    }
+    catch (Exception close_error) {
+	throw AttributeIException("Attribute::p_setId", close_error.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+}
+
 //--------------------------------------------------------------------------
 // Function:	Attribute::close
 ///\brief	Closes this attribute.
@@ -298,8 +511,10 @@ void Attribute::close()
 	{
 	    throw AttributeIException("Attribute::close", "H5Aclose failed");
 	}
-	// reset the id because the attribute that it represents is now closed
-	id = 0;
+	// reset the id when the attribute that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 

c++/src/H5Attribute.h

@@ -21,11 +21,14 @@
 namespace H5 {
 #endif
 
-class H5_DLLCPP Attribute : public AbstractDs {
+class H5_DLLCPP Attribute : public AbstractDs, public IdComponent {
    public:
 	// Closes this attribute.
 	virtual void close();
 
+	// Gets the name of the file, in which this attribute belongs.
+	H5std_string getFileName() const;
+
 	// Gets the name of this attribute.
 	ssize_t getName( size_t buf_size, H5std_string& attr_name ) const;
 	H5std_string getName( size_t buf_size ) const; // returns name, not its length
@@ -35,7 +38,10 @@ class H5_DLLCPP Attribute : public AbstractDs {
 	virtual DataSpace getSpace() const;
 
 	// Returns the amount of storage size required for this attribute.
-	hsize_t getStorageSize() const;
+	virtual hsize_t getStorageSize() const;
+
+	// Returns the in memory size of this attribute's data.
+	virtual size_t getInMemDataSize() const;
 
 	// Reads data from this attribute.
 	void read( const DataType& mem_type, void *buf ) const;
@@ -45,11 +51,11 @@ class H5_DLLCPP Attribute : public AbstractDs {
 	void write(const DataType& mem_type, const void *buf ) const;
 	void write(const DataType& mem_type, const H5std_string& strg ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("Attribute"); }
 
-        // Creates a copy of an existing attribute using the attribute id
-        Attribute( const hid_t attr_id );
+	// Creates a copy of an existing attribute using the attribute id
+	Attribute( const hid_t attr_id );
 
 	// Copy constructor: makes a copy of an existing Attribute object.
 	Attribute( const Attribute& original );
@@ -57,16 +63,29 @@ class H5_DLLCPP Attribute : public AbstractDs {
 	// Default constructor
 	Attribute();
 
+	// Gets the attribute id.
+	virtual hid_t getId() const;
+
 	// Destructor: properly terminates access to this attribute.
 	virtual ~Attribute();
 
+   protected:
+	// Sets the attribute id.
+	virtual void p_setId(const hid_t new_id);
+
    private:
+	hid_t id;	// HDF5 attribute id
+
 	// This function contains the common code that is used by
 	// getTypeClass and various API functions getXxxType
 	// defined in AbstractDs for generic datatype and specific
 	// sub-types
 	virtual hid_t p_get_type() const;
 
+	// Reads variable or fixed len strings from this attribute.
+	void p_read_variable_len(const DataType& mem_type, H5std_string& strg) const;
+	void p_read_fixed_len(const DataType& mem_type, H5std_string& strg) const;
+
 	// do not inherit H5Object::iterateAttrs
 	int iterateAttrs() { return 0; }
 

c++/src/H5Classes.h

@@ -21,7 +21,6 @@
 namespace H5 {
 #endif
 	class Exception;
-	class ReferenceCounter;
 	class IdComponent;
 	class H5Object;
 	class PropList;

c++/src/H5CommonFG.cpp

@@ -100,7 +100,7 @@ Group CommonFG::createGroup( const char* name, size_t size_hint ) const
 // Function:	CommonFG::createGroup
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 Group CommonFG::createGroup( const H5std_string& name, size_t size_hint ) const
@@ -138,7 +138,7 @@ Group CommonFG::openGroup( const char* name ) const
 // Function:	CommonFG::openGroup
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 Group CommonFG::openGroup( const H5std_string& name ) const
@@ -182,7 +182,7 @@ DataSet CommonFG::createDataSet( const char* name, const DataType& data_type, co
 // Function:	CommonFG::createDataSet
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 DataSet CommonFG::createDataSet( const H5std_string& name, const DataType& data_type, const DataSpace& data_space, const DSetCreatPropList& create_plist ) const
@@ -217,7 +217,7 @@ DataSet CommonFG::openDataSet( const char* name ) const
 // Function:	CommonFG::openDataSet
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 DataSet CommonFG::openDataSet( const H5std_string& name ) const
@@ -239,7 +239,13 @@ DataSet CommonFG::openDataSet( const H5std_string& name ) const
 ///\par Description
 ///		Note that both names are interpreted relative to the
 ///		specified location.
+///		For information on creating hard link and soft link, please
+///		refer to the C layer Reference Manual at:
+/// http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateHard and
+/// http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateSoft
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	2007: QAK modified to use H5L APIs - BMR
 //--------------------------------------------------------------------------
 void CommonFG::link( H5L_type_t link_type, const char* curr_name, const char* new_name ) const
 {
@@ -269,7 +275,7 @@ void CommonFG::link( H5L_type_t link_type, const char* curr_name, const char* ne
 // Function:	CommonFG::link
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a curr_name and \a new_name.
+///		\c H5std_string for \a curr_name and \a new_name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::link( H5L_type_t link_type, const H5std_string& curr_name, const H5std_string& new_name ) const
@@ -283,6 +289,8 @@ void CommonFG::link( H5L_type_t link_type, const H5std_string& curr_name, const
 ///\param	name  - IN: Name of the object to be removed
 ///\exception	H5::FileIException or H5::GroupIException
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	2007: QAK modified to use H5L APIs - BMR
 //--------------------------------------------------------------------------
 void CommonFG::unlink( const char* name ) const
 {
@@ -297,7 +305,7 @@ void CommonFG::unlink( const char* name ) const
 // Function:	CommonFG::unlink
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::unlink( const H5std_string& name ) const
@@ -315,8 +323,10 @@ void CommonFG::unlink( const H5std_string& name ) const
 ///		Exercise care in moving groups as it is possible to render
 ///		data in a file inaccessible with Group::move. Please refer
 ///		to the Group Interface in the HDF5 User's Guide at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/Groups.html
+/// http://www.hdfgroup.org/HDF5/doc/UG/UG_frame09Groups.html
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	2007: QAK modified to use H5L APIs - BMR
 //--------------------------------------------------------------------------
 void CommonFG::move( const char* src, const char* dst ) const
 {
@@ -331,7 +341,7 @@ void CommonFG::move( const char* src, const char* dst ) const
 // Function:	CommonFG::move
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a src and \a dst.
+///		\c H5std_string for \a src and \a dst.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::move( const H5std_string& src, const H5std_string& dst ) const
@@ -350,7 +360,7 @@ void CommonFG::move( const H5std_string& src, const H5std_string& dst ) const
 ///\par Description
 ///		For more information, please refer to the C layer Reference
 ///		Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5G.html#Group-GetObjinfo
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5G.html#Group-GetObjinfo
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::getObjinfo( const char* name, hbool_t follow_link, H5G_stat_t& statbuf ) const
@@ -366,7 +376,7 @@ void CommonFG::getObjinfo( const char* name, hbool_t follow_link, H5G_stat_t& st
 // Function:	CommonFG::getObjinfo
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::getObjinfo( const H5std_string& name, hbool_t follow_link, H5G_stat_t& statbuf ) const
@@ -380,6 +390,7 @@ void CommonFG::getObjinfo( const H5std_string& name, hbool_t follow_link, H5G_st
 ///		It differs from the above functions in that it doesn't have
 ///		the paramemter \a follow_link.
 // Programmer	Binh-Minh Ribler - Nov, 2005
+// Note: need to modify to use H5Oget_info and H5Lget_info - BMR
 //--------------------------------------------------------------------------
 void CommonFG::getObjinfo( const char* name, H5G_stat_t& statbuf ) const
 {
@@ -394,7 +405,7 @@ void CommonFG::getObjinfo( const char* name, H5G_stat_t& statbuf ) const
 // Function:	CommonFG::getObjinfo
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - Nov, 2005
 //--------------------------------------------------------------------------
 void CommonFG::getObjinfo( const H5std_string& name, H5G_stat_t& statbuf ) const
@@ -414,23 +425,44 @@ void CommonFG::getObjinfo( const H5std_string& name, H5G_stat_t& statbuf ) const
 //--------------------------------------------------------------------------
 H5std_string CommonFG::getLinkval( const char* name, size_t size ) const
 {
-   char* value_C = new char[size+1];  // temporary C-string for C API
+    H5L_info_t linkinfo;
+    char *value_C;	// value in C string
+    size_t val_size = size;
+    H5std_string value = "";
+    herr_t ret_value;
 
-   herr_t ret_value = H5Lget_val( getLocId(), name, value_C, size, H5P_DEFAULT );
-   if( ret_value < 0 )
-   {
-      throwException("getLinkval", "H5Lget_val failed");
-   }
-   H5std_string value = H5std_string( value_C );
-   delete []value_C;
-   return( value );
+    // if user doesn't provide buffer size, determine it
+    if (size == 0)
+    {
+	ret_value = H5Lget_info(getLocId(), name, &linkinfo, H5P_DEFAULT);
+	if( ret_value < 0 )
+	{
+	    throwException("getLinkval", "H5Lget_info to find buffer size failed");
+	}
+	val_size = linkinfo.u.val_size;
+    }
+
+    // if link has value, retrieve the value, otherwise, return null string
+    if (val_size > 0)
+    {
+	value_C = new char[val_size+1];  // temporary C-string for C API
+
+	ret_value = H5Lget_val(getLocId(), name, value_C, val_size, H5P_DEFAULT);
+	if( ret_value < 0 )
+	{
+	    throwException("getLinkval", "H5Lget_val failed");
+	}
+	value = H5std_string(value_C);
+	delete []value_C;
+    }
+    return(value);
 }
 
 //--------------------------------------------------------------------------
 // Function:	CommonFG::getLinkval
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 H5std_string CommonFG::getLinkval( const H5std_string& name, size_t size ) const
@@ -452,6 +484,11 @@ H5std_string CommonFG::getLinkval( const H5std_string& name, size_t size ) const
 ///		object header, e.g., data sets, groups, named data types,
 ///		and data spaces, but not symbolic links.
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	2007: QAK modified to use H5O APIs; however the first parameter is
+//		no longer just file or group, this function should be moved
+//		to another class to accommodate attribute, dataset, and named
+//		datatype. - BMR
 //--------------------------------------------------------------------------
 void CommonFG::setComment( const char* name, const char* comment ) const
 {
@@ -466,7 +503,7 @@ void CommonFG::setComment( const char* name, const char* comment ) const
 // Function:	CommonFG::setComment
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name and \a comment.
+///		\c H5std_string for \a name and \a comment.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::setComment( const H5std_string& name, const H5std_string& comment ) const
@@ -480,6 +517,10 @@ void CommonFG::setComment( const H5std_string& name, const H5std_string& comment
 ///\param	name  - IN: Name of the object
 ///\exception	H5::FileIException or H5::GroupIException
 // Programmer	Binh-Minh Ribler - May 2005
+//	2007: QAK modified to use H5O APIs; however the first parameter is
+//		no longer just file or group, this function should be moved
+//		to another class to accommodate attribute, dataset, and named
+//		datatype. - BMR
 //--------------------------------------------------------------------------
 void CommonFG::removeComment(const char* name) const
 {
@@ -494,7 +535,7 @@ void CommonFG::removeComment(const char* name) const
 // Function:	CommonFG::removeComment
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - May 2005
 //--------------------------------------------------------------------------
 void CommonFG::removeComment(const H5std_string& name) const
@@ -504,29 +545,38 @@ void CommonFG::removeComment(const H5std_string& name) const
 
 //--------------------------------------------------------------------------
 // Function:	CommonFG::getComment
-///\brief	Retrieves comment for the specified object.
+///\brief	Retrieves comment for the specified object and its comment's
+///		length.
 ///\param	name  - IN: Name of the object
+///\param	bufsize - IN: Length of the comment to retrieve
 ///\return	Comment string
 ///\exception	H5::FileIException or H5::GroupIException
-// Programmer	Binh-Minh Ribler - May 2005
+// Programmer	Binh-Minh Ribler - 2000
+//	2007: QAK modified to use H5O APIs; however the first parameter is
+//		no longer just file or group, this function should be moved
+//		to another class to accommodate attribute, dataset, and named
+//		datatype. - BMR
 //--------------------------------------------------------------------------
-H5std_string CommonFG::getComment (const H5std_string& name) const
+H5std_string CommonFG::getComment( const char* name, size_t bufsize ) const
 {
-   size_t bufsize = 256;        // anticipating the comment's length
+   // bufsize is default to 256
+   // temporary variable
    hid_t loc_id = getLocId();   // temporary variable
 
-   // temporary C-string for the object's comment
-   char* comment_C = new char[bufsize+1];
-   herr_t ret_value = H5Oget_comment_by_name(loc_id, name.c_str(), comment_C, bufsize, H5P_DEFAULT);
+   // temporary C-string for the object's comment; bufsize already including
+   // null character
+   char* comment_C = new char[bufsize];
+   ssize_t ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, bufsize, H5P_DEFAULT);
 
-   // if the actual length of the comment is longer than the anticipated
-   // value, then call H5Oget_comment_by_name again with the correct value
-   if (ret_value > bufsize)
+   // if the actual length of the comment is longer than bufsize and bufsize
+   // was the default value, i.e., not given by the user, then call
+   // H5Oget_comment_by_name again with the correct value
+   if ((size_t)ret_value > bufsize && bufsize == 256)
    {
-	bufsize = ret_value;
+	size_t new_size = ret_value;
 	delete []comment_C;
-	comment_C = new char[bufsize+1];
-	ret_value = H5Oget_comment_by_name(loc_id, name.c_str(), comment_C, bufsize, H5P_DEFAULT);
+	comment_C = new char[new_size];	// new_size including null terminator
+	ret_value = H5Oget_comment_by_name(loc_id, name, comment_C, new_size, H5P_DEFAULT);
    }
 
    // if H5Oget_comment_by_name returns SUCCEED, return the string comment,
@@ -540,38 +590,11 @@ H5std_string CommonFG::getComment (const H5std_string& name) const
    return (comment);
 }
 
-//--------------------------------------------------------------------------
-// Function:	CommonFG::getComment
-///\brief	Retrieves comment for the specified object and its comment's
-///		length.
-///\param	name  - IN: Name of the object
-///\param	bufsize - IN: Length of the comment to retrieve
-///\return	Comment string
-///\exception	H5::FileIException or H5::GroupIException
-// Programmer	Binh-Minh Ribler - 2000
-//--------------------------------------------------------------------------
-H5std_string CommonFG::getComment( const char* name, size_t bufsize ) const
-{
-   // temporary C-string for the object's comment
-   char* comment_C = new char[bufsize+1];
-
-   herr_t ret_value = H5Oget_comment_by_name( getLocId(), name, comment_C, bufsize, H5P_DEFAULT );
-
-   // if H5Oget_comment_by_name returns SUCCEED, return the string comment
-   if( ret_value < 0 )
-   {
-      throwException("getComment", "H5Oget_comment_by_name failed");
-   }
-   H5std_string comment = H5std_string(comment_C);
-   delete []comment_C;
-   return( comment );
-}
-
 //--------------------------------------------------------------------------
 // Function:	CommonFG::getComment
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 H5std_string CommonFG::getComment( const H5std_string& name, size_t bufsize ) const
@@ -608,7 +631,7 @@ void CommonFG::mount( const char* name, H5File& child, PropList& plist ) const
 // Function:	CommonFG::mount
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::mount( const H5std_string& name, H5File& child, PropList& plist ) const
@@ -639,7 +662,7 @@ void CommonFG::unmount( const char* name ) const
 // Function:	CommonFG::unmount
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void CommonFG::unmount( const H5std_string& name ) const
@@ -674,7 +697,7 @@ DataType CommonFG::openDataType( const char* name ) const
 // Function:	CommonFG::openDataType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 DataType CommonFG::openDataType( const H5std_string& name ) const
@@ -709,7 +732,7 @@ ArrayType CommonFG::openArrayType( const char* name ) const
 // Function:	CommonFG::openArrayType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - Jul, 2005
 //--------------------------------------------------------------------------
 ArrayType CommonFG::openArrayType( const H5std_string& name ) const
@@ -744,7 +767,7 @@ CompType CommonFG::openCompType( const char* name ) const
 // Function:	CommonFG::openCompType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 CompType CommonFG::openCompType( const H5std_string& name ) const
@@ -779,7 +802,7 @@ EnumType CommonFG::openEnumType( const char* name ) const
 // Function:	CommonFG::openEnumType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 EnumType CommonFG::openEnumType( const H5std_string& name ) const
@@ -814,7 +837,7 @@ IntType CommonFG::openIntType( const char* name ) const
 // Function:	CommonFG::openIntType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 IntType CommonFG::openIntType( const H5std_string& name ) const
@@ -849,7 +872,7 @@ FloatType CommonFG::openFloatType( const char* name ) const
 // Function:	CommonFG::openFloatType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 FloatType CommonFG::openFloatType( const H5std_string& name ) const
@@ -884,7 +907,7 @@ StrType CommonFG::openStrType( const char* name ) const
 // Function:	CommonFG::openStrType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 StrType CommonFG::openStrType( const H5std_string& name ) const
@@ -919,7 +942,7 @@ VarLenType CommonFG::openVarLenType( const char* name ) const
 // Function:	CommonFG::openVarLenType
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - Jul, 2005
 //--------------------------------------------------------------------------
 VarLenType CommonFG::openVarLenType( const H5std_string& name ) const
@@ -955,7 +978,7 @@ int CommonFG::iterateElems( const char* name, int *idx, H5G_iterate_t op , void*
 // Function:	CommonFG::iterateElems
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes an
-///		\c std::string for \a name.
+///		\c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 int CommonFG::iterateElems( const H5std_string& name, int *idx, H5G_iterate_t op , void* op_data )

c++/src/H5CommonFG.h

@@ -50,9 +50,8 @@ class H5_DLLCPP CommonFG {
 	DataSet openDataSet(const H5std_string& name) const;
 
 	// Retrieves comment for the HDF5 object specified by its name.
-	H5std_string getComment(const H5std_string& name) const;
-	H5std_string getComment(const char* name, size_t bufsize) const;
-	H5std_string getComment(const H5std_string& name, size_t bufsize) const;
+	H5std_string getComment(const char* name, size_t bufsize=256) const;
+	H5std_string getComment(const H5std_string& name, size_t bufsize=256) const;
 
 	// Removes the comment for the HDF5 object specified by its name.
 	void removeComment(const char* name) const;
@@ -62,9 +61,9 @@ class H5_DLLCPP CommonFG {
 	void setComment(const char* name, const char* comment) const;
 	void setComment(const H5std_string& name, const H5std_string& comment) const;
 
-	// Returns the name of the HDF5 object that the symbolic link points to.
-	H5std_string getLinkval(const char* name, size_t size) const;
-	H5std_string getLinkval(const H5std_string& name, size_t size) const;
+	// Returns the value of a symbolic link.
+	H5std_string getLinkval(const char* link_name, size_t size=0) const;
+	H5std_string getLinkval(const H5std_string& link_name, size_t size=0) const;
 
 	// Returns the number of objects in this group.
 	hsize_t getNumObjs() const;

c++/src/H5CompType.h

@@ -88,7 +88,7 @@ class H5_DLLCPP CompType : public DataType {
 	// Recursively removes padding from within this compound datatype.
 	void pack() const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("CompType"); }
 
 	// Default constructor

c++/src/H5Cpp.h

@@ -44,9 +44,9 @@
 #include "H5Group.h"
 #include "H5File.h"
 #include "H5Library.h"
- 
+
 /* Some C++ compilers do not have offsetof macro; define to bypass the problem
-   - BMR- -EIP- 2007/08/01 
+   - BMR- -EIP- 2007/08/01
 */
 #ifndef H5_CXX_HAVE_OFFSETOF
 #ifdef HOFFSET

c++/src/H5DataSet.cpp

@@ -28,11 +28,16 @@
 #include "H5PropList.h"
 #include "H5DxferProp.h"
 #include "H5DcreatProp.h"
+#include "H5FaccProp.h"
+#include "H5FcreatProp.h"
 #include "H5CommonFG.h"
 #include "H5DataType.h"
 #include "H5DataSpace.h"
 #include "H5AbstractDs.h"
+#include "H5File.h"
+#include "H5Attribute.h"
 #include "H5DataSet.h"
+#include "H5private.h"		// for HDfree
 
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
@@ -47,7 +52,7 @@ namespace H5 {
 ///\brief	Default constructor: creates a stub DataSet.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSet::DataSet() : AbstractDs() {}
+DataSet::DataSet() : AbstractDs(), H5Object(), id(0) {}
 
 //--------------------------------------------------------------------------
 // Function:	DataSet overloaded constructor
@@ -55,7 +60,10 @@ DataSet::DataSet() : AbstractDs() {}
 ///\param	existing_id - IN: Id of an existing dataset
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSet::DataSet(const hid_t existing_id) : AbstractDs(existing_id) {}
+DataSet::DataSet(const hid_t existing_id) : AbstractDs(), H5Object()
+{
+    id = existing_id;
+}
 
 //--------------------------------------------------------------------------
 // Function:	DataSet copy constructor
@@ -63,23 +71,83 @@ DataSet::DataSet(const hid_t existing_id) : AbstractDs(existing_id) {}
 ///\param	original - IN: DataSet instance to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSet::DataSet( const DataSet& original ) : AbstractDs( original ) {}
+DataSet::DataSet(const DataSet& original) : AbstractDs(original), H5Object(original)
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	DataSet overload constructor - dereference
-///\brief	Given a reference to some object, returns that dataset
-///             obj - IN: Dataset reference object is in or location of
-///                   object that the dataset is located within.
+///\brief	Given a reference, ref, to an hdf5 dataset, creates a 
+///		DataSet object
+///\param	obj - IN: Dataset reference object is in or location of
+///			  object that the dataset is located within.
 ///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
 ///\exception	H5::DataSetIException
-///\parDescription
+///\par Description
 ///		\c obj can be DataSet, Group, H5File, or named DataType, that 
 ///		is a datatype that has been named by DataType::commit.
 // Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	Jul, 2008
+//		Added for application convenience.
 //--------------------------------------------------------------------------
-DataSet::DataSet(IdComponent& obj, void* ref) : AbstractDs()
+DataSet::DataSet(H5Object& obj, const void* ref, H5R_type_t ref_type) : AbstractDs(), H5Object()
 {
-   IdComponent::dereference(obj, ref);
+    try {
+	id = p_dereference(obj.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("DataSet constructor - located by object", 
+		deref_error.getDetailMsg());
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataSet overload constructor - dereference
+///\brief	Given a reference, ref, to an hdf5 dataset, creates a 
+///		DataSet object
+///\param	h5file - IN: Location referenced object is in
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	Jul, 2008
+//		Added for application convenience.
+//--------------------------------------------------------------------------
+DataSet::DataSet(H5File& h5file, const void* ref, H5R_type_t ref_type) : AbstractDs(), H5Object()
+{
+    try {
+	id = p_dereference(h5file.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("DataSet constructor - located by HDF5 file", 
+		deref_error.getDetailMsg());
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataSet overload constructor - dereference
+///\brief	Given a reference, ref, to an hdf5 dataset, creates a 
+///		DataSet object
+///\param	attr - IN: Specifying location where the referenced object is in
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+// Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	Jul, 2008
+//		Added for application convenience.
+//--------------------------------------------------------------------------
+DataSet::DataSet(Attribute& attr, const void* ref, H5R_type_t ref_type) : AbstractDs(), H5Object()
+{
+    try {
+	id = p_dereference(attr.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("DataSet constructor - located by attribute", 
+		deref_error.getDetailMsg());
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -152,6 +220,53 @@ hsize_t DataSet::getStorageSize() const
    return(storage_size);
 }
 
+//--------------------------------------------------------------------------
+// Function:	DataSet::getInMemDataSize
+///\brief	Gets the size in memory of the dataset's data.
+///\return	Size of data (in memory)
+///\exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Apr 2009
+//--------------------------------------------------------------------------
+size_t DataSet::getInMemDataSize() const
+{
+    char *func = "DataSet::getInMemDataSize";
+
+    // Get the data type of this dataset
+    hid_t mem_type_id = H5Dget_type(id);
+    if( mem_type_id < 0 )
+    {
+	throw DataSetIException(func, "H5Dget_type failed");
+    }
+
+    // Get the data type's size
+    hid_t native_type = H5Tget_native_type(mem_type_id, H5T_DIR_DEFAULT);
+    if (native_type < 0)
+    {
+	throw DataSetIException(func, "H5Tget_native_type failed");
+    }
+    size_t type_size = H5Tget_size(native_type);
+    if (type_size == 0)
+    {
+	throw DataSetIException(func, "H5Tget_size failed");
+    }
+
+    // Get number of elements of the dataset
+    hid_t space_id = H5Dget_space(id); // first get its data space
+    if (space_id < 0)
+    {
+	throw DataSetIException(func, "H5Dget_space failed");
+    }
+    hssize_t num_elements = H5Sget_simple_extent_npoints(space_id);
+    if (num_elements < 0)
+    {
+	throw DataSetIException(func, "H5Sget_simple_extent_npoints failed");
+    }
+
+    // Calculate and return the size of the data
+    size_t data_size = type_size * num_elements;
+    return(data_size);
+}
+
 //--------------------------------------------------------------------------
 // Function:	DataSet::getOffset
 ///\brief	Returns the address of this dataset in the file.
@@ -296,21 +411,46 @@ void DataSet::read( void* buf, const DataType& mem_type, const DataSpace& mem_sp
 //--------------------------------------------------------------------------
 // Function:	DataSet::read
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It takes a reference to a \c std::string for the buffer.
+///		It takes a reference to a \c H5std_string for the buffer.
+///\param	buf - IN: Buffer for read data
+///\param	mem_type - IN: Memory datatype
+///\param	mem_space - IN: Memory dataspace
+///\param	file_space - IN: Dataset's dataspace in the file
+///\param	xfer_plist - IN: Transfer property list for this I/O operation
+///\exception	H5::DataSetIException
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	Jul 2009
+//		Follow the change to Attribute::read and use the following
+//		private functions to read datasets with fixed- and
+//		variable-length string:
+//			DataSet::p_read_fixed_len and
+//			DataSet::p_read_variable_len
 //--------------------------------------------------------------------------
-void DataSet::read( H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
+void DataSet::read(H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist) const
 {
-   // Allocate C character string for reading
-   size_t size = mem_type.getSize();
-   char* strg_C = new char[size+1];  // temporary C-string for C API
+    // Check if this dataset has variable-len string or fixed-len string and
+    // proceed appropriately.
+    htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
+    if (is_variable_len < 0)
+    {
+        throw DataSetIException("DataSet::read", "H5Tis_variable_str failed");
+    }
 
-   // Use the overloaded member to read
-   read(strg_C, mem_type, mem_space, file_space, xfer_plist);
+    // Obtain identifiers for C API
+    hid_t mem_type_id = mem_type.getId();
+    hid_t mem_space_id = mem_space.getId();
+    hid_t file_space_id = file_space.getId();
+    hid_t xfer_plist_id = xfer_plist.getId();
 
-   // Get the String and clean up
-   strg = strg_C;
-   delete []strg_C;
+    if (!is_variable_len)       // only allocate for fixed-len string
+    {
+        p_read_fixed_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg);
+    }
+    else
+    {
+        p_read_variable_len(mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg);
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -347,17 +487,48 @@ void DataSet::write( const void* buf, const DataType& mem_type, const DataSpace&
 //--------------------------------------------------------------------------
 // Function:	DataSet::write
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It takes a reference to a \c std::string for the buffer.
+///		It takes a reference to a \c H5std_string for the buffer.
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	Jul 2009
+//		Modified to pass the buffer into H5Dwrite properly depending
+//		whether the dataset has variable- or fixed-length string.
 //--------------------------------------------------------------------------
 void DataSet::write( const H5std_string& strg, const DataType& mem_type, const DataSpace& mem_space, const DataSpace& file_space, const DSetMemXferPropList& xfer_plist ) const
 {
-   // Convert string to C-string
-   const char* strg_C;
-   strg_C = strg.c_str();  // strg_C refers to the contents of strg as a C-str
+    // Check if this attribute has variable-len string or fixed-len string and
+    // proceed appropriately.
+    htri_t is_variable_len = H5Tis_variable_str(mem_type.getId());
+    if (is_variable_len < 0)
+    {
+        throw DataSetIException("DataSet::write", "H5Tis_variable_str failed");
+    }
 
-   // Use the overloaded member
-   write(strg_C, mem_type, mem_space, file_space, xfer_plist);
+   // Obtain identifiers for C API
+   hid_t mem_type_id = mem_type.getId();
+   hid_t mem_space_id = mem_space.getId();
+   hid_t file_space_id = file_space.getId();
+   hid_t xfer_plist_id = xfer_plist.getId();
+
+    // Convert string to C-string
+    const char* strg_C;
+    strg_C = strg.c_str();  // strg_C refers to the contents of strg as a C-str
+    herr_t ret_value = 0;
+
+    // Pass string in differently depends on variable or fixed length
+    if (!is_variable_len)
+    {
+        ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C );
+    }
+    else
+    {
+        // passing string argument by address
+        ret_value = H5Dwrite( id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C );
+    }
+    if (ret_value < 0)
+    {
+        throw DataSetIException("DataSet::write", "H5Dwrite failed");
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -400,7 +571,7 @@ int DataSet::iterateElems( void* buf, const DataType& type, const DataSpace& spa
 ///		For more information, please see the Description section in
 ///		C layer Reference Manual at:
 ///\par
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5D.html#Dataset-Extend
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5D.html#Dataset-Extend
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSet::extend( const hsize_t* size ) const
@@ -455,65 +626,19 @@ void DataSet::fillMemBuf(void *buf, DataType& buf_type, DataSpace& space)
     }
 }
 
-//--------------------------------------------------------------------------
-// Function:	DataSet::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use 
-///		DataSet::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* DataSet::Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type) const
-{
-   try {
-      return(p_reference(name, dataspace.getId(), ref_type));
-   }
-   catch (IdComponentException E) {
-      throw DataSetIException("DataSet::Reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	DataSet::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		DataSet::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* DataSet::Reference(const char* name) const
-{
-   try {
-      return(p_reference(name, -1, H5R_OBJECT));
-   }
-   catch (IdComponentException E) {
-      throw DataSetIException("DataSet::Reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	DataSet::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		DataSet::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* DataSet::Reference(const H5std_string& name) const
-{
-   return(Reference(name.c_str()));
-}
-
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 //--------------------------------------------------------------------------
 // Function:	DataSet::getObjType
 ///\brief	Retrieves the type of object that an object reference points to.
 ///\param	ref_type - IN: Type of reference to query, valid values are:
-///		\li \c H5R_OBJECT \tReference is an object reference.
-///		\li \c H5R_DATASET_REGION \tReference is a dataset region reference.
+///		\li \c H5R_OBJECT         - Reference is an object reference.
+///		\li \c H5R_DATASET_REGION - Reference is a dataset region reference.
 ///\param	ref      - IN: Reference to query
 ///\return	An object type, which can be one of the following:
-///		\li \c H5G_LINK (0) \tObject is a symbolic link.
-///		\li \c H5G_GROUP (1) \tObject is a group.
-///		\li \c H5G_DATASET (2) \tObject is a dataset.
-///		\li \c H5G_TYPE Object (3) \tis a named datatype
+///		\li \c H5G_LINK (0)    - Object is a symbolic link.
+///		\li \c H5G_GROUP (1)   - Object is a group.
+///		\li \c H5G_DATASET (2) - Object is a dataset.
+///		\li \c H5G_TYPE (3)    - Object is a named datatype
 ///\exception	H5::DataSetIException
 // Programmer	Binh-Minh Ribler - May, 2004
 //--------------------------------------------------------------------------
@@ -531,9 +656,9 @@ H5G_obj_t DataSet::getObjType(void *ref, H5R_type_t ref_type) const
 //--------------------------------------------------------------------------
 // Function:	DataSet::getRegion
 ///\brief	Retrieves a dataspace with the region pointed to selected.
+///\param	ref      - IN: Reference to get region of
 ///\param	ref_type - IN: Type of reference to get region of - default
 ///		to H5R_DATASET_REGION
-///\param	ref      - IN: Reference to get region of
 ///\return	DataSpace instance
 ///\exception	H5::DataSetIException
 // Programmer	Binh-Minh Ribler - May, 2004
@@ -549,6 +674,116 @@ DataSpace DataSet::getRegion(void *ref, H5R_type_t ref_type) const
    }
 }
 
+//--------------------------------------------------------------------------
+// Function:    DataSet::getId
+///\brief	Get the id of this dataset.
+// Description:
+//              Class hierarchy is revised to address bugzilla 1068.  Class
+//              AbstractDs and Attribute are moved out of H5Object.  In
+//              addition, member IdComponent::id is moved into subclasses, and
+//              IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t DataSet::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataSet::p_read_fixed_len (private)
+// brief	Reads a fixed length \a H5std_string from an dataset.
+// param	mem_type  - IN: DataSet datatype (in memory)
+// param	strg      - IN: Buffer for read string
+// exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Jul, 2009
+// Modification
+//	Jul 2009
+//		Added in follow to the change in Attribute::read
+//--------------------------------------------------------------------------
+void DataSet::p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const
+{
+    // Only allocate for fixed-len string.
+
+    // Get the size of the dataset's data
+    size_t attr_size = getInMemDataSize();
+
+    // If there is data, allocate buffer and read it.
+    if (attr_size > 0)
+    {
+	char *strg_C = NULL;
+
+	strg_C = new char [(size_t)attr_size+1];
+	herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, strg_C);
+
+	if( ret_value < 0 )
+	{
+	    delete []strg_C;	// de-allocate for fixed-len string
+	    throw DataSetIException("DataSet::read", "H5Dread failed for fixed length string");
+	}
+
+	// Get string from the C char* and release resource allocated locally
+	strg = strg_C;
+	delete []strg_C;
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataSet::p_read_variable_len (private)
+// brief	Reads a variable length \a H5std_string from an dataset.
+// param	mem_type  - IN: DataSet datatype (in memory)
+// param	strg      - IN: Buffer for read string
+// exception	H5::DataSetIException
+// Programmer	Binh-Minh Ribler - Jul, 2009
+// Modification
+//	Jul 2009
+//		Added in follow to the change in Attribute::read
+//--------------------------------------------------------------------------
+void DataSet::p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const
+{
+    // Prepare and call C API to read dataset.
+    char *strg_C;
+
+    // Read dataset, no allocation for variable-len string; C library will
+    herr_t ret_value = H5Dread(id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, &strg_C);
+
+    if( ret_value < 0 )
+    {
+	throw DataSetIException("DataSet::read", "H5Dread failed for variable length string");
+    }
+
+    // Get string from the C char* and release resource allocated by C API
+    strg = strg_C;
+    HDfree(strg_C);
+}
+
+//--------------------------------------------------------------------------
+// Function:    DataSet::p_setId (private)
+///\brief       Sets the identifier of this dataset to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///             object fails
+// Description:
+//              The underlaying reference counting in the C library ensures
+//              that the current valid id of this object is properly closed.
+//              Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void DataSet::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+        close();
+    }
+    catch (Exception close_error) {
+        throw DataSetIException(inMemFunc("p_setId"), close_error.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+
+   // increment the reference counter of the new id
+   //incRefCount();
+}
+
 //--------------------------------------------------------------------------
 // Function:	DataSet::close
 ///\brief	Closes this dataset.
@@ -565,8 +800,10 @@ void DataSet::close()
 	{
 	    throw DataSetIException("DataSet::close", "H5Dclose failed");
 	}
-	// reset the id because the dataset that it represents is now closed
-	id = 0;
+	// reset the id when the dataset that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 

c++/src/H5DataSet.h

@@ -23,7 +23,7 @@
 namespace H5 {
 #endif
 
-class H5_DLLCPP DataSet : public AbstractDs {
+class H5_DLLCPP DataSet : public H5Object, public AbstractDs {
    public:
 	// Close this dataset.
 	virtual void close();
@@ -49,7 +49,10 @@ class H5_DLLCPP DataSet : public AbstractDs {
 	void getSpaceStatus(H5D_space_status_t& status) const;
 
 	// Returns the amount of storage size required for this dataset.
-	hsize_t getStorageSize() const;
+	virtual hsize_t getStorageSize() const;
+
+	// Returns the in memory size of this attribute's data.
+	virtual size_t getInMemDataSize() const;
 
 	// Returns the number of bytes required to store VL data.
 	hsize_t getVlenBufSize( DataType& type, DataSpace& space ) const;
@@ -81,19 +84,13 @@ class H5_DLLCPP DataSet : public AbstractDs {
 	// Retrieves a dataspace with the region pointed to selected.
 	DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
 
-	// Creates a reference to a named Hdf5 object or to a dataset region
-	// in this object.
-	void* Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const;
-
-	// Creates a reference to a named Hdf5 object in this object.
-	void* Reference(const char* name) const; // will be obsolete
-	void* Reference(const H5std_string& name) const; // will be obsolete
-
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("DataSet"); }
 
 	// Creates a dataset by way of dereference.
-	DataSet(IdComponent& obj, void* ref);
+	DataSet(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+	DataSet(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+	DataSet(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
 
 	// Default constructor.
 	DataSet();
@@ -104,15 +101,30 @@ class H5_DLLCPP DataSet : public AbstractDs {
 	// Creates a copy of an existing DataSet using its id.
 	DataSet(const hid_t existing_id);
 
+        // Gets the dataset id.
+        virtual hid_t getId() const;
+
 	// Destructor: properly terminates access to this dataset.
 	virtual ~DataSet();
 
    private:
+	hid_t id;       // HDF5 dataset id
+
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
         // This function contains the common code that is used by
         // getTypeClass and various API functions getXxxType
         // defined in AbstractDs for generic datatype and specific
         // sub-types
 	virtual hid_t p_get_type() const;
+
+	// Reads variable or fixed len strings from this dataset.
+	void p_read_fixed_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const;
+	void p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id, const hid_t file_space_id, const hid_t xfer_plist_id, H5std_string& strg) const;
+
+   protected:
+        // Sets the dataset id.
+        virtual void p_setId(const hid_t new_id);
+#endif // DOXYGEN_SHOULD_SKIP_THIS
 };
 #ifndef H5_NO_NAMESPACE
 }

c++/src/H5DataSpace.cpp

@@ -47,7 +47,7 @@ const DataSpace DataSpace::ALL( H5S_ALL );
 ///\exception	H5::DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSpace::DataSpace( H5S_class_t type ) : IdComponent(0)
+DataSpace::DataSpace(H5S_class_t type) : IdComponent()
 {
    id = H5Screate( type );
    if( id < 0 )
@@ -65,7 +65,7 @@ DataSpace::DataSpace( H5S_class_t type ) : IdComponent(0)
 ///\exception	H5::DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSpace::DataSpace( int rank, const hsize_t * dims, const hsize_t * maxdims) : IdComponent(0)
+DataSpace::DataSpace( int rank, const hsize_t * dims, const hsize_t * maxdims) : IdComponent()
 {
    id = H5Screate_simple( rank, dims, maxdims );
    if( id < 0 )
@@ -82,7 +82,10 @@ DataSpace::DataSpace( int rank, const hsize_t * dims, const hsize_t * maxdims) :
 ///\exception	H5::DataSpaceIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSpace::DataSpace(const hid_t existing_id) : IdComponent(existing_id) {}
+DataSpace::DataSpace(const hid_t existing_id) : IdComponent()
+{
+    id = existing_id;
+}
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace copy constructor
@@ -90,7 +93,11 @@ DataSpace::DataSpace(const hid_t existing_id) : IdComponent(existing_id) {}
 ///\param	original - IN: DataSpace object to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataSpace::DataSpace( const DataSpace& original ) : IdComponent( original ) {}
+DataSpace::DataSpace(const DataSpace& original) : IdComponent(original)
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	DataSpace::copy
@@ -401,7 +408,7 @@ hssize_t DataSpace::getSelectElemNpoints () const
 ///\par Description
 ///		For more information, please refer to the C layer Reference
 ///		Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5S.html#Dataspace-SelectElemPointList
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5S.html#Dataspace-SelectElemPointList
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSpace::getSelectElemPointlist ( hsize_t startpoint, hsize_t numpoints, hsize_t *buf ) const
@@ -425,7 +432,7 @@ void DataSpace::getSelectElemPointlist ( hsize_t startpoint, hsize_t numpoints,
 ///\par Description
 ///		For more information, please refer to the C layer Reference
 ///		Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5S.html#Dataspace-SelectBounds
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5S.html#Dataspace-SelectBounds
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSpace::getSelectBounds ( hsize_t* start, hsize_t* end ) const
@@ -451,7 +458,7 @@ void DataSpace::getSelectBounds ( hsize_t* start, hsize_t* end ) const
 ///\par Description
 ///		For more information, please refer to the C layer Reference
 ///		Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5S.html#Dataspace-SelectElements
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5S.html#Dataspace-SelectElements
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSpace::selectElements ( H5S_seloper_t op, const size_t num_elements, const hsize_t *coord) const
@@ -533,7 +540,7 @@ bool DataSpace::selectValid () const
 ///\par Description
 ///		For more information, please refer to the C layer Reference
 ///		Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5S.html#Dataspace-SelectHyperslab
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5S.html#Dataspace-SelectHyperslab
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataSpace::selectHyperslab( H5S_seloper_t op, const hsize_t *count, const hsize_t *start, const hsize_t *stride, const hsize_t *block ) const
@@ -547,6 +554,47 @@ void DataSpace::selectHyperslab( H5S_seloper_t op, const hsize_t *count, const h
    }
 }
 
+//--------------------------------------------------------------------------
+// Function:    DataSpace::getId
+// Purpose:     Get the id of this attribute
+// Modification:
+//	May 2008 - BMR
+//              Class hierarchy is revised to address bugzilla 1068.  Class
+//              AbstractDS and Attribute are moved out of H5Object.  In
+//              addition, member IdComponent::id is moved into subclasses, and
+//              IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t DataSpace::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:    DataSpace::p_setId
+///\brief       Sets the identifier of this object to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///             object fails
+// Description:
+//              The underlaying reference counting in the C library ensures
+//              that the current valid id of this object is properly closed.
+//              Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void DataSpace::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+        close();
+    }
+    catch (Exception close_error) {
+        throw DataSpaceIException(inMemFunc("p_setId"), close_error.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+}
+
 //--------------------------------------------------------------------------
 // Function:	DataSpace::close
 ///\brief	Closes this dataspace.
@@ -564,8 +612,10 @@ void DataSpace::close()
 	{
 	    throw DataSpaceIException("DataSpace::close", "H5Sclose failed");
 	}
-	// reset the id because the dataspace that it represents is now closed
-	id = 0;
+	// reset the id when the dataspace that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 
@@ -583,8 +633,7 @@ DataSpace::~DataSpace()
 {
     try {
 	close();
-    }
-    catch (Exception close_error) {
+    } catch (Exception close_error) {
 	cerr << "DataSpace::~DataSpace - " << close_error.getDetailMsg() << endl;
     }
 }

c++/src/H5DataSpace.h

@@ -103,7 +103,7 @@ class H5_DLLCPP DataSpace : public IdComponent {
 	// Sets or resets the size of this dataspace.
 	void setExtentSimple( int rank, const hsize_t *current_size, const hsize_t *maximum_size = NULL ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("DataSpace"); }
 
 	// Creates a DataSpace object using an existing dataspace id.
@@ -112,8 +112,18 @@ class H5_DLLCPP DataSpace : public IdComponent {
 	// Copy constructor: makes a copy of the original DataSpace object.
 	DataSpace(const DataSpace& original);
 
+	// Gets the dataspace id.
+	virtual hid_t getId() const;
+
 	// Destructor: properly terminates access to this dataspace.
 	virtual ~DataSpace();
+
+   private:
+	hid_t id;       // HDF5 dataspace id
+
+   protected:
+	// Sets the dataspace id.
+	virtual void p_setId(const hid_t new_id);
 };
 #ifndef H5_NO_NAMESPACE
 }

c++/src/H5DataType.cpp

@@ -38,6 +38,7 @@
 #include "H5AbstractDs.h"
 #include "H5DataSet.h"
 #include "H5File.h"
+#include "H5Attribute.h"
 
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
@@ -51,8 +52,6 @@ namespace H5 {
 // Function:	DataType overloaded constructor
 ///\brief	Creates a datatype using an existing datatype's id
 ///\param	existing_id - IN: Id of the existing datatype
-///\param	predefined  - IN: Indicates whether or not this datatype is
-///		a predefined datatype; default to \c false
 // Description
 //		Constructor creates a copy of an existing DataType using
 //		its id.  The argument "predefined" is default to false;
@@ -62,7 +61,10 @@ namespace H5 {
 //		- BMR 5/2004
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataType::DataType(const hid_t existing_id) : H5Object(existing_id) {}
+DataType::DataType(const hid_t existing_id) : H5Object()
+{
+    id = existing_id;
+}
 
 //--------------------------------------------------------------------------
 // Function:	DataType overloaded constructor
@@ -84,17 +86,74 @@ DataType::DataType( const H5T_class_t type_class, size_t size ) : H5Object()
 
 //--------------------------------------------------------------------------
 // Function:	DataType overload constructor - dereference
-///\brief	Given a reference to some object, returns that datatype
-///\param       obj - IN: Location reference object is in
+///\brief	Given a reference, ref, to an hdf5 group, creates a
+///		DataType object
+///\param       obj - IN: Specifying location referenced object is in
 ///\param	ref - IN: Reference pointer
-///\parDescription
-///		\c obj can be DataSet, Group, H5File, or named DataType, that 
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+///\par Description
+///		\c obj can be DataSet, Group, or named DataType, that 
 ///		is a datatype that has been named by DataType::commit.
 // Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	Jul, 2008
+//		Added for application convenience.
 //--------------------------------------------------------------------------
-DataType::DataType(IdComponent& obj, void* ref) : H5Object()
+DataType::DataType(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
 {
-   IdComponent::dereference(obj, ref);
+    try {
+	id = p_dereference(obj.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("DataType constructor - located by an H5Object",
+		deref_error.getDetailMsg());
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataType overload constructor - dereference
+///\brief	Given a reference, ref, to an hdf5 group, creates a
+///		DataType object
+///\param       h5file - IN: Location referenced object is in
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+// Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	Jul, 2008
+//		Added for application convenience.
+//--------------------------------------------------------------------------
+DataType::DataType(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
+{
+    try {
+	id = p_dereference(h5file.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("DataType constructor - located by an H5File",
+		deref_error.getDetailMsg());
+    }
+}
+
+//--------------------------------------------------------------------------
+// Function:	DataType overload constructor - dereference
+///\brief	Given a reference, ref, to an hdf5 group, creates a
+///		DataType object
+///\param       attr - IN: Specifying location where the referenced object is in
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+// Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	Jul, 2008
+//		Added for application convenience.
+//--------------------------------------------------------------------------
+DataType::DataType(Attribute& attr, const void* ref, H5R_type_t ref_type) : H5Object()
+{
+    try {
+	id = p_dereference(attr.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("DataType constructor - located by an Attribute",
+		deref_error.getDetailMsg());
+    }
 }
 
 //--------------------------------------------------------------------------
@@ -102,14 +161,18 @@ DataType::DataType(IdComponent& obj, void* ref) : H5Object()
 ///\brief	Default constructor: Creates a stub datatype
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataType::DataType() : H5Object() {}
+DataType::DataType() : H5Object(), id(0) {}
 
 //--------------------------------------------------------------------------
 // Function:	DataType copy constructor
 ///\brief	Copy constructor: makes a copy of the original DataType object.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DataType::DataType(const DataType& original) : H5Object(original) {}
+DataType::DataType(const DataType& original) : H5Object(original)
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	DataType::copy
@@ -142,10 +205,10 @@ void DataType::copy( const DataType& like_type )
 //--------------------------------------------------------------------------
 // Function:	DataType::copy
 ///\brief	Copies the datatype of the given dataset to this datatype object
-///\param	dset - IN: Dataset 
+///\param	dset - IN: Dataset
 ///\exception	H5::DataTypeIException
 // Programmer	Binh-Minh Ribler - Jan, 2007
-///\parDescription
+///\par Description
 ///		The resulted dataset will be transient and modifiable.
 //--------------------------------------------------------------------------
 void DataType::copy(const DataSet& dset)
@@ -210,7 +273,7 @@ bool DataType::operator==(const DataType& compared_type ) const
 // Function:	DataType::p_commit (private)
 //\brief	Commits a transient datatype to a file, creating a new
 //		named datatype
-//\param	loc_id - IN: The id of either a file, group, dataset, named 
+//\param	loc_id - IN: The id of either a file, group, dataset, named
 //			 datatype, or attribute.
 //\param	name - IN: Name of the datatype
 //\exception	H5::DataTypeIException
@@ -452,7 +515,7 @@ DataType DataType::getSuper() const
 ///\exception	H5::DataTypeIException
 ///\par Description
 ///		For more information, please see:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5T.html#Datatype-Register
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-Register
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DataType::registerFunc( H5T_pers_t pers, const char* name, const DataType& dest, H5T_conv_t func ) const
@@ -616,52 +679,6 @@ bool DataType::isVariableStr() const
    }
 }
 
-//--------------------------------------------------------------------------
-// Function:	DataType::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		DataType::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* DataType::Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type) const
-{
-   try {
-      return(p_reference(name, dataspace.getId(), ref_type));
-   }
-   catch (IdComponentException E) {
-      throw DataTypeIException(inMemFunc("Reference"), E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	DataType::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		DataType::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* DataType::Reference(const char* name) const
-{
-   try {
-      return(p_reference(name, -1, H5R_OBJECT));
-   }
-   catch (IdComponentException E) {
-      throw DataTypeIException(inMemFunc("Reference"), E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	DataType::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		DataType::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* DataType::Reference(const H5std_string& name) const
-{
-   return(Reference(name.c_str()));
-}
-
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 //--------------------------------------------------------------------------
 // Function:	DataType::getObjType
@@ -707,6 +724,47 @@ DataSpace DataType::getRegion(void *ref, H5R_type_t ref_type) const
    }
 }
 
+//--------------------------------------------------------------------------
+// Function:    DataType::getId
+// Purpose:     Get the id of this attribute
+// Modification:
+//      May 2008 - BMR
+//              Class hierarchy is revised to address bugzilla 1068.  Class
+//              AbstractDS and Attribute are moved out of H5Object.  In
+//              addition, member IdComponent::id is moved into subclasses, and
+//              IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t DataType::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:    DataType::p_setId
+///\brief       Sets the identifier of this object to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///             object fails
+// Description:
+//              The underlaying reference counting in the C library ensures
+//              that the current valid id of this object is properly closed.
+//              Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void DataType::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+        close();
+    }
+    catch (Exception close_error) {
+        throw DataTypeIException(inMemFunc("p_setId"), close_error.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+}
+
 //--------------------------------------------------------------------------
 // Function:	DataType::close
 ///\brief	Closes the datatype if it is not a predefined type.
@@ -723,8 +781,10 @@ void DataType::close()
 	{
 	    throw DataTypeIException(inMemFunc("close"), "H5Tclose failed");
 	}
-	// reset the id because the datatype that it represents is now closed
-	id = 0;
+	// reset the id when the datatype that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 
@@ -740,14 +800,12 @@ void DataType::close()
 //--------------------------------------------------------------------------
 DataType::~DataType()
 {
-    try {
-	close();
-    }
-    catch (Exception close_error) {
-	cerr << inMemFunc("~DataType - ") << close_error.getDetailMsg() << endl;
-    }
+	try {
+	    close();
+	} catch (Exception close_error) {
+	    cerr << inMemFunc("~DataType - ") << close_error.getDetailMsg() << endl;
+	}
 }
-
 #ifndef H5_NO_NAMESPACE
 } // end namespace
 #endif

c++/src/H5DataType.h

@@ -30,7 +30,9 @@ class H5_DLLCPP DataType : public H5Object {
 	DataType( const DataType& original );
 
 	// Creates a datatype by way of dereference.
-	DataType(IdComponent& obj, void* ref);
+	DataType(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+	DataType(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+	DataType(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
 
 	// Closes this datatype.
 	virtual void close();
@@ -99,14 +101,6 @@ class H5_DLLCPP DataType : public H5Object {
 	// Checks whether this datatype is a variable-length string.
 	bool isVariableStr() const;
 
-	// Creates a reference to a named HDF5 object or to a dataset region
-	// in this object.
-	void* Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const; // will be obsolete
-
-	// Creates a reference to a named HDF5 object in this object.
-	void* Reference(const char* name) const; // will be obsolete
-	void* Reference(const H5std_string& name) const; // will be obsolete
-
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 	// Retrieves the type of object that an object reference points to.
 	H5G_obj_t getObjType(void *ref, H5R_type_t ref_type = H5R_OBJECT) const;
@@ -115,7 +109,7 @@ class H5_DLLCPP DataType : public H5Object {
 	// Retrieves a dataspace with the region pointed to selected.
 	DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("DataType"); }
 
 	// Creates a copy of an existing DataType using its id
@@ -124,8 +118,18 @@ class H5_DLLCPP DataType : public H5Object {
 	// Default constructor
 	DataType();
 
+	// Gets the datatype id.
+	virtual hid_t getId() const;
+
 	// Destructor: properly terminates access to this datatype.
 	virtual ~DataType();
+
+   protected:
+	hid_t id;	// HDF5 datatype id
+
+	// Sets the datatype id.
+	virtual void p_setId(const hid_t new_id);
+
    private:
 	void p_commit(hid_t loc_id, const char* name);
 };

c++/src/H5DcreatProp.cpp

@@ -54,7 +54,7 @@ DSetCreatPropList::DSetCreatPropList( const DSetCreatPropList& orig ) : PropList
 ///		existing dataset creation property list.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-DSetCreatPropList::DSetCreatPropList(const hid_t plist_id) : PropList( plist_id ) {}
+DSetCreatPropList::DSetCreatPropList(const hid_t plist_id) : PropList(plist_id) {}
 
 //--------------------------------------------------------------------------
 // Function:	DSetCreatPropList::setChunk
@@ -106,8 +106,8 @@ int DSetCreatPropList::getChunk( int max_ndims, hsize_t* dim ) const
 ///\param	layout - IN: Type of storage layout for raw data
 ///\exception	H5::PropListIException
 ///\par Description
-///		For information on setting layout type, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetLayout
+///		For information on valid layout types, please refer to
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetLayout
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DSetCreatPropList::setLayout(H5D_layout_t layout) const
@@ -172,16 +172,16 @@ void DSetCreatPropList::setDeflate( int level ) const
 //--------------------------------------------------------------------------
 // Function:	DSetCreatPropList::setSzip
 ///\brief	Sets up for the use of the SZIP compression filter.
-///\param	options_mask     - IN: A bit-mask conveying the desired SZIP 
-///			options.  Valid values are H5_SZIP_EC_OPTION_MASK 
+///\param	options_mask     - IN: A bit-mask conveying the desired SZIP
+///			options.  Valid values are H5_SZIP_EC_OPTION_MASK
 ///			and H5_SZIP_NN_OPTION_MASK.
-///\param	pixels_per_block - IN: Number of pixels or data elements in 
+///\param	pixels_per_block - IN: Number of pixels or data elements in
 ///			each data block.
 ///\exception	H5::PropListIException
 ///\par Description
-///		The associate C function sets an SZIP compression filter, 
+///		The associate C function sets an SZIP compression filter,
 ///		H5Z_FILTER_SZIP, for a dataset.  For more information about
-///		SZIP and usage, please refer to the C layer Reference 
+///		SZIP and usage, please refer to the C layer Reference
 ///		Manual at:
 /// http://hdfgroup.org/HDF5/doc/RM_H5P.html#Property-SetSzip
 // Programmer	Binh-Minh Ribler - Jan, 2007
@@ -211,7 +211,7 @@ void DSetCreatPropList::setSzip(unsigned int options_mask, unsigned int pixels_p
 ///\par
 ///		For information on setting fill value, please refer to the
 ///		C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFillValue
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFillValue
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DSetCreatPropList::setFillValue( const DataType& fvalue_type, const void* value ) const
@@ -459,7 +459,7 @@ bool DSetCreatPropList::allFiltersAvail()
 ///\par Description
 ///		Please refer to the Reference Manual of \c H5Pset_shuffle for
 ///		details.
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetShuffle
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetShuffle
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void DSetCreatPropList::setShuffle() const

c++/src/H5DcreatProp.h

@@ -107,7 +107,7 @@ class H5_DLLCPP DSetCreatPropList : public PropList {
 	// Sets SZIP compression method.
 	void setSzip(unsigned int options_mask, unsigned int pixels_per_block) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("DSetCreatPropList"); }
 
 	// Copy constructor: creates a copy of a DSetCreatPropList object.

c++/src/H5DxferProp.cpp

@@ -309,7 +309,7 @@ void DSetMemXferPropList::getMulti(hid_t *memb_dxpl)
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For detail, please refer to the C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetSmallData
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetSmallData
 // Programmer:	Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void DSetMemXferPropList::setSmallDataBlockSize(hsize_t size)
@@ -349,7 +349,7 @@ hsize_t DSetMemXferPropList::getSmallDataBlockSize()
 ///\par Description
 ///		For information, please refer to the C layer Reference
 ///		Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetHyperVectorSize
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetHyperVectorSize
 // Programmer:	Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void DSetMemXferPropList::setHyperVectorSize(size_t vector_size)

c++/src/H5DxferProp.h

@@ -92,7 +92,7 @@ class H5_DLLCPP DSetMemXferPropList : public PropList {
 	// Determines whether error-detection is enabled for dataset reads.
 	H5Z_EDC_t getEDCCheck();
 
-	// Returns this class name.
+	///\brief Returns this class name.
 	virtual H5std_string fromClass () const { return("DSetMemXferPropList"); }
 
 	// Copy constructor: makes a copy of a DSetMemXferPropList object.
@@ -104,7 +104,6 @@ class H5_DLLCPP DSetMemXferPropList : public PropList {
 
 	// Noop destructor
 	virtual ~DSetMemXferPropList();
-
 };
 #ifndef H5_NO_NAMESPACE
 }

c++/src/H5EnumType.h

@@ -57,7 +57,7 @@ class H5_DLLCPP EnumType : public DataType {
 	void valueOf( const char* name, void *value ) const;
 	void valueOf( const H5std_string& name, void *value ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("EnumType"); }
 
 	// Default constructor

c++/src/H5Exception.cpp

@@ -252,7 +252,7 @@ void Exception::walkErrorStack( H5E_direction_t direction, H5E_walk2_t func, voi
 // Function:	Exception::getDetailMsg
 ///\brief	Returns the detailed message set at the time the exception
 ///		is thrown.
-///\return	Text message - \c std::string
+///\return	Text message - \c H5std_string
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 H5std_string Exception::getDetailMsg() const
@@ -275,7 +275,7 @@ const char* Exception::getCDetailMsg() const
 //--------------------------------------------------------------------------
 // Function:	Exception::getFuncName
 ///\brief	Returns the name of the function, where the exception is thrown.
-///\return	Text message - \c std::string
+///\return	Text message - \c H5std_string
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 H5std_string Exception::getFuncName() const

c++/src/H5Exception.h

@@ -79,12 +79,6 @@ class H5_DLLCPP Exception {
 	virtual ~Exception();
 
    private:
-// Because 'string' is not instantiated at compilation time, this
-// warning is displayed when building DLL; but the class is exported
-// so the warning is harmless
-#if defined(_WIN32)
-#pragma warning(disable: 4251)
-#endif
 	H5std_string detail_message;
 	H5std_string func_name;
 

c++/src/H5FaccProp.cpp

@@ -76,7 +76,7 @@ void FileAccPropList::setStdio() const
 ///		driver was set for the property list.  The driver ID is
 ///		only valid as long as the file driver remains registered.
 ///		Valid driver identifiers can be found at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-GetDriver
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-GetDriver
 ///\exception	H5::PropListIException
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
@@ -99,7 +99,7 @@ hid_t FileAccPropList::getDriver() const
 ///\par Description
 ///		For a list of valid driver identifiers, please see the C
 ///		layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-GetDriver
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetDriver
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setDriver(hid_t new_driver_id, const void *new_driver_info) const
@@ -157,7 +157,7 @@ hsize_t FileAccPropList::getFamilyOffset() const
 ///\par Description
 ///		For more details on the use of \c H5FD_CORE driver, please
 ///		refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFaplCore
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFaplCore
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setCore (size_t increment, hbool_t backing_store) const
@@ -225,7 +225,7 @@ void FileAccPropList::getFamily(hsize_t& memb_size, FileAccPropList& memb_plist)
    {
       throw PropListIException("FileAccPropList::getFamily", "H5Pget_fapl_family failed");
    }
-   memb_plist.setId(memb_plist_id);
+   memb_plist.p_setId(memb_plist_id);
 }
 
 //--------------------------------------------------------------------------
@@ -261,7 +261,7 @@ FileAccPropList FileAccPropList::getFamily(hsize_t& memb_size) const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		Temporary - For information, please refer to:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFaplSplit
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFaplSplit
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setSplit( FileAccPropList& meta_plist, FileAccPropList& raw_plist, const char* meta_ext, const char* raw_ext ) const
@@ -295,11 +295,13 @@ void FileAccPropList::setSplit( FileAccPropList& meta_plist, FileAccPropList& ra
 #ifdef H5_HAVE_STREAM // for Stream Virtual File Driver
 //--------------------------------------------------------------------------
 // Function:	FileAccPropList::getStream
-///\brief	Retrieves the streaming I/O driver settings
-///\return	The streaming I/O file access property list structure
-///		For detail on this structure, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFaplStream
-///\exception	H5::PropListIException
+// Purpose:	Retrieves the streaming I/O driver settings
+// Return:	The streaming I/O file access property list structure
+// Exception:	H5::PropListIException
+// Description:
+//		This C API seems to be removed from the library; will remove
+//		this wrapper next time, only removed it from the RM in this
+//		release - Oct, 2008
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 H5FD_stream_fapl_t FileAccPropList::getStream() const
@@ -315,13 +317,14 @@ H5FD_stream_fapl_t FileAccPropList::getStream() const
 
 //--------------------------------------------------------------------------
 // Function:	FileAccPropList::setStream
-///\brief	Modifies this file access property list to use the Stream
-///		driver.
-///\param	fapl - IN: The streaming I/O file access property list
-///\exception	H5::PropListIException
-///\par Description
-///		For detail on \a fapl, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFaplStream
+// Purpose:	Modifies this file access property list to use the Stream
+//		driver.
+// Param:	fapl - IN: The streaming I/O file access property list
+// Exception:	H5::PropListIException
+// Description:
+//		This C API seems to be removed from the library; will remove
+//		this wrapper next time, only removed it from the RM in this
+//		release - Oct, 2008
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setStream(H5FD_stream_fapl_t &fapl) const
@@ -360,7 +363,7 @@ size_t FileAccPropList::getSieveBufSize() const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For detail on data sieving, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetSieveBufSize
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetSieveBufSize
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setSieveBufSize(size_t bufsize) const
@@ -380,7 +383,7 @@ void FileAccPropList::setSieveBufSize(size_t bufsize) const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For more detail, please see the C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetMetaBlockSize
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetMetaBlockSize
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setMetaBlockSize(hsize_t &block_size) const
@@ -420,7 +423,7 @@ hsize_t FileAccPropList::getMetaBlockSize() const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For detail on \a flags, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFaplStream
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetFaplLog
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setLog(const char *logfile, unsigned flags, size_t buf_size) const
@@ -477,7 +480,7 @@ void FileAccPropList::setSec2() const
 ///		The parameter \a alignment must have a positive value.
 ///
 ///		For detail on \a setting alignment, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetAlignment
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetAlignment
 // Programmer:	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void FileAccPropList::setAlignment( hsize_t threshold, hsize_t alignment ) const
@@ -514,7 +517,7 @@ void FileAccPropList::getAlignment( hsize_t &threshold, hsize_t &alignment ) con
 ///\exception	H5::PropListIException
 ///\par Description
 ///		More details and valid values for \a dtype can be found at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetMultiType
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetMultiType
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void FileAccPropList::setMultiType(H5FD_mem_t dtype) const
@@ -533,7 +536,7 @@ void FileAccPropList::setMultiType(H5FD_mem_t dtype) const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		More details and possible returned values can be found at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-GetMultiType
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-GetMultiType
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 H5FD_mem_t FileAccPropList::getMultiType() const
@@ -634,7 +637,7 @@ H5F_close_degree_t FileAccPropList::getFcloseDegree()
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For detail on \a fapl, please refer to
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetFaplStream
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetGCReferences
 // Programmer:	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void FileAccPropList::setGcReferences( unsigned gc_ref ) const

c++/src/H5FaccProp.h

@@ -123,7 +123,7 @@ class H5_DLLCPP FileAccPropList : public PropList {
 	// Returns garbage collecting references setting.
 	unsigned getGcReferences() const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("FileAccPropList"); }
 
 	// Copy constructor: creates a copy of a FileAccPropList object.

c++/src/H5FcreatProp.cpp

@@ -126,7 +126,7 @@ hsize_t FileCreatPropList::getUserblock() const
 ///\par Description
 ///		For information on setting sizes, please refer to the
 ///		C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetSizes
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetSizes
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void FileCreatPropList::setSizes( size_t sizeof_addr, size_t sizeof_size ) const
@@ -166,7 +166,7 @@ void FileCreatPropList::getSizes( size_t& sizeof_addr, size_t& sizeof_size ) con
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For information, please see the C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetSymK
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetSymK
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void FileCreatPropList::setSymk( unsigned ik, unsigned lk ) const
@@ -187,7 +187,7 @@ void FileCreatPropList::setSymk( unsigned ik, unsigned lk ) const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For information, please see
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetSymK
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-GetSymK
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void FileCreatPropList::getSymk( unsigned& ik, unsigned& lk ) const
@@ -208,7 +208,7 @@ void FileCreatPropList::getSymk( unsigned& ik, unsigned& lk ) const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For information, please see the C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetIstoreK
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetIstoreK
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void FileCreatPropList::setIstorek( unsigned ik ) const
@@ -228,7 +228,7 @@ void FileCreatPropList::setIstorek( unsigned ik ) const
 ///\exception	H5::PropListIException
 ///\par Description
 ///		For information, please see
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5P.html#Property-SetIstoreK
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-GetIstoreK
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 unsigned FileCreatPropList::getIstorek() const

c++/src/H5FcreatProp.h

@@ -60,7 +60,7 @@ class H5_DLLCPP FileCreatPropList : public PropList {
 	// indexing chunked datasets.
 	void setIstorek( unsigned ik ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("FileCreatPropList"); }
 
 	// Copy constructor: creates a copy of a FileCreatPropList object.

c++/src/H5File.cpp

@@ -50,7 +50,7 @@ namespace H5 {
 ///\brief	Default constructor: creates a stub H5File object.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-H5File::H5File() : IdComponent(0) {}
+H5File::H5File() : IdComponent(), id(0) {}
 
 //--------------------------------------------------------------------------
 // Function:	H5File overloaded constructor
@@ -76,7 +76,7 @@ H5File::H5File() : IdComponent(0) {}
 ///		For info on file creation in the case of an already-open file,
 ///		please refer to the \b Special \b case section in the C layer
 ///		Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5F.html#File-Create
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5F.html#File-Create
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 H5File::H5File( const char* name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist ) : IdComponent(0)
@@ -88,7 +88,7 @@ H5File::H5File( const char* name, unsigned int flags, const FileCreatPropList& c
 // Function:	H5File overloaded constructor
 ///\brief	This is another overloaded constructor.  It differs from the
 ///		above constructor only in the type of the \a name argument.
-///\param	name - IN: Name of the file - \c std::string
+///\param	name - IN: Name of the file - \c H5std_string
 ///\param	flags - IN: File access flags
 ///\param	create_plist - IN: File creation property list, used when
 ///		modifying default file meta-data.  Default to
@@ -140,7 +140,11 @@ void H5File::p_get_file(const char* name, unsigned int flags, const FileCreatPro
 ///\param	original - IN: H5File instance to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-H5File::H5File( const H5File& original ) : IdComponent( original ) {}
+H5File::H5File(const H5File& original) : IdComponent(original)
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	H5File::flush
@@ -187,8 +191,8 @@ bool H5File::isHdf5(const char* name)
 //--------------------------------------------------------------------------
 // Function:	H5File::isHdf5
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It takes an \c std::string for \a name.
-///\param	name - IN: Name of the file - \c std::string
+///		It takes an \c H5std_string for \a name.
+///\param	name - IN: Name of the file - \c H5std_string
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 bool H5File::isHdf5(const H5std_string& name )
@@ -227,8 +231,8 @@ void H5File::openFile(const char* name, unsigned int flags, const FileAccPropLis
 //--------------------------------------------------------------------------
 // Function:	H5File::openFile
 ///\brief	This is an overloaded member function, provided for convenience.
-///		It takes an \c std::string for \a name.
-///\param	name         - IN: Name of the file - \c std::string
+///		It takes an \c H5std_string for \a name.
+///\param	name         - IN: Name of the file - \c H5std_string
 ///\param	flags        - IN: File access flags
 ///\param	access_plist - IN: File access property list.  Default to
 ///		FileAccPropList::DEFAULT
@@ -374,9 +378,9 @@ hssize_t H5File::getFreeSpace() const
 /// Multiple object types can be combined with the logical OR operator (|).
 // Programmer   Binh-Minh Ribler - May 2004
 //--------------------------------------------------------------------------
-int H5File::getObjCount(unsigned types) const
+ssize_t H5File::getObjCount(unsigned types) const
 {
-   int num_objs = H5Fget_obj_count(id, types);
+   ssize_t num_objs = H5Fget_obj_count(id, types);
    if( num_objs < 0 )
    {
       throw FileIException("H5File::getObjCount", "H5Fget_obj_count failed");
@@ -393,9 +397,9 @@ int H5File::getObjCount(unsigned types) const
 ///\exception	H5::FileIException
 // Programmer   Binh-Minh Ribler - May 2004
 //--------------------------------------------------------------------------
-int H5File::getObjCount() const
+ssize_t H5File::getObjCount() const
 {
-   int num_objs = H5Fget_obj_count(id, H5F_OBJ_ALL);
+   ssize_t num_objs = H5Fget_obj_count(id, H5F_OBJ_ALL);
    if( num_objs < 0 )
    {
       throw FileIException("H5File::getObjCount", "H5Fget_obj_count failed");
@@ -428,9 +432,9 @@ int H5File::getObjCount() const
 // Notes: will do the overload for this one after hearing from Quincey???
 // Programmer   Binh-Minh Ribler - May 2004
 //--------------------------------------------------------------------------
-void H5File::getObjIDs(unsigned types, int max_objs, hid_t *oid_list) const
+void H5File::getObjIDs(unsigned types, size_t max_objs, hid_t *oid_list) const
 {
-   herr_t ret_value = H5Fget_obj_ids(id, types, max_objs, oid_list);
+   ssize_t ret_value = H5Fget_obj_ids(id, types, max_objs, oid_list);
    if( ret_value < 0 )
    {
       throw FileIException("H5File::getObjIDs", "H5Fget_obj_ids failed");
@@ -502,60 +506,14 @@ H5std_string H5File::getFileName() const
    }
 }
 
-//--------------------------------------------------------------------------
-// Function:	H5File::Reference
-///\brief	Important!!! - This functions does not work correctly, it 
-///		will be removed in the near future.  Please use 
-///		H5File::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* H5File::Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type) const
-{
-   try {
-      return(p_reference(name, dataspace.getId(), ref_type));
-   }
-   catch (IdComponentException E) {
-      throw FileIException("H5File::Reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	H5File::Reference
-///\brief	Important!!! - This functions does not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		H5File::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* H5File::Reference(const char* name) const
-{
-   try {
-      return(p_reference(name, -1, H5R_OBJECT));
-   }
-   catch (IdComponentException E) {
-      throw FileIException("H5File::Reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	H5File::Reference
-///\brief	Important!!! - This functions does not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		H5File::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* H5File::Reference(const H5std_string& name) const
-{
-   return(Reference(name.c_str()));
-}
-
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 //--------------------------------------------------------------------------
 // Function:	H5File::getObjType
 ///\brief	Retrieves the type of object that an object reference points to.
 ///\param	ref      - IN: Reference to query
 ///\param	ref_type - IN: Type of reference, valid values are:
-///		\li \c H5R_OBJECT \tReference is an object reference.
-///		\li \c H5R_DATASET_REGION \tReference is a dataset region reference.
+///		\li \c H5R_OBJECT         - Reference is an object reference.
+///		\li \c H5R_DATASET_REGION - Reference is a dataset region reference.
 ///\return	Object type, which can be one of the following:
 ///		\li \c H5G_LINK    - Object is a symbolic link.
 ///		\li \c H5G_GROUP   - Object is a group.
@@ -616,6 +574,134 @@ hsize_t H5File::getFileSize() const
    return (file_size);
 }
 
+//--------------------------------------------------------------------------
+// Function:    H5File::p_reference (protected)
+// Purpose      Creates a reference to an HDF5 object or a dataset region.
+// Parameters
+//              name - IN: Name of the object to be referenced
+//              dataspace - IN: Dataspace with selection
+//              ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
+// Exception    H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5File::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
+{
+   herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
+   if (ret_value < 0)
+   {
+      throw IdComponentException("", "H5Rcreate failed");
+   }
+}
+
+//--------------------------------------------------------------------------
+// Function:    H5File::reference
+///\brief       Creates a reference to an HDF5 object or a dataset region.
+///\param       ref - IN: Reference pointer
+///\param       name - IN: Name of the object to be referenced
+///\param       dataspace - IN: Dataspace with selection
+///\param       ref_type - IN: Type of reference to query, valid values are:
+///             \li \c H5R_OBJECT         - Reference is an object reference.
+///             \li \c H5R_DATASET_REGION - Reference is a dataset region
+///                     reference. - this is the default
+///\exception   H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5File::reference(void* ref, const char* name, const DataSpace& dataspace, H5R_type_t ref_type) const
+{
+   try {
+      p_reference(ref, name, dataspace.getId(), ref_type);
+   }
+   catch (IdComponentException E) {
+      throw IdComponentException("H5File::reference", E.getDetailMsg());
+   }
+}
+
+//--------------------------------------------------------------------------
+// Function:    H5File::reference
+///\brief       This is an overloaded function, provided for your convenience.
+///             It differs from the above function in that it only creates
+///             a reference to an HDF5 object, not to a dataset region.
+///\param       ref - IN: Reference pointer
+///\param       name - IN: Name of the object to be referenced - \c char pointer
+///\exception   H5::IdComponentException
+///\par Description
+//              This function passes H5R_OBJECT and -1 to the protected
+//              function for it to pass to the C API H5Rcreate
+//              to create a reference to the named object.
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5File::reference(void* ref, const char* name) const
+{
+   try {
+      p_reference(ref, name, -1, H5R_OBJECT);
+   }
+   catch (IdComponentException E) {
+      throw IdComponentException("H5File::reference", E.getDetailMsg());
+   }
+}
+//--------------------------------------------------------------------------
+// Function:    H5File::reference
+///\brief       This is an overloaded function, provided for your convenience.
+///             It differs from the above function in that it takes an
+///             \c H5std_string for the object's name.
+///\param       ref - IN: Reference pointer
+///\param       name - IN: Name of the object to be referenced - \c H5std_string
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5File::reference(void* ref, const H5std_string& name) const
+{
+   reference(ref, name.c_str());
+}
+
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+//--------------------------------------------------------------------------
+// Function:    H5File::p_get_obj_type (protected)
+// Purpose      Retrieves the type of object that an object reference points to.
+// Parameters
+//              ref      - IN: Reference to query
+//              ref_type - IN: Type of reference to query
+// Return       An object type, which can be one of the following:
+//                      H5G_LINK Object is a symbolic link.
+//                      H5G_GROUP Object is a group.
+//                      H5G_DATASET   Object is a dataset.
+//                      H5G_TYPE Object is a named datatype
+// Exception    H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+H5G_obj_t H5File::p_get_obj_type(void *ref, H5R_type_t ref_type) const
+{
+   H5G_obj_t obj_type = H5Rget_obj_type1(getId(), ref_type, ref);
+
+   if (obj_type == H5G_UNKNOWN)
+   {
+      throw IdComponentException("", "H5Rget_obj_type failed");
+   }
+   return(obj_type);
+}
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+
+//--------------------------------------------------------------------------
+// Function:    H5File::p_get_region (protected)
+// Purpose      Retrieves a dataspace with the region pointed to selected.
+// Parameters
+//              ref_type - IN: Type of reference to get region of - default
+//                              to H5R_DATASET_REGION
+//              ref      - IN: Reference to get region of
+// Return       Dataspace id
+// Exception    H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+hid_t H5File::p_get_region(void *ref, H5R_type_t ref_type) const
+{
+   hid_t space_id = H5Rget_region(getId(), ref_type, ref);
+   if (space_id < 0)
+   {
+      throw IdComponentException("", "H5Rget_region failed");
+   }
+   return(space_id);
+}
+
 //--------------------------------------------------------------------------
 // Function:	H5File::getLocId
 // Purpose:	Get the id of this file
@@ -629,6 +715,47 @@ hid_t H5File::getLocId() const
    return( getId() );
 }
 
+//--------------------------------------------------------------------------
+// Function:    H5File::getId
+// Purpose:     Get the id of this attribute
+// Modification:
+//      May 2008 - BMR
+//              Class hierarchy is revised to address bugzilla 1068.  Class
+//              AbstractDS and Attribute are moved out of H5Object.  In
+//              addition, member IdComponent::id is moved into subclasses, and
+//              IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t H5File::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:    H5File::p_setId
+///\brief       Sets the identifier of this object to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///             object fails
+// Description:
+//              The underlaying reference counting in the C library ensures
+//              that the current valid id of this object is properly closed.
+//              Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void H5File::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+        close();
+    }
+    catch (Exception E) {
+        throw FileIException("H5File::p_setId", E.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+}
+
 //--------------------------------------------------------------------------
 // Function:	H5File::close
 ///\brief	Closes this HDF5 file.
@@ -645,8 +772,10 @@ void H5File::close()
 	{
 	    throw FileIException("H5File::close", "H5Fclose failed");
 	}
-	// reset the id because the file that it represents is now closed
-	id = 0;
+	// reset the id when the file that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 
@@ -685,8 +814,7 @@ H5File::~H5File()
 {
     try {
 	close();
-    }
-    catch (Exception close_error) {
+    } catch (Exception close_error) {
 	cerr << "H5File::~H5File - " << close_error.getDetailMsg() << endl;
     }
 }

c++/src/H5File.h

@@ -60,12 +60,12 @@ class H5_DLLCPP H5File : public IdComponent, public CommonFG {
 
 	// Returns the number of opened object IDs (files, datasets, groups
 	// and datatypes) in the same file.
-	int getObjCount(unsigned types) const;
-	int getObjCount() const;
+	ssize_t getObjCount(unsigned types) const;
+	ssize_t getObjCount() const;
 
 	// Retrieves a list of opened object IDs (files, datasets, groups
 	// and datatypes) in the same file.
-	void getObjIDs(unsigned types, int max_objs, hid_t *oid_list) const;
+	void getObjIDs(unsigned types, size_t max_objs, hid_t *oid_list) const;
 
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 	// Retrieves the type of object that an object reference points to.
@@ -89,13 +89,12 @@ class H5_DLLCPP H5File : public IdComponent, public CommonFG {
 
 	// Creates a reference to a named HDF5 object or to a dataset region
 	// in this object.
-	void* Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const; // will be obsolete
+	void reference(void* ref, const char* name, const DataSpace& dataspace,
+			H5R_type_t ref_type = H5R_DATASET_REGION) const;
+	void reference(void* ref, const char* name) const;
+	void reference(void* ref, const H5std_string& name) const;
 
-	// Creates a reference to a named Hdf5 object in this object.
-	void* Reference(const char* name) const; // will be obsolete
-	void* Reference(const H5std_string& name) const; // will be obsolete
-
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("H5File"); }
 
 	// Throw file exception.
@@ -110,14 +109,38 @@ class H5_DLLCPP H5File : public IdComponent, public CommonFG {
 	// Copy constructor: makes a copy of the original H5File object.
 	H5File(const H5File& original);
 
+	// Gets the HDF5 file id.
+	virtual hid_t getId() const;
+
 	// H5File destructor.
 	virtual ~H5File();
 
    private:
+	hid_t id;	// HDF5 file id
+
+#ifndef DOXYGEN_SHOULD_SKIP_THIS
+
 	// This function is private and contains common code between the
 	// constructors taking a string or a char*
 	void p_get_file( const char* name, unsigned int flags, const FileCreatPropList& create_plist, const FileAccPropList& access_plist );
 
+	// Creates a reference to an HDF5 object or a dataset region.
+	void p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const;
+
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+	// Retrieves the type of object that an object reference points to.
+	H5G_obj_t p_get_obj_type(void *ref, H5R_type_t ref_type) const;
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+	// Retrieves a dataspace with the region pointed to selected.
+	hid_t p_get_region(void *ref, H5R_type_t ref_type) const;
+
+   protected:
+	// Sets the HDF5 file id.
+	virtual void p_setId(const hid_t new_id);
+
+#endif // DOXYGEN_SHOULD_SKIP_THIS
+
 };
 #ifndef H5_NO_NAMESPACE
 }

c++/src/H5FloatType.h

@@ -53,7 +53,7 @@ class H5_DLLCPP FloatType : public AtomType {
 	// Sets the mantissa normalization of a floating-point datatype.
 	void setNorm( H5T_norm_t norm ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("FloatType"); }
 
 	// Default constructor

c++/src/H5Group.cpp

@@ -33,6 +33,7 @@
 #include "H5DataSpace.h"
 #include "H5DataSet.h"
 #include "H5CommonFG.h"
+#include "H5Attribute.h"
 #include "H5Group.h"
 #include "H5File.h"
 #include "H5Alltypes.h"
@@ -50,7 +51,7 @@ namespace H5 {
 ///\brief	Default constructor: creates a stub Group.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-Group::Group() : H5Object() {}
+Group::Group() : H5Object(), id(0) {}
 
 //--------------------------------------------------------------------------
 // Function:	Group copy constructor
@@ -58,7 +59,11 @@ Group::Group() : H5Object() {}
 ///\param	original - IN: Original group to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-Group::Group( const Group& original ) : H5Object( original ) {}
+Group::Group(const Group& original) : H5Object(original)
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	Group::getLocId
@@ -74,70 +79,72 @@ hid_t Group::getLocId() const
 //--------------------------------------------------------------------------
 // Function:	Group overloaded constructor
 ///\brief	Creates a Group object using the id of an existing group.
-///\param	group_id - IN: Id of an existing group
+///\param	existing_id - IN: Id of an existing group
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-Group::Group( const hid_t group_id ) : H5Object( group_id ) {}
+Group::Group(const hid_t existing_id) : H5Object()
+{
+    id = existing_id;
+}
 
 //--------------------------------------------------------------------------
 // Function:	Group overload constructor - dereference
-///\brief	Given a reference to some object, returns that group
-///             obj - IN: Location reference object is in
+///\brief	Given a reference, ref, to an hdf5 group, creates a Group object
+///\param	obj - IN: Specifying location referenced object is in
 ///\param	ref - IN: Reference pointer
-///\parDescription
-///		\c obj can be DataSet, Group, H5File, or named DataType, that 
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+///\par Description
+///		\c obj can be DataSet, Group, or named DataType, that 
 ///		is a datatype that has been named by DataType::commit.
 // Programmer	Binh-Minh Ribler - Oct, 2006
 //--------------------------------------------------------------------------
-Group::Group(IdComponent& obj, void* ref) : H5Object()
+Group::Group(H5Object& obj, const void* ref, H5R_type_t ref_type) : H5Object()
 {
-   IdComponent::dereference(obj, ref);
+    try {
+	id = p_dereference(obj.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("Group constructor - located by an H5Object",
+		deref_error.getDetailMsg());
+    }
 }
 
 //--------------------------------------------------------------------------
-// Function:	Group::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		Group::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
+// Function:	Group overload constructor - dereference
+///\brief	Given a reference, ref, to an hdf5 group, creates a Group object
+///\param	h5file - IN: Location referenced object is in
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+// Programmer	Binh-Minh Ribler - Oct, 2006
 //--------------------------------------------------------------------------
-void* Group::Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type) const
+Group::Group(H5File& h5file, const void* ref, H5R_type_t ref_type) : H5Object()
 {
-   try {
-      return(p_reference(name, dataspace.getId(), ref_type));
-   }
-   catch (IdComponentException E) {
-      throw GroupIException("Group::Reference", E.getDetailMsg());
-   }
+    try {
+	id = p_dereference(h5file.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("Group constructor - located by an H5File",
+		deref_error.getDetailMsg());
+    }
 }
 
 //--------------------------------------------------------------------------
-// Function:	Group::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		Group::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
+// Function:	Group overload constructor - dereference
+///\brief	Given a reference, ref, to an hdf5 group, creates a Group object
+///\param	attr - IN: Specifying location where the referenced object is in
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type - default to H5R_OBJECT
+///\exception	H5::ReferenceException
+// Programmer	Binh-Minh Ribler - Oct, 2006
 //--------------------------------------------------------------------------
-void* Group::Reference(const char* name) const
+Group::Group(Attribute& attr, const void* ref, H5R_type_t ref_type) : H5Object()
 {
-   try {
-      return(p_reference(name, -1, H5R_OBJECT));
-   }
-   catch (IdComponentException E) {
-      throw GroupIException("Group::Reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:	Group::Reference
-///\brief	Important!!! - This functions may not work correctly, it 
-///		will be removed in the near future.  Please use similar
-///		Group::reference instead!
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* Group::Reference(const H5std_string& name) const
-{
-   return(Reference(name.c_str()));
+    try {
+	id = p_dereference(attr.getId(), ref, ref_type);
+    } catch (ReferenceException deref_error) {
+	throw ReferenceException("Group constructor - located by an Attribute",
+		deref_error.getDetailMsg());
+    }
 }
 
 #ifndef H5_NO_DEPRECATED_SYMBOLS
@@ -146,13 +153,13 @@ void* Group::Reference(const H5std_string& name) const
 ///\brief	Retrieves the type of object that an object reference points to.
 ///\param	ref      - IN: Reference to query
 ///\param	ref_type - IN: Type of reference to query, valid values are:
-///		\li \c H5R_OBJECT \tReference is an object reference.
-///		\li \c H5R_DATASET_REGION \tReference is a dataset region reference.
+///		\li \c H5R_OBJECT         - Reference is an object reference.
+///		\li \c H5R_DATASET_REGION - Reference is a dataset region reference.
 ///\return	An object type, which can be one of the following:
-///			H5G_LINK Object is a symbolic link.
-///			H5G_GROUP Object is a group.
-///			H5G_DATASET   Object is a dataset.
-///			H5G_TYPE Object is a named datatype
+///		\li \c H5G_LINK (0)    - Object is a symbolic link.
+///		\li \c H5G_GROUP (1)   - Object is a group.
+///		\li \c H5G_DATASET (2) - Object is a dataset.
+///		\li \c H5G_TYPE (3)    - Object is a named datatype
 ///\exception	H5::GroupIException
 // Programmer	Binh-Minh Ribler - May, 2004
 //--------------------------------------------------------------------------
@@ -187,6 +194,47 @@ DataSpace Group::getRegion(void *ref, H5R_type_t ref_type) const
    }
 }
 
+//--------------------------------------------------------------------------
+// Function:    Group::getId
+// Purpose:     Get the id of this attribute
+// Modification:
+//      May 2008 - BMR
+//		Class hierarchy is revised to address bugzilla 1068.  Class
+//		AbstractDS and Attribute are moved out of H5Object.  In
+//		addition, member IdComponent::id is moved into subclasses, and
+//		IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t Group::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:    Group::p_setId
+///\brief       Sets the identifier of this object to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///		object fails
+// Description:
+//		The underlaying reference counting in the C library ensures
+//		that the current valid id of this object is properly closed.
+//		Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void Group::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+        close();
+    }
+    catch (Exception close_error) {
+        throw GroupIException("Group::p_setId", close_error.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+}
+
 //--------------------------------------------------------------------------
 // Function:	Group::close
 ///\brief	Closes this group.
@@ -203,8 +251,10 @@ void Group::close()
 	{
 	    throw GroupIException("Group::close", "H5Gclose failed");
 	}
-	// reset the id because the group that it represents is now closed
-	id = 0;
+	// reset the id when the group that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 

c++/src/H5Group.h

@@ -34,15 +34,7 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
 	// Retrieves a dataspace with the region pointed to selected.
 	DataSpace getRegion(void *ref, H5R_type_t ref_type = H5R_DATASET_REGION) const;
 
-	// Creates a reference to a named Hdf5 object or to a dataset region
-	// in this object.
-	void* Reference(const char* name, DataSpace& dataspace, H5R_type_t ref_type = H5R_DATASET_REGION) const; // will be obsolete
-
-	// Creates a reference to a named Hdf5 object in this object.
-	void* Reference(const char* name) const; // will be obsolete
-	void* Reference(const H5std_string& name) const; // will be obsolete
-
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("Group"); }
 
 	// Throw group exception.
@@ -52,7 +44,9 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
 	virtual hid_t getLocId() const;
 
 	// Creates a group by way of dereference.
-	Group(IdComponent& obj, void* ref);
+	Group(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+        Group(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+        Group(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
 
 	// default constructor
 	Group();
@@ -60,12 +54,21 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
 	// Copy constructor: makes a copy of the original object
 	Group(const Group& original);
 
+	// Gets the group id.
+	virtual hid_t getId() const;
+
 	// Destructor
 	virtual ~Group();
 
 	// Creates a copy of an existing group using its id.
 	Group( const hid_t group_id );
 
+   private:
+	hid_t id;	// HDF5 group id
+
+   protected:
+	// Sets the group id.
+	virtual void p_setId(const hid_t new_id);
 };
 #ifndef H5_NO_NAMESPACE
 }

c++/src/H5IdComponent.cpp

@@ -18,7 +18,6 @@
 #endif /*H5_VMS*/
 
 #include <string>
-
 #include "H5Include.h"
 #include "H5Exception.h"
 #include "H5Library.h"
@@ -36,7 +35,7 @@ namespace H5 {
 ///\exception	H5::DataTypeIException
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-IdComponent::IdComponent(const hid_t h5_id) : id(h5_id) {}
+IdComponent::IdComponent(const hid_t h5_id) {}
 
 //--------------------------------------------------------------------------
 // Function:	IdComponent copy constructor
@@ -44,11 +43,7 @@ IdComponent::IdComponent(const hid_t h5_id) : id(h5_id) {}
 ///\param	original - IN: IdComponent instance to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-IdComponent::IdComponent( const IdComponent& original )
-{
-    id = original.id;
-    incRefCount(); // increment number of references to this id
-}
+IdComponent::IdComponent( const IdComponent& original ) {}
 
 //--------------------------------------------------------------------------
 // Function:	IdComponent::incRefCount
@@ -69,7 +64,7 @@ void IdComponent::incRefCount(const hid_t obj_id) const
 //--------------------------------------------------------------------------
 void IdComponent::incRefCount() const
 {
-    incRefCount(id);
+    incRefCount(getId());
 }
 
 //--------------------------------------------------------------------------
@@ -99,7 +94,7 @@ void IdComponent::decRefCount(const hid_t obj_id) const
 //--------------------------------------------------------------------------
 void IdComponent::decRefCount() const
 {
-    decRefCount(id);
+    decRefCount(getId());
 }
 
 //--------------------------------------------------------------------------
@@ -128,13 +123,13 @@ int IdComponent::getCounter(const hid_t obj_id) const
 //--------------------------------------------------------------------------
 int IdComponent::getCounter() const
 {
-    return (getCounter(id));
+    return (getCounter(getId()));
 }
 
 //--------------------------------------------------------------------------
 // Function:	hdfObjectType
 ///\brief	Given an id, returns the type of the object.
-///return	a valid HDF object type, which may be one of the following:
+///\return	a valid HDF object type, which may be one of the following:
 ///		\li \c H5I_FILE
 ///		\li \c H5I_GROUP
 ///		\li \c H5I_DATATYPE
@@ -173,7 +168,7 @@ IdComponent& IdComponent::operator=( const IdComponent& rhs )
     if (this != &rhs)
     {
 	// handling references to this id
-	try {
+  	try {
 	    close();
 	}
 	catch (Exception close_error) {
@@ -181,10 +176,9 @@ IdComponent& IdComponent::operator=( const IdComponent& rhs )
 	}
 
 	// copy the data members from the rhs object
-	id = rhs.id;
-
-	// increment the reference counter
-	incRefCount();
+	setId(rhs.getId());
+//	incRefCount(getId()); // a = b, so there are two objects with the same
+			      // hdf5 id
     }
     return *this;
 }
@@ -196,39 +190,30 @@ IdComponent& IdComponent::operator=( const IdComponent& rhs )
 ///\exception	H5::IdComponentException when the attempt to close the HDF5
 ///		object fails
 // Description:
-// 		The underlaying reference counting in the C library ensures
-// 		that the current valid id of this object is properly closed.
-// 		Then the object's id is reset to the new id.
+//		The underlaying reference counting in the C library ensures
+//		that the current valid id of this object is properly closed.
+//		Then the object's id is reset to the new id.
 // Programmer	Binh-Minh Ribler - 2000
+// Modification
+//	2008/7/23 - BMR
+//		Changed all subclasses' setId to p_setId and put back setId
+//		here.  p_setId is used in the library where the id provided
+//		by a C API passed on to user's application in the form of a
+//		C++ API object, which will be destroyed properly, and so
+//		p_setId does not call incRefCount.  On the other hand, the
+//		public version setId is used by other applications, in which
+//		the id passed to setId already has a reference count, so setId
+//		must call incRefCount.
 //--------------------------------------------------------------------------
 void IdComponent::setId(const hid_t new_id)
 {
-    // handling references to this old id
-    try {
-	close();
-    }
-    catch (Exception close_error) {
-	throw IdComponentException(inMemFunc("copy"), close_error.getDetailMsg());
-    }
-
-   // reset object's id to the given id
-   id = new_id;
+   // set to new_id
+   p_setId(new_id);
 
    // increment the reference counter of the new id
    incRefCount();
 }
 
-//--------------------------------------------------------------------------
-// Function:	IdComponent::getId
-///\brief	Returns the id of this object
-///\return	HDF5 id
-// Programmer	Binh-Minh Ribler - 2000
-//--------------------------------------------------------------------------
-hid_t IdComponent::getId () const
-{
-   return(id);
-}
-
 //--------------------------------------------------------------------------
 // Function:	IdComponent destructor
 ///\brief	Noop destructor.
@@ -273,7 +258,7 @@ H5std_string IdComponent::inMemFunc(const char* func_name) const
 ///\brief	Default constructor.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-IdComponent::IdComponent() : id(-1) {}
+IdComponent::IdComponent() {}
 
 //--------------------------------------------------------------------------
 // Function:	IdComponent::p_get_file_name (protected)
@@ -287,8 +272,10 @@ IdComponent::IdComponent() : id(-1) {}
 //--------------------------------------------------------------------------
 H5std_string IdComponent::p_get_file_name() const
 {
+   hid_t temp_id = getId();
+
    // Preliminary call to H5Fget_name to get the length of the file name
-   ssize_t name_size = H5Fget_name(id, NULL, 0);
+   ssize_t name_size = H5Fget_name(temp_id, NULL, 0);
 
    // If H5Aget_name returns a negative value, raise an exception,
    if( name_size < 0 )
@@ -298,7 +285,7 @@ H5std_string IdComponent::p_get_file_name() const
 
    // Call H5Fget_name again to get the actual file name
    char* name_C = new char[name_size+1];  // temporary C-string for C API
-   name_size = H5Fget_name(id, name_C, name_size+1);
+   name_size = H5Fget_name(temp_id, name_C, name_size+1);
 
    // Check for failure again
    if( name_size < 0 )
@@ -312,178 +299,6 @@ H5std_string IdComponent::p_get_file_name() const
    return(file_name);
 }
 
-//--------------------------------------------------------------------------
-// Function:	IdComponent::p_reference (protected)
-// Purpose	Creates a reference to an HDF5 object or a dataset region.
-// Parameters
-//		name - IN: Name of the object to be referenced
-//		dataspace - IN: Dataspace with selection
-//		ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
-// Exception	H5::IdComponentException
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void IdComponent::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
-{
-   herr_t ret_value = H5Rcreate(ref, id, name, ref_type, space_id);
-   if (ret_value < 0)
-   {
-      throw IdComponentException("", "H5Rcreate failed");
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:    IdComponent::reference
-///\brief       Creates a reference to an HDF5 object or a dataset region.
-///\param       ref - IN: Reference pointer
-///\param       name - IN: Name of the object to be referenced
-///\param       dataspace - IN: Dataspace with selection
-///\param       ref_type - IN: Type of reference to query, valid values are:
-///             \li \c H5R_OBJECT \tReference is an object reference.
-///             \li \c H5R_DATASET_REGION \tReference is a dataset region
-///                     reference. - this is the default
-///\exception   H5::IdComponentException
-// Programmer   Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void IdComponent::reference(void* ref, const char* name, const DataSpace& dataspace, H5R_type_t ref_type) const
-{
-   try {
-      p_reference(ref, name, dataspace.getId(), ref_type);
-   }
-   catch (IdComponentException E) {
-      throw IdComponentException("IdComponent::reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:    IdComponent::reference
-///\brief       This is an overloaded function, provided for your convenience.
-///             It differs from the above function in that it only creates
-///             a reference to an HDF5 object, not to a dataset region.
-///\param       ref - IN: Reference pointer
-///\param       name - IN: Name of the object to be referenced - \c char pointer
-///\exception   H5::IdComponentException
-///\par Description
-//              This function passes H5R_OBJECT and -1 to the protected
-//              function for it to pass to the C API H5Rcreate
-//              to create a reference to the named object.
-// Programmer   Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void IdComponent::reference(void* ref, const char* name) const
-{
-   try {
-      p_reference(ref, name, -1, H5R_OBJECT);
-   }
-   catch (IdComponentException E) {
-      throw IdComponentException("IdComponent::reference", E.getDetailMsg());
-   }
-}
-
-//--------------------------------------------------------------------------
-// Function:    IdComponent::reference
-///\brief       This is an overloaded function, provided for your convenience.
-///             It differs from the above function in that it takes an
-///             \c std::string for the object's name.
-///\param       ref - IN: Reference pointer
-///\param       name - IN: Name of the object to be referenced - \c std::string
-// Programmer   Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void IdComponent::reference(void* ref, const H5std_string& name) const
-{
-   reference(ref, name.c_str());
-}
-
-//--------------------------------------------------------------------------
-// Function:	IdComponent::p_reference (protected)
-// Purpose	Creates a reference to an HDF5 object or a dataset region.
-// Parameters
-//		name - IN: Name of the object to be referenced
-//		dataspace - IN: Dataspace with selection
-//		ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
-// Return	A reference
-// Exception	H5::IdComponentException
-// Notes	This function is incorrect, and will be removed in the near
-//		future after notifying users of the new APIs ::reference's.
-//		BMR - Oct 8, 2006
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-void* IdComponent::p_reference(const char* name, hid_t space_id, H5R_type_t ref_type) const
-{
-   hobj_ref_t ref;
-   herr_t ret_value = H5Rcreate(&ref, id, name, ref_type, space_id);
-   if (ret_value < 0)
-   {
-      throw IdComponentException("", "H5Rcreate failed");
-   }
-   return (reinterpret_cast<void*>(ref));
-}
-
-//--------------------------------------------------------------------------
-// Function:	IdComponent::dereference
-// Purpose	Opens the HDF5 object referenced.
-// Parameters
-//		obj - IN: Dataset reference object is in or location of
-//                            object that the dataset is located within.
-//		ref - IN: Reference pointer
-// Exception	H5::IdComponentException
-// Programmer	Binh-Minh Ribler - Oct, 2006
-//--------------------------------------------------------------------------
-void IdComponent::dereference(IdComponent& obj, void* ref)
-{
-   id = H5Rdereference(obj.getId(), H5R_OBJECT, ref);
-   if (id < 0)
-   {
-      throw IdComponentException("", "H5Rdereference failed");
-   }
-}
-
-#ifndef H5_NO_DEPRECATED_SYMBOLS
-//--------------------------------------------------------------------------
-// Function:	IdComponent::p_get_obj_type (protected)
-// Purpose	Retrieves the type of object that an object reference points to.
-// Parameters
-//		ref      - IN: Reference to query
-//		ref_type - IN: Type of reference to query
-// Return	An object type, which can be one of the following:
-//			H5G_LINK Object is a symbolic link.
-//			H5G_GROUP Object is a group.
-//			H5G_DATASET   Object is a dataset.
-//			H5G_TYPE Object is a named datatype
-// Exception	H5::IdComponentException
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-H5G_obj_t IdComponent::p_get_obj_type(void *ref, H5R_type_t ref_type) const
-{
-   H5G_obj_t obj_type = H5Rget_obj_type1(id, ref_type, ref);
-
-   if (obj_type == H5G_UNKNOWN)
-   {
-      throw IdComponentException("", "H5Rget_obj_type failed");
-   }
-   return(obj_type);
-}
-#endif /* H5_NO_DEPRECATED_SYMBOLS */
-
-//--------------------------------------------------------------------------
-// Function:	IdComponent::p_get_region (protected)
-// Purpose	Retrieves a dataspace with the region pointed to selected.
-// Parameters
-//		ref_type - IN: Type of reference to get region of - default
-//				to H5R_DATASET_REGION
-//		ref      - IN: Reference to get region of
-// Return	Dataspace id
-// Exception	H5::IdComponentException
-// Programmer	Binh-Minh Ribler - May, 2004
-//--------------------------------------------------------------------------
-hid_t IdComponent::p_get_region(void *ref, H5R_type_t ref_type) const
-{
-   hid_t space_id = H5Rget_region(id, ref_type, ref);
-   if (space_id < 0)
-   {
-      throw IdComponentException("", "H5Rget_region failed");
-   }
-   return(space_id);
-}
-
 //
 // Local functions used in this class
 //
@@ -495,7 +310,7 @@ hid_t IdComponent::p_get_region(void *ref, H5R_type_t ref_type) const
 // Return	true if id is valid, false, otherwise
 // Programmer	Binh-Minh Ribler - May, 2005
 //--------------------------------------------------------------------------
-bool IdComponent::p_valid_id(const hid_t obj_id) const
+bool IdComponent::p_valid_id(const hid_t obj_id)
 {
     H5I_type_t id_type = H5Iget_type(obj_id);
     if (id_type <= H5I_BADID || id_type >= H5I_NTYPES)

c++/src/H5IdComponent.h

@@ -44,13 +44,8 @@ class H5_DLLCPP IdComponent {
 	// Assignment operator.
 	IdComponent& operator=( const IdComponent& rhs );
 
-        void reference(void* ref, const char* name, const DataSpace& dataspace,
-                        H5R_type_t ref_type = H5R_DATASET_REGION) const;
-        void reference(void* ref, const char* name) const;
-        void reference(void* ref, const H5std_string& name) const;
-
-	// Open a referenced HDF5 object.
-	void dereference(IdComponent& obj, void* ref);
+	// Gets the identifier of this object.
+	virtual hid_t getId () const = 0;
 
 	// Sets the identifier of this object to a new value.
 	void setId(const hid_t new_id);
@@ -61,9 +56,6 @@ class H5_DLLCPP IdComponent {
 	// Copy constructor: makes copy of the original IdComponent object.
 	IdComponent( const IdComponent& original );
 
-	// Gets the value of IdComponent's data member.
-	virtual hid_t getId () const;
-
 #ifndef DOXYGEN_SHOULD_SKIP_THIS
 	// Pure virtual function for there are various H5*close for the
 	// subclasses.
@@ -73,7 +65,7 @@ class H5_DLLCPP IdComponent {
 	// <class-name> is returned by fromClass().
 	H5std_string inMemFunc(const char* func_name) const;
 
-	// Returns this class name.
+	///\brief Returns this class name.
 	virtual H5std_string fromClass() const { return("IdComponent");}
 
 #endif // DOXYGEN_SHOULD_SKIP_THIS
@@ -83,7 +75,6 @@ class H5_DLLCPP IdComponent {
 
    protected:
 #ifndef DOXYGEN_SHOULD_SKIP_THIS
-	hid_t id;	// HDF5 object id
 
 	// Default constructor.
 	IdComponent();
@@ -91,23 +82,12 @@ class H5_DLLCPP IdComponent {
 	// Gets the name of the file, in which an HDF5 object belongs.
 	H5std_string p_get_file_name() const;
 
-	// Gets the id of the H5 file in which the given object is located.
-	hid_t p_get_file_id();
-
-	// Creates a reference to an HDF5 object or a dataset region.
-	void p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const;
-	void* p_reference(const char* name, hid_t space_id, H5R_type_t ref_type) const; // will be removed
-
-#ifndef H5_NO_DEPRECATED_SYMBOLS
-	// Retrieves the type of object that an object reference points to.
-	H5G_obj_t p_get_obj_type(void *ref, H5R_type_t ref_type) const;
-#endif /* H5_NO_DEPRECATED_SYMBOLS */
-
-	// Retrieves a dataspace with the region pointed to selected.
-	hid_t p_get_region(void *ref, H5R_type_t ref_type) const;
-
 	// Verifies that the given id is valid.
-	bool p_valid_id(const hid_t obj_id) const;
+	static bool p_valid_id(const hid_t obj_id);
+
+	// Sets the identifier of this object to a new value. - this one
+	// doesn't increment reference count
+	virtual void p_setId(const hid_t new_id) = 0;
 
 #endif // DOXYGEN_SHOULD_SKIP_THIS
 

c++/src/H5IntType.h

@@ -35,7 +35,7 @@ class H5_DLLCPP IntType : public AtomType {
 	// Sets the sign proprety for an integer type.
 	void setSign( H5T_sign_t sign ) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("IntType"); }
 
 	// Default constructor

c++/src/H5Library.cpp

@@ -106,7 +106,7 @@ void H5Library::getLibVersion( unsigned& majnum, unsigned& minnum, unsigned& rel
 ///\par Description
 ///		For information about library version, please refer to
 ///		the C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5.html#Library-VersCheck
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5.html#Library-VersCheck
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void H5Library::checkVersion(unsigned majnum, unsigned minnum, unsigned relnum)
@@ -161,7 +161,7 @@ void H5Library::garbageCollect()
 ///		Setting a value of -1 for a limit means no limit of that type.
 ///		For more information on free list limits, please refer to C
 ///		layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5.html#Library-SetFreeListLimits
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5.html#Library-SetFreeListLimits
 // Programmer	Binh-Minh Ribler - May, 2004
 //--------------------------------------------------------------------------
 void H5Library::setFreeListLimits(int reg_global_lim, int reg_list_lim,

c++/src/H5Object.cpp

@@ -21,10 +21,15 @@
 #include "H5PropList.h"
 #include "H5Object.h"
 #include "H5DcreatProp.h"
+#include "H5DxferProp.h"
+#include "H5FaccProp.h"
+#include "H5FcreatProp.h"
 #include "H5CommonFG.h"
 #include "H5DataType.h"
 #include "H5DataSpace.h"
 #include "H5AbstractDs.h"
+#include "H5File.h"
+#include "H5DataSet.h"
 #include "H5Attribute.h"
 
 #ifndef H5_NO_NAMESPACE
@@ -103,7 +108,7 @@ Attribute H5Object::createAttribute( const char* name, const DataType& data_type
    hid_t type_id = data_type.getId();
    hid_t space_id = data_space.getId();
    hid_t plist_id = create_plist.getId();
-   hid_t attr_id = H5Acreate2(id, name, type_id, space_id, plist_id, H5P_DEFAULT );
+   hid_t attr_id = H5Acreate2(getId(), name, type_id, space_id, plist_id, H5P_DEFAULT );
 
    // If the attribute id is valid, create and return the Attribute object
    if( attr_id > 0 )
@@ -119,7 +124,7 @@ Attribute H5Object::createAttribute( const char* name, const DataType& data_type
 // Function:	H5Object::createAttribute
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes
-///		a reference to an \c std::string for \a name.
+///		a reference to an \c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 Attribute H5Object::createAttribute( const H5std_string& name, const DataType& data_type, const DataSpace& data_space, const PropList& create_plist ) const
@@ -137,7 +142,7 @@ Attribute H5Object::createAttribute( const H5std_string& name, const DataType& d
 //--------------------------------------------------------------------------
 Attribute H5Object::openAttribute( const char* name ) const
 {
-   hid_t attr_id = H5Aopen( id, name, H5P_DEFAULT );
+   hid_t attr_id = H5Aopen(getId(), name, H5P_DEFAULT);
    if( attr_id > 0 )
    {
       Attribute attr( attr_id );
@@ -153,7 +158,7 @@ Attribute H5Object::openAttribute( const char* name ) const
 // Function:	H5Object::openAttribute
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes
-///		a reference to an \c std::string for \a name.
+///		a reference to an \c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 Attribute H5Object::openAttribute( const H5std_string& name ) const
@@ -171,7 +176,8 @@ Attribute H5Object::openAttribute( const H5std_string& name ) const
 //--------------------------------------------------------------------------
 Attribute H5Object::openAttribute( const unsigned int idx ) const
 {
-   hid_t attr_id = H5Aopen_by_idx(id, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)idx, H5P_DEFAULT, H5P_DEFAULT);
+   hid_t attr_id = H5Aopen_by_idx(getId(), ".", H5_INDEX_CRT_ORDER,
+			H5_ITER_INC, (hsize_t)idx, H5P_DEFAULT, H5P_DEFAULT);
    if( attr_id > 0 )
    {
       Attribute attr( attr_id );
@@ -188,7 +194,7 @@ Attribute H5Object::openAttribute( const unsigned int idx ) const
 ///\brief	Iterates a user's function over all the attributes of an H5
 ///		object, which may be a group, dataset or named datatype.
 ///\param	user_op - IN: User's function to operate on each attribute
-///\param	idx - IN/OUT: Starting (IN) and ending (OUT) attribute indices
+///\param	_idx - IN/OUT: Starting (IN) and ending (OUT) attribute indices
 ///\param	op_data - IN: User's data to pass to user's operator function
 ///\return	Returned value of the last operator if it was non-zero, or
 ///		zero if all attributes were processed
@@ -196,7 +202,7 @@ Attribute H5Object::openAttribute( const unsigned int idx ) const
 ///\par Description
 ///		For information, please refer to the C layer Reference Manual
 ///		at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5A.html#Annot-Iterate
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5A.html#Annot-Create2
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 int H5Object::iterateAttrs( attr_operator_t user_op, unsigned *_idx, void *op_data )
@@ -208,15 +214,17 @@ int H5Object::iterateAttrs( attr_operator_t user_op, unsigned *_idx, void *op_da
    userData->object = this;
 
    // call the C library routine H5Aiterate2 to iterate the attributes
-   hsize_t idx = (hsize_t)*_idx;
-   int ret_value = H5Aiterate2(id, H5_INDEX_NAME, H5_ITER_INC, &idx, userAttrOpWrpr, (void *) userData);
+   hsize_t idx = _idx ? (hsize_t)*_idx : 0;
+   int ret_value = H5Aiterate2(getId(), H5_INDEX_NAME, H5_ITER_INC, &idx,
+			userAttrOpWrpr, (void *) userData);
 
    // release memory
    delete userData;
 
    if( ret_value >= 0 ) {
       /* Pass back update index value to calling code */
-      *_idx = (unsigned)idx;
+      if (_idx)
+	 *_idx = (unsigned)idx;
 
       return( ret_value );
    }
@@ -235,7 +243,7 @@ int H5Object::getNumAttrs() const
 {
    H5O_info_t oinfo;    /* Object info */
 
-   if(H5Oget_info(id, &oinfo) < 0)
+   if(H5Oget_info(getId(), &oinfo) < 0)
       throw AttributeIException(inMemFunc("getNumAttrs"), "H5Oget_info failed");
    else
       return( (int)oinfo.num_attrs );
@@ -250,7 +258,7 @@ int H5Object::getNumAttrs() const
 //--------------------------------------------------------------------------
 void H5Object::removeAttr( const char* name ) const
 {
-   herr_t ret_value = H5Adelete(id, name);
+   herr_t ret_value = H5Adelete(getId(), name);
    if( ret_value < 0 )
       throw AttributeIException(inMemFunc("removeAttr"), "H5Adelete failed");
 }
@@ -259,7 +267,7 @@ void H5Object::removeAttr( const char* name ) const
 // Function:	H5Object::removeAttr
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes
-///		a reference to an \c std::string for \a name.
+///		a reference to an \c H5std_string for \a name.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void H5Object::removeAttr( const H5std_string& name ) const
@@ -277,7 +285,7 @@ void H5Object::removeAttr( const H5std_string& name ) const
 //--------------------------------------------------------------------------
 void H5Object::renameAttr(const char* oldname, const char* newname) const
 {
-   herr_t ret_value = H5Arename(id, oldname, newname);
+   herr_t ret_value = H5Arename(getId(), oldname, newname);
    if (ret_value < 0)
       throw AttributeIException(inMemFunc("renameAttr"), "H5Arename failed");
 }
@@ -286,7 +294,7 @@ void H5Object::renameAttr(const char* oldname, const char* newname) const
 // Function:	H5Object::renameAttr
 ///\brief	This is an overloaded member function, provided for convenience.
 ///		It differs from the above function in that it takes
-///		a reference to an \c std::string for the names.
+///		a reference to an \c H5std_string for the names.
 // Programmer	Binh-Minh Ribler - Mar, 2005
 //--------------------------------------------------------------------------
 void H5Object::renameAttr(const H5std_string& oldname, const H5std_string& newname) const
@@ -306,9 +314,9 @@ void H5Object::renameAttr(const H5std_string& oldname, const H5std_string& newna
 ///		This object is used to identify the file to be flushed.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-void H5Object::flush(H5F_scope_t scope ) const
+void H5Object::flush(H5F_scope_t scope) const
 {
-   herr_t ret_value = H5Fflush( id, scope );
+   herr_t ret_value = H5Fflush(getId(), scope);
    if( ret_value < 0 )
    {
       throw FileIException(inMemFunc("flush"), "H5Fflush failed");
@@ -332,6 +340,235 @@ H5std_string H5Object::getFileName() const
    }
 }
 
+//--------------------------------------------------------------------------
+// Function:    H5Object::p_reference (protected)
+// Purpose      Creates a reference to an HDF5 object or a dataset region.
+// Parameters
+//              name - IN: Name of the object to be referenced
+//              dataspace - IN: Dataspace with selection
+//              ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
+// Exception    H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5Object::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
+{
+   herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
+   if (ret_value < 0)
+   {
+      throw IdComponentException("", "H5Rcreate failed");
+   }
+}
+
+//--------------------------------------------------------------------------
+// Function:    H5Object::reference
+///\brief       Creates a reference to an HDF5 object or a dataset region.
+///\param       ref - IN: Reference pointer
+///\param       name - IN: Name of the object to be referenced
+///\param       dataspace - IN: Dataspace with selection
+///\param       ref_type - IN: Type of reference to query, valid values are:
+///             \li \c H5R_OBJECT         - Reference is an object reference.
+///             \li \c H5R_DATASET_REGION - Reference is a dataset region
+///                     reference. - this is the default
+///\exception   H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5Object::reference(void* ref, const char* name, const DataSpace& dataspace, H5R_type_t ref_type) const
+{
+   try {
+      p_reference(ref, name, dataspace.getId(), ref_type);
+   }
+   catch (IdComponentException E) {
+      throw IdComponentException("H5Object::reference", E.getDetailMsg());
+   }
+}
+
+//--------------------------------------------------------------------------
+// Function:    H5Object::reference
+///\brief       This is an overloaded function, provided for your convenience.
+///             It differs from the above function in that it only creates
+///             a reference to an HDF5 object, not to a dataset region.
+///\param       ref - IN: Reference pointer
+///\param       name - IN: Name of the object to be referenced - \c char pointer
+///\exception   H5::IdComponentException
+///\par Description
+//              This function passes H5R_OBJECT and -1 to the protected
+//              function for it to pass to the C API H5Rcreate
+//              to create a reference to the named object.
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5Object::reference(void* ref, const char* name) const
+{
+   try {
+      p_reference(ref, name, -1, H5R_OBJECT);
+   }
+   catch (IdComponentException E) {
+      throw IdComponentException("H5Object::reference", E.getDetailMsg());
+   }
+}
+
+//--------------------------------------------------------------------------
+// Function:    H5Object::reference
+///\brief       This is an overloaded function, provided for your convenience.
+///             It differs from the above function in that it takes an
+///             \c H5std_string for the object's name.
+///\param       ref - IN: Reference pointer
+///\param       name - IN: Name of the object to be referenced - \c H5std_string
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+void H5Object::reference(void* ref, const H5std_string& name) const
+{
+   reference(ref, name.c_str());
+}
+
+//--------------------------------------------------------------------------
+// Function:	H5Object::p_dereference (protected)
+// Purpose	Dereference a ref into an hdf5 object.
+// Parameters
+//		loc_id - IN: An hdf5 identifier specifying the location of the 
+//			 referenced object
+//		ref - IN: Reference pointer
+//		ref_type - IN: Reference type
+// Exception	H5::ReferenceException
+// Programmer	Binh-Minh Ribler - Oct, 2006
+// Modification
+//	May 2008 - BMR
+//		Moved from IdComponent.
+//--------------------------------------------------------------------------
+hid_t H5Object::p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type)
+{
+   hid_t temp_id;
+   temp_id = H5Rdereference(loc_id, ref_type, ref);
+   if (temp_id < 0)
+   {
+      throw ReferenceException("", "H5Rdereference failed");
+   }
+
+   // No failure, set id to the object
+   return(temp_id);
+}
+
+//--------------------------------------------------------------------------
+// Function:	H5Object::dereference
+///\brief	Dereferences a reference into an HDF5 object, given an HDF5 object.
+///\param	obj - IN: Object specifying the location of the referenced object
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type
+///\exception	H5::ReferenceException
+// Programmer   Binh-Minh Ribler - Oct, 2006
+// Modification
+//	May, 2008
+//		Corrected missing parameters. - BMR
+//--------------------------------------------------------------------------
+void H5Object::dereference(H5Object& obj, const void* ref, H5R_type_t ref_type)
+{
+   hid_t temp_id;
+   try {
+      temp_id = p_dereference(obj.getId(), ref, ref_type);
+   }
+   catch (ReferenceException E) {
+      throw ReferenceException("H5Object::dereference - located by object", E.getDetailMsg());
+   }
+   p_setId(temp_id);
+}
+
+//--------------------------------------------------------------------------
+// Function:	H5Object::dereference
+///\brief	Dereferences a reference into an HDF5 object, given an HDF5 file.
+///\param	h5file - IN: HDF5 file specifying the location of the referenced object
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type
+///\exception	H5::ReferenceException
+// Programmer   Binh-Minh Ribler - Oct, 2006
+// Modification
+//	May, 2008
+//		Corrected missing parameters. - BMR
+//--------------------------------------------------------------------------
+void H5Object::dereference(H5File& h5file, const void* ref, H5R_type_t ref_type)
+{
+   hid_t temp_id;
+   try {
+      temp_id = p_dereference(h5file.getId(), ref, ref_type);
+   }
+   catch (ReferenceException E) {
+      throw ReferenceException("H5Object::dereference - located by file", E.getDetailMsg());
+   }
+   p_setId(temp_id);
+}
+
+//--------------------------------------------------------------------------
+// Function:	H5Object::dereference
+///\brief	Dereferences a reference into an HDF5 object, given an attribute.
+///\param	attr - IN: Attribute specifying the location of the referenced object
+///\param	ref - IN: Reference pointer
+///\param	ref_type - IN: Reference type
+///\exception	H5::ReferenceException
+// Programmer   Binh-Minh Ribler - Oct, 2006
+// Modification
+//	May, 2008
+//		Corrected missing parameters. - BMR
+//--------------------------------------------------------------------------
+void H5Object::dereference(Attribute& attr, const void* ref, H5R_type_t ref_type)
+{
+   hid_t temp_id;
+   try {
+      temp_id = p_dereference(attr.getId(), ref, ref_type);
+   }
+   catch (ReferenceException E) {
+      throw ReferenceException("H5Object::dereference - located by attribute", E.getDetailMsg());
+   }
+   p_setId(temp_id);
+}
+
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+//--------------------------------------------------------------------------
+// Function:    H5Object::p_get_obj_type (protected)
+// Purpose      Retrieves the type of object that an object reference points to.
+// Parameters
+//              ref      - IN: Reference to query
+//              ref_type - IN: Type of reference to query
+// Return       An object type, which can be one of the following:
+//                      H5G_LINK Object is a symbolic link.
+//                      H5G_GROUP Object is a group.
+//                      H5G_DATASET   Object is a dataset.
+//                      H5G_TYPE Object is a named datatype
+// Exception    H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+H5G_obj_t H5Object::p_get_obj_type(void *ref, H5R_type_t ref_type) const
+{
+   H5G_obj_t obj_type = H5Rget_obj_type1(getId(), ref_type, ref);
+
+   if (obj_type == H5G_UNKNOWN)
+   {
+      throw IdComponentException("", "H5Rget_obj_type failed");
+   }
+   return(obj_type);
+}
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+
+//--------------------------------------------------------------------------
+// Function:    H5Object::p_get_region (protected)
+// Purpose      Retrieves a dataspace with the region pointed to selected.
+// Parameters
+//              ref_type - IN: Type of reference to get region of - default
+//                              to H5R_DATASET_REGION
+//              ref      - IN: Reference to get region of
+// Return       Dataspace id
+// Exception    H5::IdComponentException
+// Programmer   Binh-Minh Ribler - May, 2004
+//--------------------------------------------------------------------------
+hid_t H5Object::p_get_region(void *ref, H5R_type_t ref_type) const
+{
+   hid_t space_id = H5Rget_region(getId(), ref_type, ref);
+   if (space_id < 0)
+   {
+      throw IdComponentException("", "H5Rget_region failed");
+   }
+   return(space_id);
+}
+
+
 //--------------------------------------------------------------------------
 // Function:	H5Object destructor
 ///\brief	Noop destructor.

c++/src/H5Object.h

@@ -20,8 +20,7 @@
 #include "H5Classes.h"		// constains forward class declarations
 
 // H5Object is a baseclass.  It has these subclasses:
-// Group, AbstractDs, and DataType.
-// AbstractDs, in turn, has subclasses DataSet and Attribute.
+// Group, DataSet, and DataType.
 // DataType, in turn, has several specific datatypes as subclasses.
 
 #ifndef H5_NO_NAMESPACE
@@ -80,6 +79,19 @@ class H5_DLLCPP H5Object : public IdComponent {
 	void renameAttr(const char* oldname, const char* newname) const;
 	void renameAttr(const H5std_string& oldname, const H5std_string& newname) const;
 
+	// Creates a reference to a named Hdf5 object or to a dataset region
+	// in this object.
+	void reference(void* ref, const char* name, const DataSpace& dataspace,
+			H5R_type_t ref_type = H5R_DATASET_REGION) const;
+	void reference(void* ref, const char* name) const;
+	void reference(void* ref, const H5std_string& name) const;
+
+	// Open a referenced HDF5 object whose location is specified by either
+	// a file, an HDF5 object, or an attribute.
+	void dereference(H5File& h5file, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+	void dereference(H5Object& obj, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+	void dereference(Attribute& attr, const void* ref, H5R_type_t ref_type = H5R_OBJECT);
+
 	// Copy constructor: makes copy of an H5Object object.
 	H5Object(const H5Object& original);
 
@@ -93,6 +105,24 @@ class H5_DLLCPP H5Object : public IdComponent {
 
 	// Creates a copy of an existing object giving the object id
 	H5Object( const hid_t object_id );
+
+	// Gets the id of the H5 file in which the given object is located.
+	hid_t p_get_file_id();
+
+	// Creates a reference to an HDF5 object or a dataset region.
+	void p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const;
+
+	// Dereferences a ref into an hdf5 id.
+	hid_t p_dereference(hid_t loc_id, const void* ref, H5R_type_t ref_type);
+
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+	// Retrieves the type of object that an object reference points to.
+	H5G_obj_t p_get_obj_type(void *ref, H5R_type_t ref_type) const;
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+
+	// Retrieves a dataspace with the region pointed to selected.
+	hid_t p_get_region(void *ref, H5R_type_t ref_type) const;
+
 #endif // DOXYGEN_SHOULD_SKIP_THIS
 
 }; /* end class H5Object */

c++/src/H5PredType.cpp

@@ -289,7 +289,6 @@ void PredType::commit( H5Object& loc, const H5std_string& name )
 bool PredType::committed()
 {
    throw DataTypeIException("PredType::committed", "Error: Attempting to check for commit status on a predefined datatype." );
-   return (0);
 }
 #endif // DOXYGEN_SHOULD_SKIP_THIS
 

c++/src/H5PredType.h

@@ -28,7 +28,7 @@ namespace H5 {
 
 class H5_DLLCPP PredType : public AtomType {
    public:
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("PredType"); }
 
 	// Makes a copy of the predefined type and stores the new

c++/src/H5PropList.cpp

@@ -25,6 +25,7 @@
 #include "H5Exception.h"
 #include "H5IdComponent.h"
 #include "H5PropList.h"
+#include "H5private.h"		// for HDfree
 
 #ifndef H5_NO_NAMESPACE
 namespace H5 {
@@ -44,7 +45,7 @@ const PropList PropList::DEFAULT( H5P_DEFAULT );
 ///\brief	Default constructor: creates a stub property list object.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-PropList::PropList() : IdComponent( 0 ) {}
+PropList::PropList() : IdComponent(), id(0) {}
 
 //--------------------------------------------------------------------------
 // Function:	PropList copy constructor
@@ -52,7 +53,11 @@ PropList::PropList() : IdComponent( 0 ) {}
 ///\param	original - IN: The original property list to copy
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-PropList::PropList( const PropList& original ) : IdComponent( original ) {}
+PropList::PropList(const PropList& original) : IdComponent(original)
+{
+    id = original.getId();
+    incRefCount(); // increment number of references to this id
+}
 
 //--------------------------------------------------------------------------
 // Function:	PropList overloaded constructor
@@ -68,7 +73,7 @@ PropList::PropList( const PropList& original ) : IdComponent( original ) {}
 //		description was what I came up with from reading the code.
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
-PropList::PropList( const hid_t plist_id ) : IdComponent(0)
+PropList::PropList( const hid_t plist_id ) : IdComponent()
 {
     if (H5I_GENPROP_CLS == H5Iget_type(plist_id)) {
 	// call C routine to create the new property
@@ -157,7 +162,7 @@ void PropList::copyProp(PropList& dest, const char *name) const
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
 ///\param	dest - IN: Destination property list or class
-///\param	name - IN: Name of the property to copy - \c std::string
+///\param	name - IN: Name of the property to copy - \c H5std_string
 // Programmer	Binh-Minh Ribler - Jul, 2005
 //--------------------------------------------------------------------------
 void PropList::copyProp( PropList& dest, const H5std_string& name ) const
@@ -194,7 +199,7 @@ void PropList::copyProp( PropList& dest, PropList& src, const char *name ) const
 ///		accepts. - Obsolete
 ///\param	dest - IN: Destination property list or class
 ///\param	src  - IN: Source property list or class
-///\param	name - IN: Name of the property to copy - \c std::string
+///\param	name - IN: Name of the property to copy - \c H5std_string
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void PropList::copyProp( PropList& dest, PropList& src, const H5std_string& name ) const
@@ -202,6 +207,46 @@ void PropList::copyProp( PropList& dest, PropList& src, const H5std_string& name
    copyProp( dest, src, name.c_str());
 }
 
+//--------------------------------------------------------------------------
+// Function:    PropList::getId
+// Purpose:     Get the id of this attribute
+// Description:
+//              Class hierarchy is revised to address bugzilla 1068.  Class
+//              AbstractDS and Attribute are moved out of H5Object.  In
+//              addition, member IdComponent::id is moved into subclasses, and
+//              IdComponent::getId now becomes pure virtual function.
+// Programmer   Binh-Minh Ribler - May, 2008
+//--------------------------------------------------------------------------
+hid_t PropList::getId() const
+{
+   return(id);
+}
+
+//--------------------------------------------------------------------------
+// Function:    PropList::p_setId
+///\brief       Sets the identifier of this object to a new value.
+///
+///\exception   H5::IdComponentException when the attempt to close the HDF5
+///             object fails
+// Description:
+//              The underlaying reference counting in the C library ensures
+//              that the current valid id of this object is properly closed.
+//              Then the object's id is reset to the new id.
+// Programmer   Binh-Minh Ribler - 2000
+//--------------------------------------------------------------------------
+void PropList::p_setId(const hid_t new_id)
+{
+    // handling references to this old id
+    try {
+        close();
+    }
+    catch (Exception close_error) {
+        throw PropListIException(inMemFunc("p_setId"), close_error.getDetailMsg());
+    }
+   // reset object's id to the given id
+   id = new_id;
+}
+
 //--------------------------------------------------------------------------
 // Function:	PropList::close
 ///\brief	Closes the property list if it is not a default one.
@@ -218,8 +263,10 @@ void PropList::close()
 	{
 	    throw PropListIException(inMemFunc("close"), "H5Pclose failed");
 	}
-	// reset the id because the property list that it represents is now closed
-	id = 0;
+	// reset the id when the property list that it represents is no longer
+	// referenced
+	if (getCounter() == 0)
+	    id = 0;
     }
 }
 
@@ -273,7 +320,7 @@ bool PropList::propExist(const char* name ) const
 ///\brief	This is an overloaded member function, provided for convenience.
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name - IN: Name of property to check for - \c std::string
+///\param	name - IN: Name of property to check for - \c H5std_string
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 bool PropList::propExist(const H5std_string& name ) const
@@ -326,7 +373,7 @@ void PropList::getProperty(const char* name, void* value) const
 ///   		It differs from the above function only in what arguments it
 ///		accepts.
 ///\param	name -  IN: Name of property to query - \c char pointer
-///\return	The property that is a \c std::string.
+///\return	The property that is a \c H5std_string.
 ///\exception	H5::PropListIException
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
@@ -343,7 +390,7 @@ H5std_string PropList::getProperty(const char* name) const
    }
 
    // Return propety value as a string after deleting temp C-string
-   H5std_string prop_strg = H5std_string(prop_strg_C);
+   H5std_string prop_strg(prop_strg_C);
    delete []prop_strg_C;
    return (prop_strg);
 }
@@ -352,7 +399,7 @@ H5std_string PropList::getProperty(const char* name) const
 ///\brief	This is an overloaded member function, provided for convenience.
 ///   		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name -   IN: Name of property to query - \c std::string
+///\param	name -   IN: Name of property to query - \c H5std_string
 ///\param	value - OUT: Pointer to the buffer for the property value
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
@@ -365,8 +412,8 @@ void PropList::getProperty(const H5std_string& name, void* value) const
 ///\brief	This is an overloaded member function, provided for convenience.
 ///   		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name -  IN: Name of property to query - \c std::string
-///\return	The property that is a \c std::string.
+///\param	name -  IN: Name of property to query - \c H5std_string
+///\return	The property that is a \c H5std_string.
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 H5std_string PropList::getProperty(const H5std_string& name) const
@@ -402,7 +449,7 @@ size_t PropList::getPropSize(const char *name) const
 ///\brief	This is an overloaded member function, provided for convenience.
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name - IN: Name of property to query - \c std::string
+///\param	name - IN: Name of property to query - \c H5std_string
 ///
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
@@ -421,12 +468,13 @@ size_t PropList::getPropSize(const H5std_string& name) const
 H5std_string PropList::getClassName() const
 {
    char* temp_str;
-   temp_str = H5Pget_class_name(id);
+   temp_str = H5Pget_class_name(id); // this API specified that temp_str must
+				     // be freed.
 
    if (temp_str != NULL)
    {
-      H5std_string class_name = H5std_string(temp_str);
-      free(temp_str);
+      H5std_string class_name(temp_str);
+      HDfree(temp_str);
       return(class_name);
    }
    else
@@ -489,7 +537,7 @@ void PropList::setProperty(const char* name, const char* charptr) const
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
 ///\param	name - IN: Name of property to set - \c char pointer
-///\param	strg - IN: Value for the property is a \c std::string
+///\param	strg - IN: Value for the property is a \c H5std_string
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void PropList::setProperty(const char* name, H5std_string& strg) const
@@ -502,7 +550,7 @@ void PropList::setProperty(const char* name, H5std_string& strg) const
 ///\brief	This is an overloaded member function, provided for convenience.
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name  - IN: Name of property to set - \c std::string
+///\param	name  - IN: Name of property to set - \c H5std_string
 ///\param	value - IN: Void pointer to the value for the property
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
@@ -516,8 +564,8 @@ void PropList::setProperty(const H5std_string& name, void* value) const
 ///\brief	This is an overloaded member function, provided for convenience.
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name - IN: Name of property to set - \c std::string
-///\param	strg - IN: Value for the property is a \c std::string
+///\param	name - IN: Name of property to set - \c H5std_string
+///\param	strg - IN: Value for the property is a \c H5std_string
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void PropList::setProperty(const H5std_string& name, H5std_string& strg) const
@@ -569,7 +617,7 @@ void PropList::removeProp(const char *name) const
 ///\brief	This is an overloaded member function, provided for convenience.
 /// 		It differs from the above function only in what arguments it
 ///		accepts.
-///\param	name - IN: Name of property to remove - \c std::string
+///\param	name - IN: Name of property to remove - \c H5std_string
 // Programmer:  Binh-Minh Ribler - April, 2004
 //--------------------------------------------------------------------------
 void PropList::removeProp(const H5std_string& name) const

c++/src/H5PropList.h

@@ -94,7 +94,7 @@ class H5_DLLCPP PropList : public IdComponent {
 	void removeProp(const char *name) const;
 	void removeProp(const H5std_string& name) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("PropList"); }
 
 	// Default constructor: creates a stub PropList object.
@@ -103,8 +103,17 @@ class H5_DLLCPP PropList : public IdComponent {
 	// Copy constructor: creates a copy of a PropList object.
 	PropList(const PropList& original);
 
+	// Gets the property list id.
+	virtual hid_t getId() const;
+
 	// Destructor: properly terminates access to this property list.
 	virtual ~PropList();
+
+   protected:
+	hid_t id;	// HDF5 property list id
+
+	// Sets the property list id.
+	virtual void p_setId(const hid_t new_id);
 };
 
 #ifndef H5_NO_NAMESPACE

c++/src/H5StrType.cpp

@@ -87,7 +87,7 @@ StrType::StrType( const PredType& pred_type, const size_t& size ) : AtomType()
 // Function:	StrType overloaded constructor
 ///\brief	Creates a string datatype with a specified length
 ///\param	dummy - IN: To simplify calling the previous constructor
-//			and avoid prototype clash with another constructor
+///			and avoid prototype clash with another constructor
 ///\param	size  - IN: Length of the new string type
 ///\exception	H5::DataTypeIException
 ///\par Description
@@ -209,7 +209,7 @@ H5T_str_t StrType::getStrpad() const
 ///\exception	H5::DataTypeIException
 ///\par Description
 ///		For detail, please refer to the C layer Reference Manual at:
-/// http://hdf.ncsa.uiuc.edu/HDF5/doc/RM_H5T.html#Datatype-SetStrpad
+/// http://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-SetStrpad
 // Programmer	Binh-Minh Ribler - 2000
 //--------------------------------------------------------------------------
 void StrType::setStrpad( H5T_str_t strpad ) const

c++/src/H5StrType.h

@@ -47,7 +47,7 @@ class H5_DLLCPP StrType : public AtomType {
 	// Defines the storage mechanism for character strings.
 	void setStrpad(H5T_str_t strpad) const;
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("StrType"); }
 
 	// default constructor

c++/src/H5VarLenType.h

@@ -30,7 +30,7 @@ class H5_DLLCPP VarLenType : public DataType {
 	// on the specified base type.
 	VarLenType(const DataType* base_type);
 
-	// Returns this class name
+	///\brief Returns this class name
 	virtual H5std_string fromClass () const { return("VarLenType"); }
 
 	// Copy constructor: makes copy of the original object.

c++/src/Makefile.am

@@ -19,6 +19,7 @@
 #
 
 include $(top_srcdir)/config/commence.am
+include $(top_srcdir)/config/lt_vers.am
 
 # Include src directory
 INCLUDES=-I$(top_srcdir)/src
@@ -26,10 +27,13 @@ INCLUDES=-I$(top_srcdir)/src
 # This is our main target
 lib_LTLIBRARIES=libhdf5_cpp.la
 
+# Add libtool numbers to the HDF5 C++ library (from config/lt_vers.am)
+libhdf5_cpp_la_LDFLAGS= -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
+
 # Shared C++ libraries aren't universally supported.
 if CXX_SHARED_CONDITIONAL
 else
-  AM_LDFLAGS=-static
+  AM_LDFLAGS+=-static
 endif
 
 bin_SCRIPTS=h5c++
@@ -64,6 +68,6 @@ mostlyclean-local:
 	fi
 
 # Mark this directory as part of the C++ API
-HDF_CXX=yes
+CXX_API=yes
 
 include $(top_srcdir)/config/conclude.am

c++/src/Makefile.in

@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006  Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -35,8 +36,9 @@
 
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
 install_sh_DATA = $(install_sh) -c -m 644
 install_sh_PROGRAM = $(install_sh) -c
@@ -54,7 +56,11 @@ host_triplet = @host@
 DIST_COMMON = $(include_HEADERS) $(srcdir)/Makefile.am \
 	$(srcdir)/Makefile.in $(srcdir)/h5c++.in \
 	$(top_srcdir)/config/commence.am \
-	$(top_srcdir)/config/conclude.am
+	$(top_srcdir)/config/conclude.am \
+	$(top_srcdir)/config/lt_vers.am
+
+# Shared C++ libraries aren't universally supported.
+@CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 TESTS =
 subdir = c++/src
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -64,15 +70,30 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
 CONFIG_CLEAN_FILES = h5c++
+CONFIG_CLEAN_VPATH_FILES =
 am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
 am__vpath_adj = case $$p in \
     $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
     *) f=$$p;; \
   esac;
-am__strip_dir = `echo $$p | sed -e 's|^.*/||'`;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
 am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)" \
 	"$(DESTDIR)$(includedir)"
-libLTLIBRARIES_INSTALL = $(INSTALL)
 LTLIBRARIES = $(lib_LTLIBRARIES)
 libhdf5_cpp_la_LIBADD =
 am_libhdf5_cpp_la_OBJECTS = H5Exception.lo H5IdComponent.lo \
@@ -83,11 +104,14 @@ am_libhdf5_cpp_la_OBJECTS = H5Exception.lo H5IdComponent.lo \
 	H5StrType.lo H5ArrayType.lo H5VarLenType.lo H5CompType.lo \
 	H5DataSet.lo H5CommonFG.lo H5Group.lo H5File.lo
 libhdf5_cpp_la_OBJECTS = $(am_libhdf5_cpp_la_OBJECTS)
-binSCRIPT_INSTALL = $(INSTALL_SCRIPT)
+libhdf5_cpp_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \
+	$(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \
+	$(CXXFLAGS) $(libhdf5_cpp_la_LDFLAGS) $(LDFLAGS) -o $@
 SCRIPTS = $(bin_SCRIPTS)
-DEFAULT_INCLUDES = -I. -I$(top_builddir)/src@am__isrc@
+DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src
 depcomp = $(SHELL) $(top_srcdir)/bin/depcomp
 am__depfiles_maybe = depfiles
+am__mv = mv -f
 CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
 	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
 LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
@@ -99,14 +123,25 @@ CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
 	$(LDFLAGS) -o $@
 SOURCES = $(libhdf5_cpp_la_SOURCES)
 DIST_SOURCES = $(libhdf5_cpp_la_SOURCES)
-includeHEADERS_INSTALL = $(INSTALL_HEADER)
 HEADERS = $(include_HEADERS)
 ETAGS = etags
 CTAGS = ctags
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -120,46 +155,47 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
+CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
+DIRECT_VFD = @DIRECT_VFD@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
 DYNAMIC_DIRS = @DYNAMIC_DIRS@
-ECHO = @ECHO@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
 EXEEXT = @EXEEXT@
-F77 = @F77@
+EXTERNAL_FILTERS = @EXTERNAL_FILTERS@
 
 # Make sure that these variables are exported to the Makefiles
 F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FGREP = @FGREP@
 FILTERS = @FILTERS@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+GPFS = @GPFS@
 GREP = @GREP@
 H5_CFLAGS = @H5_CFLAGS@
 H5_CPPFLAGS = @H5_CPPFLAGS@
@@ -168,11 +204,14 @@ H5_FCFLAGS = @H5_FCFLAGS@
 H5_LONE_COLON = @H5_LONE_COLON@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
+HAVE_DMALLOC = @HAVE_DMALLOC@
+HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
+HDF_CXX = @HDF_CXX@
+HDF_FORTRAN = @HDF_FORTRAN@
 HID_T = @HID_T@
 HL = @HL@
 HL_FOR = @HL_FOR@
-HSIZET = @HSIZET@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
 INSTALL = @INSTALL@
@@ -180,11 +219,16 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+INSTRUMENT = @INSTRUMENT@
 INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@
+LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
+LINUX_LFS = @LINUX_LFS@
+LIPO = @LIPO@
+LL_PATH = @LL_PATH@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 LT_STATIC_EXEC = @LT_STATIC_EXEC@
@@ -193,13 +237,19 @@ MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 MPI_GET_SIZE = @MPI_GET_SIZE@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
 OBJECT_NAMELEN_DEFAULT_F = @OBJECT_NAMELEN_DEFAULT_F@
 OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PARALLEL = @PARALLEL@
 PATH_SEPARATOR = @PATH_SEPARATOR@
@@ -212,22 +262,21 @@ RUNSERIAL = @RUNSERIAL@
 R_INTEGER = @R_INTEGER@
 R_LARGE = @R_LARGE@
 SEARCH = @SEARCH@
+SED = @SED@
 SETX = @SETX@
 SET_MAKE = @SET_MAKE@
-
-# Hardcode SHELL to be /bin/sh.  Most machines have this shell, and
-# on at least one machine configure fails to detect its existence (janus).
-# Also, when HDF5 is configured on one machine but run on another,
-# configure's automatic SHELL detection may not work on the build machine.
-SHELL = /bin/sh
+SHELL = @SHELL@
 SIZE_T = @SIZE_T@
+STATIC_EXEC = @STATIC_EXEC@
 STATIC_SHARED = @STATIC_SHARED@
 STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@
 STRIP = @STRIP@
 TESTPARALLEL = @TESTPARALLEL@
+THREADSAFE = @THREADSAFE@
 TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
+UNAME_INFO = @UNAME_INFO@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_FLETCHER32 = @USE_FILTER_FLETCHER32@
 USE_FILTER_NBIT = @USE_FILTER_NBIT@
@@ -236,13 +285,14 @@ USE_FILTER_SHUFFLE = @USE_FILTER_SHUFFLE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
 VERSION = @VERSION@
+WORDS_BIGENDIAN = @WORDS_BIGENDIAN@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_CXX = @ac_ct_CXX@
-ac_ct_F77 = @ac_ct_F77@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 ac_ct_FC = @ac_ct_FC@
 am__include = @am__include@
 am__leading_dot = @am__leading_dot@
@@ -258,8 +308,12 @@ build_vendor = @build_vendor@
 builddir = @builddir@
 datadir = @datadir@
 datarootdir = @datarootdir@
+
+# Install directories that automake doesn't know about
 docdir = $(exec_prefix)/doc
 dvidir = @dvidir@
+enable_shared = @enable_shared@
+enable_static = @enable_static@
 exec_prefix = @exec_prefix@
 host = @host@
 host_alias = @host_alias@
@@ -267,15 +321,14 @@ host_cpu = @host_cpu@
 host_os = @host_os@
 host_vendor = @host_vendor@
 htmldir = @htmldir@
-
-# Install directories that automake doesn't know about
-includedir = $(exec_prefix)/include
+includedir = @includedir@
 infodir = @infodir@
 install_sh = @install_sh@
 libdir = @libdir@
 libexecdir = @libexecdir@
 localedir = @localedir@
 localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
 mandir = @mandir@
 mkdir_p = @mkdir_p@
 oldincludedir = @oldincludedir@
@@ -288,6 +341,7 @@ sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 
@@ -333,14 +387,20 @@ TRACE = perl $(top_srcdir)/bin/trace
 # *.clog are from the MPE option.
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog
 
+# Add libtool shared library version numbers to the HDF5 library
+# See libtool versioning documentation online.
+LT_VERS_INTERFACE = 6
+LT_VERS_REVISION = 3
+LT_VERS_AGE = 0
+
 # Include src directory
 INCLUDES = -I$(top_srcdir)/src
 
 # This is our main target
 lib_LTLIBRARIES = libhdf5_cpp.la
 
-# Shared C++ libraries aren't universally supported.
-@CXX_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
+# Add libtool numbers to the HDF5 C++ library (from config/lt_vers.am)
+libhdf5_cpp_la_LDFLAGS = -version-info $(LT_VERS_INTERFACE):$(LT_VERS_REVISION):$(LT_VERS_AGE) $(AM_LDFLAGS)
 bin_SCRIPTS = h5c++
 
 # Source files for the library
@@ -367,7 +427,7 @@ include_HEADERS = H5Cpp.h H5AbstractDs.h H5AtomType.h H5Attribute.h H5Classes.h
 DISTCLEANFILES = h5c++ libhdf5.settings
 
 # Mark this directory as part of the C++ API
-HDF_CXX = yes
+CXX_API = yes
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -388,18 +448,18 @@ all: all-am
 
 .SUFFIXES:
 .SUFFIXES: .cpp .lo .o .obj
-$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir)/config/commence.am $(top_srcdir)/config/conclude.am $(am__configure_deps)
+$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir)/config/commence.am $(top_srcdir)/config/lt_vers.am $(top_srcdir)/config/conclude.am $(am__configure_deps)
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
-	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
-		&& exit 0; \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  c++/src/Makefile'; \
-	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign  c++/src/Makefile
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign c++/src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign c++/src/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
@@ -417,25 +477,30 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
 h5c++: $(top_builddir)/config.status $(srcdir)/h5c++.in
 	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 install-libLTLIBRARIES: $(lib_LTLIBRARIES)
 	@$(NORMAL_INSTALL)
 	test -z "$(libdir)" || $(MKDIR_P) "$(DESTDIR)$(libdir)"
-	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	list2=; for p in $$list; do \
 	  if test -f $$p; then \
-	    f=$(am__strip_dir) \
-	    echo " $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \
-	    $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \
+	    list2="$$list2 $$p"; \
 	  else :; fi; \
-	done
+	done; \
+	test -z "$$list2" || { \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
+	}
 
 uninstall-libLTLIBRARIES:
 	@$(NORMAL_UNINSTALL)
-	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
-	  p=$(am__strip_dir) \
-	  echo " $(LIBTOOL) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$p'"; \
-	  $(LIBTOOL) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$p"; \
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	for p in $$list; do \
+	  $(am__strip_dir) \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f '$(DESTDIR)$(libdir)/$$f'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
 	done
 
 clean-libLTLIBRARIES:
@@ -447,26 +512,41 @@ clean-libLTLIBRARIES:
 	  rm -f "$${dir}/so_locations"; \
 	done
 libhdf5_cpp.la: $(libhdf5_cpp_la_OBJECTS) $(libhdf5_cpp_la_DEPENDENCIES) 
-	$(CXXLINK) -rpath $(libdir) $(libhdf5_cpp_la_OBJECTS) $(libhdf5_cpp_la_LIBADD) $(LIBS)
+	$(libhdf5_cpp_la_LINK) -rpath $(libdir) $(libhdf5_cpp_la_OBJECTS) $(libhdf5_cpp_la_LIBADD) $(LIBS)
 install-binSCRIPTS: $(bin_SCRIPTS)
 	@$(NORMAL_INSTALL)
 	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-	@list='$(bin_SCRIPTS)'; for p in $$list; do \
+	@list='$(bin_SCRIPTS)'; test -n "$(bindir)" || list=; \
+	for p in $$list; do \
 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  if test -f $$d$$p; then \
-	    f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
-	    echo " $(binSCRIPT_INSTALL) '$$d$$p' '$(DESTDIR)$(bindir)/$$f'"; \
-	    $(binSCRIPT_INSTALL) "$$d$$p" "$(DESTDIR)$(bindir)/$$f"; \
-	  else :; fi; \
-	done
+	  if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \
+	done | \
+	sed -e 'p;s,.*/,,;n' \
+	    -e 'h;s|.*|.|' \
+	    -e 'p;x;s,.*/,,;$(transform)' | sed 'N;N;N;s,\n, ,g' | \
+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1; } \
+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+	    if ($$2 == $$4) { files[d] = files[d] " " $$1; \
+	      if (++n[d] == $(am__install_max)) { \
+		print "f", d, files[d]; n[d] = 0; files[d] = "" } } \
+	    else { print "f", d "/" $$4, $$1 } } \
+	  END { for (d in files) print "f", d, files[d] }' | \
+	while read type dir files; do \
+	     if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+	     test -z "$$files" || { \
+	       echo " $(INSTALL_SCRIPT) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+	       $(INSTALL_SCRIPT) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+	     } \
+	; done
 
 uninstall-binSCRIPTS:
 	@$(NORMAL_UNINSTALL)
-	@list='$(bin_SCRIPTS)'; for p in $$list; do \
-	  f=`echo "$$p" | sed 's|^.*/||;$(transform)'`; \
-	  echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
-	  rm -f "$(DESTDIR)$(bindir)/$$f"; \
-	done
+	@list='$(bin_SCRIPTS)'; test -n "$(bindir)" || exit 0; \
+	files=`for p in $$list; do echo "$$p"; done | \
+	       sed -e 's,.*/,,;$(transform)'`; \
+	test -n "$$list" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(bindir)" && rm -f $$files
 
 mostlyclean-compile:
 	-rm -f *.$(OBJEXT)
@@ -503,21 +583,21 @@ distclean-compile:
 
 .cpp.o:
 @am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ $<
 
 .cpp.obj:
 @am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-@am__fastdepCXX_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
 
 .cpp.lo:
 @am__fastdepCXX_TRUE@	$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(LTCXXCOMPILE) -c -o $@ $<
@@ -530,65 +610,72 @@ clean-libtool:
 install-includeHEADERS: $(include_HEADERS)
 	@$(NORMAL_INSTALL)
 	test -z "$(includedir)" || $(MKDIR_P) "$(DESTDIR)$(includedir)"
-	@list='$(include_HEADERS)'; for p in $$list; do \
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	for p in $$list; do \
 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-	  f=$(am__strip_dir) \
-	  echo " $(includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(includedir)/$$f'"; \
-	  $(includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(includedir)/$$f"; \
+	  echo "$$d$$p"; \
+	done | $(am__base_list) | \
+	while read files; do \
+	  echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
+	  $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
 	done
 
 uninstall-includeHEADERS:
 	@$(NORMAL_UNINSTALL)
-	@list='$(include_HEADERS)'; for p in $$list; do \
-	  f=$(am__strip_dir) \
-	  echo " rm -f '$(DESTDIR)$(includedir)/$$f'"; \
-	  rm -f "$(DESTDIR)$(includedir)/$$f"; \
-	done
+	@list='$(include_HEADERS)'; test -n "$(includedir)" || list=; \
+	files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
+	test -n "$$files" || exit 0; \
+	echo " ( cd '$(DESTDIR)$(includedir)' && rm -f" $$files ")"; \
+	cd "$(DESTDIR)$(includedir)" && rm -f $$files
 
 ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
 	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
 	mkid -fID $$unique
 tags: TAGS
 
 TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
+	set x; \
 	here=`pwd`; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
 	  test -n "$$unique" || unique=$$empty_fix; \
-	  $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	    $$tags $$unique; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
 	fi
 ctags: CTAGS
 CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
-	here=`pwd`; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	test -z "$(CTAGS_ARGS)$$tags$$unique" \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
 	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$tags $$unique
+	     $$unique
 
 GTAGS:
 	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && cd $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) $$here
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
 
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
@@ -609,13 +696,17 @@ distdir: $(DISTFILES)
 	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
 	  if test -d $$d/$$file; then \
 	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
 	    fi; \
-	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
 	  else \
-	    test -f $(distdir)/$$file \
-	    || cp -p $$d/$$file $(distdir)/$$file \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
 	    || exit 1; \
 	  fi; \
 	done
@@ -647,6 +738,7 @@ clean-generic:
 
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
 	-test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
 
 maintainer-clean-generic:
@@ -669,6 +761,8 @@ dvi-am:
 
 html: html-am
 
+html-am:
+
 info: info-am
 
 info-am:
@@ -677,18 +771,28 @@ install-data-am: install-includeHEADERS
 
 install-dvi: install-dvi-am
 
+install-dvi-am:
+
 install-exec-am: install-binSCRIPTS install-libLTLIBRARIES
 
 install-html: install-html-am
 
+install-html-am:
+
 install-info: install-info-am
 
+install-info-am:
+
 install-man:
 
 install-pdf: install-pdf-am
 
+install-pdf-am:
+
 install-ps: install-ps-am
 
+install-ps-am:
+
 installcheck-am:
 
 maintainer-clean: maintainer-clean-am
@@ -712,7 +816,7 @@ ps-am:
 uninstall-am: uninstall-binSCRIPTS uninstall-includeHEADERS \
 	uninstall-libLTLIBRARIES
 
-.MAKE: install-am install-strip
+.MAKE: check-am install-am install-strip
 
 .PHONY: CTAGS GTAGS all all-am all-local check check-TESTS check-am \
 	clean clean-generic clean-libLTLIBRARIES clean-libtool ctags \
@@ -743,6 +847,19 @@ uninstall-am: uninstall-binSCRIPTS uninstall-includeHEADERS \
 help:
 	@$(top_srcdir)/bin/makehelp
 
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+
 # Some C++ compilers/linkers (PGI?) create a directory named "ii_files" that
 # holds *.ii files, which are template entity instantiations.
 # This entire directory should be cleaned.
@@ -839,10 +956,10 @@ $(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
 	      else \
@@ -878,10 +995,10 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
 	      else \
@@ -945,6 +1062,7 @@ check-vfd: $(LIB) $(PROGS) $(TESTS)
 	        HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1;    \
 	    fi;                                                               \
 	done
+
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:

c++/src/h5c++.in

@@ -56,9 +56,9 @@ get_output_file="no"
 SHOW="eval"
 CXXBASE="@CXX@"
 CXXLINKERBASE="@CXX@"
-CXXFLAGS="@CXXFLAGS@"
-CPPFLAGS="@CPPFLAGS@"
-LDFLAGS="@LDFLAGS@"
+CXXFLAGS="@AM_CXXFLAGS@ @CXXFLAGS@"
+CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
 LIBS="@LIBS@"
 
 CXX="${HDF5_CXX:-$CXXBASE}"
@@ -317,7 +317,7 @@ if test "x$do_link" = "xyes"; then
   # module. It's okay if they're included twice in the compile line.
   link_args="$link_args $LIBS"
 
-  $SHOW $CXXLINKER $CPPFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $link_args $shared_link
+  $SHOW $CXXLINKER $CPPFLAGS $CXXFLAGS $clibpath $link_objs $link_args $shared_link $LDFLAGS
 
   status=$?
 fi

c++/test/Makefile.am

@@ -26,7 +26,7 @@ INCLUDES=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/c++/src
 # Shared C++ libraries aren't universally supported.
 if CXX_SHARED_CONDITIONAL
 else
-  AM_LDFLAGS=-static
+  AM_LDFLAGS+=-static
 endif
 
 # These are our main targets.  They should be listed in the order to be
@@ -39,10 +39,10 @@ LDADD=$(LIBH5TEST) $(LIBH5CPP) $(LIBHDF5)
 
 dsets_SOURCES=dsets.cpp h5cpputil.cpp
 testhdf5_SOURCES=testhdf5.cpp tattr.cpp tcompound.cpp tfile.cpp tfilter.cpp \
-	th5s.cpp trefer.cpp ttypes.cpp tvlstr.cpp h5cpputil.cpp
+	th5s.cpp tlinks.cpp trefer.cpp ttypes.cpp tvlstr.cpp h5cpputil.cpp
 
 # Tell conclude.am that these are C++ tests.
-HDF_CXX=yes
+CXX_API=yes
 
 # Some C++ compilers/linkers (PGI?) create a directory named "ii_files" that
 # holds *.ii files, which are template entity instantiations.

c++/test/Makefile.in

@@ -1,8 +1,9 @@
-# Makefile.in generated by automake 1.10 from Makefile.am.
+# Makefile.in generated by automake 1.11 from Makefile.am.
 # @configure_input@
 
 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006  Free Software Foundation, Inc.
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
 # with or without modifications, as long as this notice is preserved.
@@ -32,8 +33,9 @@
 #
 VPATH = @srcdir@
 pkgdatadir = $(datadir)/@PACKAGE@
-pkglibdir = $(libdir)/@PACKAGE@
 pkgincludedir = $(includedir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkglibexecdir = $(libexecdir)/@PACKAGE@
 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
 install_sh_DATA = $(install_sh) -c -m 644
 install_sh_PROGRAM = $(install_sh) -c
@@ -51,6 +53,9 @@ host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
+
+# Shared C++ libraries aren't universally supported.
+@CXX_SHARED_CONDITIONAL_FALSE@am__append_1 = -static
 check_PROGRAMS = $(am__EXEEXT_1)
 TESTS = $(check_PROGRAMS)
 subdir = c++/test
@@ -61,6 +66,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
 CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
 am__EXEEXT_1 = dsets$(EXEEXT) testhdf5$(EXEEXT)
 am_dsets_OBJECTS = dsets.$(OBJEXT) h5cpputil.$(OBJEXT)
 dsets_OBJECTS = $(am_dsets_OBJECTS)
@@ -68,14 +74,15 @@ dsets_LDADD = $(LDADD)
 dsets_DEPENDENCIES = $(LIBH5TEST) $(LIBH5CPP) $(LIBHDF5)
 am_testhdf5_OBJECTS = testhdf5.$(OBJEXT) tattr.$(OBJEXT) \
 	tcompound.$(OBJEXT) tfile.$(OBJEXT) tfilter.$(OBJEXT) \
-	th5s.$(OBJEXT) trefer.$(OBJEXT) ttypes.$(OBJEXT) \
-	tvlstr.$(OBJEXT) h5cpputil.$(OBJEXT)
+	th5s.$(OBJEXT) tlinks.$(OBJEXT) trefer.$(OBJEXT) \
+	ttypes.$(OBJEXT) tvlstr.$(OBJEXT) h5cpputil.$(OBJEXT)
 testhdf5_OBJECTS = $(am_testhdf5_OBJECTS)
 testhdf5_LDADD = $(LDADD)
 testhdf5_DEPENDENCIES = $(LIBH5TEST) $(LIBH5CPP) $(LIBHDF5)
-DEFAULT_INCLUDES = -I. -I$(top_builddir)/src@am__isrc@
+DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src
 depcomp = $(SHELL) $(top_srcdir)/bin/depcomp
 am__depfiles_maybe = depfiles
+am__mv = mv -f
 CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
 	$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
 LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
@@ -89,10 +96,22 @@ SOURCES = $(dsets_SOURCES) $(testhdf5_SOURCES)
 DIST_SOURCES = $(dsets_SOURCES) $(testhdf5_SOURCES)
 ETAGS = etags
 CTAGS = ctags
+am__tty_colors = \
+red=; grn=; lgn=; blu=; std=
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@ $(am__append_1)
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -106,46 +125,47 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
-CFLAGS = @CFLAGS@ @H5_CFLAGS@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
+CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
 DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
+DIRECT_VFD = @DIRECT_VFD@
+DSYMUTIL = @DSYMUTIL@
+DUMPBIN = @DUMPBIN@
 DYNAMIC_DIRS = @DYNAMIC_DIRS@
-ECHO = @ECHO@
 ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
 EXEEXT = @EXEEXT@
-F77 = @F77@
+EXTERNAL_FILTERS = @EXTERNAL_FILTERS@
 
 # Make sure that these variables are exported to the Makefiles
 F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FGREP = @FGREP@
 FILTERS = @FILTERS@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+GPFS = @GPFS@
 GREP = @GREP@
 H5_CFLAGS = @H5_CFLAGS@
 H5_CPPFLAGS = @H5_CPPFLAGS@
@@ -154,11 +174,14 @@ H5_FCFLAGS = @H5_FCFLAGS@
 H5_LONE_COLON = @H5_LONE_COLON@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
+HAVE_DMALLOC = @HAVE_DMALLOC@
+HDF5_HL = @HDF5_HL@
 HDF5_INTERFACES = @HDF5_INTERFACES@
+HDF_CXX = @HDF_CXX@
+HDF_FORTRAN = @HDF_FORTRAN@
 HID_T = @HID_T@
 HL = @HL@
 HL_FOR = @HL_FOR@
-HSIZET = @HSIZET@
 HSIZE_T = @HSIZE_T@
 HSSIZE_T = @HSSIZE_T@
 INSTALL = @INSTALL@
@@ -166,11 +189,16 @@ INSTALL_DATA = @INSTALL_DATA@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
 INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
+INSTRUMENT = @INSTRUMENT@
 INSTRUMENT_LIBRARY = @INSTRUMENT_LIBRARY@
+LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
+LINUX_LFS = @LINUX_LFS@
+LIPO = @LIPO@
+LL_PATH = @LL_PATH@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 LT_STATIC_EXEC = @LT_STATIC_EXEC@
@@ -179,13 +207,19 @@ MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 MPI_GET_SIZE = @MPI_GET_SIZE@
+NM = @NM@
+NMEDIT = @NMEDIT@
+OBJDUMP = @OBJDUMP@
 OBJECT_NAMELEN_DEFAULT_F = @OBJECT_NAMELEN_DEFAULT_F@
 OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
 PACKAGE_STRING = @PACKAGE_STRING@
 PACKAGE_TARNAME = @PACKAGE_TARNAME@
+PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PARALLEL = @PARALLEL@
 PATH_SEPARATOR = @PATH_SEPARATOR@
@@ -198,22 +232,21 @@ RUNSERIAL = @RUNSERIAL@
 R_INTEGER = @R_INTEGER@
 R_LARGE = @R_LARGE@
 SEARCH = @SEARCH@
+SED = @SED@
 SETX = @SETX@
 SET_MAKE = @SET_MAKE@
-
-# Hardcode SHELL to be /bin/sh.  Most machines have this shell, and
-# on at least one machine configure fails to detect its existence (janus).
-# Also, when HDF5 is configured on one machine but run on another,
-# configure's automatic SHELL detection may not work on the build machine.
-SHELL = /bin/sh
+SHELL = @SHELL@
 SIZE_T = @SIZE_T@
+STATIC_EXEC = @STATIC_EXEC@
 STATIC_SHARED = @STATIC_SHARED@
 STRICT_FORMAT_CHECKS = @STRICT_FORMAT_CHECKS@
 STRIP = @STRIP@
 TESTPARALLEL = @TESTPARALLEL@
+THREADSAFE = @THREADSAFE@
 TIME = @TIME@
 TR = @TR@
 TRACE_API = @TRACE_API@
+UNAME_INFO = @UNAME_INFO@
 USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
 USE_FILTER_FLETCHER32 = @USE_FILTER_FLETCHER32@
 USE_FILTER_NBIT = @USE_FILTER_NBIT@
@@ -222,13 +255,14 @@ USE_FILTER_SHUFFLE = @USE_FILTER_SHUFFLE@
 USE_FILTER_SZIP = @USE_FILTER_SZIP@
 USINGMEMCHECKER = @USINGMEMCHECKER@
 VERSION = @VERSION@
+WORDS_BIGENDIAN = @WORDS_BIGENDIAN@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
 abs_top_builddir = @abs_top_builddir@
 abs_top_srcdir = @abs_top_srcdir@
 ac_ct_CC = @ac_ct_CC@
 ac_ct_CXX = @ac_ct_CXX@
-ac_ct_F77 = @ac_ct_F77@
+ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
 ac_ct_FC = @ac_ct_FC@
 am__include = @am__include@
 am__leading_dot = @am__leading_dot@
@@ -244,8 +278,12 @@ build_vendor = @build_vendor@
 builddir = @builddir@
 datadir = @datadir@
 datarootdir = @datarootdir@
+
+# Install directories that automake doesn't know about
 docdir = $(exec_prefix)/doc
 dvidir = @dvidir@
+enable_shared = @enable_shared@
+enable_static = @enable_static@
 exec_prefix = @exec_prefix@
 host = @host@
 host_alias = @host_alias@
@@ -253,15 +291,14 @@ host_cpu = @host_cpu@
 host_os = @host_os@
 host_vendor = @host_vendor@
 htmldir = @htmldir@
-
-# Install directories that automake doesn't know about
-includedir = $(exec_prefix)/include
+includedir = @includedir@
 infodir = @infodir@
 install_sh = @install_sh@
 libdir = @libdir@
 libexecdir = @libexecdir@
 localedir = @localedir@
 localstatedir = @localstatedir@
+lt_ECHO = @lt_ECHO@
 mandir = @mandir@
 mkdir_p = @mkdir_p@
 oldincludedir = @oldincludedir@
@@ -274,6 +311,7 @@ sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
 sysconfdir = @sysconfdir@
 target_alias = @target_alias@
+top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 
@@ -322,9 +360,6 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog
 # Include src, test, and c++/src directories
 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/c++/src
 
-# Shared C++ libraries aren't universally supported.
-@CXX_SHARED_CONDITIONAL_FALSE@AM_LDFLAGS = -static
-
 # These are our main targets.  They should be listed in the order to be
 # executed, generally most specific tests to least specific tests.
 TEST_PROG = dsets testhdf5
@@ -333,11 +368,11 @@ TEST_PROG = dsets testhdf5
 LDADD = $(LIBH5TEST) $(LIBH5CPP) $(LIBHDF5)
 dsets_SOURCES = dsets.cpp h5cpputil.cpp
 testhdf5_SOURCES = testhdf5.cpp tattr.cpp tcompound.cpp tfile.cpp tfilter.cpp \
-	th5s.cpp trefer.cpp ttypes.cpp tvlstr.cpp h5cpputil.cpp
+	th5s.cpp tlinks.cpp trefer.cpp ttypes.cpp tvlstr.cpp h5cpputil.cpp
 
 
 # Tell conclude.am that these are C++ tests.
-HDF_CXX = yes
+CXX_API = yes
 
 # Automake needs to be taught how to build lib, progs, and tests targets.
 # These will be filled in automatically for the most part (e.g.,
@@ -362,14 +397,14 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
-	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
-		&& exit 0; \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
 	      exit 1;; \
 	  esac; \
 	done; \
-	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  c++/test/Makefile'; \
-	cd $(top_srcdir) && \
-	  $(AUTOMAKE) --foreign  c++/test/Makefile
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign c++/test/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign c++/test/Makefile
 .PRECIOUS: Makefile
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	@case '$?' in \
@@ -387,13 +422,16 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
 
 clean-checkPROGRAMS:
-	@list='$(check_PROGRAMS)'; for p in $$list; do \
-	  f=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
-	  echo " rm -f $$p $$f"; \
-	  rm -f $$p $$f ; \
-	done
+	@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
+	echo " rm -f" $$list; \
+	rm -f $$list || exit $$?; \
+	test -n "$(EXEEXT)" || exit 0; \
+	list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
+	echo " rm -f" $$list; \
+	rm -f $$list
 dsets$(EXEEXT): $(dsets_OBJECTS) $(dsets_DEPENDENCIES) 
 	@rm -f dsets$(EXEEXT)
 	$(CXXLINK) $(dsets_OBJECTS) $(dsets_LDADD) $(LIBS)
@@ -415,27 +453,28 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tfile.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tfilter.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/th5s.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tlinks.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/trefer.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ttypes.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tvlstr.Po@am__quote@
 
 .cpp.o:
 @am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ $<
 
 .cpp.obj:
 @am__fastdepCXX_TRUE@	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-@am__fastdepCXX_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
 
 .cpp.lo:
 @am__fastdepCXX_TRUE@	$(LTCXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-@am__fastdepCXX_TRUE@	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
+@am__fastdepCXX_TRUE@	$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	source='$<' object='$@' libtool=yes @AMDEPBACKSLASH@
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(LTCXXCOMPILE) -c -o $@ $<
@@ -451,45 +490,49 @@ ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
 	mkid -fID $$unique
 tags: TAGS
 
 TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
+	set x; \
 	here=`pwd`; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	shift; \
+	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
 	  test -n "$$unique" || unique=$$empty_fix; \
-	  $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-	    $$tags $$unique; \
+	  if test $$# -gt 0; then \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      "$$@" $$unique; \
+	  else \
+	    $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+	      $$unique; \
+	  fi; \
 	fi
 ctags: CTAGS
 CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
 		$(TAGS_FILES) $(LISP)
-	tags=; \
-	here=`pwd`; \
 	list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
 	unique=`for i in $$list; do \
 	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
 	  done | \
-	  $(AWK) '    { files[$$0] = 1; } \
-	       END { for (i in files) print i; }'`; \
-	test -z "$(CTAGS_ARGS)$$tags$$unique" \
+	  $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+	      END { if (nonempty) { for (i in files) print i; }; }'`; \
+	test -z "$(CTAGS_ARGS)$$unique" \
 	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-	     $$tags $$unique
+	     $$unique
 
 GTAGS:
 	here=`$(am__cd) $(top_builddir) && pwd` \
-	  && cd $(top_srcdir) \
-	  && gtags -i $(GTAGS_ARGS) $$here
+	  && $(am__cd) $(top_srcdir) \
+	  && gtags -i $(GTAGS_ARGS) "$$here"
 
 distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
@@ -510,13 +553,17 @@ distdir: $(DISTFILES)
 	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
 	  if test -d $$d/$$file; then \
 	    dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
 	    fi; \
-	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
 	  else \
-	    test -f $(distdir)/$$file \
-	    || cp -p $$d/$$file $(distdir)/$$file \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
 	    || exit 1; \
 	  fi; \
 	done
@@ -546,6 +593,7 @@ clean-generic:
 
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
 
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
@@ -567,6 +615,8 @@ dvi-am:
 
 html: html-am
 
+html-am:
+
 info: info-am
 
 info-am:
@@ -575,18 +625,28 @@ install-data-am:
 
 install-dvi: install-dvi-am
 
+install-dvi-am:
+
 install-exec-am:
 
 install-html: install-html-am
 
+install-html-am:
+
 install-info: install-info-am
 
+install-info-am:
+
 install-man:
 
 install-pdf: install-pdf-am
 
+install-pdf-am:
+
 install-ps: install-ps-am
 
+install-ps-am:
+
 installcheck-am:
 
 maintainer-clean: maintainer-clean-am
@@ -609,7 +669,7 @@ ps-am:
 
 uninstall-am:
 
-.MAKE: install-am install-strip
+.MAKE: check-am install-am install-strip
 
 .PHONY: CTAGS GTAGS all all-am all-local check check-TESTS check-am \
 	clean clean-checkPROGRAMS clean-generic clean-libtool ctags \
@@ -733,10 +793,10 @@ $(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
 	      else \
@@ -772,10 +832,10 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
 	      else \
@@ -839,6 +899,7 @@ check-vfd: $(LIB) $(PROGS) $(TESTS)
 	        HDF5_DRIVER=$$vfd $(MAKE) $(AM_MAKEFLAGS) check || exit 1;    \
 	    fi;                                                               \
 	done
+
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:

c++/test/dsets.cpp

@@ -352,7 +352,7 @@ test_tconv( H5File& file)
 }   // test_tconv
 
 /* This message derives from H5Z */
-const H5Z_class_t H5Z_BOGUS[1] = {{
+const H5Z_class2_t H5Z_BOGUS[1] = {{
     H5Z_CLASS_T_VERS,		/* H5Z_class_t version number   */
     H5Z_FILTER_BOGUS,		/* Filter id number		*/
     1, 1,			/* Encode and decode enabled    */
@@ -413,8 +413,10 @@ filter_bogus(unsigned int flags, size_t cd_nelmts,
 static herr_t
 test_compression(H5File& file)
 {
+#ifndef H5_HAVE_FILTER_DEFLATE
     const char		*not_supported;
     not_supported = "    Deflate compression is not enabled.";
+#endif /* H5_HAVE_FILTER_DEFLATE */
     int		points[100][200];
     int		check[100][200];
     hsize_t	i, j, n;
@@ -423,7 +425,7 @@ test_compression(H5File& file)
     for (i = n = 0; i < 100; i++)
     {
 	for (j = 0; j < 200; j++) {
-	    points[i][j] = n++;
+	    points[i][j] = (int)n++;
 	}
     }
     char* tconv_buf = new char [1000];
@@ -487,7 +489,7 @@ test_compression(H5File& file)
 	{
 	    for (j=0; j<size[1]; j++)
 	    {
-		points[i][j] = n++;
+		points[i][j] = (int)n++;
 	    }
 	}
 

c++/test/h5cpputil.cpp

@@ -112,7 +112,7 @@ void issue_fail_msg(const char* where, int line, const char* file_name,
  *		different, the function will print out a message and the
  *		different values.  This function is made to reuse the code
  *		segment that is used in various places throughout
- *		the test code.  Where the C version of this code segment 
+ *		the test code.  Where the C version of this code segment
  *		"goto error," this function will return -1.
  *
  * Return:	Success:	0

c++/test/h5cpputil.h

@@ -113,25 +113,27 @@ template <class Type1, class Type2>
 #ifdef __cplusplus
 extern "C" {
 #endif
-void test_attr(void);
-void test_compound(void);
-void test_file(void);
-void test_filters(void);
-void test_h5s(void);
-void test_reference(void);
-void test_types(void);
-void test_vlstrings(void);
+void test_attr();
+void test_compound();
+void test_file();
+void test_filters();
+void test_links();
+void test_h5s();
+void test_reference();
+void test_types();
+void test_vlstrings();
 
 /* Prototypes for the cleanup routines */
-void cleanup_attr(void);
-void cleanup_compound(void);
-void cleanup_dsets(void);
-void cleanup_file(void);
-void cleanup_filters(void);
-void cleanup_h5s(void);
-void cleanup_reference(void);
-void cleanup_types(void);
-void cleanup_vlstrings(void);
+void cleanup_attr();
+void cleanup_compound();
+void cleanup_dsets();
+void cleanup_file();
+void cleanup_filters();
+void cleanup_links();
+void cleanup_h5s();
+void cleanup_reference();
+void cleanup_types();
+void cleanup_vlstrings();
 
 #ifdef __cplusplus
 }

c++/test/tattr.cpp

@@ -356,7 +356,7 @@ static void test_attr_basic_read()
 	for(i=0; i<ATTR2_DIM1; i++)
             for(j=0; j<ATTR2_DIM2; j++)
         	if(attr_data2[i][j]!=read_data2[i][j]) {
-		    TestErrPrintf("%d: attribute data different: attr_data2[%d][%d]=%d, read_data2[%d][%d]=%d\n",__LINE__, i,j,attr_data2[i][j],i,j,read_data1[i]);
+		    TestErrPrintf("%d: attribute data different: attr_data2[%d][%d]=%d, read_data2[%d][%d]=%d\n",__LINE__, i,j,attr_data2[i][j],i,j,read_data2[i][j]);
 		}
 	PASSED();
     } // end try block
@@ -1043,13 +1043,18 @@ static void test_attr_dtype_shared()
 
 	// Get size of file
 	h5_stat_size_t empty_filesize;       // Size of empty file
-	empty_filesize = h5_get_file_size(FILENAME.c_str());
+	empty_filesize = h5_get_file_size(FILENAME.c_str(), H5P_DEFAULT);
 	if (empty_filesize < 0)
-    	TestErrPrintf("Line %d: file size wrong!\n",__LINE__);
+            TestErrPrintf("Line %d: file size wrong!\n", __LINE__);
 
 	// Open the file again
 	fid1.openFile(FILENAME, H5F_ACC_RDWR);
 
+	// Enclosing to work around the issue of unused variables and/or
+	// objects created by copy constructors stay around until end of
+	// scope, causing incorrect number of ref counts.
+	{ // First enclosed block
+
 	// Create a datatype to commit and use
 	IntType dtype(PredType::NATIVE_INT);
 
@@ -1065,13 +1070,6 @@ static void test_attr_dtype_shared()
 	// Create dataspace for dataset
 	DataSpace dspace;
 
-	// Enclose the following so that all temporary objects can be
-	// destroyed before testing reference count - this is to overcome
-	// the different time when the temporary objects are to be destroyed
-	// by different compilers.
-	{
-
-	// Create dataset
 	DataSet dset = fid1.createDataSet(DSET1_NAME, dtype, dspace);
 
 #ifndef H5_NO_DEPRECATED_SYMBOLS
@@ -1089,8 +1087,8 @@ static void test_attr_dtype_shared()
 	verify_val((int)statbuf.nlink, 3, "DataSet::getObjinfo", __LINE__, __FILE__);
 #endif /* H5_NO_DEPRECATED_SYMBOLS */
 
-	// Close attribute
-	attr.close();
+        // Close attribute
+        attr.close();
 
 	// Delete attribute
 	dset.removeAttr(ATTR1_NAME);
@@ -1101,8 +1099,8 @@ static void test_attr_dtype_shared()
 	verify_val((int)statbuf.nlink, 2, "DataSet::getObjinfo after DataSet::removeAttr", __LINE__, __FILE__);
 #endif /* H5_NO_DEPRECATED_SYMBOLS */
 
-	// Create attribute on dataset
-	attr = dset.createAttribute(ATTR1_NAME,dtype,dspace);
+        // Create attribute on dataset
+        attr = dset.createAttribute(ATTR1_NAME,dtype,dspace);
 
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 	// Check reference count on named datatype
@@ -1118,11 +1116,15 @@ static void test_attr_dtype_shared()
 	dset.close();
 	dspace.close();
 	dtype.close();
+	} // end of first enclosing
+
 	fid1.close();
 
 	// Open the file again
 	fid1.openFile(FILENAME, H5F_ACC_RDWR);
 
+	{ // Second enclosed block...
+
 	// Open dataset
 	DataSet *dset2 = new DataSet (fid1.openDataSet(DSET1_NAME));
 
@@ -1142,12 +1144,11 @@ static void test_attr_dtype_shared()
 	fid1.getObjinfo(TYPE1_NAME, statbuf);
 	verify_val((int)statbuf.nlink, 3, "DataSet::openAttribute", __LINE__, __FILE__);
 #endif /* H5_NO_DEPRECATED_SYMBOLS */
+	} // end of second enclosing
 
 	// Unlink the dataset
 	fid1.unlink(DSET1_NAME);
 
-        } // end of enclosing to test reference counts
-
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 	// Check reference count on named datatype
 	fid1.getObjinfo(TYPE1_NAME, statbuf);
@@ -1161,7 +1162,7 @@ static void test_attr_dtype_shared()
 	fid1.close();
 
 	// Check size of file
-	filesize=h5_get_file_size(FILENAME.c_str());
+	filesize = h5_get_file_size(FILENAME.c_str(), H5P_DEFAULT);
 	verify_val((long)filesize, (long)empty_filesize, "Checking file size", __LINE__, __FILE__);
 
 	PASSED();
@@ -1179,20 +1180,26 @@ static void test_attr_dtype_shared()
 **
 ****************************************************************/
 /* Info for a string attribute */
-const H5std_string ATTRSTR_NAME("String_attr");
+const H5std_string ATTR1_FL_STR_NAME("String_attr 1");
+const H5std_string ATTR2_FL_STR_NAME("String_attr 2");
+const H5std_string ATTR_VL_STR_NAME("String_attr");
 const H5std_string ATTRSTR_DATA("String Attribute");
+const int ATTR_LEN = 17;
 
 static void test_string_attr()
 {
     // Output message about test being performed
-    SUBTEST("Testing Basic Attribute Writing Functions");
+    SUBTEST("Testing I/O on FL and VL String Attributes");
 
     try {
 	// Create file
 	H5File fid1(FILENAME, H5F_ACC_RDWR);
 
-	// Create a variable length string datatype to refer to.
-	StrType type(0, H5T_VARIABLE);
+	//
+	// Fixed-lenth string attributes
+	//
+	// Create a fixed-length string datatype to refer to.
+	StrType fls_type(0, ATTR_LEN);
 
 	// Open the root group.
 	Group root = fid1.openGroup("/");
@@ -1200,24 +1207,88 @@ static void test_string_attr()
 	// Create dataspace for the attribute.
 	DataSpace att_space (H5S_SCALAR);
 
+	/* Test Attribute::write(...,const void *buf) with Fixed len string */
+
 	// Create an attribute for the root group.
-	Attribute gr_attr = root.createAttribute(ATTRSTR_NAME, type, att_space);
+	Attribute gr_flattr1 = root.createAttribute(ATTR1_FL_STR_NAME, fls_type, att_space);
 
 	// Write data to the attribute.
-	gr_attr.write(type, ATTRSTR_DATA);
+	gr_flattr1.write(fls_type, ATTRSTR_DATA.c_str());
+
+	/* Test Attribute::write(...,const H5std_string& strg) with FL string */
+
+	// Create an attribute for the root group.
+	Attribute gr_flattr2 = root.createAttribute(ATTR2_FL_STR_NAME, fls_type, att_space);
+
+	// Write data to the attribute.
+	gr_flattr2.write(fls_type, ATTRSTR_DATA);
+
+	/* Test Attribute::read(...,void *buf) with FL string */
 
 	// Read and verify the attribute string as a string of chars.
-	char *string_att_check;
-	gr_attr.read(type, &string_att_check);
-	if(HDstrcmp(string_att_check, ATTRSTR_DATA.c_str())!=0)
-	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,string_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), string_att_check);
+	char flstring_att_check[ATTR_LEN];
+	gr_flattr1.read(fls_type, flstring_att_check);
+	if(HDstrcmp(flstring_att_check, ATTRSTR_DATA.c_str())!=0)
+	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,flstring_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), flstring_att_check);
+
+	// Read and verify the attribute string as a string of chars; buffer
+	// is dynamically allocated.
+	size_t attr_size = gr_flattr1.getInMemDataSize();
+	char *fl_dyn_string_att_check;
+	fl_dyn_string_att_check = new char[attr_size+1];
+	gr_flattr1.read(fls_type, fl_dyn_string_att_check);
+	if(HDstrcmp(fl_dyn_string_att_check, ATTRSTR_DATA.c_str())!=0)
+	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,flstring_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), fl_dyn_string_att_check);
+	delete []fl_dyn_string_att_check;
+
+	/* Test Attribute::read(...,H5std_string& strg) with FL string */
 
+	// Read and verify the attribute string as an std::string.
+	H5std_string read_flstr1;
+	gr_flattr1.read(fls_type, read_flstr1);
+	if (read_flstr1 != ATTRSTR_DATA)
+	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,read_flstr1=%s\n",__LINE__, ATTRSTR_DATA.c_str(), read_flstr1.c_str());
+
+	// Read and verify the attribute string as a string of chars.
+	HDstrcpy(flstring_att_check, "");
+	gr_flattr2.read(fls_type, flstring_att_check);
+	if(HDstrcmp(flstring_att_check, ATTRSTR_DATA.c_str())!=0)
+	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,flstring_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), flstring_att_check);
+
+	/* Test Attribute::read(...,H5std_string& strg) with FL string */
+
+	// Read and verify the attribute string as an std::string.
+	H5std_string read_flstr2;
+	gr_flattr2.read(fls_type, read_flstr2);
+	if (read_flstr2 != ATTRSTR_DATA)
+	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,read_flstr2=%s\n",__LINE__, ATTRSTR_DATA.c_str(), read_flstr2.c_str());
+
+	//
+	// Variable-lenth string attributes
+	//
+	// Create a variable length string datatype to refer to.
+	StrType vls_type(0, H5T_VARIABLE);
+
+	// Create an attribute for the root group.
+	Attribute gr_vlattr = root.createAttribute(ATTR_VL_STR_NAME, vls_type, att_space);
+
+	// Write data to the attribute.
+	gr_vlattr.write(vls_type, ATTRSTR_DATA);
+
+	/* Test Attribute::read(...,void *buf) with Variable len string */
+	// Read and verify the attribute string as a string of chars.
+	char *string_att_check;
+	gr_vlattr.read(vls_type, &string_att_check);
+	if(HDstrcmp(string_att_check, ATTRSTR_DATA.c_str())!=0)
+	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,string_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), string_att_check);
+	HDfree(string_att_check);
+
+	/* Test Attribute::read(...,H5std_string& strg) with VL string */
 	// Read and verify the attribute string as an std::string.
 	H5std_string read_str;
-	gr_attr.read(type, read_str);
+	gr_vlattr.read(vls_type, read_str);
 	if (read_str != ATTRSTR_DATA)
 	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,read_str=%s\n",__LINE__, ATTRSTR_DATA.c_str(), read_str.c_str());
-
 	PASSED();
     } // end try block
 

c++/test/tcompound.cpp

@@ -178,13 +178,13 @@ static void test_compound_2()
 		s_ptr->e    != d_ptr->e) {
 		H5_FAILED();
 		cerr << "    i=" << i << endl;
-		cerr << "    src={a=" << s_ptr->a << ", b=" << s_ptr->b 
-		     << "c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << "," 
-		     << s_ptr->c[2] << "," << s_ptr->c[3] << ", d=" 
+		cerr << "    src={a=" << s_ptr->a << ", b=" << s_ptr->b
+		     << "c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << ","
+		     << s_ptr->c[2] << "," << s_ptr->c[3] << ", d="
 		     << s_ptr->d << ", e=" << s_ptr->e << "}" << endl;
-		cerr << "    dst={a=" << s_ptr->a << ", b=" << s_ptr->b 
-		     << "c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << "," 
-		     << s_ptr->c[2] << "," << s_ptr->c[3] << ", d=" 
+		cerr << "    dst={a=" << s_ptr->a << ", b=" << s_ptr->b
+		     << "c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << ","
+		     << s_ptr->c[2] << "," << s_ptr->c[3] << ", d="
 		     << s_ptr->d << ", e=" << s_ptr->e << "}" << endl;
 	    }
     	}
@@ -294,13 +294,13 @@ static void test_compound_3()
 		s_ptr->e    != d_ptr->e) {
 		H5_FAILED();
 		cerr << "    i=" << i << endl;
-		cerr << "    src={a=" << s_ptr->a << ", b=" << s_ptr->b 
-		     << ", c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << "," 
-		     << s_ptr->c[2] << "," << s_ptr->c[3] << "], d=" 
+		cerr << "    src={a=" << s_ptr->a << ", b=" << s_ptr->b
+		     << ", c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << ","
+		     << s_ptr->c[2] << "," << s_ptr->c[3] << "], d="
 		     << s_ptr->d << ", e=" << s_ptr->e << "}" << endl;
 		cerr << "    dst={a=" << d_ptr->a
-		     << ", c=[" << d_ptr->c[0] << "," << d_ptr->c[1] << "," 
-		     << d_ptr->c[2] << "," << d_ptr->c[3] << "], e=" 
+		     << ", c=[" << d_ptr->c[0] << "," << d_ptr->c[1] << ","
+		     << d_ptr->c[2] << "," << d_ptr->c[3] << "], e="
 		     << d_ptr->e << "}" << endl;
 	    } // if
 	} // for
@@ -391,7 +391,7 @@ static void test_compound_4()
 	st.insertMember("d", HOFFSET(src_typ_t, d), PredType::NATIVE_INT);
 	st.insertMember("e", HOFFSET(src_typ_t, e), PredType::NATIVE_INT);
 	array_dt->close();
-    
+
 	array_dt = new ArrayType(PredType::NATIVE_INT, 1, &four);
 
 	// Create an empty compound datatype
@@ -402,7 +402,7 @@ static void test_compound_4()
 	dt.insertMember("d", HOFFSET(dst_typ_t, d), PredType::NATIVE_SHORT);
 	dt.insertMember("e", HOFFSET(dst_typ_t, e), PredType::NATIVE_INT);
 	array_dt->close();
-    
+
 	/* Perform the conversion */
 	st.convert(dt, (size_t)nelmts, buf, bkg);
 
@@ -421,17 +421,17 @@ static void test_compound_4()
 	    {
 		H5_FAILED();
 		cerr << "    i=" << i << endl;
-		cerr << "    src={a=" << s_ptr->a << ", b=" << s_ptr->b 
-		     << "c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << "," 
-		     << s_ptr->c[2] << "," << s_ptr->c[3] << ", d=" 
+		cerr << "    src={a=" << s_ptr->a << ", b=" << s_ptr->b
+		     << "c=[" << s_ptr->c[0] << "," << s_ptr->c[1] << ","
+		     << s_ptr->c[2] << "," << s_ptr->c[3] << ", d="
 		     << s_ptr->d << ", e=" << s_ptr->e << "}" << endl;
-		cerr << "    dst={a=" << d_ptr->a << ", b=" << d_ptr->b 
-		     << "c=[" << d_ptr->c[0] << "," << d_ptr->c[1] << "," 
-		     << d_ptr->c[2] << "," << d_ptr->c[3] << ", d=" 
+		cerr << "    dst={a=" << d_ptr->a << ", b=" << d_ptr->b
+		     << "c=[" << d_ptr->c[0] << "," << d_ptr->c[1] << ","
+		     << d_ptr->c[2] << "," << d_ptr->c[3] << ", d="
 		     << d_ptr->d << ", e=" << d_ptr->e << "}" << endl;
 	    } // if
 	} // for
-    
+
 	/* Release resources */
 	free(buf);
 	free(bkg);
@@ -493,13 +493,13 @@ static void test_compound_5()
     try {
 
 	/* Build datatypes */
-	ArrayType* array_dt = new ArrayType(PredType::NATIVE_SHORT, 1, dims);	
+	ArrayType* array_dt = new ArrayType(PredType::NATIVE_SHORT, 1, dims);
 	CompType short_array(4*sizeof(short));
 	short_array.insertMember("_", 0, *array_dt);
 	array_dt->close();
 
 	CompType int_array(4*sizeof(int));
-	array_dt = new ArrayType(PredType::NATIVE_INT, 1, dims);	
+	array_dt = new ArrayType(PredType::NATIVE_INT, 1, dims);
 	int_array.insertMember("_", 0, *array_dt);
 	array_dt->close();
 
@@ -532,7 +532,7 @@ static void test_compound_5()
 	    src[1].coll_ids[0]!=dst[1].coll_ids[0] ||
 	    src[1].coll_ids[1]!=dst[1].coll_ids[1] ||
 	    src[1].coll_ids[2]!=dst[1].coll_ids[2] ||
-	    src[1].coll_ids[3]!=dst[1].coll_ids[3]) 
+	    src[1].coll_ids[3]!=dst[1].coll_ids[3])
 	{ H5_FAILED(); }
 
 	/* Free memory buffers */
@@ -614,17 +614,17 @@ static void test_compound_6()
 	    s_ptr = ((src_typ_t*)orig) + i;
 	    d_ptr = ((dst_typ_t*)buf)  + i;
 	    if (s_ptr->b    != d_ptr->b    ||
-		s_ptr->d    != d_ptr->d) 
+		s_ptr->d    != d_ptr->d)
 	    {
 		H5_FAILED();
 		cerr << "    i=" << i << endl;
-		cerr << "    src={b=" << s_ptr->b << ", d=" << s_ptr->d 
+		cerr << "    src={b=" << s_ptr->b << ", d=" << s_ptr->d
 		     << "}" << endl;
-		cerr << "    dst={b=" << d_ptr->b << ", d=" << d_ptr->d 
+		cerr << "    dst={b=" << d_ptr->b << ", d=" << d_ptr->d
 		     << "}" << endl;
 	    } // if
 	} // for
-    
+
 	/* Release resources */
 	free(buf);
 	free(bkg);

c++/test/testhdf5.cpp

@@ -85,6 +85,7 @@ main(int argc, char *argv[])
     AddTest("types", test_types, cleanup_types,  "Generic Data Types", NULL);
     AddTest("compound", test_compound, cleanup_compound,  "Compound Data Types", NULL);
     AddTest("filter", test_filters, cleanup_filters,  "Various Filters", NULL);
+    AddTest("links", test_links, cleanup_links,  "Various Links", NULL);
 /* Comment out tests that are not done yet. - BMR, Feb 2001
     AddTest("select", test_select, cleanup_select,  "Selections", NULL);
     AddTest("time", test_time, cleanup_time,  "Time Datatypes", NULL);

c++/test/tfilter.cpp

@@ -48,7 +48,7 @@
 #define FILTER_CHUNK_DIM2 25
 
 // will do this function later or use it as guideline - BMR - 2007/01/26
-static herr_t test_filter_internal(hid_t fid, const char *name, hid_t dcpl, 
+static herr_t test_filter_internal(hid_t fid, const char *name, hid_t dcpl,
 		int if_fletcher32, int corrupted, hsize_t *dset_size)
 {
     cerr << "do nothing right now" << endl;
@@ -58,9 +58,9 @@ static herr_t test_filter_internal(hid_t fid, const char *name, hid_t dcpl,
 /* Temporary filter IDs used for testing */
 #define H5Z_FILTER_BOGUS        305
 static size_t filter_bogus(unsigned int flags, size_t cd_nelmts,
-    const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf); 
+    const unsigned int *cd_values, size_t nbytes, size_t *buf_size, void **buf);
 /* This message derives from H5Z */
-const H5Z_class_t H5Z_BOGUS[1] = {{
+const H5Z_class2_t H5Z_BOGUS[1] = {{
     H5Z_CLASS_T_VERS,       /* H5Z_class_t version */
     H5Z_FILTER_BOGUS,           /* Filter id number             */
     1, 1,               /* Encoding and decoding enabled */
@@ -118,7 +118,7 @@ static void test_null_filter()
     // Output message about test being performed
     SUBTEST("'Null' filter");
     try {
-	hsize_t  null_size;          // Size of dataset with null filter
+	//hsize_t  null_size;          // Size of dataset with null filter
 
 	// Prepare dataset create property list
 	DSetCreatPropList dsplist;
@@ -168,7 +168,6 @@ void test_szip_filter(H5File& file1)
 {
 #ifdef H5_HAVE_FILTER_SZIP
     int      points[DSET_DIM1][DSET_DIM2], check[DSET_DIM1][DSET_DIM2];
-    hsize_t  szip_size;       /* Size of dataset with szip filter */
     unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
     unsigned szip_pixels_per_block=4;
 
@@ -203,7 +202,7 @@ void test_szip_filter(H5File& file1)
         {
             for (j=0; j<size[1]; j++)
             {
-                points[i][j] = n++;
+                points[i][j] = (int)n++;
             }
         }
 
@@ -228,7 +227,7 @@ void test_szip_filter(H5File& file1)
     {
         issue_fail_msg("test_szip_filter()", __LINE__, __FILE__, E.getCDetailMsg());
     }
-    } // if szip presents 
+    } // if szip presents
     else {
 	SKIPPED();
     }

c++/test/th5s.cpp

@@ -300,7 +300,7 @@ static void test_h5s_scalar_write()
 	verify_val(ext_type, H5S_SCALAR, "DataSpace::getSimpleExtentType", __LINE__, __FILE__);
 
 	// Create and write a dataset
-	DataSet dataset = fid1.createDataSet("Dataset1", PredType::NATIVE_UINT,sid1); 
+	DataSet dataset = fid1.createDataSet("Dataset1", PredType::NATIVE_UINT,sid1);
 	dataset.write(&space3_data, PredType::NATIVE_UINT);
 
 	PASSED();

c++/test/tlinks.cpp

@@ -0,0 +1,722 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*****************************************************************************
+   FILE
+   tlinks.cpp - HDF5 C++ testing functionalities associated with the
+        C attribute interface (H5L)
+
+ ***************************************************************************/
+
+#ifdef OLD_HEADER_FILENAME
+#include <iostream.h>
+#else
+#include <iostream>
+#endif
+#include <string>
+
+#ifndef H5_NO_NAMESPACE
+#ifndef H5_NO_STD
+    using std::cerr;
+    using std::endl;
+#endif  // H5_NO_STD
+#endif
+
+#include "testhdf5.h"   // C test header file
+#include "H5Cpp.h"      // C++ API header file
+
+#ifndef H5_NO_NAMESPACE
+    using namespace H5;
+#endif
+
+#include "h5cpputil.h"  // C++ test utilility header file
+
+// A lot of the definition inherited from C test links.c is left here until
+// the H5L API is implemented and tests are completed - BMR 10/19/2009
+/*
+ * This file needs to access private information from the H5G package.
+ * This file also needs to access the group testing code.
+ */
+//#define H5G_PACKAGE
+//#define H5G_TESTING
+
+//#include "h5test.h"
+//#include "H5Gpkg.h"		/* Groups 				*/
+//#include "H5Iprivate.h"		/* IDs			  		*/
+//#include "H5Lprivate.h"         /* Links                                */
+
+/* File for external link test.  Created with gen_udlinks.c */
+#define LINKED_FILE  "be_extlink2.h5"
+
+#ifdef H5_VMS
+#if 0
+const char *FILENAME[] = {
+    "links0",
+    "links1",
+    "links2",
+    "links3",
+    "links4a", /* 4 */
+    "links4b", /* 5 */
+    "links4c", /* 6 */
+    "links4d", /* 7 */
+    "links5",  /* 8 */
+    "links6",  /* 9 */
+    "links7",  /* 10 */
+    "links8",  /* 11 */
+    "extlinks0",	/* 12: main files */
+    "[.tmp]extlinks0",	/* 13: */
+    "extlinks1",	/* 14: target files */
+    "[.tmp]extlinks1",	/* 15: */
+    "extlinks2",	/* 16: */
+    "[.tmp]extlinks2",	/* 17: */
+    "extlinks3",	/* 18: */
+    "[.tmp]extlinks3",	/* 19: */
+    "extlinks4",	/* 20: */
+    "[.tmp]extlinks4",	/* 21: */
+    "extlinks5",	/* 22: */
+    "[.tmp]extlinks6",	/* 23: */
+    "extlinks7",	/* 24: */
+    "[.tmp]extlinks7",	/* 25: */
+    "[.tmp]extlinks8",	/* 26: */
+    "extlinks9",	/* 27: */
+    "[.tmp]extlinks9",	/* 28: */
+    "extlinks10",	/* 29: */ /* TESTS for windows */
+    "[.tmp]extlinks10",	/* 30: */
+    "[.tmp]extlinks11",	/* 31: */
+    "[.tmp]extlinks12",	/* 32: */
+    "extlinks13",	/* 33: */
+    "[.tmp]extlinks13",	/* 34: */
+    "[.tmp]extlinks14",	/* 35: */
+    "[.tmp]extlinks15",	/* 36: */
+    "extlinks16A",	/* 37: */ /* TESTS for H5P_set_elink_fapl */
+    "extlinks16B",	/* 38: */
+    "extlinks17",	/* 39: */
+    "extlinks18A",	/* 40: */
+    "extlinks18B",	/* 41: */
+    "extlinks19A",	/* 42: */
+    "extlinks19B",	/* 43: */
+    "extlinks20",	/* 44: */
+    NULL
+};
+#endif // 0
+
+#define TMPDIR          "[.tmp]"
+#else
+#if 0
+const char *FILENAME[] = {
+    "links0",
+    "links1",
+    "links2",
+    "links3",
+    "links4a", /* 4 */
+    "links4b", /* 5 */
+    "links4c", /* 6 */
+    "links4d", /* 7 */
+    "links5",  /* 8 */
+    "links6",  /* 9 */
+    "links7",  /* 10 */
+    "links8",  /* 11 */
+    "extlinks0",	/* 12: main files */
+    "tmp/extlinks0",	/* 13: */
+    "extlinks1",	/* 14: target files */
+    "tmp/extlinks1",	/* 15: */
+    "extlinks2",	/* 16: */
+    "tmp/extlinks2",	/* 17: */
+    "extlinks3",	/* 18: */
+    "tmp/extlinks3",	/* 19: */
+    "extlinks4",	/* 20: */
+    "tmp/extlinks4",	/* 21: */
+    "extlinks5",	/* 22: */
+    "tmp/extlinks6",	/* 23: */
+    "extlinks7",	/* 24: */
+    "tmp/extlinks7",	/* 25: */
+    "tmp/extlinks8",	/* 26: */
+    "extlinks9",	/* 27: */
+    "tmp/extlinks9",	/* 28: */
+    "extlinks10",	/* 29: */ /* TESTS for windows */
+    "tmp/extlinks10",	/* 30: */
+    "tmp/extlinks11",	/* 31: */
+    "tmp/extlinks12",	/* 32: */
+    "extlinks13",	/* 33: */
+    "tmp/extlinks13",	/* 34: */
+    "tmp/extlinks14",	/* 35: */
+    "tmp/extlinks15",	/* 36: */
+    "extlinks16A",	/* 37: */ /* TESTS for H5P_set_elink_fapl */
+    "extlinks16B",	/* 38: */
+    "extlinks17",	/* 39: */
+    "extlinks18A",	/* 40: */
+    "extlinks18B",	/* 41: */
+    "extlinks19A",	/* 42: */
+    "extlinks19B",	/* 43: */
+    "extlinks20",	/* 44: */
+    NULL
+};
+
+#endif // 0
+
+#define TMPDIR          "tmp"
+#endif
+
+#define FAMILY_SIZE	1024
+#define CORE_INCREMENT  1024
+#define NUM400		400
+
+/* do not do check_all_closed() for "ext*" files and "tmp/ext*" */
+#define EXTSTOP		12
+
+#define LINK_BUF_SIZE   1024
+#define NAME_BUF_SIZE   1024
+#define MAX_NAME_LEN    ((64*1024)+1024)
+
+/* Link type IDs */
+#define UD_HARD_TYPE 201
+#define UD_CB_TYPE H5L_TYPE_MAX
+#define UD_PLIST_TYPE 128
+#define UD_CBFAIL_TYPE UD_PLIST_TYPE
+#define UD_ERROR_TYPE 189
+#define UD_BAD_TYPE1 H5L_TYPE_HARD
+#define UD_BAD_TYPE2 (H5L_TYPE_UD_MIN - 5)
+#define UD_BAD_VERS (H5L_LINK_CLASS_T_VERS + 1)
+
+#define DEST_PROP_NAME "destination_group"
+#define REREG_TARGET_NAME "rereg_target"
+
+#define UD_CB_LINK_NAME "ud_callback_link"
+#define NEW_UD_CB_LINK_NAME "ud_callback_link2"
+#define UD_CB_TARGET "ud_target"
+#define UD_CB_TARGET_LEN 10
+
+#define LE_FILENAME "le_extlink1.h5"
+#define BE_FILENAME "be_extlink1.h5"
+
+#define ELINK_CB_FAM_SIZE (hsize_t) 100
+
+#define H5L_DIM1 100
+#define H5L_DIM2 100
+
+/* Creation order macros */
+#define CORDER_GROUP_NAME       "corder_group"
+#define CORDER_SOFT_GROUP_NAME  "corder_soft_group"
+#define CORDER_NLINKS               18
+#define CORDER_ITER_STOP            3
+#define CORDER_EST_ENTRY_LEN        9
+
+/* Timestamp macros */
+#define TIMESTAMP_GROUP_1       "timestamp1"
+#define TIMESTAMP_GROUP_2       "timestamp2"
+
+/* Link iteration struct */
+typedef struct {
+    H5_iter_order_t order;      /* Direction of iteration */
+    unsigned ncalled;           /* # of times callback is entered */
+    unsigned nskipped;          /* # of links skipped */
+    int stop;                   /* # of iterations to stop after */
+    int64_t curr;               /* Current creation order value */
+    size_t max_visit;           /* Size of "visited link" flag array */
+    hbool_t *visited;           /* Pointer to array of "visited link" flags */
+} link_iter_info_t;
+
+/* Link visit structs */
+typedef struct {
+    const char *path;           /* Path to link */
+    H5L_type_t type;            /* Type of link */
+} link_visit_t;
+static const link_visit_t lvisit0[] = {
+    {"Dataset_zero", H5L_TYPE_HARD},
+    {"Group1", H5L_TYPE_HARD},
+    {"Group1/Dataset_one", H5L_TYPE_HARD},
+    {"Group1/Group2", H5L_TYPE_HARD},
+    {"Group1/Group2/Dataset_two", H5L_TYPE_HARD},
+    {"Group1/Group2/Type_two", H5L_TYPE_HARD},
+    {"Group1/Group2/hard_zero", H5L_TYPE_HARD},
+    {"Group1/Type_one", H5L_TYPE_HARD},
+    {"Group1/hard_one", H5L_TYPE_HARD},
+    {"Type_zero", H5L_TYPE_HARD},
+    {"ext_dangle", H5L_TYPE_EXTERNAL},
+    {"ext_one", H5L_TYPE_EXTERNAL},
+    {"hard_one", H5L_TYPE_HARD},
+    {"hard_two", H5L_TYPE_HARD},
+    {"hard_zero", H5L_TYPE_HARD},
+    {"soft_dangle", H5L_TYPE_SOFT},
+    {"soft_one", H5L_TYPE_SOFT},
+    {"soft_two", H5L_TYPE_SOFT}
+};
+static const link_visit_t lvisit1[] = {
+    {"Dataset_one", H5L_TYPE_HARD},
+    {"Group2", H5L_TYPE_HARD},
+    {"Group2/Dataset_two", H5L_TYPE_HARD},
+    {"Group2/Type_two", H5L_TYPE_HARD},
+    {"Group2/hard_zero", H5L_TYPE_HARD},
+    {"Group2/hard_zero/Dataset_zero", H5L_TYPE_HARD},
+    {"Group2/hard_zero/Group1", H5L_TYPE_HARD},
+    {"Group2/hard_zero/Type_zero", H5L_TYPE_HARD},
+    {"Group2/hard_zero/ext_dangle", H5L_TYPE_EXTERNAL},
+    {"Group2/hard_zero/ext_one", H5L_TYPE_EXTERNAL},
+    {"Group2/hard_zero/hard_one", H5L_TYPE_HARD},
+    {"Group2/hard_zero/hard_two", H5L_TYPE_HARD},
+    {"Group2/hard_zero/hard_zero", H5L_TYPE_HARD},
+    {"Group2/hard_zero/soft_dangle", H5L_TYPE_SOFT},
+    {"Group2/hard_zero/soft_one", H5L_TYPE_SOFT},
+    {"Group2/hard_zero/soft_two", H5L_TYPE_SOFT},
+    {"Type_one", H5L_TYPE_HARD},
+    {"hard_one", H5L_TYPE_HARD}
+};
+static const link_visit_t lvisit2[] = {
+    {"Dataset_two", H5L_TYPE_HARD},
+    {"Type_two", H5L_TYPE_HARD},
+    {"hard_zero", H5L_TYPE_HARD},
+    {"hard_zero/Dataset_zero", H5L_TYPE_HARD},
+    {"hard_zero/Group1", H5L_TYPE_HARD},
+    {"hard_zero/Group1/Dataset_one", H5L_TYPE_HARD},
+    {"hard_zero/Group1/Group2", H5L_TYPE_HARD},
+    {"hard_zero/Group1/Type_one", H5L_TYPE_HARD},
+    {"hard_zero/Group1/hard_one", H5L_TYPE_HARD},
+    {"hard_zero/Type_zero", H5L_TYPE_HARD},
+    {"hard_zero/ext_dangle", H5L_TYPE_EXTERNAL},
+    {"hard_zero/ext_one", H5L_TYPE_EXTERNAL},
+    {"hard_zero/hard_one", H5L_TYPE_HARD},
+    {"hard_zero/hard_two", H5L_TYPE_HARD},
+    {"hard_zero/hard_zero", H5L_TYPE_HARD},
+    {"hard_zero/soft_dangle", H5L_TYPE_SOFT},
+    {"hard_zero/soft_one", H5L_TYPE_SOFT},
+    {"hard_zero/soft_two", H5L_TYPE_SOFT}
+};
+
+typedef struct {
+    unsigned idx;               /* Index in link visit structure */
+    const link_visit_t *info;   /* Pointer to the link visit structure to use */
+} lvisit_ud_t;
+
+
+/* Object visit structs */
+typedef struct {
+    const char *path;           /* Path to object */
+    H5O_type_t type;            /* Type of object */
+} obj_visit_t;
+static const obj_visit_t ovisit0_old[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Dataset_zero", H5O_TYPE_DATASET},
+    {"Group1", H5O_TYPE_GROUP},
+    {"Group1/Dataset_one", H5O_TYPE_DATASET},
+    {"Group1/Group2", H5O_TYPE_GROUP},
+    {"Group1/Group2/Dataset_two", H5O_TYPE_DATASET},
+    {"Group1/Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
+    {"Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
+    {"Type_zero", H5O_TYPE_NAMED_DATATYPE}
+};
+static const obj_visit_t ovisit0_new[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Dataset_zero", H5O_TYPE_DATASET},
+    {"Group1", H5O_TYPE_GROUP},
+    {"Group1/Dataset_one", H5O_TYPE_DATASET},
+    {"Group1/Group2", H5O_TYPE_GROUP},
+    {"Group1/Group2/Dataset_two", H5O_TYPE_DATASET},
+    {"Group1/Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
+    {"Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
+    {"Type_zero", H5O_TYPE_NAMED_DATATYPE}
+};
+static const obj_visit_t ovisit1_old[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Dataset_one", H5O_TYPE_DATASET},
+    {"Group2", H5O_TYPE_GROUP},
+    {"Group2/Dataset_two", H5O_TYPE_DATASET},
+    {"Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
+    {"Group2/hard_zero", H5O_TYPE_GROUP},
+    {"Group2/hard_zero/Dataset_zero", H5O_TYPE_DATASET},
+    {"Group2/hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE},
+    {"Type_one", H5O_TYPE_NAMED_DATATYPE}
+};
+static const obj_visit_t ovisit1_new[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Dataset_one", H5O_TYPE_DATASET},
+    {"Group2", H5O_TYPE_GROUP},
+    {"Group2/Dataset_two", H5O_TYPE_DATASET},
+    {"Group2/Type_two", H5O_TYPE_NAMED_DATATYPE},
+    {"Group2/hard_zero", H5O_TYPE_GROUP},
+    {"Group2/hard_zero/Dataset_zero", H5O_TYPE_DATASET},
+    {"Group2/hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE},
+    {"Type_one", H5O_TYPE_NAMED_DATATYPE}
+};
+static const obj_visit_t ovisit2_old[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Dataset_two", H5O_TYPE_DATASET},
+    {"Type_two", H5O_TYPE_NAMED_DATATYPE},
+    {"hard_zero", H5O_TYPE_GROUP},
+    {"hard_zero/Dataset_zero", H5O_TYPE_DATASET},
+    {"hard_zero/Group1", H5O_TYPE_GROUP},
+    {"hard_zero/Group1/Dataset_one", H5O_TYPE_DATASET},
+    {"hard_zero/Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
+    {"hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE}
+};
+static const obj_visit_t ovisit2_new[] = {
+    {".", H5O_TYPE_GROUP},
+    {"Dataset_two", H5O_TYPE_DATASET},
+    {"Type_two", H5O_TYPE_NAMED_DATATYPE},
+    {"hard_zero", H5O_TYPE_GROUP},
+    {"hard_zero/Dataset_zero", H5O_TYPE_DATASET},
+    {"hard_zero/Group1", H5O_TYPE_GROUP},
+    {"hard_zero/Group1/Dataset_one", H5O_TYPE_DATASET},
+    {"hard_zero/Group1/Type_one", H5O_TYPE_NAMED_DATATYPE},
+    {"hard_zero/Type_zero", H5O_TYPE_NAMED_DATATYPE}
+};
+
+typedef struct {
+    unsigned idx;               /* Index in object visit structure */
+    const obj_visit_t *info;    /* Pointer to the object visit structure to use */
+} ovisit_ud_t;
+
+static const char *FILENAME[] = {
+    "link0",
+    "link1.h5",
+    "link2.h5",
+    NULL
+};
+
+
+/*-------------------------------------------------------------------------
+ * Function:	test_basic_links
+ *
+ * Purpose:	Test building a file with assorted links.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Binh-Minh Ribler
+ *		October 16, 2009
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void test_basic_links(hid_t fapl_id, hbool_t new_format)
+{
+    hsize_t	        size[1] = {1};
+    char		filename[NAME_BUF_SIZE];
+    char* tconv_buf = new char [1000];
+
+    // Use the file access template id to create a file access prop. list.
+    FileAccPropList fapl(fapl_id);
+
+    try
+    {
+	if(new_format)
+	    SUBTEST("Link creation (w/new group format)")
+	else
+	    SUBTEST("Link creation")
+
+	h5_fixname(FILENAME[0], fapl_id, filename, sizeof filename);
+	H5File file(filename, H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, fapl);
+
+	// Create simple dataspace
+	DataSpace scalar (1, size, size);
+
+	// Create a group then close it by letting the object go out of scope
+	{
+	    Group group(file.createGroup("grp1", 0));
+	}
+
+	// Create a dataset then close it by letting the object go out of scope
+	{
+	    DataSet dset1(file.createDataSet("dset1", PredType::NATIVE_INT, scalar));
+	}
+
+	hid_t file_id = file.getId();
+
+	// Because these are not implemented in the C++ API yet, they are
+	// used so CommonFG::getLinkval can be tested.
+	// Create a hard link
+	if(H5Lcreate_hard(
+		file_id, "dset1", H5L_SAME_LOC, "grp1/hard1",
+		H5P_DEFAULT, H5P_DEFAULT) < 0)
+	    throw Exception("test_basic_links", "H5Lcreate_hard failed");
+
+	// Create a symbolic link
+	if(H5Lcreate_soft(
+		"/dset1", file_id, "grp1/soft", H5P_DEFAULT, H5P_DEFAULT) < 0)
+	    throw Exception("test_basic_links", "H5Lcreate_soft failed");
+
+	// Create a symbolic link to something that doesn't exist
+	if(H5Lcreate_soft(
+		"foobar", file_id, "grp1/dangle", H5P_DEFAULT, H5P_DEFAULT) < 0)
+	    throw Exception("test_basic_links", "H5Lcreate_soft failed");
+
+	// Create a recursive symbolic link
+	if(H5Lcreate_soft(
+		"/grp1/recursive", file_id, "/grp1/recursive",
+		H5P_DEFAULT, H5P_DEFAULT) < 0)
+	    throw Exception("test_basic_links", "H5Lcreate_soft failed");
+
+	// Verify link values before closing the file
+
+	H5std_string softlink_val = file.getLinkval("grp1/soft");
+	verify_val(softlink_val, "/dset1", "H5File::getLinkval grp1/soft", __LINE__, __FILE__);
+
+	H5std_string dngllink_val = file.getLinkval("grp1/dangle");
+	verify_val(dngllink_val, "foobar", "H5File::getLinkval grp1/dangle", __LINE__, __FILE__);
+
+	H5std_string reclink_val = file.getLinkval("grp1/recursive");
+	verify_val(reclink_val, "/grp1/recursive", "H5File::getLinkval grp1/recursive", __LINE__, __FILE__);
+
+    } // end of try block
+    catch (Exception E)
+    {
+	issue_fail_msg("test_basic_links()", __LINE__, __FILE__, E.getCDetailMsg());
+    }
+
+    // Open the file and check on the links in it
+    try
+    {
+	// Open the file above
+	H5File file(filename, H5F_ACC_RDWR, FileCreatPropList::DEFAULT, fapl);
+
+	// Verify link existence
+	if(H5Lexists(file.getId(), "dset1", H5P_DEFAULT) != TRUE)
+	    throw InvalidActionException("H5Lexists", "dset1 doesn't exist");
+	if(H5Lexists(file.getId(), "grp1/soft", H5P_DEFAULT) != TRUE) 
+	    throw InvalidActionException("H5Lexists", "grp1/soft doesn't exist");
+
+	// Verify link values
+	H5std_string softlink_val = file.getLinkval("grp1/soft");
+	verify_val(softlink_val, "/dset1", "H5File::getLinkval grp1/soft", __LINE__, __FILE__);
+
+	H5std_string reclink_val = file.getLinkval("grp1/recursive");
+	verify_val(reclink_val, "/grp1/recursive", "H5File::getLinkval grp1/recursive", __LINE__, __FILE__);
+
+	PASSED();
+    } // end of try block
+    catch (Exception E)
+    {
+	issue_fail_msg("test_basic_links()", __LINE__, __FILE__, E.getCDetailMsg());
+    }
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	test_links
+ *
+ * Purpose:	Test links
+ *
+ * Return:	None
+ *
+ * Programmer:	Binh-Minh Ribler
+ *              October 16, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+#ifdef __cplusplus
+extern "C"
+#endif
+void test_links()
+{
+    hid_t	fapl_id, fapl2_id;    /* File access property lists */
+    hbool_t new_format;     /* Whether to use the new format or not */
+    const char  *envval;
+
+    envval = HDgetenv("HDF5_DRIVER");
+    if(envval == NULL)
+        envval = "nomatch";
+
+    fapl_id = h5_fileaccess();
+
+    // Output message about test being performed
+    MESSAGE(5, ("Testing Various Links\n"));
+    try
+    {
+	/* Copy the file access property list */
+	if((fapl2_id = H5Pcopy(fapl_id)) < 0)
+	    throw Exception("test_links", "H5Pcopy failed");
+
+	/* Set the "use the latest version of the format" bounds for creating objects in the file */
+	if(H5Pset_libver_bounds(fapl2_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
+	throw Exception("test_links", "H5Pset_libver_bounds failed");
+
+	/* Loop over using new group format */
+	for(new_format = FALSE; new_format <= TRUE; new_format++)
+	{
+	    hid_t my_fapl_id;
+
+	    /* Check for FAPL to use */
+	    if(new_format)
+		my_fapl_id = fapl2_id;
+	    else
+		my_fapl_id = fapl_id;
+
+	    /* General tests... (on both old & new format groups */
+	    // FileAccPropList may be passed in instead of fapl id
+	    test_basic_links(my_fapl_id, new_format);
+#if 0
+// these tests are from the C test links.c and left here for future
+// implementation of H5L API
+	nerrors += test_basic_links(fapl_id, new_format) < 0 ? 1 : 0;
+	nerrors += cklinks(my_fapl, new_format) < 0 ? 1 : 0;
+	nerrors += new_links(my_fapl, new_format) < 0 ? 1 : 0;
+	nerrors += ck_new_links(my_fapl, new_format) < 0 ? 1 : 0;
+	nerrors += long_links(my_fapl, new_format) < 0 ? 1 : 0;
+	nerrors += toomany(my_fapl, new_format) < 0 ? 1 : 0;
+
+	/* Test new H5L link creation routine */
+	nerrors += test_lcpl(my_fapl, new_format);
+        nerrors += test_move(my_fapl, new_format);
+        nerrors += test_copy(my_fapl, new_format);
+        nerrors += test_move_preserves(my_fapl, new_format);
+#ifndef H5_NO_DEPRECATED_SYMBOLS
+        nerrors += test_deprec(my_fapl, new_format);
+#endif /* H5_NO_DEPRECATED_SYMBOLS */
+#ifndef H5_CANNOT_OPEN_TWICE
+        nerrors += external_link_root(my_fapl, new_format) < 0 ? 1 : 0;
+#endif /* H5_CANNOT_OPEN_TWICE */
+        nerrors += external_link_path(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_mult(my_fapl, new_format) < 0 ? 1 : 0;
+#ifndef H5_CANNOT_OPEN_TWICE
+        nerrors += external_link_self(envval, my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_pingpong(envval, my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_toomany(my_fapl, new_format) < 0 ? 1 : 0;
+#endif /* H5_CANNOT_OPEN_TWICE */
+        nerrors += external_link_dangling(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_recursive(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_query(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_unlink_compact(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_unlink_dense(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_move(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_ride(my_fapl, new_format) < 0 ? 1 : 0;
+#ifndef H5_CANNOT_OPEN_TWICE
+        nerrors += external_link_closing(envval, my_fapl, new_format) < 0 ? 1 : 0;
+#endif /* H5_CANNOT_OPEN_TWICE */
+        nerrors += external_link_endian(new_format) < 0 ? 1 : 0;
+        nerrors += external_link_strong(my_fapl, new_format) < 0 ? 1 : 0;
+
+        /* tests for external link */
+        nerrors += external_link_env(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_prefix(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_abs_mainpath(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_rel_mainpath(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_cwd(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_abstar(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_abstar_cur(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_reltar(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_chdir(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_set_elink_fapl1(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_set_elink_fapl2(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_set_elink_fapl3(new_format) < 0 ? 1 : 0;
+        nerrors += external_set_elink_acc_flags(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_set_elink_cb(my_fapl, new_format) < 0 ? 1 : 0;
+
+#ifdef H5_HAVE_WINDOW_PATH
+        nerrors += external_link_win1(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win2(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win3(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win4(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win5(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win6(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win7(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win8(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += external_link_win9(my_fapl, new_format) < 0 ? 1 : 0;
+#endif
+        /* These tests assume that external links are a form of UD links,
+         * so assume that everything that passed for external links
+         * above has already been tested for UD links.
+         */
+        if(new_format == TRUE) {
+            nerrors += ud_hard_links(fapl2) < 0 ? 1 : 0;     /* requires new format groups */
+            nerrors += ud_link_reregister(fapl2) < 0 ? 1 : 0;        /* requires new format groups */
+        } /* end if */
+
+        nerrors += ud_callbacks(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += ud_link_errors(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += lapl_udata(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += lapl_nlinks(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += linkinfo(my_fapl, new_format) < 0 ? 1 : 0;
+
+        /* Misc. extra tests, useful for both new & old format files */
+        nerrors += link_visit(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += link_visit_by_name(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += obj_visit(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += obj_visit_by_name(my_fapl, new_format) < 0 ? 1 : 0;
+        nerrors += obj_visit_stop(my_fapl, new_format) < 0 ? 1 : 0;
+
+        /* Keep this test last, it's testing files that are used above */
+        /* do not do this for files used by external link tests */
+        nerrors += check_all_closed(my_fapl, new_format, EXTSTOP) < 0 ? 1 : 0;
+#endif // 0
+	} /* end for */
+
+#if 0
+    /* New group revision feature tests */
+    nerrors += corder_create_empty(fapl2) < 0 ? 1 : 0;
+/* XXX: when creation order indexing is fully working, go back and add checks
+*      to these tests to make certain that the creation order values are
+*      correct.
+*/
+    nerrors += corder_create_compact(fapl2) < 0 ? 1 : 0;
+    nerrors += corder_create_dense(fapl2) < 0 ? 1 : 0;
+    nerrors += corder_transition(fapl2) < 0 ? 1 : 0;
+    nerrors += corder_delete(fapl2) < 0 ? 1 : 0;
+    nerrors += link_info_by_idx(fapl2) < 0 ? 1 : 0;
+    nerrors += delete_by_idx(fapl2) < 0 ? 1 : 0;
+    nerrors += link_iterate(fapl2) < 0 ? 1 : 0;
+    nerrors += open_by_idx(fapl2) < 0 ? 1 : 0;
+    nerrors += object_info(fapl2) < 0 ? 1 : 0;
+    nerrors += group_info(fapl2) < 0 ? 1 : 0;
+    nerrors += timestamps(fapl2) < 0 ? 1 : 0;
+
+    /* Test new API calls on old-style groups */
+    nerrors += link_info_by_idx_old(fapl) < 0 ? 1 : 0;
+    nerrors += delete_by_idx_old(fapl) < 0 ? 1 : 0;
+    nerrors += link_iterate_old(fapl) < 0 ? 1 : 0;
+    nerrors += open_by_idx_old(fapl) < 0 ? 1 : 0;
+    nerrors += object_info_old(fapl) < 0 ? 1 : 0;
+    nerrors += group_info_old(fapl) < 0 ? 1 : 0;
+
+#endif
+	/* Close 2nd FAPL */
+	H5Pclose(fapl2_id);
+
+	h5_cleanup(FILENAME, fapl_id);
+
+	/* Test that external links can be used after a library reset.  MUST be
+	* called last so the reset doesn't interfere with the property lists.  This
+	* routine will delete its own file. */
+	/* nerrors += external_reset_register() < 0 ? 1 : 0;
+ */ 
+    }
+    catch (Exception E)
+    {
+	issue_fail_msg("test_links()", __LINE__, __FILE__, E.getCDetailMsg());
+    }
+
+}
+
+/*-------------------------------------------------------------------------
+ * Function:	cleanup_links
+ *
+ * Purpose:	Cleanup temporary test files
+ *
+ * Return:	none
+ *
+ * Programmer:	Binh-Minh Ribler
+ *		October 16, 2009
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+#ifdef __cplusplus
+extern "C"
+#endif
+void cleanup_links()
+{
+    HDremove(FILENAME[0]);
+}
+

c++/test/trefer.cpp

@@ -59,17 +59,9 @@ const int SPACE1_DIM1 = 4;
 
 // 2-D dataset with fixed dimensions
 const H5std_string      SPACE2_NAME("Space2");
-const int SPACE2_RANK = 2;
-const int SPACE2_DIM1 = 10;
-const int SPACE2_DIM2 = 10;
 
 // Larger 1-D dataset with fixed dimensions
 const H5std_string      SPACE3_NAME("Space3");
-const int SPACE3_RANK = 1;
-const int SPACE3_DIM1 = 100;
-
-// Element selection information
-const int POINT1_NPOINTS = 10;
 
 // Compound datatype
 typedef struct s1_t {
@@ -84,7 +76,7 @@ typedef struct s1_t {
 **      Tests references to various kinds of objects
 **
 ****************************************************************/
-static void test_reference_obj()
+static void test_reference_obj(void)
 {
     int    i;          // counting variables
     const  H5std_string write_comment="Foo!"; // Comments for group
@@ -100,9 +92,9 @@ static void test_reference_obj()
 
 	// Allocate write & read buffers
 	int temp_size = MAX(sizeof(unsigned),sizeof(hobj_ref_t));
-	wbuf=(hobj_ref_t*)malloc(temp_size*SPACE1_DIM1);
-	rbuf=(hobj_ref_t*)malloc(temp_size*SPACE1_DIM1);
-	tbuf=(hobj_ref_t*)malloc(temp_size*SPACE1_DIM1);
+	wbuf=(hobj_ref_t*)HDmalloc(temp_size*SPACE1_DIM1);
+	rbuf=(hobj_ref_t*)HDmalloc(temp_size*SPACE1_DIM1);
+	tbuf=(hobj_ref_t*)HDmalloc(temp_size*SPACE1_DIM1);
 
         // Create file FILE1
         file1 = new H5File (FILE1, H5F_ACC_TRUNC);
@@ -190,7 +182,7 @@ static void test_reference_obj()
 	sid1.close();
 	dataset.close();
 	delete file1;
-	
+
 	// Re-open the file
 	file1 = new H5File(FILE1, H5F_ACC_RDWR);
 
@@ -198,16 +190,16 @@ static void test_reference_obj()
 	dataset = file1->openDataSet("/Dataset3");
 
 	// Read selection from disk
-	dataset.read(rbuf, PredType::STD_REF_OBJ); 
+	dataset.read(rbuf, PredType::STD_REF_OBJ);
 
-	// Dereference dataset object by ctor, from the location where 
+	// Dereference dataset object by ctor, from the location where
 	// 'dataset' is located
 	DataSet dset2(dataset, &rbuf[0]);
 
 	// Check information in the referenced dataset
 	sid1 = dset2.getSpace();
 	hssize_t n_elements = sid1.getSimpleExtentNpoints();
-	verify_val((long)n_elements, (long)4, "DataSpace::getSimpleExtentNpoints", __LINE__, __FILE__);
+	verify_val((long)n_elements, 4, "DataSpace::getSimpleExtentNpoints", __LINE__, __FILE__);
 
 	// Read from disk
 	dset2.read(tbuf, PredType::NATIVE_UINT);
@@ -234,14 +226,14 @@ static void test_reference_obj()
 	verify_val(read_comment2, write_comment, "Group::getComment", __LINE__, __FILE__);
 	group.close();
 
-	// Dereference group object by ctor and using dataset to specify 
+	// Dereference group object by ctor and using dataset to specify
 	// location
 	Group new_group(dataset, &rbuf[2]);
 	H5std_string read_comment3 = new_group.getComment(".", 10);
 	verify_val(read_comment3, write_comment, "Group::getComment", __LINE__, __FILE__);
-	group.close();
+	new_group.close();
 
-	// Dereference datatype object from the location where 'dataset' 
+	// Dereference datatype object from the location where 'dataset'
 	// is located
 	dtype1.dereference(dataset, &rbuf[3]);
 
@@ -270,9 +262,9 @@ static void test_reference_obj()
 	file1->close();
 
 	// Free memory buffers
-	free(wbuf);
-	free(rbuf);
-	free(tbuf);
+	HDfree(wbuf);
+	HDfree(rbuf);
+	HDfree(tbuf);
 
 	PASSED();
     } // end try
@@ -289,7 +281,7 @@ static void test_reference_obj()
 #ifdef __cplusplus
 extern "C"
 #endif
-void test_reference()
+void test_reference(void)
 {
     // Output message about test being performed
     MESSAGE(5, ("Testing References\n"));
@@ -307,7 +299,7 @@ void test_reference()
 #ifdef __cplusplus
 extern "C"
 #endif
-void cleanup_reference()
+void cleanup_reference(void)
 {
     HDremove(FILE1.c_str());
 }

c++/test/ttypes.cpp

@@ -121,7 +121,7 @@ static void test_classes()
 	}
 	PASSED();
     }   // end of try block
-    catch (Exception E) { 
+    catch (Exception E) {
 	issue_fail_msg("test_classes", __LINE__, __FILE__, E.getCDetailMsg());
     }
 }
@@ -178,8 +178,8 @@ static void test_copy()
         another_int_type = new_int_type;
 
 	PASSED();
-    } 
-    catch (Exception E) { 
+    }
+    catch (Exception E) {
 	issue_fail_msg("test_copy", __LINE__, __FILE__, E.getCDetailMsg());
     }
 }
@@ -191,12 +191,12 @@ static void test_copy()
  * Purpose:	Tests query functions of compound and enumeration types.
  *
  * Return:	Success: 	0
- * 	
+ *
  *		Failure:	number of errors
  *
  * Programmer:	Binh-Minh Ribler (use C version)
  *		January, 2007
- *  
+ *
  * Modifications:
  *
  *-------------------------------------------------------------------------
@@ -289,7 +289,7 @@ static void test_query()
         issue_fail_msg("test_query", __LINE__, __FILE__, E.getCDetailMsg());
     }
 }   // test_query
- 
+
 
 /*-------------------------------------------------------------------------
  * Function:	test_transient
@@ -311,7 +311,7 @@ const char* filename1 = "dtypes1.h5";
 static void test_transient ()
 {
     static hsize_t	ds_size[2] = {10, 20};
-    
+
     SUBTEST("Transient datatypes");
     try {
 
@@ -345,7 +345,7 @@ static void test_transient ()
 	} catch (DataTypeIException err) {}
 	itype.close();
 
-	// Get a copy of the dataset's datatype by applying DataType::copy() 
+	// Get a copy of the dataset's datatype by applying DataType::copy()
 	// to the dataset. The resulted datatype should be modifiable.
 	itype.copy(dset);
 	itype.setPrecision(256);
@@ -393,7 +393,7 @@ static void test_named ()
     hsize_t		i;
     unsigned 		attr_data[10][20];
     char		filename[1024];
-    
+
     SUBTEST("Named datatypes");
     try {
 	// Create the file.
@@ -416,7 +416,7 @@ static void test_named ()
         itype.commit(file, "native-int");
 
 	// Check that it is committed.
-	if (itype.committed() <= 0)
+	if (itype.committed() == false)
 	    cerr << "IntType::committed() returned false" << endl;
 
 	// We should not be able to modify a type after it has been committed.
@@ -437,7 +437,7 @@ static void test_named ()
 
 	// It should be possible to define an attribute for the named type
 	Attribute attr1 = itype.createAttribute("attr1", PredType::NATIVE_UCHAR, space);
-	for (i=0; i<ds_size[0]*ds_size[1]; i++) 
+	for (i=0; i<ds_size[0]*ds_size[1]; i++)
 	    attr_data[0][i] = (int)i;/*tricky*/
 	attr1.write(PredType::NATIVE_UINT, attr_data);
 	attr1.close();
@@ -454,7 +454,7 @@ static void test_named ()
     /*
      * Close the committed type and reopen it.  It should return a named type.
 * This had something to do with the way IntType was returned and assigned
-and caused itype.committed not working correctly.  So, use another_type for 
+and caused itype.committed not working correctly.  So, use another_type for
 now.
 	itype.close();
 	itype = file.openIntType("native-int");
@@ -475,7 +475,7 @@ now.
 	dset.close();
 	ds_type->close();
 
-	// Reopen the dataset and its type, then make sure the type is 
+	// Reopen the dataset and its type, then make sure the type is
 	// a named type.
 	dset = file.openDataSet("dset1");
 	ds_type = new DataType(dset.getDataType());
@@ -497,7 +497,7 @@ now.
 	if (!iscommitted)
 	    throw InvalidActionException("DataType::iscommitted()", "Dataset type should be named type!");
 	ds_type->close();
-    
+
 	// Get the dataset datatype by applying DataType::copy() to the
 	// dataset. The resulted datatype should be modifiable.
 	IntType copied_type;

c++/test/tvlstr.cpp

@@ -18,7 +18,6 @@
    tvlstr.cpp - HDF5 C++ testing the Variable-Length String functionality
 
    EXTERNAL ROUTINES/VARIABLES:
-     These routines are in the test directory of the C library:
 
  ***************************************************************************/
 
@@ -40,7 +39,7 @@
 #include "H5Cpp.h"      // C++ API header file
 
 #ifndef H5_NO_NAMESPACE
-using namespace H5;
+    using namespace H5;
 #endif
 
 #include "h5cpputil.h"  // C++ utilility header file
@@ -52,47 +51,48 @@ const H5std_string FILENAME("tvlstr.h5");
 const int SPACE1_RANK = 1;
 const hsize_t SPACE1_DIM1 = 4;
 
-// Utility functions
+// Utility functions - not used now, later though.
 void *test_vlstr_alloc_custom(size_t size, void *info);
 void test_vlstr_free_custom(void *mem, void *info);
 
 /****************************************************************
 **
 **  test_vlstr_alloc_custom(): Test VL datatype custom memory
-**      allocation routines.  This routine just uses malloc to
-**      allocate the memory and increments the amount of memory
-**      allocated.  It is passed into setVlenMemManager.
+**	allocation routines.  This routine just uses malloc to
+**	allocate the memory and increments the amount of memory
+**	allocated.  It is passed into setVlenMemManager.
 **
 **  Note: exact copy from the C version.
 **
 ****************************************************************/
 void *test_vlstr_alloc_custom(size_t size, void *info)
 {
-    void *ret_value=NULL;   	// Pointer to return
-    int *mem_used=(int *)info;  // Get the pointer to the memory used
-    size_t extra;           	// Extra space needed
+    void *ret_value=NULL;	// Pointer to return
+    size_t *mem_used=(size_t *)info;  // Get the pointer to the memory used
+    size_t extra;		// Extra space needed
 
     /*
      *  This weird contortion is required on the DEC Alpha to keep the
      *  alignment correct - QAK
      */
-    
+
     extra=MAX(sizeof(void *),sizeof(size_t));
 
     if((ret_value=HDmalloc(extra+size))!=NULL) {
-        *(size_t *)ret_value=size;
-        *mem_used+=size;
+	*(size_t *)ret_value=size;
+	*mem_used+=size;
     } // end if
-    ret_value=((unsigned char *)ret_value)+extra;
+    ret_value = ((unsigned char *)ret_value) + extra;
+
     return(ret_value);
 }
 
 /****************************************************************
 **
 **  test_vlstr_free_custom(): Test VL datatype custom memory
-**      allocation routines.  This routine just uses free to
-**      release the memory and decrements the amount of memory
-**      allocated.  It is passed into setVlenMemManager.
+**	allocation routines.  This routine just uses free to
+**	release the memory and decrements the amount of memory
+**	allocated.  It is passed into setVlenMemManager.
 **
 **  Note: exact copy from the C version.
 **
@@ -100,14 +100,14 @@ void *test_vlstr_alloc_custom(size_t size, void *info)
 void test_vlstr_free_custom(void *_mem, void *info)
 {
     unsigned char *mem;
-    int *mem_used=(int *)info;  // Get the pointer to the memory used
-    size_t extra;           	// Extra space needed
+    size_t *mem_used=(size_t *)info;  // Get the pointer to the memory used
+    size_t extra;		// Extra space needed
 
     /*
      *  This weird contortion is required on the DEC Alpha to keep the
      *  alignment correct - QAK
      */
-    
+
     extra=MAX(sizeof(void *),sizeof(size_t));
 
     if(_mem!=NULL) {
@@ -118,9 +118,9 @@ void test_vlstr_free_custom(void *_mem, void *info)
 }
 
 /*-------------------------------------------------------------------------
- * Function:	test_vlstrings_basic
+ * Function:	test_vlstring_dataset
  *
- * Purpose:	Test simple VL string I/O.
+ * Purpose:	Test writing/reading VL strings on datasets.
  *
  * Return:	None
  *
@@ -129,98 +129,171 @@ void test_vlstr_free_custom(void *_mem, void *info)
  *
  *-------------------------------------------------------------------------
  */
-static void test_vlstrings_basic()
+// String for testing datasets
+static char *dynstring_ds_write=NULL;
+static char stastring_ds_write[1]={'A'};
+
+// Info for a string dataset
+const H5std_string DSET1_NAME("String_ds");
+const H5std_string DSET1_DATA("String Dataset");
+
+static void test_vlstring_dataset()
 {
-    const char *wdata[SPACE1_DIM1]= {
-        "Four score and seven years ago our forefathers brought forth on this continent a new nation,",
-        "conceived in liberty and dedicated to the proposition that all men are created equal.",
-        "Now we are engaged in a great civil war,",
-        "testing whether that nation or any nation so conceived and so dedicated can long endure."
+    // Output message about test being performed
+    SUBTEST("Testing VL String on Datasets");
+
+    try {
+	// Open the file
+	H5File file1(FILENAME, H5F_ACC_TRUNC);
+
+	// Create a datatype to refer to.
+	StrType vlst(0, H5T_VARIABLE);
+
+	// Open the root group.
+	Group root = file1.openGroup("/");
+
+	// Create dataspace for the dataset.
+	DataSpace ds_space (H5S_SCALAR);
+
+	// Create an dataset in the root group.
+	DataSet dset1 = root.createDataSet(DSET1_NAME, vlst, ds_space);
+
+	// Write data to the dataset.
+	dset1.write(DSET1_DATA, vlst);
+
+	// Read and verify the dataset string as a string of chars.
+	char *string_ds_check;
+	dset1.read(&string_ds_check, vlst);
+	if(HDstrcmp(string_ds_check, DSET1_DATA.c_str())!=0)
+	    TestErrPrintf("Line %d: Attribute data different: DSET1_DATA=%s,string_ds_check=%s\n",__LINE__, DSET1_DATA.c_str(), string_ds_check);
+
+	HDfree(string_ds_check);  // note: no need for std::string test
+
+	// Read and verify the dataset string as an std::string.
+	H5std_string read_str;
+	dset1.read(read_str, vlst);
+	if (read_str != DSET1_DATA)
+	    TestErrPrintf("Line %d: Attribute data different: DSET1_DATA=%s,read_str=%s\n",__LINE__, DSET1_DATA.c_str(), read_str.c_str());
+
+	// Close the dataset.
+	dset1.close();
+
+	// Test scalar type dataset with 1 value.
+	dset1 = root.createDataSet("test_scalar_small", vlst, ds_space);
+
+	dynstring_ds_write = (char*)HDcalloc(1, sizeof(char));
+	HDmemset(dynstring_ds_write, 'A', 1);
+
+	// Write data to the dataset, then read it back.
+	dset1.write(&dynstring_ds_write, vlst);
+	dset1.read(&string_ds_check, vlst);
+
+	// Verify data read.
+	if(HDstrcmp(string_ds_check,dynstring_ds_write)!=0)
+	    TestErrPrintf("VL string datasets don't match!, dynstring_ds_write=%s, string_ds_check=%s\n",dynstring_ds_write,string_ds_check);
+	HDfree(string_ds_check);
+	dset1.close();
+
+	// Open dataset DSET1_NAME again.
+	dset1 = root.openDataSet(DSET1_NAME);
+
+	// Close dataset and file
+	dset1.close();
+	file1.close();
+
+	PASSED();
+    } // end try block
+
+    // Catch all exceptions.
+    catch (Exception E) {
+	issue_fail_msg("test_vlstring_dataset()", __LINE__, __FILE__, E.getCDetailMsg());
+    }
+}   // test_vlstring_dataset()
+
+/*-------------------------------------------------------------------------
+ * Function:	test_vlstring_array_dataset
+ *
+ * Purpose:	Test writing/reading VL string array to/from datasets.
+ *
+ * Return:	None
+ *
+ * Programmer:	Binh-Minh Ribler
+ *		July, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+const H5std_string DSSTRARR_NAME("StringArray_dset");
+static void test_vlstring_array_dataset()
+{
+    const char *string_ds_array[SPACE1_DIM1]= {
+        "Line 1", "Line 2", "Line 3", "Line 4"
         };   // Information to write
 
     // Output message about test being performed
-    SUBTEST("Testing Basic VL String Functionality");
+    SUBTEST("Testing VL String Array on Datasets");
 
-    H5File* file1 = NULL;
+    H5File* file1;
     try {
         // Create file.
-        file1 = new H5File (FILENAME, H5F_ACC_TRUNC);
+	file1 = new H5File (FILENAME, H5F_ACC_RDWR);
 
-	// Create dataspace for datasets.
-	hsize_t	dims1[] = {SPACE1_DIM1};
-	DataSpace sid1(SPACE1_RANK, dims1);
+        // Create dataspace for datasets.
+        hsize_t dims1[] = {SPACE1_DIM1};
+        DataSpace ds_space(SPACE1_RANK, dims1);
 
 	// Create a datatype to refer to.
-	StrType tid1(0, H5T_VARIABLE);
+	StrType vlst(0, H5T_VARIABLE);
 
 	// Create and write a dataset.
-	DataSet dataset(file1->createDataSet("Dataset1", tid1, sid1));
-	dataset.write(wdata, tid1);
+	DataSet dataset(file1->createDataSet(DSSTRARR_NAME, vlst, ds_space));
+	dataset.write(string_ds_array, vlst);
+
+	// Read and verify the dataset using strings of chars as buffer.
+	// Note: reading by array of H5std_string doesn't work yet.
+	char *string_ds_check[SPACE1_DIM1];
+	dataset.read(string_ds_check, vlst);
+
+	int ii;
+	for (ii = 0; ii < SPACE1_DIM1; ii++)
+	{
+	    if(HDstrcmp(string_ds_check[ii], string_ds_array[ii])!=0)
+		TestErrPrintf("Line %d: Dataset data different: written=%s,read=%s\n",__LINE__, string_ds_array[ii], string_ds_check[ii]);
+
+	    HDfree(string_ds_check[ii]);
+	}
+
+	// Close objects that are no longer needed.
+	dataset.close();
+	ds_space.close();
+
+	//
+	// Test with scalar data space.
+	//
 
 	// Create H5S_SCALAR data space.
 	DataSpace scalar_space;
 
 	// Create and write another dataset.
-	DataSet dataset2(file1->createDataSet("Dataset2", tid1, scalar_space));
+	DataSet dataset2(file1->createDataSet("Dataset2", vlst, scalar_space));
 	char *wdata2 = (char*)HDcalloc(65534, sizeof(char));
 	HDmemset(wdata2, 'A', 65533);
-	dataset2.write(&wdata2, tid1);
+	dataset2.write(&wdata2, vlst);
+
+	char *rdata2 = (char*)HDcalloc(65534, sizeof(char));
+	HDmemset(rdata2, 0, 65533);
+	dataset2.read(&rdata2, vlst);
+	if (HDstrcmp(wdata2, rdata2)!=0)
+	    TestErrPrintf("Line %d: Dataset data different: written=%s,read=%s\n",__LINE__, wdata2, rdata2);
 
 	// Release resources from second dataset operation.
 	scalar_space.close();
 	dataset2.close();
 	HDfree(wdata2);
-
-	// Change to the custom memory allocation routines for reading 
-	// VL string.
-	DSetMemXferPropList xfer;
-	int mem_used = 0;	// Memory used during allocation
-	xfer.setVlenMemManager(test_vlstr_alloc_custom, &mem_used, test_vlstr_free_custom, &mem_used);
-
-	// Make certain the correct amount of memory will be used.
-	hsize_t vlsize = dataset.getVlenBufSize(tid1, sid1);
-
-	// Count the actual number of bytes used by the strings.
-	int str_used;   // String data in memory
-	hsize_t i;	// counting variable
-	for (i=0,str_used=0; i<SPACE1_DIM1; i++)
-	    str_used+=HDstrlen(wdata[i])+1;
-
-	// Compare against the strings actually written.
-	verify_val((int)vlsize,str_used,"DataSet::getVlenBufSize", __LINE__, __FILE__);
-
-	// Read dataset from disk.
-	char *rdata[SPACE1_DIM1];   // Data read in
-	dataset.read(rdata, tid1, DataSpace::ALL, DataSpace::ALL, xfer);
-
-	// Make certain the correct amount of memory has been used.
-	verify_val(mem_used, str_used, "DataSet::read", __LINE__, __FILE__);
-
-	// Compare data read in.
-	for (i=0; i<SPACE1_DIM1; i++) {
-	    int wlen = HDstrlen(wdata[i]);
-	    int rlen = HDstrlen(rdata[i]);
-	    if(wlen != rlen) {
-		TestErrPrintf("VL data lengths don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n", (int)i, wlen, (int)i, rlen);
-		continue;
-	    } // end if
-	    if( HDstrcmp(wdata[i],rdata[i]) != 0 ) {
-		TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n", (int)i, wdata[i], (int)i, rdata[i]);
-		continue;
-	    } // end if
-	} // end for
-
-	// Reclaim the read VL data.
-	DataSet::vlenReclaim((void *)rdata, tid1, sid1, xfer);
-
-	// Make certain the VL memory has been freed.
-	verify_val(mem_used, 0, "DataSet::vlenReclaim", __LINE__, __FILE__);
+	HDfree(rdata2);
 
 	// Close objects and file.
-	dataset.close();
-	tid1.close();
-	sid1.close();
-	xfer.close();
+	dataset2.close();
+	vlst.close();
 	file1->close();
 
 	PASSED();
@@ -229,16 +302,15 @@ static void test_vlstrings_basic()
     // Catch all exceptions.
     catch (Exception E)
     {
-	issue_fail_msg("test_vlstrings_basic()", __LINE__, __FILE__, E.getCDetailMsg());
-        if (file1 != NULL) // clean up
-            delete file1;
+	issue_fail_msg("test_vlstring_array_dataset()", __LINE__, __FILE__, E.getCDetailMsg());
+	delete file1;
     }
-} // end test_vlstrings_basic()
+} // end test_vlstring_array_dataset()
 
 /*-------------------------------------------------------------------------
  * Function:	test_vlstrings_special
  *
- * Purpose:	Test VL string code for special string cases, nil and 
+ * Purpose:	Test VL string code for special string cases, nil and
  *		zero-sized.
  *
  * Return:	None
@@ -266,71 +338,71 @@ static void test_vlstrings_special()
         DataSpace sid1(SPACE1_RANK, dims1);
 
 	// Create a datatype to refer to.
-	StrType tid1(0, H5T_VARIABLE);
+	StrType vlst(0, H5T_VARIABLE);
 
 	// Create a dataset.
-	DataSet dataset(file1.createDataSet("Dataset3", tid1, sid1));
+	DataSet dataset(file1.createDataSet("Dataset3", vlst, sid1));
 
 	// Read from the dataset before writing data.
-	dataset.read(rdata, tid1);
+	dataset.read(rdata, vlst);
 
 	// Check data read in.
 	hsize_t i;      	// counting variable
 	for (i=0; i<SPACE1_DIM1; i++)
-	    if(rdata[i] != NULL)
+	    if(rdata[i]!=NULL)
 		TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i,rdata[i]);
 
 	// Write dataset to disk, then read it back.
-	dataset.write(wdata, tid1);
-	dataset.read(rdata, tid1);
+	dataset.write(wdata, vlst);
+	dataset.read(rdata, vlst);
 
 	// Compare data read in.
-	for (i=0; i<SPACE1_DIM1; i++) {
-	    int wlen = HDstrlen(wdata[i]);
-	    int rlen = HDstrlen(rdata[i]);
+	for (i = 0; i < SPACE1_DIM1; i++) {
+	    size_t wlen = HDstrlen(wdata[i]);
+	    size_t rlen = HDstrlen(rdata[i]);
 	    if(wlen != rlen) {
-		TestErrPrintf("VL data lengths don't match!, strlen(wdata[%d])=%d, strlen(rdata[%d])=%d\n", (int)i, wlen, (int)i, rlen);
+		TestErrPrintf("VL data lengths don't match!, strlen(wdata[%d])=%u, strlen(rdata[%d])=%u\n", (int)i, (unsigned)wlen, (int)i, (unsigned)rlen);
 		continue;
 	    } // end if
-	    if( HDstrcmp(wdata[i],rdata[i]) != 0 ) {
+	    if(HDstrcmp(wdata[i],rdata[i]) != 0) {
 		TestErrPrintf("VL data values don't match!, wdata[%d]=%s, rdata[%d]=%s\n", (int)i, wdata[i], (int)i, rdata[i]);
 		continue;
 	    } // end if
 	} // end for
 
 	// Reclaim the read VL data.
-	DataSet::vlenReclaim((void *)rdata, tid1, sid1);
+	DataSet::vlenReclaim((void *)rdata, vlst, sid1);
 
 	// Close Dataset.
 	dataset.close();
 
-	/* 
+	/*
 	 * Create another dataset to test nil strings.
 	 */
 
-	// Create the property list and set the fill value for the second 
+	// Create the property list and set the fill value for the second
 	// dataset.
 	DSetCreatPropList dcpl;
 	char *fill = NULL;	// Fill value
-	dcpl.setFillValue(tid1, &fill);
-	dataset = file1.createDataSet("Dataset4", tid1, sid1, dcpl);
+	dcpl.setFillValue(vlst, &fill);
+	dataset = file1.createDataSet("Dataset4", vlst, sid1, dcpl);
 
 	// Close dataset creation property list.
 	dcpl.close();
 
 	// Read from dataset before writing data.
-	dataset.read(rdata, tid1);
+	dataset.read(rdata, vlst);
 
 	// Check data read in.
 	for (i=0; i<SPACE1_DIM1; i++)
-	  if(rdata[i] != NULL)
-	    TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i, rdata[i]);
+	  if(rdata[i]!=NULL)
+	    TestErrPrintf("VL doesn't match!, rdata[%d]=%p\n",(int)i,rdata[i]);
 
 	// Try to write nil strings to disk.
-	dataset.write(wdata2, tid1);
+	dataset.write(wdata2, vlst);
 
 	// Read nil strings back from disk.
-	dataset.read(rdata, tid1);
+	dataset.read(rdata, vlst);
 
 	// Check data read in.
 	for (i=0; i<SPACE1_DIM1; i++)
@@ -339,7 +411,7 @@ static void test_vlstrings_special()
 
 	// Close objects and file.
 	dataset.close();
-	tid1.close();
+	vlst.close();
 	sid1.close();
 	file1.close();
 
@@ -349,7 +421,7 @@ static void test_vlstrings_special()
     // Catch all exceptions.
     catch (Exception E)
     {
-	issue_fail_msg(E.getCFuncName(), __LINE__, __FILE__, E.getCDetailMsg());
+	issue_fail_msg("test_vlstrings_special()", __LINE__, __FILE__, E.getCDetailMsg());
     }
 } // test_vlstrings_special
 
@@ -369,7 +441,7 @@ const H5std_string      VLSTR_TYPE("vl_string_type");
 static void test_vlstring_type()
 {
     // Output message about test being performed.
-    SUBTEST("Testing VL String type");
+    SUBTEST("Testing VL String Type");
 
     H5File* file1 = NULL;
     try {
@@ -377,55 +449,55 @@ static void test_vlstring_type()
 	file1 = new H5File(FILENAME, H5F_ACC_RDWR);
 
 	// Create a datatype to refer to.
-	StrType vlstr_type(PredType::C_S1);
+	StrType vlst(PredType::C_S1);
 
 	// Change padding and verify it.
-	vlstr_type.setStrpad(H5T_STR_NULLPAD);
-	H5T_str_t pad = vlstr_type.getStrpad();
+	vlst.setStrpad(H5T_STR_NULLPAD);
+	H5T_str_t pad = vlst.getStrpad();
 	verify_val(pad, H5T_STR_NULLPAD, "StrType::getStrpad", __LINE__, __FILE__);
 
 	// Convert to variable-length string.
-	vlstr_type.setSize(H5T_VARIABLE);
+	vlst.setSize(H5T_VARIABLE);
 
 	// Check if datatype is VL string.
-	H5T_class_t type_class = vlstr_type.getClass();
+	H5T_class_t type_class = vlst.getClass();
 	verify_val(type_class, H5T_STRING, "DataType::getClass", __LINE__, __FILE__);
-	bool is_variable_str = vlstr_type.isVariableStr();
-	verify_val(is_variable_str, TRUE, "DataType::isVariableStr", __LINE__, __FILE__);
+	bool is_variable_str = vlst.isVariableStr();
+	verify_val(is_variable_str, true, "DataType::isVariableStr", __LINE__, __FILE__);
 
 	// Check default character set and padding.
-	H5T_cset_t cset = vlstr_type.getCset();
+	H5T_cset_t cset = vlst.getCset();
 	verify_val(cset, H5T_CSET_ASCII, "StrType::getCset", __LINE__, __FILE__);
-	pad = vlstr_type.getStrpad();
+	pad = vlst.getStrpad();
 	verify_val(pad, H5T_STR_NULLPAD, "StrType::getStrpad", __LINE__, __FILE__);
 
 	// Commit variable-length string datatype to storage.
-	vlstr_type.commit(*file1, VLSTR_TYPE);
+	vlst.commit(*file1, VLSTR_TYPE);
 
 	// Close datatype.
-	vlstr_type.close();
+	vlst.close();
 
 	// Try opening datatype again.
-	vlstr_type = file1->openStrType(VLSTR_TYPE);
+	vlst = file1->openStrType(VLSTR_TYPE);
 
 	// Close datatype and file.
-	vlstr_type.close();
+	vlst.close();
 	file1->close();
 
 	// Open file.
 	file1 = new H5File(FILENAME, H5F_ACC_RDWR);
 
 	// Open the variable-length string datatype just created
-	vlstr_type.setId((file1->openStrType(VLSTR_TYPE)).getId());
+	vlst = file1->openStrType(VLSTR_TYPE);
 
 	// Verify character set and padding
-	cset = vlstr_type.getCset();
+	cset = vlst.getCset();
 	verify_val(cset, H5T_CSET_ASCII, "StrType::getCset", __LINE__, __FILE__);
-	pad = vlstr_type.getStrpad();
+	pad = vlst.getStrpad();
 	verify_val(pad, H5T_STR_NULLPAD, "StrType::getStrpad", __LINE__, __FILE__);
 
 	// Close datatype and file
-	vlstr_type.close();
+	vlst.close();
 	file1->close();
 
 	PASSED();
@@ -435,6 +507,7 @@ static void test_vlstring_type()
     catch (Exception E)
     {
         issue_fail_msg("test_vlstring_type()", __LINE__, __FILE__, E.getCDetailMsg());
+	delete file1;
     }
 } // end test_vlstring_type()
 
@@ -453,7 +526,7 @@ static void test_vlstring_type()
 static void test_compact_vlstring()
 {
     // Output message about test being performed
-    SUBTEST("Testing VL Strings in compact dataset");
+    SUBTEST("Testing VL Strings on Compact Dataset");
 
     try {
 	// Create file
@@ -464,22 +537,22 @@ static void test_compact_vlstring()
         DataSpace sid1(SPACE1_RANK, dims1);
 
 	// Create a datatype to refer to
-	StrType tid1(0, H5T_VARIABLE);
+	StrType vlst(0, H5T_VARIABLE);
 
 	// Create dataset create property list and set layout
 	DSetCreatPropList plist;
 	plist.setLayout(H5D_COMPACT);
 
 	// Create a dataset
-	DataSet dataset(file1.createDataSet("Dataset5", tid1, sid1, plist));
+	DataSet dataset(file1.createDataSet("Dataset5", vlst, sid1, plist));
 
 	// Write dataset to disk
 	const char *wdata[SPACE1_DIM1] = {"one", "two", "three", "four"};
-	dataset.write(wdata, tid1);
+	dataset.write(wdata, vlst);
 
 	// Read dataset from disk
 	char *rdata[SPACE1_DIM1];   // Information read in
-	dataset.read(rdata, tid1);
+	dataset.read(rdata, vlst);
 
 	// Compare data read in
 	hsize_t i;
@@ -495,11 +568,11 @@ static void test_compact_vlstring()
 	} // end for
 
 	// Reclaim the read VL data
-	DataSet::vlenReclaim((void *)rdata, tid1, sid1);
+	DataSet::vlenReclaim((void *)rdata, vlst, sid1);
 
 	// Close objects and file
 	dataset.close();
-	tid1.close();
+	vlst.close();
 	sid1.close();
 	plist.close();
 	file1.close();
@@ -515,9 +588,9 @@ static void test_compact_vlstring()
 }   // test_compact_vlstrings
 
 /*-------------------------------------------------------------------------
- * Function:	test_write_vl_string_attribute
+ * Function:	test_vlstring_attribute
  *
- * Purpose:	Test writing VL strings as attributes.
+ * Purpose:	Test writing/reading VL strings on attributes.
  *
  * Return:	None
  *
@@ -526,25 +599,24 @@ static void test_compact_vlstring()
  *
  *-------------------------------------------------------------------------
  */
-// String for testing attributes
-static const char *string_att = "This is the string for the attribute";
+// String for writing to attribute
 static char *string_att_write=NULL;
 
 // Info for a string attribute
 const H5std_string ATTRSTR_NAME("String_attr");
 const H5std_string ATTRSTR_DATA("String Attribute");
 
-static void test_write_vl_string_attribute()
+static void test_vlstring_attribute()
 {
     // Output message about test being performed
-    SUBTEST("Testing writing VL String as attributes");
+    SUBTEST("Testing VL String on Attributes");
 
     try {
 	// Open the file
 	H5File file1(FILENAME, H5F_ACC_RDWR);
 
 	// Create a datatype to refer to.
-	StrType tid1(0, H5T_VARIABLE);
+	StrType vlst(0, H5T_VARIABLE);
 
 	// Open the root group.
 	Group root = file1.openGroup("/");
@@ -553,14 +625,14 @@ static void test_write_vl_string_attribute()
 	DataSpace att_space (H5S_SCALAR);
 
 	// Create an attribute for the root group.
-	Attribute gr_attr = root.createAttribute(ATTRSTR_NAME, tid1, att_space);
+	Attribute gr_attr = root.createAttribute(ATTRSTR_NAME, vlst, att_space);
 
 	// Write data to the attribute.
-	gr_attr.write(tid1, ATTRSTR_DATA);
+	gr_attr.write(vlst, ATTRSTR_DATA);
 
 	// Read and verify the attribute string as a string of chars.
 	char *string_att_check;
-	gr_attr.read(tid1, &string_att_check);
+	gr_attr.read(vlst, &string_att_check);
 	if(HDstrcmp(string_att_check, ATTRSTR_DATA.c_str())!=0)
 	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,string_att_check=%s\n",__LINE__, ATTRSTR_DATA.c_str(), string_att_check);
 
@@ -568,7 +640,7 @@ static void test_write_vl_string_attribute()
 
 	// Read and verify the attribute string as an std::string.
 	H5std_string read_str;
-	gr_attr.read(tid1, read_str);
+	gr_attr.read(vlst, read_str);
 	if (read_str != ATTRSTR_DATA)
 	    TestErrPrintf("Line %d: Attribute data different: ATTRSTR_DATA=%s,read_str=%s\n",__LINE__, ATTRSTR_DATA.c_str(), read_str.c_str());
 
@@ -576,28 +648,22 @@ static void test_write_vl_string_attribute()
 	gr_attr.close();
 
 	// Test creating a "large" sized string attribute
-	gr_attr = root.createAttribute("test_scalar_large", tid1, att_space);
+	gr_attr = root.createAttribute("test_scalar_large", vlst, att_space);
 
 	string_att_write = (char*)HDcalloc(8192, sizeof(char));
 	HDmemset(string_att_write, 'A', 8191);
 
 	// Write data to the attribute, then read it back.
-	gr_attr.write(tid1, &string_att_write);
-	gr_attr.read(tid1, &string_att_check);
+	gr_attr.write(vlst, &string_att_write);
+	gr_attr.read(vlst, &string_att_check);
 
 	// Verify data read.
 	if(HDstrcmp(string_att_check,string_att_write)!=0)
 	    TestErrPrintf("VL string attributes don't match!, string_att_write=%s, string_att_check=%s\n",string_att_write,string_att_check);
+
+	// Release resources.
 	HDfree(string_att_check);
-	gr_attr.close();
-
-	// Open attribute ATTRSTR_NAME again.
-	gr_attr = root.openAttribute(ATTRSTR_NAME);
-
-	// The attribute string written is freed below, in the 
-	// test_read_vl_string_attribute() test
-
-	// Close attribute and file
+	HDfree(string_att_write);
 	gr_attr.close();
 	file1.close();
 
@@ -606,9 +672,9 @@ static void test_write_vl_string_attribute()
 
     // Catch all exceptions.
     catch (Exception E) {
-	issue_fail_msg("test_string_attr()", __LINE__, __FILE__, E.getCDetailMsg());
+	issue_fail_msg("test_vlstring_attribute()", __LINE__, __FILE__, E.getCDetailMsg());
     }
-}   // test_string_attr()
+}   // test_vlstring_attribute()
 
 /*-------------------------------------------------------------------------
  * Function:	test_read_vl_string_attribute
@@ -633,7 +699,7 @@ static void test_read_vl_string_attribute()
 	H5File file1(FILENAME, H5F_ACC_RDONLY);
 
 	// Create a datatype to refer to.
-	StrType tid1(0, H5T_VARIABLE);
+	StrType vlst(0, H5T_VARIABLE);
 
 	// Open the root group and its attribute named ATTRSTR_NAME.
 	Group root = file1.openGroup("/");
@@ -641,7 +707,7 @@ static void test_read_vl_string_attribute()
 
 	// Test reading "normal" sized string attribute
 	char *string_att_check;
-	att.read(tid1, &string_att_check);
+	att.read(vlst, &string_att_check);
 	if(HDstrcmp(string_att_check,ATTRSTR_DATA.c_str())!=0)
 	    TestErrPrintf("VL string attributes don't match!, string_att=%s, string_att_check=%s\n",ATTRSTR_DATA.c_str(),string_att_check);
 	HDfree(string_att_check);
@@ -649,7 +715,7 @@ static void test_read_vl_string_attribute()
 
 	// Test reading "large" sized string attribute
 	att = root.openAttribute("test_scalar_large");
-	att.read(tid1, &string_att_check);
+	att.read(vlst, &string_att_check);
 	if(HDstrcmp(string_att_check,string_att_write)!=0)
 	    TestErrPrintf("VL string attributes don't match!, string_att_write=%s, string_att_check=%s\n",string_att_write,string_att_check);
 	HDfree(string_att_check);
@@ -657,7 +723,7 @@ static void test_read_vl_string_attribute()
 
 	// Close objects and file.
 	att.close();
-	tid1.close();
+	vlst.close();
 	root.close();
 	file1.close();
 
@@ -670,8 +736,78 @@ static void test_read_vl_string_attribute()
     }
 } // test_read_vl_string_attribute
 
+/*-------------------------------------------------------------------------
+ * Function:	test_vlstring_array_attribute
+ *
+ * Purpose:	Test writing/reading VL string array to/from attributes.
+ *
+ * Return:	None
+ *
+ * Programmer:	Binh-Minh Ribler
+ *		July, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+const H5std_string ATTRSTRARR_NAME("StringArray_attr");
+
+static void test_vlstring_array_attribute()
+{
+    const char *string_att_array[SPACE1_DIM1]= {
+        "Line 1", "Line 2", "Line 3", "Line 4"
+        };   // Information to write
+
+    // Output message about test being performed
+    SUBTEST("Testing VL String Array on Attributes");
+
+    try {
+	// Open the file
+	H5File file1(FILENAME, H5F_ACC_RDWR);
+
+	// Create a datatype to refer to.
+	StrType vlst(0, H5T_VARIABLE);
+
+	// Open the root group.
+	Group root = file1.openGroup("/");
+
+        // Create dataspace for datasets.
+        hsize_t dims1[] = {SPACE1_DIM1};
+        DataSpace att_space(SPACE1_RANK, dims1);
+
+	// Create an attribute for the root group.
+	Attribute gr_attr = root.createAttribute(ATTRSTRARR_NAME, vlst, att_space);
+
+	// Write data to the attribute.
+	gr_attr.write(vlst, string_att_array);
+
+	// Read and verify the attribute string as a string of chars.
+	// Note: reading by array of H5std_string doesn't work yet.
+	char *string_att_check[SPACE1_DIM1];
+	gr_attr.read(vlst, &string_att_check);
+
+	int ii;
+	for (ii = 0; ii < SPACE1_DIM1; ii++)
+	{
+	    if(HDstrcmp(string_att_check[ii], string_att_array[ii])!=0)
+		TestErrPrintf("Line %d: Attribute data different: written=%s,read=%s\n",__LINE__, string_att_check[ii], string_att_check[ii]);
+
+	    HDfree(string_att_check[ii]);  // note: no need for std::string test
+	}
+
+	// Close group's attribute.
+	gr_attr.close();
+	file1.close();
+
+	PASSED();
+    } // end try block
+
+    // Catch all exceptions.
+    catch (Exception E) {
+	issue_fail_msg("test_vlstring_array_attribute()", __LINE__, __FILE__, E.getCDetailMsg());
+    }
+}   // test_vlstring_array_attribute()
+
 /* Helper routine for test_vl_rewrite() */
-static void write_scalar_dset(H5File& file, DataType& type, DataSpace& space, 
+static void write_scalar_dset(H5File& file, DataType& type, DataSpace& space,
 				char *name, char *data)
 {
     DataSet dset;
@@ -689,7 +825,7 @@ static void write_scalar_dset(H5File& file, DataType& type, DataSpace& space,
 }
 
 /* Helper routine for test_vl_rewrite() */
-static void read_scalar_dset(H5File& file, DataType& type, DataSpace& space, 
+static void read_scalar_dset(H5File& file, DataType& type, DataSpace& space,
 				char *name, char *data)
 {
     char *data_read;
@@ -814,14 +950,17 @@ void test_vlstrings()
 
     // These tests use the same file
     // Test basic VL string datatype
-    test_vlstrings_basic();
+    test_vlstring_dataset();
     test_vlstrings_special();
     test_vlstring_type();
     test_compact_vlstring();
 
     // Test using VL strings in attributes
-    test_write_vl_string_attribute();
-    test_read_vl_string_attribute();
+    test_vlstring_attribute();
+
+    // Test using VL string array in attributes and datasets
+    test_vlstring_array_attribute();
+    test_vlstring_array_dataset();
 
     // Test writing VL datasets in files with lots of unlinking
     test_vl_rewrite();

config/BlankForm

@@ -72,7 +72,7 @@ fi
 # 			`-pg').  This may or may not include debugging 
 # 			or production flags.
 #			
-# CFLAGS		Flags can be added to this variable which
+# H5_CFLAGS		Flags can be added to this variable which
 #			might already be partially initialized.  These 
 #			flags will always be passed to the compiler
 #			and should include switches to turn on full
@@ -81,16 +81,14 @@ fi
 #			practices resulting in few if any
 #			warnings.
 #
-#			Warning flags do not have to be added to CFLAGS
+#			Warning flags do not have to be added to H5_CFLAGS
 #			variable if the compiler is the GNU gcc
 #			compiler or a descendent of gcc such as EGCS or PGCC.
 #
-#			The CFLAGS should contains *something* or else 
-#			configure will probably add `-g'.  For most
-#			systems this isn't a problem but some systems
-#			will disable optimizations in favor of the
-#			`-g'.
-#			
+# AM_CFLAGS             Flags added directly into this variable will
+#                       be propogated to the compiler wrapper scripts (h5cc,
+#                       h5c++, et cetera) in addition to being used to compile 
+#                       the library.
 #
 # These flags should be set according to the compiler being used.
 # There are two ways to check the compiler.  You can try using `-v' or 
@@ -101,7 +99,7 @@ fi
 
 case $CC_BASENAME in
     gcc)
-	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	H5_CFLAGS="$H5_CFLAGS -Wsign-compare" #Only works for some versions
 	DEBUG_CFLAGS="-g -fverbose-asm"
 	DEBUG_CPPFLAGS=
 	PROD_CFLAGS="-O3 -fomit-frame-pointer"
@@ -111,7 +109,7 @@ case $CC_BASENAME in
 	;;
 
     *)
-	CFLAGS="$CFLAGS -ansi"
+	H5_CFLAGS="$H5_CFLAGS -ansi"
 	DEBUG_CFLAGS="-g"
 	DEBUG_CPPFLAGS=
 	PROD_CFLAGS="-O"

config/COPYING

@@ -1,5 +1,5 @@
 
-  Copyright by  The HDF Group (THG) and 
+  Copyright by  The HDF Group and 
                 The Board of Trustees of the University of Illinois. 
   All rights reserved. 
 

config/apple

@@ -28,54 +28,30 @@ fi
 
 # Figure out compiler flags
 . $srcdir/config/gnu-flags
-
-# The default Fortran 90 compiler
+ 
+. $srcdir/config/intel-flags
 if test "X-" = "X-$FC"; then
-    # Assume Absoft compiler
-    FC=xlf
-    FC_BASENAME=xlf
-  else
+    case $CC_BASENAME in
+        gcc*)
+            FC=gfortran
+            FC_BASENAME=gfortran
+            ;;
+        icc*)
+            FC=ifort
+            FC_BASENAME=ifort
+            ;;
+    esac
+fi
+# Figure out compiler flags
+. $srcdir/config/gnu-fflags
+ 
+. $srcdir/config/intel-fflags
 
-    # Neither xlf nor f95 have a working "version" command.
-    # If FC is set, try to guess which one is being used by examining
-    # the last element in the path to the compiler.
-
-    TEMP_BASENAME=`basename $FC`
-    if test "xlf" = "${TEMP_BASENAME}"; then
-      FC_BASENAME=xlf
-    else
-      FC_BASENAME=f95
-    fi
+# Fortran doesn't work with shared libraries
+# 
+if test "X-" != "X-$enable_fortran"; then
+        echo '    Warning: shared libraries are not supported with Fortran'
+        echo '    Disabling shared libraries'
+        enable_shared="no"
 fi
 
-case $FC_BASENAME in
-    xlf) 
-        F9XSUFFIXFLAG="-qsuffix=f=f90 -qfree=f90"
-        FCFLAGS="$FCFLAGS ${F9XSUFFIXFLAG}"
-        H5_FCFLAGS="$H5_FCFLAGS -qmoddir=./ "
-        FSEARCH_DIRS="-I./ -I../src"
-        DEBUG_FCFLAGS="-g"
-        PROD_FCFLAGS="-O"
-        PROFILE_FCFLAGS="-g"
-        f9x_flags_set=yes
-        ;;
-
-    f95)
-
-        F9XSUFFIXFLAG=""
-# We force compiler to use upper case for external names 
-# (just in case since this should be a default EIP)
-        H5_FCFLAGS="$H5_FCFLAGS"
-        FSEARCH_DIRS=""
-        DEBUG_FCFLAGS="-g"
-        PROD_FCFLAGS="-O"
-        PROFILE_FCFLAGS="-g -pg"
-        f9x_flags_set=yes
-
-# f95 doesn't support shared libraries
-        echo '    warning: shared libraries are not supported for f95!'
-        echo '    disabling shared libraries'
-        enable_shared="no"
-        ;;
-
-esac  

config/commence.am

@@ -22,12 +22,6 @@
 RM=rm -f
 CP=cp
 
-# Hardcode SHELL to be /bin/sh.  Most machines have this shell, and
-# on at least one machine configure fails to detect its existence (janus).
-# Also, when HDF5 is configured on one machine but run on another,
-# configure's automatic SHELL detection may not work on the build machine.
-SHELL=/bin/sh
-
 # Some machines need a command to run executables; this is that command
 # so that our tests will run.
 # We use RUNTESTS instead of RUNSERIAL directly because it may be that
@@ -49,7 +43,6 @@ LIBH5F_HL=$(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
 LIBH5CPP_HL=$(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
 
 # Install directories that automake doesn't know about
-includedir = $(exec_prefix)/include
 docdir = $(exec_prefix)/doc
 
 # Scripts used to build examples
@@ -62,13 +55,15 @@ H5FC_PP=$(bindir)/h5pfc
 H5CPP=$(bindir)/h5c++
   
 
-# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
-# but which shouldn't be exported to h5cc for building other programs.
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
 
-CFLAGS=@CFLAGS@ @H5_CFLAGS@
-CPPFLAGS=@CPPFLAGS@ @H5_CPPFLAGS@
-FCFLAGS=@FCFLAGS@ @H5_FCFLAGS@
-CXXFLAGS=@CXXFLAGS@ @H5_CXXFLAGS@
+AM_CFLAGS=@AM_CFLAGS@ @H5_CFLAGS@
+AM_FCFLAGS=@AM_FCFLAGS@ @H5_FCFLAGS@
+AM_CXXFLAGS=@AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_CPPFLAGS=@AM_CPPFLAGS@ @H5_CPPFLAGS@
 
 # The trace script; this is used on source files from the C library to
 # insert tracing macros.

config/conclude.am

@@ -122,10 +122,10 @@ $(TEST_PROG_CHKEXE) $(TEST_PROG_PARA_CHKEXE) dummy.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $(HDF5_DRIVER) $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $(HDF5_DRIVER) $${tname} $(TEST_FLAGS) Test Log" >> $${log};\
 	      else \
@@ -161,10 +161,10 @@ $(TEST_SCRIPT_CHKSH) $(TEST_SCRIPT_PARA_CHKSH) dummysh.chkexe_:
 	      echo "No need to test $${tname} again."; \
 	   else \
 	      echo "============================" > $${log}; \
-	      if test "X$(HDF_FORTRAN)" = "Xyes"; then \
+	      if test "X$(FORTRAN_API)" = "Xyes"; then \
 	         echo "Fortran API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "Fortran API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
-	      elif test "X$(HDF_CXX)" = "Xyes"; then \
+	      elif test "X$(CXX_API)" = "Xyes"; then \
 	         echo "C++ API: Testing $${tname} $(TEST_FLAGS)"; \
 	         echo "C++ API: $${tname} $(TEST_FLAGS) Test Log" >> $${log}; \
 	      else \

config/craynv

@@ -21,7 +21,7 @@
 # Disabling Dependency Tracking
 # ---------------------
 #
-# The Cray X1 machines that THG tests on seem to have trouble doing
+# The Cray X1 machines that The HDF Group tests on seem to have trouble doing
 # dependency tracking (probably because they use Cray's C++ compiler,
 # which autoconf may not recognize).  Until this is fixed by autoconf
 # or a user complains, disable dependency tracking on Crays.
@@ -68,25 +68,23 @@ RANLIB=:
 #                      `-pg').  This may or may not include debugging 
 #                      or production flags.
 #                      
-# CFLAGS               Flags can be added to this variable which
-#                      might already be partially initialized.  These 
-#                      flags will always be passed to the compiler
-#                      and should include switches to turn on full
-#                      warnings.  HDF5 attempts to be ANSI and Posix
-#                      compliant and employ good programming
-#                      practices resulting in few if any
-#                      warnings.
+# H5_CFLAGS		Flags can be added to this variable which
+#			might already be partially initialized.  These 
+#			flags will always be passed to the compiler
+#			and should include switches to turn on full
+#			warnings.  HDF5 attempts to be ANSI and Posix
+#			compliant and employ good programming
+#			practices resulting in few if any
+#			warnings.
 #
-#                      Warning flags do not have to be added to CFLAGS
-#                      variable if the compiler is the GNU gcc
-#                      compiler or a descendent of gcc such as EGCS or PGCC.
+#			Warning flags do not have to be added to H5_CFLAGS
+#			variable if the compiler is the GNU gcc
+#			compiler or a descendent of gcc such as EGCS or PGCC.
 #
-#                      The CFLAGS should contains *something* or else 
-#                      configure will probably add `-g'.  For most
-#                      systems this isn't a problem but some systems
-#                      will disable optimizations in favor of the
-#                      `-g'.
-#                      
+# AM_CFLAGS             Flags added directly into this variable will
+#                       be propogated to the compiler wrapper scripts (h5cc,
+#                       h5c++, et cetera) in addition to being used to compile 
+#                       the library.
 #
 # These flags should be set according to the compiler being used.
 # There are two ways to check the compiler.  You can try using `-v' or 
@@ -162,7 +160,7 @@ if test "X-" = "X-$f9x_flags_set"; then
     # The -em flag enables .mod files, which is what HDF5 builds.
     F9XSUFFIXFLAG=""
     FSEARCH_DIRS=""
-    FCFLAGS="$FCFLAGS -em"
+    H5_FCFLAGS="$H5_FCFLAGS -em"
     DEBUG_FCFLAGS="-g"
     PROD_FCFLAGS=""
     PROFILE_FCFLAGS=""

config/dec-flags

@@ -26,7 +26,7 @@
 #
 if test X = "X$cc_flags_set"; then
     cc_vendor=DEC
-    cc_version="`$CC $CFLAGS -V 2>&1 |head -1`"
+    cc_version="`$CC $CFLAGS $H5_CFLAGS -V 2>&1 |head -1`"
     case "$cc_version" in
 	DEC*)
 	    cc_version="`echo $cc_version |\
@@ -111,7 +111,7 @@ fi
 if test "X-" = "X-$f9x_flags_set"; then
   F9XSUFFIXFLAG=""
   FSEARCH_DIRS=""
-  FCFLAGS="$FCFLAGS -Olimit 2048 -std1"
+  H5_FCFLAGS="$H5_FCFLAGS -Olimit 2048 -std1"
   DEBUG_FCFLAGS="-Olimit 2048 -std1"
   PROD_FCFLAGS="-Olimit 2048 -std1"
   PROFILE_FCFLAGS="-Olimit 2048 -std1"
@@ -128,7 +128,7 @@ fi
 
 case $CXX_BASENAME in
     g++)
-	CXXFLAGS="$CXXFLAGS -Wsign-compare" #Only works for some versions
+	H5_CXXFLAGS="$H5_CXXFLAGS -Wsign-compare" #Only works for some versions
 	DEBUG_CXXFLAGS="-g -fverbose-asm"
 	DEBUG_CPPFLAGS=
 	PROD_CXXFLAGS="-O3 -fomit-frame-pointer"
@@ -138,7 +138,7 @@ case $CXX_BASENAME in
 	;;
 
     *)
-	CXXFLAGS="$CXXFLAGS -tlocal -D__USE_STD_IOSTREAM"
+	H5_CXXFLAGS="$H5_CXXFLAGS -tlocal -D__USE_STD_IOSTREAM"
 	DEBUG_CXXFLAGS="-g"
 	DEBUG_CPPFLAGS=
 	PROD_CXXFLAGS="-O"