[svn-r24205] Merge HDFFV-8513/8522 from trunk (via cmake branch), h5repack UD plugins.

Also warning session fixes.

Tested: CMake local linux

20 files changed, 4811 insertions, 3812 deletions

diff --git a/tools/h5repack/CMakeLists.txt b/tools/h5repack/CMakeLists.txt
index f03ad69..176fc2b 100644
--- a/tools/h5repack/CMakeLists.txt
+++ b/tools/h5repack/CMakeLists.txt
@@ -44,6 +44,41 @@ IF (BUILD_TESTING)
   TARGET_LINK_LIBRARIES (h5repacktest  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
   SET_TARGET_PROPERTIES (h5repacktest PROPERTIES FOLDER tools)
 
+  #-----------------------------------------------------------------------------
+  # If plugin library tests can be tested
+  #-----------------------------------------------------------------------------
+  IF (BUILD_SHARED_LIBS)
+    SET (HDF5_TOOL_PLUGIN_LIB_CORENAME         "dynlibadd")
+    SET (HDF5_TOOL_PLUGIN_LIB_NAME             "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_CORENAME}")
+    SET (HDF5_TOOL_PLUGIN_LIB_TARGET           ${HDF5_TOOL_PLUGIN_LIB_CORENAME})
+    ADD_DEFINITIONS (${HDF5_EXTRA_C_FLAGS})
+    INCLUDE_DIRECTORIES (${HDF5_SRC_DIR})
+
+    ADD_LIBRARY (${HDF5_TOOL_PLUGIN_LIB_TARGET} ${LIB_TYPE} ${HDF5_TEST_SRC_DIR}/dynlib1.c)
+    TARGET_C_PROPERTIES (${HDF5_TOOL_PLUGIN_LIB_TARGET} " " " ")
+    TARGET_LINK_LIBRARIES (${HDF5_TOOL_PLUGIN_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
+    H5_SET_LIB_OPTIONS (
+        ${HDF5_TOOL_PLUGIN_LIB_TARGET} ${HDF5_TOOL_PLUGIN_LIB_NAME}
+        ${LIB_TYPE}
+        HDF5_TOOL_PLUGIN_LIB_NAME_RELEASE
+        HDF5_TOOL_PLUGIN_LIB_NAME_DEBUG
+    )
+
+    # make plugins dir
+    FILE (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/plugins")
+    #-----------------------------------------------------------------------------
+    # Copy plugin library to a plugins folder
+    #-----------------------------------------------------------------------------
+    ADD_CUSTOM_COMMAND (
+        TARGET     ${HDF5_TOOL_PLUGIN_LIB_TARGET}
+        POST_BUILD
+        COMMAND    ${CMAKE_COMMAND}
+        ARGS       -E copy_if_different 
+          "$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
+          "${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
+    )
+  ENDIF (BUILD_SHARED_LIBS)
+
   INCLUDE (CMakeTests.cmake)
   
 ENDIF (BUILD_TESTING)
diff --git a/tools/h5repack/CMakeTests.cmake b/tools/h5repack/CMakeTests.cmake
index 3f7ec7c..7f8f71b 100644
--- a/tools/h5repack/CMakeTests.cmake
+++ b/tools/h5repack/CMakeTests.cmake
@@ -86,6 +86,8 @@
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/deflate_limit.h5repack_layout.h5.ddl
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5.ddl
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_filters.h5.tst
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_test.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_test.h5repack_layout.h5.tst
   )
 
   FOREACH (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
@@ -335,6 +337,51 @@
       SET_TESTS_PROPERTIES (H5REPACK_META-${testname} PROPERTIES DEPENDS H5REPACK_META-${testname}_M)
   ENDMACRO (ADD_H5_TEST_META)
 
+  MACRO (ADD_H5_UD_TEST testname resultcode resultfile)
+    IF (HDF5_BUILD_TOOLS AND NOT HDF5_ENABLE_USING_MEMCHECKER)
+      # Remove any output file left over from previous test run
+      ADD_TEST (
+          NAME H5REPACK_UD-clearall-objects
+          COMMAND    ${CMAKE_COMMAND}
+              -E remove 
+              testfiles/out-${testname}.${resultfile}
+              testfiles/${testname}.${resultfile}.out
+              testfiles/${testname}.${resultfile}.out.err
+              testfiles/${resultfile}-${testname}.out
+              testfiles/${resultfile}-${testname}.out.err
+      )
+      ADD_TEST (
+          NAME H5REPACK_UD-${testname}
+          COMMAND "${CMAKE_COMMAND}"
+              -D "TEST_PROGRAM=$<TARGET_FILE:h5repack>"
+              -D "TEST_ARGS:STRING=${ARGN};${PROJECT_BINARY_DIR}/testfiles/${resultfile};${PROJECT_BINARY_DIR}/testfiles/out-${testname}.${resultfile}"
+              -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+              -D "TEST_EXPECT=${resultcode}"
+              -D "TEST_FILTER:STRING=O?...ing file[^\n]+\n"
+              -D "TEST_OUTPUT=./testfiles/${testname}.${resultfile}.out"
+              -D "TEST_REFERENCE=testfiles/${testname}.${resultfile}.tst"
+              -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH"
+              -D "TEST_ENV_VALUE=${CMAKE_BINARY_DIR}/plugins"
+              -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+      )
+      SET_TESTS_PROPERTIES (H5REPACK_UD-${testname} PROPERTIES DEPENDS H5REPACK_UD-clearall-objects)
+      ADD_TEST (
+          NAME H5REPACK_UD-h5dump-${testname}
+          COMMAND "${CMAKE_COMMAND}"
+              -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
+              -D "TEST_ARGS:STRING=-pH;testfiles/out-${testname}.${resultfile}"
+              -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+              -D "TEST_OUTPUT=./testfiles/${resultfile}-${testname}.out"
+              -D "TEST_EXPECT=${resultcode}"
+              -D "TEST_REFERENCE=testfiles/${resultfile}-${testname}.ddl"
+              -D "TEST_ENV_VAR=HDF5_PLUGIN_PATH"
+              -D "TEST_ENV_VALUE=${CMAKE_BINARY_DIR}/plugins"
+              -P "${HDF5_RESOURCES_DIR}/runTest.cmake"
+      )
+      SET_TESTS_PROPERTIES (H5REPACK_UD-h5dump-${testname} PROPERTIES DEPENDS "H5REPACK_UD-${testname}")
+    ENDIF (HDF5_BUILD_TOOLS AND NOT HDF5_ENABLE_USING_MEMCHECKER)
+  ENDMACRO (ADD_H5_UD_TEST)
+
 ##############################################################################
 ##############################################################################
 ###           T H E   T E S T S                                            ###
@@ -365,7 +412,7 @@
   SET (FILE18 h5repack_layout2.h5)
   SET (FILE_REF h5repack_refs.h5)
   SET (FILE_ATTR_REF h5repack_attr_refs.h5)
-
+  
   # Remove any output file left over from previous test run
   ADD_TEST (
       NAME H5REPACK-clearall-objects
@@ -410,6 +457,8 @@
          ./testfiles/h5repack_layout.h5-layout_long_switches-v.out.err
          ./testfiles/h5repack_layout.h5-layout_short_switches-v.out
          ./testfiles/h5repack_layout.h5-layout_short_switches-v.out.err
+         ./testfiles/h5repack_layout.h5-plugin_test.out
+         ./testfiles/h5repack_layout.h5-plugin_test.out.err
          ./testfiles/h5repack_layout2.h5-contig_small_compa-v.out
          ./testfiles/h5repack_layout2.h5-contig_small_compa-v.out.err
          ./testfiles/h5repack_layout2.h5-contig_small_fixed_compa-v.out
@@ -470,6 +519,7 @@
          ./testfiles/out-layout_long_switches.h5repack_layout.h5
          ./testfiles/out-layout_short_switches.h5repack_layout.h5
          ./testfiles/out-old_style_layout_short_switches.h5repack_layout.h5
+         ./testfiles/out-plugin_test.h5repack_layout.h5
          ./testfiles/out-shuffle_all.h5repack_layout.h5
          ./testfiles/out-shuffle_individual.h5repack_layout.h5
          ./testfiles/out-upgrade_layout.h5repack_layouto.h5
@@ -1008,6 +1058,19 @@ ADD_H5_VERIFY_TEST (ckdim_smaller "TEST" 0 h5repack_layout3.h5 chunk_unlimit3 CO
   ADD_H5_TEST_META (meta_short h5repack_layout.h5 -M 8192)
   ADD_H5_TEST_META (meta_long h5repack_layout.h5 --metadata_block_size=8192)
 
+##############################################################################
+###    P L U G I N  T E S T S
+##############################################################################
+IF (BUILD_SHARED_LIBS)
+  ADD_H5_UD_TEST (plugin_test 0 h5repack_layout.h5 -v -f UD=257,1,9)
+ELSE (BUILD_SHARED_LIBS)
+  MESSAGE (STATUS " **** Plugins libraries must be built as shared libraries **** ")
+  ADD_TEST (
+      NAME H5REPACK-plugin
+      COMMAND ${CMAKE_COMMAND} -E echo "SKIP H5PLUGIN TESTING"
+  )
+ENDIF (BUILD_SHARED_LIBS)
+
   IF (HDF5_TEST_VFD)
     # Run test with different Virtual File Driver
     FOREACH (vfd ${VFD_LIST})
diff --git a/tools/h5repack/Makefile.am b/tools/h5repack/Makefile.am
index 96f0082..663e501 100644
--- a/tools/h5repack/Makefile.am
+++ b/tools/h5repack/Makefile.am
@@ -28,11 +28,16 @@ TEST_SCRIPT=h5repack.sh
 TEST_PROG=h5repacktst
 noinst_PROGRAMS=testh5repack_detect_szip
 
+SCRIPT_DEPEND=h5repack$(EXEEXT)
+if HAVE_SHARED_CONDITIONAL
+if USE_PLUGINS_CONDITIONAL
+   TEST_SCRIPT += h5repack_plugin.sh
+endif
+endif
+
 check_SCRIPTS=$(TEST_SCRIPT)
 check_PROGRAMS=$(TEST_PROG)
 
-SCRIPT_DEPEND=h5repack$(EXEEXT)
-
 # Our main target, h5repack tool
 bin_PROGRAMS=h5repack
 
@@ -56,9 +61,18 @@ testh5repack_detect_szip_SOURCES=testh5repack_detect_szip.c
 # The h5repack.sh script needs h5repacktst to run first.
 h5repack.sh.chkexe_: h5repacktst.chkexe_
 
+if HAVE_SHARED_CONDITIONAL
+  # Build it as shared library if configure is enabled for shared library.
+  lib_LTLIBRARIES=libdynlibadd.la
+  libdynlibadd_la_SOURCES=$(top_srcdir)/test/dynlib1.c
+
+install-exec-hook:
+	$(RM) $(DESTDIR)$(libdir)/*dynlib*
+endif
+
 # Temporary files.  *.h5 are generated by h5repack.  They should
 # copied to the testfiles/ directory if update is required.
 CHECK_CLEANFILES+=*.h5 *.bin
-DISTCLEANFILES=h5repack.sh
+DISTCLEANFILES=h5repack.sh h5repack_plugin.sh
 
 include $(top_srcdir)/config/conclude.am
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index fe3a11c..aa51cd1 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -31,6 +31,7 @@
 # HDF5 Library Makefile(.in)
 #
 
+
 VPATH = @srcdir@
 am__make_dryrun = \
   { \
@@ -68,11 +69,12 @@ POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
-	$(srcdir)/h5repack.sh.in $(top_srcdir)/bin/depcomp \
-	$(top_srcdir)/bin/mkinstalldirs \
+	$(srcdir)/h5repack.sh.in $(srcdir)/h5repack_plugin.sh.in \
+	$(top_srcdir)/bin/depcomp $(top_srcdir)/bin/mkinstalldirs \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 noinst_PROGRAMS = testh5repack_detect_szip$(EXEEXT)
+@HAVE_SHARED_CONDITIONAL_TRUE@@USE_PLUGINS_CONDITIONAL_TRUE@am__append_1 = h5repack_plugin.sh
 check_PROGRAMS = $(am__EXEEXT_1)
 bin_PROGRAMS = h5repack$(EXEEXT)
 TESTS = $(am__EXEEXT_1) $(TEST_SCRIPT)
@@ -83,9 +85,47 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(SHELL) $(top_srcdir)/bin/mkinstalldirs
 CONFIG_HEADER = $(top_builddir)/src/H5config.h
-CONFIG_CLEAN_FILES = h5repack.sh
+CONFIG_CLEAN_FILES = h5repack.sh h5repack_plugin.sh
 CONFIG_CLEAN_VPATH_FILES =
-am__installdirs = "$(DESTDIR)$(bindir)"
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = 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__uninstall_files_from_dir = { \
+  test -z "$$files" \
+    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
+    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
+         $(am__cd) "$$dir" && rm -f $$files; }; \
+  }
+am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"
+LTLIBRARIES = $(lib_LTLIBRARIES)
+libdynlibadd_la_LIBADD =
+am__libdynlibadd_la_SOURCES_DIST = $(top_srcdir)/test/dynlib1.c
+@HAVE_SHARED_CONDITIONAL_TRUE@am_libdynlibadd_la_OBJECTS = dynlib1.lo
+libdynlibadd_la_OBJECTS = $(am_libdynlibadd_la_OBJECTS)
+AM_V_lt = $(am__v_lt_@AM_V@)
+am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
+am__v_lt_0 = --silent
+am__v_lt_1 = 
+@HAVE_SHARED_CONDITIONAL_TRUE@am_libdynlibadd_la_rpath = -rpath \
+@HAVE_SHARED_CONDITIONAL_TRUE@	$(libdir)
 am__EXEEXT_1 = h5repacktst$(EXEEXT)
 PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
 am__objects_1 = h5repack.$(OBJEXT) h5repack_copy.$(OBJEXT) \
@@ -96,10 +136,6 @@ am_h5repack_OBJECTS = $(am__objects_1) h5repack_main.$(OBJEXT)
 h5repack_OBJECTS = $(am_h5repack_OBJECTS)
 h5repack_LDADD = $(LDADD)
 h5repack_DEPENDENCIES = $(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
-AM_V_lt = $(am__v_lt_@AM_V@)
-am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
-am__v_lt_0 = --silent
-am__v_lt_1 = 
 h5repack_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
 	$(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
 	$(h5repack_LDFLAGS) $(LDFLAGS) -o $@
@@ -148,10 +184,10 @@ AM_V_CCLD = $(am__v_CCLD_@AM_V@)
 am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
 am__v_CCLD_0 = @echo "  CCLD    " $@;
 am__v_CCLD_1 = 
-SOURCES = $(h5repack_SOURCES) $(h5repacktst_SOURCES) \
-	$(testh5repack_detect_szip_SOURCES)
-DIST_SOURCES = $(h5repack_SOURCES) $(h5repacktst_SOURCES) \
-	$(testh5repack_detect_szip_SOURCES)
+SOURCES = $(libdynlibadd_la_SOURCES) $(h5repack_SOURCES) \
+	$(h5repacktst_SOURCES) $(testh5repack_detect_szip_SOURCES)
+DIST_SOURCES = $(am__libdynlibadd_la_SOURCES_DIST) $(h5repack_SOURCES) \
+	$(h5repacktst_SOURCES) $(testh5repack_detect_szip_SOURCES)
 am__can_run_installinfo = \
   case $$AM_UPDATE_INFO_DIR in \
     n|no|NO) false;; \
@@ -450,10 +486,10 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog *.h5 *.bin
 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
 
 # Test programs and scripts
-TEST_SCRIPT = h5repack.sh
+TEST_SCRIPT = h5repack.sh $(am__append_1)
 TEST_PROG = h5repacktst
-check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5repack$(EXEEXT)
+check_SCRIPTS = $(TEST_SCRIPT)
 
 # Add h5repack specific linker flags here
 h5repack_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
@@ -469,7 +505,9 @@ COMMON_SOURCES = h5repack.c h5repack_copy.c h5repack_filters.c \
 h5repack_SOURCES = $(COMMON_SOURCES) h5repack_main.c
 h5repacktst_SOURCES = $(COMMON_SOURCES) h5repacktst.c 
 testh5repack_detect_szip_SOURCES = testh5repack_detect_szip.c
-DISTCLEANFILES = h5repack.sh
+@HAVE_SHARED_CONDITIONAL_TRUE@lib_LTLIBRARIES = libdynlibadd.la
+@HAVE_SHARED_CONDITIONAL_TRUE@libdynlibadd_la_SOURCES = $(top_srcdir)/test/dynlib1.c
+DISTCLEANFILES = h5repack.sh h5repack_plugin.sh
 
 # 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.,
@@ -527,6 +565,44 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 $(am__aclocal_m4_deps):
 h5repack.sh: $(top_builddir)/config.status $(srcdir)/h5repack.sh.in
 	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+h5repack_plugin.sh: $(top_builddir)/config.status $(srcdir)/h5repack_plugin.sh.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+install-libLTLIBRARIES: $(lib_LTLIBRARIES)
+	@$(NORMAL_INSTALL)
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	list2=; for p in $$list; do \
+	  if test -f $$p; then \
+	    list2="$$list2 $$p"; \
+	  else :; fi; \
+	done; \
+	test -z "$$list2" || { \
+	  echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
+	  $(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
+	  echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
+	  $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
+	}
+
+uninstall-libLTLIBRARIES:
+	@$(NORMAL_UNINSTALL)
+	@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
+	for p in $$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:
+	-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
+	@list='$(lib_LTLIBRARIES)'; \
+	locs=`for p in $$list; do echo $$p; done | \
+	      sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
+	      sort -u`; \
+	test -z "$$locs" || { \
+	  echo rm -f $${locs}; \
+	  rm -f $${locs}; \
+	}
+libdynlibadd.la: $(libdynlibadd_la_OBJECTS) $(libdynlibadd_la_DEPENDENCIES) $(EXTRA_libdynlibadd_la_DEPENDENCIES) 
+	$(AM_V_CCLD)$(LINK) $(am_libdynlibadd_la_rpath) $(libdynlibadd_la_OBJECTS) $(libdynlibadd_la_LIBADD) $(LIBS)
 install-binPROGRAMS: $(bin_PROGRAMS)
 	@$(NORMAL_INSTALL)
 	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
@@ -607,6 +683,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/dynlib1.Plo@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_copy.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_filters.Po@am__quote@
@@ -639,6 +716,13 @@ distclean-compile:
 @AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(LTCOMPILE) -c -o $@ $<
 
+dynlib1.lo: $(top_srcdir)/test/dynlib1.c
+@am__fastdepCC_TRUE@	$(AM_V_CC)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -MT dynlib1.lo -MD -MP -MF $(DEPDIR)/dynlib1.Tpo -c -o dynlib1.lo `test -f '$(top_srcdir)/test/dynlib1.c' || echo '$(srcdir)/'`$(top_srcdir)/test/dynlib1.c
+@am__fastdepCC_TRUE@	$(AM_V_at)$(am__mv) $(DEPDIR)/dynlib1.Tpo $(DEPDIR)/dynlib1.Plo
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	$(AM_V_CC)source='$(top_srcdir)/test/dynlib1.c' object='dynlib1.lo' libtool=yes @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@	$(AM_V_CC@am__nodep@)$(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -c -o dynlib1.lo `test -f '$(top_srcdir)/test/dynlib1.c' || echo '$(srcdir)/'`$(top_srcdir)/test/dynlib1.c
+
 mostlyclean-libtool:
 	-rm -f *.lo
 
@@ -745,9 +829,11 @@ check-am: all-am
 	$(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS) $(check_SCRIPTS)
 	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
 check: check-am
-all-am: Makefile $(PROGRAMS) all-local
+all-am: Makefile $(LTLIBRARIES) $(PROGRAMS) all-local
+install-binPROGRAMS: install-libLTLIBRARIES
+
 installdirs:
-	for dir in "$(DESTDIR)$(bindir)"; do \
+	for dir in "$(DESTDIR)$(libdir)" "$(DESTDIR)$(bindir)"; do \
 	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
 	done
 install: install-am
@@ -781,10 +867,12 @@ distclean-generic:
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
 	@echo "it deletes files that may require special tools to rebuild."
+@HAVE_SHARED_CONDITIONAL_FALSE@install-exec-hook:
 clean: clean-am
 
 clean-am: clean-binPROGRAMS clean-checkPROGRAMS clean-generic \
-	clean-libtool clean-noinstPROGRAMS mostlyclean-am
+	clean-libLTLIBRARIES clean-libtool clean-noinstPROGRAMS \
+	mostlyclean-am
 
 distclean: distclean-am
 	-rm -rf ./$(DEPDIR)
@@ -810,8 +898,9 @@ install-dvi: install-dvi-am
 
 install-dvi-am:
 
-install-exec-am: install-binPROGRAMS
-
+install-exec-am: install-binPROGRAMS install-libLTLIBRARIES
+	@$(NORMAL_INSTALL)
+	$(MAKE) $(AM_MAKEFLAGS) install-exec-hook
 install-html: install-html-am
 
 install-html-am:
@@ -850,25 +939,26 @@ ps: ps-am
 
 ps-am:
 
-uninstall-am: uninstall-binPROGRAMS
+uninstall-am: uninstall-binPROGRAMS uninstall-libLTLIBRARIES
 
-.MAKE: check-am install-am install-strip
+.MAKE: check-am install-am install-exec-am install-strip
 
 .PHONY: CTAGS GTAGS all all-am all-local check check-TESTS check-am \
 	clean clean-binPROGRAMS clean-checkPROGRAMS clean-generic \
-	clean-libtool clean-noinstPROGRAMS cscopelist ctags distclean \
-	distclean-compile distclean-generic distclean-libtool \
-	distclean-tags distdir dvi dvi-am html html-am info info-am \
-	install install-am install-binPROGRAMS install-data \
-	install-data-am install-dvi install-dvi-am install-exec \
-	install-exec-am install-html install-html-am install-info \
-	install-info-am install-man install-pdf install-pdf-am \
+	clean-libLTLIBRARIES clean-libtool clean-noinstPROGRAMS \
+	cscopelist ctags distclean distclean-compile distclean-generic \
+	distclean-libtool distclean-tags distdir dvi dvi-am html \
+	html-am info info-am install install-am install-binPROGRAMS \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-exec-hook install-html \
+	install-html-am install-info install-info-am \
+	install-libLTLIBRARIES install-man install-pdf install-pdf-am \
 	install-ps install-ps-am install-strip installcheck \
 	installcheck-am installdirs maintainer-clean \
 	maintainer-clean-generic mostlyclean mostlyclean-compile \
 	mostlyclean-generic mostlyclean-libtool mostlyclean-local pdf \
 	pdf-am ps ps-am tags uninstall uninstall-am \
-	uninstall-binPROGRAMS
+	uninstall-binPROGRAMS uninstall-libLTLIBRARIES
 
 
 # List all build rules defined by HDF5 Makefiles as "PHONY" targets here.
@@ -885,6 +975,11 @@ help:
 # The h5repack.sh script needs h5repacktst to run first.
 h5repack.sh.chkexe_: h5repacktst.chkexe_
 
+@HAVE_SHARED_CONDITIONAL_TRUE@  # Build it as shared library if configure is enabled for shared library.
+
+@HAVE_SHARED_CONDITIONAL_TRUE@install-exec-hook:
+@HAVE_SHARED_CONDITIONAL_TRUE@	$(RM) $(DESTDIR)$(libdir)/*dynlib*
+
 # lib/progs/tests targets recurse into subdirectories. build-* targets
 # build files in this directory.
 build-lib: $(LIB)
diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index e014f49..a195f6c 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -1,17 +1,17 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* 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.     *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * 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.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include <stdlib.h>
 #include <string.h>
@@ -23,218 +23,194 @@
 #include "h5tools_utils.h"
 
 /*-------------------------------------------------------------------------
-* File: h5repack.c
-* Purpose: Public API functions
-*-------------------------------------------------------------------------
-*/
+ * File: h5repack.c
+ * Purpose: Public API functions
+ *-------------------------------------------------------------------------
+ */
 
 static int check_options(pack_opt_t *options);
 static int check_objects(const char* fname, pack_opt_t *options);
-static const char* get_sfilter (H5Z_filter_t filtn);
+static const char* get_sfilter(H5Z_filter_t filtn);
 static int have_request(pack_opt_t *options);
 
+/*-------------------------------------------------------------------------
+ * Function: h5repack
+ *
+ * Purpose: locate all high-level HDF5 objects in the file
+ *  and compress/chunk them using options
+ *
+ * Algorithm: 2 traversals are made to the file; the 1st builds a list of
+ *  the objects, the 2nd makes a copy of them, using the options;
+ *  the reason for the 1st traversal is to check for invalid
+ *  object name requests
+ *
+ * Return: 0, ok, -1, fail
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+	/* check input */
+	if (check_options(options) < 0)
+		return -1;
 
+	/* check for objects in input that are in the file */
+	if (check_objects(infile, options) < 0)
+		return -1;
 
-/*-------------------------------------------------------------------------
-* Function: h5repack
-*
-* Purpose: locate all high-level HDF5 objects in the file
-*  and compress/chunk them using options
-*
-* Algorithm: 2 traversals are made to the file; the 1st builds a list of
-*  the objects, the 2nd makes a copy of them, using the options;
-*  the reason for the 1st traversal is to check for invalid
-*  object name requests
-*
-* Return: 0, ok, -1, fail
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack(const char* infile,
-             const char* outfile,
-             pack_opt_t *options)
-{
-    /* check input */
-    if (check_options(options)<0)
-        return -1;
-
-    /* check for objects in input that are in the file */
-    if (check_objects(infile,options) < 0)
-        return -1;
-
-    /* copy the objects  */
-    if (copy_objects(infile,outfile,options) < 0)
-        return -1;
-
-
-    return 0;
+	/* copy the objects  */
+	if (copy_objects(infile, outfile, options) < 0)
+		return -1;
+
+	return 0;
 }
 
+/*-------------------------------------------------------------------------
+ * Function: h5repack_init
+ *
+ * Purpose: initialize options
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
 
+int h5repack_init(pack_opt_t *options, int verbose) {
+	int k, n;
 
-/*-------------------------------------------------------------------------
-* Function: h5repack_init
-*
-* Purpose: initialize options
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack_init(pack_opt_t *options,
-                   int verbose)
-{
-    int k, n;
-
-    HDmemset(options, 0, sizeof(pack_opt_t));
-    options->min_comp = 0;
-    options->verbose  = verbose;
-    options->layout_g = H5D_LAYOUT_ERROR;
-
-    for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
-    {
-        options->filter_g[n].filtn  = -1;
-        options->filter_g[n].cd_nelmts  = 0;
-        for ( k = 0; k < CD_VALUES; k++)
-            options->filter_g[n].cd_values[k] = 0;
-    }
-
-    return (options_table_init(&(options->op_tbl)));
-}
+	HDmemset(options, 0, sizeof(pack_opt_t));
+	options->min_comp = 0;
+	options->verbose = verbose;
+	options->layout_g = H5D_LAYOUT_ERROR;
 
+	for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
+		options->filter_g[n].filtn = -1;
+		options->filter_g[n].cd_nelmts = 0;
+		for (k = 0; k < CD_VALUES; k++)
+			options->filter_g[n].cd_values[k] = 0;
+	}
 
-/*-------------------------------------------------------------------------
-* Function: h5repack_end
-*
-* Purpose: free options table
-*
-*-------------------------------------------------------------------------
-*/
-
-int h5repack_end  (pack_opt_t *options)
-{
-    return options_table_free(options->op_tbl);
+	return (options_table_init(&(options->op_tbl)));
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: h5repack_addfilter
-*
-* Purpose: add a compression -f option to table
-*   Example: -f dset:GZIP=6
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack_addfilter(const char* str,
-                       pack_opt_t *options)
-{
-    obj_list_t      *obj_list=NULL; /* one object list for the -f and -l option entry */
-    filter_info_t   filter;         /* filter info for the current -f option entry */
-    int             n_objs;         /* number of objects in the current -f or -l option entry */
-    int             is_glb;         /* is the filter global */
-
-
-
-    /* parse the -f option */
-    if(NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
-        return -1;
-
-    /* if it applies to all objects */
-    if(is_glb)
-    {
-        int n;
-
-        n = options->n_filter_g++; /* increase # of global filters */
-
-        if(options->n_filter_g > H5_REPACK_MAX_NFILTERS)
-        {
-            error_msg("maximum number of filters exceeded for <%s>\n", str);
-            HDfree(obj_list);
-            return -1;
-        }
-
-        options->filter_g[n] = filter;
-    }
-    else
-        options_add_filter(obj_list, n_objs, filter, options->op_tbl);
-
-    HDfree(obj_list);
-    return 0;
+ * Function: h5repack_end
+ *
+ * Purpose: free options table
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_end(pack_opt_t *options) {
+	return options_table_free(options->op_tbl);
 }
 
+/*-------------------------------------------------------------------------
+ * Function: h5repack_addfilter
+ *
+ * Purpose: add a compression -f option to table
+ *   Example: -f dset:GZIP=6
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_addfilter(const char* str, pack_opt_t *options) {
+	obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
+	filter_info_t filter; /* filter info for the current -f option entry */
+	int n_objs; /* number of objects in the current -f or -l option entry */
+	int is_glb; /* is the filter global */
+
+	/* parse the -f option */
+	if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
+		return -1;
+
+	/* if it applies to all objects */
+	if (is_glb) {
+		int n;
+
+		n = options->n_filter_g++; /* increase # of global filters */
+
+		if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
+			error_msg("maximum number of filters exceeded for <%s>\n", str);
+			HDfree(obj_list);
+			return -1;
+		}
+
+		options->filter_g[n] = filter;
+	}
+	else
+		options_add_filter(obj_list, n_objs, filter, options->op_tbl);
+
+	HDfree(obj_list);
+	return 0;
+}
 
 /*-------------------------------------------------------------------------
-* Function: h5repack_addlayout
-*
-* Purpose: add a layout option
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-
-int h5repack_addlayout(const char* str,
-                       pack_opt_t *options)
-{
-
-    obj_list_t  *obj_list=NULL;     /*one object list for the -t and -c option entry */
-    int         n_objs;             /*number of objects in the current -t or -c option entry */
-    pack_info_t pack;               /*info about layout to extract from parse */
-    int         j;
-
-    init_packobject(&pack);
-
-    if (options->all_layout==1){
-        error_msg("invalid layout input: 'all' option \
-                            is present with other objects <%s>\n",str);
-        return -1;
-    }
-
-    /* parse the layout option */
-    obj_list=parse_layout(str,&n_objs,&pack,options);
-    if (obj_list==NULL)
-        return -1;
-
-    /* set layout option */
-    options->layout_g = pack.layout;
-
-    /* no individual dataset specified */
-    if (options->all_layout==1 )
-    {
-        if (pack.layout==H5D_CHUNKED)
-        {
-            /* -2 means the NONE option, remove chunking
-            and set the global layout to contiguous */
-            if (pack.chunk.rank==-2)
-            {
-                options->layout_g = H5D_CONTIGUOUS;
-            }
-            /* otherwise set the global chunking type */
-            else
-            {
-                options->chunk_g.rank=pack.chunk.rank;
-                for (j = 0; j < pack.chunk.rank; j++)
-                    options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
-            }
-        }
-    }
-
-    /* individual dataset specified */
-    if (options->all_layout==0)
-        options_add_layout(obj_list,
-        n_objs,
-        &pack,
-        options->op_tbl);
-
-    HDfree(obj_list);
-    return 0;
+ * Function: h5repack_addlayout
+ *
+ * Purpose: add a layout option
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_addlayout(const char* str, pack_opt_t *options) {
+
+	obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
+	int n_objs; /*number of objects in the current -t or -c option entry */
+	pack_info_t pack; /*info about layout to extract from parse */
+	int j;
+	int ret_value = -1;
+
+	init_packobject(&pack);
+
+	if (options->all_layout == 1) {
+		error_msg(
+				"invalid layout input: 'all' option \
+                            is present with other objects <%s>\n",
+				str);
+		return ret_value;
+	}
+
+	/* parse the layout option */
+	obj_list = parse_layout(str, &n_objs, &pack, options);
+	if (obj_list) {
+
+		/* set layout option */
+		options->layout_g = pack.layout;
+
+		/* no individual dataset specified */
+		if (options->all_layout == 1) {
+			if (pack.layout == H5D_CHUNKED) {
+				/* -2 means the NONE option, remove chunking
+				 and set the global layout to contiguous */
+				if (pack.chunk.rank == -2) {
+					options->layout_g = H5D_CONTIGUOUS;
+				}
+				/* otherwise set the global chunking type */
+				else {
+					options->chunk_g.rank = pack.chunk.rank;
+					for (j = 0; j < pack.chunk.rank; j++)
+						options->chunk_g.chunk_lengths[j] =
+								pack.chunk.chunk_lengths[j];
+				}
+			}
+		}
+
+		/* individual dataset specified */
+		if (options->all_layout == 0)
+			ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
+
+		HDfree(obj_list);
+		ret_value = 0;
+	}
+
+	return ret_value;
 }
 
 /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
@@ -244,766 +220,720 @@ int h5repack_addlayout(const char* str,
  * others to static in h5repack_copy.c.
  */
 /*-------------------------------------------------------------------------
-* Function: copy_named_datatype
-*
-* Purpose: Copies the specified datatype anonymously, and returns an open
-*          id for that datatype in the output file.  The first time this
-*          is called it scans every named datatype in travt into a
-*          private stack, afterwards it simply scans that stack.  The id
-*          returned must be closed after it is no longer needed.
-*          named_datatype_free must be called before the program exits
-*          to free the stack.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
-{
-    named_dt_t  *dt = *named_dt_head_p; /* Stack pointer */
-    named_dt_t  *dt_ret = NULL;     /* Datatype to return */
-    H5O_info_t  oinfo;              /* Object info of input dtype */
-    hid_t       ret_value = -1;     /* The identifier of the named dtype in the out file */
-
-    if(H5Oget_info(type_in, &oinfo) < 0)
-        goto error;
-
-    if(*named_dt_head_p)
-    {
-        /* Stack already exists, search for the datatype */
-        while(dt && dt->addr_in != oinfo.addr)
-            dt = dt->next;
-
-        dt_ret = dt;
-    }
-    else
-    {
-        /* Create the stack */
-        size_t  i;
-
-        for(i=0; i<travt->nobjs; i++)
-            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
-            {
-                /* Push onto the stack */
-                if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
-                    goto error;
-                dt->next = *named_dt_head_p;
-                *named_dt_head_p = dt;
-
-                /* Update the address and id */
-                dt->addr_in = travt->objs[i].objno;
-                dt->id_out = -1;
-
-                /* Check if this type is the one requested */
-                if(oinfo.addr == dt->addr_in)
-                {
-                    HDassert(!dt_ret);
-                    dt_ret = dt;
-                } /* end if */
-            } /* end if */
-    } /* end else */
-
-    /* Handle the case that the requested datatype was not found.  This is
-     * possible if the datatype was committed anonymously in the input file. */
-    if(!dt_ret)
-    {
-        /* Push the new datatype onto the stack */
-        if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
-            goto error;
-        dt_ret->next = *named_dt_head_p;
-        *named_dt_head_p = dt_ret;
-
-        /* Update the address and id */
-        dt_ret->addr_in = oinfo.addr;
-        dt_ret->id_out = -1;
-    } /* end if */
-
-    /* If the requested datatype does not yet exist in the output file, copy it
-     * anonymously */
-    if(dt_ret->id_out < 0)
-    {
-        if (options->use_native==1)
-            dt_ret->id_out = h5tools_get_native_type(type_in);
-        else
-            dt_ret->id_out = H5Tcopy(type_in);
-        if(dt_ret->id_out < 0)
-            goto error;
-        if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
-            goto error;
-    } /* end if */
-
-    /* Set return value */
-    ret_value = dt_ret->id_out;
-
-    /* Increment the ref count on id_out, because the calling function will try
-     * to close it */
-    if(H5Iinc_ref(ret_value) < 0)
-        goto error;
-
-    return(ret_value);
-
-error:
-    return(-1);
+ * Function: copy_named_datatype
+ *
+ * Purpose: Copies the specified datatype anonymously, and returns an open
+ *          id for that datatype in the output file.  The first time this
+ *          is called it scans every named datatype in travt into a
+ *          private stack, afterwards it simply scans that stack.  The id
+ *          returned must be closed after it is no longer needed.
+ *          named_datatype_free must be called before the program exits
+ *          to free the stack.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
+		named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+	named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+	named_dt_t *dt_ret = NULL; /* Datatype to return */
+	H5O_info_t oinfo; /* Object info of input dtype */
+	hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
+
+	if (H5Oget_info(type_in, &oinfo) < 0)
+		goto done;
+
+	if (*named_dt_head_p) {
+		/* Stack already exists, search for the datatype */
+		while (dt && dt->addr_in != oinfo.addr)
+			dt = dt->next;
+
+		dt_ret = dt;
+	}
+	else {
+		/* Create the stack */
+		size_t i;
+
+		for (i = 0; i < travt->nobjs; i++) {
+			if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+				/* Push onto the stack */
+				if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+					goto done;
+				}
+				dt->next = *named_dt_head_p;
+				*named_dt_head_p = dt;
+
+				/* Update the address and id */
+				dt->addr_in = travt->objs[i].objno;
+				dt->id_out = -1;
+
+				/* Check if this type is the one requested */
+				if (oinfo.addr == dt->addr_in) {
+					HDassert(!dt_ret);
+					dt_ret = dt;
+				} /* end if */
+			} /* end if */
+		} /* end for */
+	} /* end else */
+
+	/* Handle the case that the requested datatype was not found.  This is
+	 * possible if the datatype was committed anonymously in the input file. */
+	if (!dt_ret) {
+		/* Push the new datatype onto the stack */
+		if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+			goto done;
+		}
+		dt_ret->next = *named_dt_head_p;
+		*named_dt_head_p = dt_ret;
+
+		/* Update the address and id */
+		dt_ret->addr_in = oinfo.addr;
+		dt_ret->id_out = -1;
+	} /* end if */
+
+	/* If the requested datatype does not yet exist in the output file, copy it
+	 * anonymously */
+	if (dt_ret->id_out < 0) {
+		if (options->use_native == 1)
+			dt_ret->id_out = h5tools_get_native_type(type_in);
+		else
+			dt_ret->id_out = H5Tcopy(type_in);
+		if (dt_ret->id_out < 0)
+			goto done;
+		if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+			goto done;
+	} /* end if */
+
+	/* Set return value */
+	ret_value = dt_ret->id_out;
+
+	/* Increment the ref count on id_out, because the calling function will try
+	 * to close it */
+	if(H5Iinc_ref(ret_value) < 0) {
+		ret_value = -1;
+	}
+
+done:
+	return (ret_value);
 } /* end copy_named_datatype */
 
-
 /*-------------------------------------------------------------------------
-* Function: named_datatype_free
-*
-* Purpose: Frees the stack of named datatypes.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
-{
-    named_dt_t *dt = *named_dt_head_p;
-
-    while(dt)
-    {
-        /* Pop the datatype off the stack and free it */
-        if(H5Tclose(dt->id_out) < 0 && !ignore_err)
-            goto error;
-        dt = dt->next;
-        HDfree(*named_dt_head_p);
-        *named_dt_head_p = dt;
-    } /* end while */
-
-    return 0;
-
-error:
-    return -1;
+ * Function: named_datatype_free
+ *
+ * Purpose: Frees the stack of named datatypes.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
+	named_dt_t *dt = *named_dt_head_p;
+	hid_t ret_value = -1;
+
+	while (dt) {
+		/* Pop the datatype off the stack and free it */
+		if (H5Tclose(dt->id_out) < 0 && !ignore_err)
+			goto done;
+		dt = dt->next;
+		HDfree(*named_dt_head_p);
+		*named_dt_head_p = dt;
+	} /* end while */
+
+	ret_value = 0;
+
+done:
+	return (ret_value);
 } /* end named_datatype_free */
 
 /*-------------------------------------------------------------------------
-* Function: copy_attr
-*
-* Purpose: copy attributes located in LOC_IN, which is obtained either from
-* loc_id = H5Gopen2( fid, name);
-* loc_id = H5Dopen2( fid, name);
-* loc_id = H5Topen2( fid, name);
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 28, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int copy_attr(hid_t loc_in,
-              hid_t loc_out,
-              named_dt_t **named_dt_head_p,
-              trav_table_t *travt,
-              pack_opt_t *options)
-{
-    hid_t      attr_id=-1;        /* attr ID */
-    hid_t      attr_out=-1;       /* attr ID */
-    hid_t      space_id=-1;       /* space ID */
-    hid_t      ftype_id=-1;       /* file type ID */
-    hid_t      wtype_id=-1;       /* read/write type ID */
-    size_t     msize;             /* size of type */
-    void       *buf = NULL;       /* data buffer */
-    hsize_t    nelmts;            /* number of elements in dataset */
-    int        rank;              /* rank of dataset */
-    htri_t     is_named;          /* Whether the datatype is named */
-    hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
-    char       name[255];
-    H5O_info_t oinfo;             /* object info */
-    int        j;
-    unsigned   u;
-    hbool_t    is_ref=0;
-    H5T_class_t type_class = -1;
-
-    if(H5Oget_info(loc_in, &oinfo) < 0)
-        goto error;
-
-    /*-------------------------------------------------------------------------
-    * copy all attributes
-    *-------------------------------------------------------------------------
-    */
-    for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
-        /* open attribute */
-        if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-            goto error;
-
-        /* get name */
-        if(H5Aget_name(attr_id, (size_t)255, name) < 0)
-            goto error;
-
-        /* get the file datatype  */
-        if((ftype_id = H5Aget_type(attr_id)) < 0 )
-            goto error;
-
-        /* Check if the datatype is committed */
-        if((is_named = H5Tcommitted(ftype_id)) < 0)
-            goto error;
-        if(is_named && travt) {
-            hid_t fidout;
-
-            /* Create out file id */
-            if((fidout = H5Iget_file_id(loc_out)) < 0)
-                goto error;
-
-            /* Copy named dt */
-            if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
-                    travt, options)) < 0)
-            {
-                H5Fclose(fidout);
-                goto error;
-            } /* end if */
-
-            if(H5Fclose(fidout) < 0)
-                goto error;
-        } /* end if */
-        else {
-            if(options->use_native == 1)
-                wtype_id = h5tools_get_native_type(ftype_id);
-            else
-                wtype_id = H5Tcopy(ftype_id);
-        } /* end else */
-
-
-        /* get the dataspace handle  */
-        if((space_id = H5Aget_space(attr_id)) < 0)
-            goto error;
-
-        /* get dimensions  */
-        if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
-            goto error;
-
-        nelmts = 1;
-        for(j = 0; j < rank; j++)
-            nelmts *= dims[j];
-
-        if((msize = H5Tget_size(wtype_id)) == 0)
-            goto error;
-
-        /*-------------------------------------------------------------------------
-        * object references are a special case. We cannot just copy the buffers,
-        * but instead we recreate the reference.
-        * This is done on a second sweep of the file that just copies the referenced
-        * objects at copy_refs_attr()
-        *-------------------------------------------------------------------------
-        */
-        type_class = H5Tget_class(wtype_id);
-        is_ref = (type_class == H5T_REFERENCE);
-        if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
-        	hid_t base_type = -1;
-        	base_type = H5Tget_super(ftype_id);
-        	is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
-        	H5Tclose(base_type);
-        }
-
-        if (type_class == H5T_COMPOUND) {
-        	int nmembers = H5Tget_nmembers(wtype_id) ;
-        	for (j=0; j<nmembers; j++) {
-        		hid_t mtid = H5Tget_member_type( wtype_id, (unsigned) j );
-        		H5T_class_t mtclass = H5Tget_class(mtid);
-        		H5Tclose(mtid);
-
-        		if (mtclass==H5T_REFERENCE) {
-        			is_ref = 1;
-        			break;
-        		}
-        	} /* for (j=0; i<nmembers; j++) */
-        } /* if (type_class == H5T_COMPOUND) */
-
-        if(is_ref) {
-            ; /* handled by copy_refs_attr() */
-        }
-        else {
-            /*-------------------------------------------------------------------------
-            * read to memory
-            *-------------------------------------------------------------------------
-            */
-
-            buf = (void *)HDmalloc((size_t)(nelmts * msize));
-            if(buf == NULL) {
-                error_msg("h5repack", "cannot read into memory\n" );
-                goto error;
-            } /* end if */
-            if(H5Aread(attr_id, wtype_id, buf) < 0)
-                goto error;
-
-            /*-------------------------------------------------------------------------
-            * copy
-            *-------------------------------------------------------------------------
-            */
-
-            if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-                goto error;
-            if(H5Awrite(attr_out, wtype_id, buf) < 0)
-                goto error;
-
-            /*close*/
-            if(H5Aclose(attr_out) < 0)
-                goto error;
-
-            /* Check if we have VL data and string in the attribute's  datatype that must
-             * be reclaimed */
-            if (TRUE == h5tools_detect_vlen(wtype_id))
-                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-            HDfree(buf);
-            buf = NULL;
-        } /*H5T_REFERENCE*/
-
-
-        if(options->verbose)
-            printf(FORMAT_OBJ_ATTR, "attr", name);
-
-        /*-------------------------------------------------------------------------
-        * close
-        *-------------------------------------------------------------------------
-        */
-
-        if(H5Tclose(ftype_id) < 0)
-            goto error;
-        if(H5Tclose(wtype_id) < 0)
-            goto error;
-        if(H5Sclose(space_id) < 0)
-            goto error;
-        if(H5Aclose(attr_id) < 0)
-            goto error;
-    } /* u */
-
-    return 0;
+ * Function: copy_attr
+ *
+ * Purpose: copy attributes located in LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2( fid, name);
+ * loc_id = H5Dopen2( fid, name);
+ * loc_id = H5Topen2( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
+		trav_table_t *travt, pack_opt_t *options) {
+	hid_t attr_id = -1; /* attr ID */
+	hid_t attr_out = -1; /* attr ID */
+	hid_t space_id = -1; /* space ID */
+	hid_t ftype_id = -1; /* file type ID */
+	hid_t wtype_id = -1; /* read/write type ID */
+	size_t msize; /* size of type */
+	void *buf = NULL; /* data buffer */
+	hsize_t nelmts; /* number of elements in dataset */
+	int rank; /* rank of dataset */
+	htri_t is_named; /* Whether the datatype is named */
+	hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+	char name[255];
+	H5O_info_t oinfo; /* object info */
+	int j;
+	unsigned u;
+	hbool_t is_ref = 0;
+	H5T_class_t type_class = -1;
+
+	if (H5Oget_info(loc_in, &oinfo) < 0)
+		goto error;
+
+	/*-------------------------------------------------------------------------
+	 * copy all attributes
+	 *-------------------------------------------------------------------------
+	 */
+	for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
+		/* open attribute */
+		if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER,
+				H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+			goto error;
+
+		/* get name */
+		if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
+			goto error;
+
+		/* get the file datatype  */
+		if ((ftype_id = H5Aget_type(attr_id)) < 0)
+			goto error;
+
+		/* Check if the datatype is committed */
+		if ((is_named = H5Tcommitted(ftype_id)) < 0)
+			goto error;
+		if (is_named && travt) {
+			hid_t fidout;
+
+			/* Create out file id */
+			if ((fidout = H5Iget_file_id(loc_out)) < 0)
+				goto error;
+
+			/* Copy named dt */
+			if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+					named_dt_head_p, travt, options)) < 0) {
+				H5Fclose(fidout);
+				goto error;
+			} /* end if */
+
+			if (H5Fclose(fidout) < 0)
+				goto error;
+		} /* end if */
+		else {
+			if (options->use_native == 1)
+				wtype_id = h5tools_get_native_type(ftype_id);
+			else
+				wtype_id = H5Tcopy(ftype_id);
+		} /* end else */
+
+		/* get the dataspace handle  */
+		if ((space_id = H5Aget_space(attr_id)) < 0)
+			goto error;
+
+		/* get dimensions  */
+		if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+			goto error;
+
+		nelmts = 1;
+		for (j = 0; j < rank; j++)
+			nelmts *= dims[j];
+
+		if ((msize = H5Tget_size(wtype_id)) == 0)
+			goto error;
+
+		/*-------------------------------------------------------------------------
+		 * object references are a special case. We cannot just copy the buffers,
+		 * but instead we recreate the reference.
+		 * This is done on a second sweep of the file that just copies the referenced
+		 * objects at copy_refs_attr()
+		 *-------------------------------------------------------------------------
+		 */
+		type_class = H5Tget_class(wtype_id);
+		is_ref = (type_class == H5T_REFERENCE);
+		if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
+			hid_t base_type = -1;
+			base_type = H5Tget_super(ftype_id);
+			is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
+			H5Tclose(base_type);
+		}
+
+		if (type_class == H5T_COMPOUND) {
+			int nmembers = H5Tget_nmembers(wtype_id);
+			for (j = 0; j < nmembers; j++) {
+				hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+				H5T_class_t mtclass = H5Tget_class(mtid);
+				H5Tclose(mtid);
+
+				if (mtclass == H5T_REFERENCE) {
+					is_ref = 1;
+					break;
+				}
+			} /* for (j=0; i<nmembers; j++) */
+		} /* if (type_class == H5T_COMPOUND) */
+
+		if (is_ref) {
+			; /* handled by copy_refs_attr() */
+		}
+		else {
+			/*-------------------------------------------------------------------------
+			 * read to memory
+			 *-------------------------------------------------------------------------
+			 */
+
+			buf = (void *) HDmalloc((size_t)(nelmts * msize));
+			if (buf == NULL) {
+				error_msg("h5repack", "cannot read into memory\n");
+				goto error;
+			} /* end if */
+			if (H5Aread(attr_id, wtype_id, buf) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * copy
+			 *-------------------------------------------------------------------------
+			 */
+
+			if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id,
+					H5P_DEFAULT, H5P_DEFAULT)) < 0)
+				goto error;
+			if (H5Awrite(attr_out, wtype_id, buf) < 0)
+				goto error;
+
+			/*close*/
+			if (H5Aclose(attr_out) < 0)
+				goto error;
+
+			/* Check if we have VL data and string in the attribute's  datatype that must
+			 * be reclaimed */
+			if (TRUE == h5tools_detect_vlen(wtype_id))
+				H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+			HDfree(buf);
+			buf = NULL;
+		} /*H5T_REFERENCE*/
+
+		if (options->verbose)
+			printf(FORMAT_OBJ_ATTR, "attr", name);
+
+		/*-------------------------------------------------------------------------
+		 * close
+		 *-------------------------------------------------------------------------
+		 */
+
+		if (H5Tclose(ftype_id) < 0)
+			goto error;
+		if (H5Tclose(wtype_id) < 0)
+			goto error;
+		if (H5Sclose(space_id) < 0)
+			goto error;
+		if (H5Aclose(attr_id) < 0)
+			goto error;
+	} /* u */
+
+	return 0;
 
 error:
-    H5E_BEGIN_TRY {
-        if(buf) {
-            /* Check if we have VL data and string in the attribute's  datatype that must
-             * be reclaimed */
-            if (TRUE == h5tools_detect_vlen(wtype_id))
-                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-
-            /* Free buf */
-            HDfree(buf);
-        } /* end if */
-
-        H5Tclose(ftype_id);
-        H5Tclose(wtype_id);
-        H5Sclose(space_id);
-        H5Aclose(attr_id);
-        H5Aclose(attr_out);
-    } H5E_END_TRY;
-
-    return -1;
+	H5E_BEGIN_TRY
+		{
+			if (buf) {
+				/* Check if we have VL data and string in the attribute's  datatype that must
+				 * be reclaimed */
+				if (TRUE == h5tools_detect_vlen(wtype_id))
+					H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+
+				/* Free buf */
+				HDfree(buf);
+			} /* end if */
+
+			H5Tclose(ftype_id);
+			H5Tclose(wtype_id);
+			H5Sclose(space_id);
+			H5Aclose(attr_id);
+			H5Aclose(attr_out);
+		} H5E_END_TRY;
+
+	return -1;
 } /* end copy_attr() */
 
 /*-------------------------------------------------------------------------
-* Function: check_options
-*
-* Purpose: print options, checks for invalid options
-*
-* Return: void, return -1 on error
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-* Modification:
-*   Peter Cao, July 9, 2007
-*   Add "-L, --latest" and other options to pack a file with the latest file format
-*
-*-------------------------------------------------------------------------
-*/
-static int check_options(pack_opt_t *options)
-{
-    unsigned int   i;
-    int            k, j, has_cp=0, has_ck=0;
-    char           slayout[30];
-
-    /*-------------------------------------------------------------------------
-    * objects to layout
-    *-------------------------------------------------------------------------
-    */
-    if (options->verbose && have_request(options) /* only print if requested */)
-    {
-        printf("Objects to modify layout are...\n");
-        if (options->all_layout==1)
-        {
-            switch (options->layout_g)
-            {
-            case H5D_COMPACT:
-                strcpy(slayout,"compact");
-                break;
-            case H5D_CONTIGUOUS:
-                strcpy(slayout,"contiguous");
-                break;
-            case H5D_CHUNKED:
-                strcpy(slayout,"chunked");
-                break;
-            case H5D_LAYOUT_ERROR:
-            case H5D_NLAYOUTS:
-                error_msg("invalid layout\n");
-                return -1;
-            default:
-                strcpy(slayout,"invalid layout\n");
-                return -1;
-            }
-            printf(" Apply %s layout to all\n", slayout);
-            if (H5D_CHUNKED==options->layout_g)
-            {
-                printf("with dimension [");
-                for ( j = 0; j < options->chunk_g.rank; j++)
-                    printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
-                printf("]\n");
-            }
-        }
-    }/* verbose */
-
-    for ( i = 0; i < options->op_tbl->nelems; i++)
-    {
-        char* name=options->op_tbl->objs[i].path;
-
-        if (options->op_tbl->objs[i].chunk.rank>0)
-        {
-            if (options->verbose){
-                printf(" <%s> with chunk size ",name);
-                for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
-                    printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
-                printf("\n");
-            }
-            has_ck=1;
-        }
-        else if (options->op_tbl->objs[i].chunk.rank==-2)
-        {
-            if (options->verbose)
-                printf(" <%s> %s\n",name,"NONE (contigous)");
-            has_ck=1;
-        }
-    }
-
-    if (options->all_layout==1 && has_ck)
-    {
-        error_msg("invalid chunking input: 'all' option\
+ * Function: check_options
+ *
+ * Purpose: print options, checks for invalid options
+ *
+ * Return: void, return -1 on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ * Modification:
+ *   Peter Cao, July 9, 2007
+ *   Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_options(pack_opt_t *options) {
+	unsigned int i;
+	int k, j, has_cp = 0, has_ck = 0;
+	char slayout[30];
+
+	/*-------------------------------------------------------------------------
+	 * objects to layout
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->verbose && have_request(options) /* only print if requested */) {
+		printf("Objects to modify layout are...\n");
+		if (options->all_layout == 1) {
+			switch (options->layout_g) {
+			case H5D_COMPACT:
+				strcpy(slayout, "compact");
+				break;
+			case H5D_CONTIGUOUS:
+				strcpy(slayout, "contiguous");
+				break;
+			case H5D_CHUNKED:
+				strcpy(slayout, "chunked");
+				break;
+			case H5D_LAYOUT_ERROR:
+			case H5D_NLAYOUTS:
+				error_msg("invalid layout\n");
+				return -1;
+			default:
+				strcpy(slayout, "invalid layout\n");
+				return -1;
+			}
+			printf(" Apply %s layout to all\n", slayout);
+			if (H5D_CHUNKED == options->layout_g) {
+				printf("with dimension [");
+				for (j = 0; j < options->chunk_g.rank; j++)
+					printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+				printf("]\n");
+			}
+		}
+	}/* verbose */
+
+	for (i = 0; i < options->op_tbl->nelems; i++) {
+		char* name = options->op_tbl->objs[i].path;
+
+		if (options->op_tbl->objs[i].chunk.rank > 0) {
+			if (options->verbose) {
+				printf(" <%s> with chunk size ", name);
+				for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
+					printf("%d ",
+							(int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+				printf("\n");
+			}
+			has_ck = 1;
+		}
+		else if (options->op_tbl->objs[i].chunk.rank == -2) {
+			if (options->verbose)
+				printf(" <%s> %s\n", name, "NONE (contigous)");
+			has_ck = 1;
+		}
+	}
+
+	if (options->all_layout == 1 && has_ck) {
+		error_msg(
+				"invalid chunking input: 'all' option\
                             is present with other objects\n");
-        return -1;
-    }
-
-    /*-------------------------------------------------------------------------
-    * objects to filter
-    *-------------------------------------------------------------------------
-    */
-
-    if (options->verbose && have_request(options) /* only print if requested */)
-    {
-        printf("Objects to apply filter are...\n");
-        if (options->all_filter==1)
-        {
-
-            for (k = 0; k < options->n_filter_g; k++ )
-            {
-                H5Z_filter_t filtn=options->filter_g[k].filtn;
-                switch (filtn)
-                {
-                case H5Z_FILTER_NONE:
-                    printf(" Uncompress all\n");
-                    break;
-                case H5Z_FILTER_SHUFFLE:
-                case H5Z_FILTER_FLETCHER32:
-                    printf(" All with %s\n",get_sfilter(filtn));
-                    break;
-                case H5Z_FILTER_SZIP:
-                case H5Z_FILTER_DEFLATE:
-                    printf(" All with %s, parameter %d\n",
-                        get_sfilter(filtn),
-                        options->filter_g[k].cd_values[0]);
-                    break;
-                default:
-                    break;
-                } /* k */
-            };
-        }
-    } /* verbose */
-
-    for ( i = 0; i < options->op_tbl->nelems; i++)
-    {
-        pack_info_t pack  = options->op_tbl->objs[i];
-        char*       name  = pack.path;
-
-        for ( j=0; j<pack.nfilters; j++)
-        {
-            if (options->verbose)
-            {
-                printf(" <%s> with %s filter\n",
-                    name,
-                    get_sfilter(pack.filter[j].filtn));
-            }
-
-            has_cp=1;
-
-        } /* j */
-    } /* i */
-
-    if (options->all_filter==1 && has_cp)
-    {
-        error_msg("invalid compression input: 'all' option\
+		return -1;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * objects to filter
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (options->verbose && have_request(options) /* only print if requested */) {
+		printf("Objects to apply filter are...\n");
+		if (options->all_filter == 1) {
+			for (k = 0; k < options->n_filter_g; k++) {
+				H5Z_filter_t filtn = options->filter_g[k].filtn;
+				switch (filtn) {
+				case H5Z_FILTER_NONE:
+					printf(" Uncompress all\n");
+					break;
+				case H5Z_FILTER_SHUFFLE:
+				case H5Z_FILTER_FLETCHER32:
+					printf(" All with %s\n", get_sfilter(filtn));
+					break;
+				case H5Z_FILTER_SZIP:
+				case H5Z_FILTER_DEFLATE:
+					printf(" All with %s, parameter %d\n", get_sfilter(filtn),
+							options->filter_g[k].cd_values[0]);
+					break;
+				default:
+					printf(" User Defined %d\n", filtn);
+					break;
+				} /* k */
+			};
+		}
+	} /* verbose */
+
+	for (i = 0; i < options->op_tbl->nelems; i++) {
+		pack_info_t pack = options->op_tbl->objs[i];
+		char* name = pack.path;
+
+		for (j = 0; j < pack.nfilters; j++) {
+			if (options->verbose) {
+				printf(" <%s> with %s filter\n", name,
+						get_sfilter(pack.filter[j].filtn));
+			}
+
+			has_cp = 1;
+
+		} /* j */
+	} /* i */
+
+	if (options->all_filter == 1 && has_cp) {
+		error_msg(
+				"invalid compression input: 'all' option\
                             is present with other objects\n");
-        return -1;
-    }
-
-    /*-------------------------------------------------------------------------
-    * check options for the latest format
-    *-------------------------------------------------------------------------
-    */
-
-    if (options->grp_compact < 0)
-    {
-        error_msg("invalid maximum number of links to store as header messages\n");
-        return -1;
-    }
-    if (options->grp_indexed < 0)
-    {
-        error_msg("invalid minimum number of links to store in the indexed format\n");
-        return -1;
-    }
-    if (options->grp_indexed > options->grp_compact)
-    {
-        error_msg("minimum indexed size is greater than the maximum compact size\n");
-        return -1;
-    }
-    for (i=0; i<8; i++)
-    {
-        if (options->msg_size[i]<0)
-        {
-            error_msg("invalid shared message size\n");
-            return -1;
-        }
-    }
-
-
-    /*--------------------------------------------------------------------------------
-    * verify new user userblock options; file name must be present
-    *---------------------------------------------------------------------------------
-    */
-    if ( options->ublock_filename != NULL && options->ublock_size == 0 )
-    {
-        if ( options->verbose )
-        {
-            printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
-                options->ublock_filename);
-            options->ublock_size = 1024;
-        }
-    }
-
-    if ( options->ublock_filename == NULL && options->ublock_size != 0 )
-    {
-        error_msg("file name missing for user block\n",
-            options->ublock_filename);
-        return -1;
-    }
-
-
-    /*--------------------------------------------------------------------------------
-    * verify alignment options; threshold is zero default but alignment not
-    *---------------------------------------------------------------------------------
-    */
-
-    if ( options->alignment == 0 && options->threshold != 0 )
-    {
-        error_msg("alignment for H5Pset_alignment missing\n");
-        return -1;
-    }
-
-    return 0;
+		return -1;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * check options for the latest format
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (options->grp_compact < 0) {
+		error_msg(
+				"invalid maximum number of links to store as header messages\n");
+		return -1;
+	}
+	if (options->grp_indexed < 0) {
+		error_msg(
+				"invalid minimum number of links to store in the indexed format\n");
+		return -1;
+	}
+	if (options->grp_indexed > options->grp_compact) {
+		error_msg(
+				"minimum indexed size is greater than the maximum compact size\n");
+		return -1;
+	}
+	for (i = 0; i < 8; i++) {
+		if (options->msg_size[i] < 0) {
+			error_msg("invalid shared message size\n");
+			return -1;
+		}
+	}
+
+	/*--------------------------------------------------------------------------------
+	 * verify new user userblock options; file name must be present
+	 *---------------------------------------------------------------------------------
+	 */
+	if (options->ublock_filename != NULL && options->ublock_size == 0) {
+		if (options->verbose) {
+			printf(
+					"Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
+					options->ublock_filename);
+			options->ublock_size = 1024;
+		}
+	}
+
+	if (options->ublock_filename == NULL && options->ublock_size != 0) {
+		error_msg("file name missing for user block\n",
+				options->ublock_filename);
+		return -1;
+	}
+
+	/*--------------------------------------------------------------------------------
+	 * verify alignment options; threshold is zero default but alignment not
+	 *---------------------------------------------------------------------------------
+	 */
+
+	if (options->alignment == 0 && options->threshold != 0) {
+		error_msg("alignment for H5Pset_alignment missing\n");
+		return -1;
+	}
+
+	return 0;
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: check_objects
-*
-* Purpose: locate all HDF5 objects in the file and compare with user
-*  supplied list
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: September, 23, 2003
-*
-*-------------------------------------------------------------------------
-*/
-static int check_objects(const char* fname,
-                         pack_opt_t *options)
-{
-    hid_t         fid;
-    unsigned int  i;
-    trav_table_t  *travt = NULL;
-
-    /* nothing to do */
-    if(options->op_tbl->nelems == 0)
-        return 0;
-
-    /*-------------------------------------------------------------------------
-    * open the file
-    *-------------------------------------------------------------------------
-    */
-    if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
-    {
-        printf("<%s>: %s\n", fname, H5FOPENERROR );
-        return -1;
-    }
-
-    /*-------------------------------------------------------------------------
-    * get the list of objects in the file
-    *-------------------------------------------------------------------------
-    */
-
-    /* init table */
-    trav_table_init(&travt);
-
-    /* get the list of objects in the file */
-    if(h5trav_gettable(fid, travt) < 0)
-        goto out;
-
-    /*-------------------------------------------------------------------------
-    * compare with user supplied list
-    *-------------------------------------------------------------------------
-    */
-
-    if(options->verbose)
-        printf("Opening file <%s>. Searching for objects to modify...\n", fname);
-
-    for(i = 0; i < options->op_tbl->nelems; i++)
-    {
-        char* name=options->op_tbl->objs[i].path;
-        if(options->verbose)
-            printf(" <%s>",name);
-
-        /* the input object names are present in the file and are valid */
-        if(h5trav_getindext(name, travt) < 0)
-        {
-            error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
-                (options->verbose?"\n":""),name,fname);
-            goto out;
-        }
-        if(options->verbose)
-            printf("...Found\n");
-
-        /* check for extra filter conditions */
-        switch(options->op_tbl->objs[i].filter->filtn)
-        {
-            /* chunk size must be smaller than pixels per block */
-        case H5Z_FILTER_SZIP:
-            {
-                int      j;
-                hsize_t  csize = 1;
-                unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
-                hsize_t  dims[H5S_MAX_RANK];
-                int      rank;
-                hid_t    did;
-                hid_t    sid;
-
-                if(options->op_tbl->objs[i].chunk.rank > 0) {
-                    rank = options->op_tbl->objs[i].chunk.rank;
-                    for(j = 0; j < rank; j++)
-                        csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
-                }
-                else {
-                    if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
-                        goto out;
-                    if((sid = H5Dget_space(did)) < 0)
-                        goto out;
-                    if((rank = H5Sget_simple_extent_ndims(sid)) < 0)
-                        goto out;
-                    HDmemset(dims, 0, sizeof dims);
-                    if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
-                        goto out;
-                    for(j = 0; j < rank; j++)
-                        csize *= dims[j];
-                    if(H5Sclose(sid) < 0)
-                        goto out;
-                    if(H5Dclose(did) < 0)
-                        goto out;
-                }
-
-                if (csize < ppb ) {
-                    printf(" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
-                    goto out;
-                }
-            }
-            break;
-        default:
-            break;
-        }
-    } /* i */
-
-    /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-    H5Fclose(fid);
-    trav_table_free(travt);
-    return 0;
+ * Function: check_objects
+ *
+ * Purpose: locate all HDF5 objects in the file and compare with user
+ *  supplied list
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_objects(const char* fname, pack_opt_t *options) {
+	hid_t fid;
+	unsigned int i;
+	trav_table_t *travt = NULL;
+
+	/* nothing to do */
+	if (options->op_tbl->nelems == 0)
+		return 0;
+
+	/*-------------------------------------------------------------------------
+	 * open the file
+	 *-------------------------------------------------------------------------
+	 */
+	if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
+			< 0) {
+		printf("<%s>: %s\n", fname, H5FOPENERROR);
+		return -1;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * get the list of objects in the file
+	 *-------------------------------------------------------------------------
+	 */
+
+	/* init table */
+	trav_table_init(&travt);
+
+	/* get the list of objects in the file */
+	if (h5trav_gettable(fid, travt) < 0)
+		goto out;
+
+	/*-------------------------------------------------------------------------
+	 * compare with user supplied list
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (options->verbose)
+		printf("Opening file <%s>. Searching for objects to modify...\n",
+				fname);
+
+	for (i = 0; i < options->op_tbl->nelems; i++) {
+		char* name = options->op_tbl->objs[i].path;
+		if (options->verbose)
+			printf(" <%s>", name);
+
+		/* the input object names are present in the file and are valid */
+		if (h5trav_getindext(name, travt) < 0) {
+			error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
+					(options->verbose ? "\n" : ""), name, fname);
+			goto out;
+		}
+		if (options->verbose)
+			printf("...Found\n");
+
+		/* check for extra filter conditions */
+		switch (options->op_tbl->objs[i].filter->filtn) {
+		/* chunk size must be smaller than pixels per block */
+		case H5Z_FILTER_SZIP:
+			{
+				int j;
+				hsize_t csize = 1;
+				unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
+				hsize_t dims[H5S_MAX_RANK];
+				int rank;
+				hid_t did;
+				hid_t sid;
+
+				if (options->op_tbl->objs[i].chunk.rank > 0) {
+					rank = options->op_tbl->objs[i].chunk.rank;
+					for (j = 0; j < rank; j++)
+						csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+				}
+				else {
+					if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+						goto out;
+					if ((sid = H5Dget_space(did)) < 0)
+						goto out;
+					if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
+						goto out;
+					HDmemset(dims, 0, sizeof dims);
+					if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+						goto out;
+					for (j = 0; j < rank; j++)
+						csize *= dims[j];
+					if (H5Sclose(sid) < 0)
+						goto out;
+					if (H5Dclose(did) < 0)
+						goto out;
+				}
+
+				if (csize < ppb) {
+					printf(
+							" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
+					goto out;
+				}
+			}
+			break;
+		default:
+			break;
+		}
+	} /* i */
+
+	/*-------------------------------------------------------------------------
+	 * close
+	 *-------------------------------------------------------------------------
+	 */
+	H5Fclose(fid);
+	trav_table_free(travt);
+	return 0;
 
 out:
-    H5Fclose(fid);
-    trav_table_free(travt);
-    return -1;
+	H5Fclose(fid);
+	trav_table_free(travt);
+	return -1;
 }
 
+/*-------------------------------------------------------------------------
+ * Function: have_request
+ *
+ * Purpose: check if a filter or layout was requested
+ *
+ * Return: 1 yes, 0 no
+ *
+ * Date: May, 24, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int have_request(pack_opt_t *options) {
 
+	if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+		return 1;
 
-
-
-/*-------------------------------------------------------------------------
-* Function: have_request
-*
-* Purpose: check if a filter or layout was requested
-*
-* Return: 1 yes, 0 no
-*
-* Date: May, 24, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int have_request(pack_opt_t *options)
-{
-
-    if (options->all_filter || options->all_layout || options->op_tbl->nelems)
-        return 1;
-
-    return 0;
+	return 0;
 
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: get_sfilter
-*
-* Purpose: return the filter as a string name
-*
-* Return: name of filter, exit on error
-*
-*-------------------------------------------------------------------------
-*/
-
-static const char* get_sfilter(H5Z_filter_t filtn)
-{
-    if (filtn==H5Z_FILTER_NONE)
-        return "NONE";
-    else if (filtn==H5Z_FILTER_DEFLATE)
-        return "GZIP";
-    else if (filtn==H5Z_FILTER_SZIP)
-        return "SZIP";
-    else if (filtn==H5Z_FILTER_SHUFFLE)
-        return "SHUFFLE";
-    else if (filtn==H5Z_FILTER_FLETCHER32)
-        return "FLETCHER32";
-    else if (filtn==H5Z_FILTER_NBIT)
-        return "NBIT";
-    else if (filtn==H5Z_FILTER_SCALEOFFSET)
-        return "SOFF";
-    else {
-        error_msg("input error in filter type\n");
-        HDexit(EXIT_FAILURE);
-    }
+ * Function: get_sfilter
+ *
+ * Purpose: return the filter as a string name
+ *
+ * Return: name of filter, exit on error
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static const char* get_sfilter(H5Z_filter_t filtn) {
+	if (filtn == H5Z_FILTER_NONE)
+		return "NONE";
+	else if (filtn == H5Z_FILTER_DEFLATE)
+		return "GZIP";
+	else if (filtn == H5Z_FILTER_SZIP)
+		return "SZIP";
+	else if (filtn == H5Z_FILTER_SHUFFLE)
+		return "SHUFFLE";
+	else if (filtn == H5Z_FILTER_FLETCHER32)
+		return "FLETCHER32";
+	else if (filtn == H5Z_FILTER_NBIT)
+		return "NBIT";
+	else if (filtn == H5Z_FILTER_SCALEOFFSET)
+		return "SOFF";
+	else
+		return "UD";
 }
 
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 81a883d..250121e 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -133,14 +133,13 @@ typedef struct named_dt_t {
 extern "C" {
 #endif
 
-int h5repack           (const char* infile, const char* outfile, pack_opt_t *options);
-int h5repack_addfilter (const char* str, pack_opt_t *options);
-int h5repack_addlayout (const char* str, pack_opt_t *options);
-int h5repack_init      (pack_opt_t *options, int verbose);
-int h5repack_end       (pack_opt_t *options);
-int h5repack_verify    (const char *fname,pack_opt_t *options);
-int h5repack_cmp_pl   (const char *fname1,
-                        const char *fname2);
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options);
+int h5repack_addfilter(const char* str, pack_opt_t *options);
+int h5repack_addlayout(const char* str, pack_opt_t *options);
+int h5repack_init(pack_opt_t *options, int verbose);
+int h5repack_end(pack_opt_t *options);
+int h5repack_verify(const char *out_fname, pack_opt_t *options);
+int h5repack_cmp_pl(const char *fname1, const char *fname2);
 
 /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() 
  * and struct named_dt_t were located in h5repack_copy.c as static prior to 
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 2a17436..583b6ef 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -124,6 +124,8 @@ $SRC_H5REPACK_TESTFILES/h5repack.info
 $SRC_H5REPACK_TESTFILES/deflate_limit.h5repack_layout.h5.ddl
 $SRC_H5REPACK_TESTFILES/h5repack_layout.h5.ddl
 $SRC_H5REPACK_TESTFILES/h5repack_filters.h5.tst
+$SRC_H5REPACK_TESTFILES/h5repack_layout.h5-plugin_test.ddl
+$SRC_H5REPACK_TESTFILES/plugin_test.h5repack_layout.h5.tst
 "
 
 #
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index b2a8641..63b5373 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -1,36 +1,36 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* 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.     *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * 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.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
 #include "h5tools.h"
 #include "h5tools_utils.h"
 
 /*-------------------------------------------------------------------------
-* typedefs
-*-------------------------------------------------------------------------
-*/
+ * typedefs
+ *-------------------------------------------------------------------------
+ */
 
 /*-------------------------------------------------------------------------
-* globals
-*-------------------------------------------------------------------------
-*/
+ * globals
+ *-------------------------------------------------------------------------
+ */
 
 /*-------------------------------------------------------------------------
-* macros
-*-------------------------------------------------------------------------
-*/
+ * macros
+ *-------------------------------------------------------------------------
+ */
 
 /* size of buffer/# of bytes to xfer at a time when copying userblock */
 #define USERBLOCK_XFER_SIZE     512     
@@ -48,1658 +48,1597 @@
         } \
     } H5E_END_TRY; \
 }
-   
+
 /*-------------------------------------------------------------------------
-* local functions
-*-------------------------------------------------------------------------
-*/
-static int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
-static void  print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
-static int   do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
-static int   copy_user_block(const char *infile, const char *outfile, hsize_t size);
+ * local functions
+ *-------------------------------------------------------------------------
+ */
+static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+		size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
+static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
+static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+		pack_opt_t *options);
+static int copy_user_block(const char *infile, const char *outfile,
+		hsize_t size);
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
-static void  print_user_block(const char *filename, hid_t fid);
+static void print_user_block(const char *filename, hid_t fid);
 #endif
 static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
 
 /* get the major number from the error stack. */
-static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata)
-{
-    if (err_desc) 
-        *((int *)udata) = err_desc->maj_num;
-        
-    return 0;
+static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
+	if (err_desc)
+		*((int *) udata) = err_desc->maj_num;
+
+	return 0;
 }
 
 /*-------------------------------------------------------------------------
-* Function: copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modification:
-*   Peter Cao, June 13, 2007
-*   Add "-L, --latest" and other options to pack a file with the latest file format
-*
-*   Peter Cao, September 25, 2007
-*   Copy user block when repacking a file
-*
-*   Pedro Vicente, August 20, 2008
-*   Add a user block to file if requested
-*
-*-------------------------------------------------------------------------
-*/
-
-int copy_objects(const char* fnamein,
-                 const char* fnameout,
-                 pack_opt_t *options)
-{
-    hid_t         fidin;
-    hid_t         fidout = -1;
-    trav_table_t  *travt = NULL;
-    hsize_t       ub_size = 0;        /* size of user block */
-    hid_t         fcpl = H5P_DEFAULT; /* file creation property list ID */
-    hid_t         fapl = H5P_DEFAULT; /* file access property list ID */
-
-    /*-------------------------------------------------------------------------
-    * open input file
-    *-------------------------------------------------------------------------
-    */
-    if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0)
-    {
-        error_msg("<%s>: %s\n", fnamein, H5FOPENERROR );
-        goto out;
-    }
-
-    /* get user block size */
-    {
-        hid_t fcpl_in; /* file creation property list ID for input file */
-
-        if((fcpl_in = H5Fget_create_plist(fidin)) < 0)
-        {
-            error_msg("failed to retrieve file creation property list\n");
-            goto out;
-        }
-
-        if(H5Pget_userblock(fcpl_in, &ub_size) < 0)
-        {
-            error_msg("failed to retrieve userblock size\n");
-            goto out;
-        }
-
-        if(H5Pclose(fcpl_in) < 0)
-        {
-            error_msg("failed to close property list\n");
-            goto out;
-        }
-    }
-
-    /* Check if we need to create a non-default file creation property list */
-    if(options->latest || ub_size > 0)
-    {
-        /* Create file creation property list */
-        if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
-        {
-            error_msg("fail to create a file creation property list\n");
-            goto out;
-        }
-
-        if(ub_size > 0)
-        {
-            if(H5Pset_userblock(fcpl, ub_size) < 0)
-            {
-                error_msg("failed to set non-default userblock size\n");
-                goto out;
-            }
-        }
-
-        if(options->latest)
-        {
-            unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
-
-            /* Adjust group creation parameters for root group */
-            /* (So that it is created in "dense storage" form) */
-            if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
-            {
-                error_msg("fail to adjust group creation parameters for root group\n");
-                goto out;
-            }
-
-            for(i = 0; i < 5; i++)
-            {
-                if(options->msg_size[i] > 0)
-                {
-                    switch(i)
-                    {
-                    case 0:
-                        mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
-                        break;
-
-                    case 1:
-                        mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
-                        break;
-
-                    case 2:
-                        mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
-                        break;
-
-                    case 3:
-                        mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
-                        break;
-
-                    case 4:
-                        mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
-                        break;
-                    default:
-                        break;
-                    } /* end switch */
-                    min_mesg_sizes[nindex] = (unsigned)options->msg_size[i];
-
-                    nindex++;
-                } /* end if */
-            } /* end for */
-
-            if(nindex > 0)
-            {
-                if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
-                {
-                    error_msg("fail to set the number of shared object header message indexes\n");
-                    goto out;
-                }
-
-                /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
-                for(i = 0; i < (nindex - 1); i++)
-                {
-                    if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
-                        error_msg("fail to configure the specified shared object header message index\n");
-                        goto out;
-                    } /* end if */
-                } /* end for */
-            } /* if (nindex>0) */
-
-            /* Create file access property list */
-            if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-            {
-                error_msg("Could not create file access property list\n");
-                goto out;
-            } /* end if */
-
-            if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
-            {
-                error_msg("Could not set property for using latest version of the format\n");
-                goto out;
-            } /* end if */
-        } /* end if */
-    } /* end if */
+ * Function: copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modification:
+ *   Peter Cao, June 13, 2007
+ *   Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ *   Peter Cao, September 25, 2007
+ *   Copy user block when repacking a file
+ *
+ *   Pedro Vicente, August 20, 2008
+ *   Add a user block to file if requested
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) {
+	hid_t fidin;
+	hid_t fidout = -1;
+	trav_table_t *travt = NULL;
+	hsize_t ub_size = 0; /* size of user block */
+	hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
+	hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+
+	/*-------------------------------------------------------------------------
+	 * open input file
+	 *-------------------------------------------------------------------------
+	 */
+	if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL,
+			(size_t) 0)) < 0) {
+		error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
+		goto out;
+	}
+
+	/* get user block size and file space strategy/threshold */
+	{
+		hid_t fcpl_in; /* file creation property list ID for input file */
+
+		if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
+			error_msg("failed to retrieve file creation property list\n");
+			goto out;
+		}
+
+		if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
+			error_msg("failed to retrieve userblock size\n");
+			goto out;
+		}
+
+		if (H5Pclose(fcpl_in) < 0) {
+			error_msg("failed to close property list\n");
+			goto out;
+		}
+	}
+
+	/* Check if we need to create a non-default file creation property list */
+	if (options->latest || ub_size > 0) {
+		/* Create file creation property list */
+		if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+			error_msg("fail to create a file creation property list\n");
+			goto out;
+		}
+
+		if (ub_size > 0) {
+			if (H5Pset_userblock(fcpl, ub_size) < 0) {
+				error_msg("failed to set non-default userblock size\n");
+				goto out;
+			}
+		}
+
+		if (options->latest) {
+			unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
+
+			/* Adjust group creation parameters for root group */
+			/* (So that it is created in "dense storage" form) */
+			if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
+					(unsigned) options->grp_indexed) < 0) {
+				error_msg(
+						"fail to adjust group creation parameters for root group\n");
+				goto out;
+			}
+
+			for (i = 0; i < 5; i++) {
+				if (options->msg_size[i] > 0) {
+					switch (i) {
+					case 0:
+						mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
+						break;
+
+					case 1:
+						mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
+						break;
+
+					case 2:
+						mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
+						break;
+
+					case 3:
+						mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
+						break;
+
+					case 4:
+						mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
+						break;
+					default:
+						break;
+					} /* end switch */
+					min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
+
+					nindex++;
+				} /* end if */
+			} /* end for */
+
+			if (nindex > 0) {
+				if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
+					error_msg(
+							"fail to set the number of shared object header message indexes\n");
+					goto out;
+				}
+
+				/* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
+				for (i = 0; i < (nindex - 1); i++) {
+					if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i],
+							min_mesg_sizes[i]) < 0) {
+						error_msg(
+								"fail to configure the specified shared object header message index\n");
+						goto out;
+					} /* end if */
+				} /* end for */
+			} /* if (nindex>0) */
+
+			/* Create file access property list */
+			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+				error_msg("Could not create file access property list\n");
+				goto out;
+			} /* end if */
+
+			if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+				error_msg(
+						"Could not set property for using latest version of the format\n");
+				goto out;
+			} /* end if */
+		} /* end if */
+	} /* end if */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
-    print_user_block(fnamein, fidin);
+	print_user_block(fnamein, fidin);
 #endif
 
-    /*-------------------------------------------------------------------------
-    * set the new user userblock options in the FCPL (before H5Fcreate )
-    *-------------------------------------------------------------------------
-    */
-    if ( options->ublock_size > 0 )
-    {
-        /* either use the FCPL already created or create a new one */
-        if(fcpl == H5P_DEFAULT)
-        {
-            /* create a file creation property list */
-            if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
-            {
-                error_msg("fail to create a file creation property list\n");
-                goto out;
-            }
-        }
-
-        /* set user block size */
-        if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
-        {
-            error_msg("failed to set userblock size\n");
-            goto out;
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * set alignment options
-    *-------------------------------------------------------------------------
-    */
-    if (  options->alignment > 0 )
-    {
-        /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT)
-        {
-            /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-            {
-                error_msg("Could not create file access property list\n");
-                goto out;
-            }
-        }
-
-        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
-        {
-            error_msg("failed to set alignment\n");
-            goto out;
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * set metadata block size option
-    *-------------------------------------------------------------------------
-    */
-    if ( options->meta_block_size > 0 )
-    {
-        /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT)
-        {
-            /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-            {
-                error_msg("Could not create file access property list\n");
-                goto out;
-            }
-        }
-
-        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
-        {
-            error_msg("failed to set metadata block size\n");
-            goto out;
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * create the output file
-    *-------------------------------------------------------------------------
-    */
-    if(options->verbose)
-        printf("Making file <%s>...\n",fnameout);
-
-    if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0)
-    {
-        error_msg("<%s>: Could not create file\n", fnameout );
-        goto out;
-    }
-
-
-    /*-------------------------------------------------------------------------
-    * write a new user block if requested
-    *-------------------------------------------------------------------------
-    */
-    if ( options->ublock_size > 0  )
-    {
-        if ( copy_user_block( options->ublock_filename, fnameout, options->ublock_size) < 0 )
-        {
-            error_msg("Could not copy user block. Exiting...\n");
-            goto out;
-
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * get list of objects
-    *-------------------------------------------------------------------------
-    */
-
-    /* init table */
-    trav_table_init(&travt);
-
-    /* get the list of objects in the file */
-    if(h5trav_gettable(fidin, travt) < 0)
-        goto out;
-
-    /*-------------------------------------------------------------------------
-    * do the copy
-    *-------------------------------------------------------------------------
-    */
-    if(do_copy_objects(fidin, fidout, travt, options) < 0)
-    {
-        error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        goto out;
-    } /* end if */
-
-    /*-------------------------------------------------------------------------
-    * do the copy of referenced objects
-    * and create hard links
-    *-------------------------------------------------------------------------
-    */
-    if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 )
-    {
-        printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        goto out;
-    }
-
-    /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-
-    if(fapl > 0)
-        H5Pclose(fapl);
-
-    if(fcpl > 0)
-        H5Pclose(fcpl);
-
-    H5Fclose(fidin);
-    H5Fclose(fidout);
-
-    /* free table */
-    trav_table_free(travt);
-    travt = NULL;
-
-    /*-------------------------------------------------------------------------
-    * write only the input file user block if there is no user block file input
-    *-------------------------------------------------------------------------
-    */
-
-    if( ub_size > 0 && options->ublock_size == 0 )
-    {
-        if ( copy_user_block(fnamein, fnameout, ub_size) < 0 )
-        {
-            error_msg("Could not copy user block. Exiting...\n");
-            goto out;
-
-        }
-    }
-
-    return 0;
-
-    /*-------------------------------------------------------------------------
-    * out
-    *-------------------------------------------------------------------------
-    */
+	/*-------------------------------------------------------------------------
+	 * set the new user userblock options in the FCPL (before H5Fcreate )
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->ublock_size > 0) {
+		/* either use the FCPL already created or create a new one */
+		if (fcpl == H5P_DEFAULT) {
+			/* create a file creation property list */
+			if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+				error_msg("fail to create a file creation property list\n");
+				goto out;
+			}
+		}
+
+		/* set user block size */
+		if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
+			error_msg("failed to set userblock size\n");
+			goto out;
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * set alignment options
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->alignment > 0) {
+		/* either use the FAPL already created or create a new one */
+		if (fapl == H5P_DEFAULT) {
+			/* create a file access property list */
+			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+				error_msg("Could not create file access property list\n");
+				goto out;
+			}
+		}
+
+		if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
+			error_msg("failed to set alignment\n");
+			goto out;
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * set metadata block size option
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->meta_block_size > 0) {
+		/* either use the FAPL already created or create a new one */
+		if (fapl == H5P_DEFAULT) {
+			/* create a file access property list */
+			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+				error_msg("Could not create file access property list\n");
+				goto out;
+			}
+		}
+
+		if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
+			error_msg("failed to set metadata block size\n");
+			goto out;
+		}
+	}
+
+
+	/*-------------------------------------------------------------------------
+	 * create the output file
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->verbose)
+		printf("Making file <%s>...\n", fnameout);
+
+	if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
+		error_msg("<%s>: Could not create file\n", fnameout);
+		goto out;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * write a new user block if requested
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->ublock_size > 0) {
+		if (copy_user_block(options->ublock_filename, fnameout,
+				options->ublock_size) < 0) {
+			error_msg("Could not copy user block. Exiting...\n");
+			goto out;
+
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * get list of objects
+	 *-------------------------------------------------------------------------
+	 */
+
+	/* init table */
+	trav_table_init(&travt);
+
+	/* get the list of objects in the file */
+	if (h5trav_gettable(fidin, travt) < 0)
+		goto out;
+
+	/*-------------------------------------------------------------------------
+	 * do the copy
+	 *-------------------------------------------------------------------------
+	 */
+	if (do_copy_objects(fidin, fidout, travt, options) < 0) {
+		error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+		goto out;
+	} /* end if */
+
+	/*-------------------------------------------------------------------------
+	 * do the copy of referenced objects
+	 * and create hard links
+	 *-------------------------------------------------------------------------
+	 */
+	if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
+		printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein,
+				fnameout);
+		goto out;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * close
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (fapl > 0)
+		H5Pclose(fapl);
+
+	if (fcpl > 0)
+		H5Pclose(fcpl);
+
+	H5Fclose(fidin);
+	H5Fclose(fidout);
+
+	/* free table */
+	trav_table_free(travt);
+	travt = NULL;
+
+	/*-------------------------------------------------------------------------
+	 * write only the input file user block if there is no user block file input
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (ub_size > 0 && options->ublock_size == 0) {
+		if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
+			error_msg("Could not copy user block. Exiting...\n");
+			goto out;
+
+		}
+	}
+
+	return 0;
+
+	/*-------------------------------------------------------------------------
+	 * out
+	 *-------------------------------------------------------------------------
+	 */
 
 out:
-    H5E_BEGIN_TRY
-    {
-        H5Pclose(fapl);
-        H5Pclose(fcpl);
-        H5Fclose(fidin);
-        H5Fclose(fidout);
-    } H5E_END_TRY;
-    if(travt)
-        trav_table_free(travt);
-
-    return -1;
+	H5E_BEGIN_TRY
+		{
+			H5Pclose(fapl);
+			H5Pclose(fcpl);
+			H5Fclose(fidin);
+			H5Fclose(fidout);
+		}H5E_END_TRY;
+	if (travt)
+		trav_table_free(travt);
+
+	return -1;
 }
 
 /*-------------------------------------------------------------------------
-* Function: Get_hyperslab
-*
-* Purpose: Calulate a hyperslab from a dataset for higher performance.
-*          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
-*          Return the hyperslab dimentions and size in byte.
-*
-* Return: 0 - SUCCEED, -1 FAILED
-*
-* Parameters:
-*   dcpl_id : [IN] dataset creation property.
-*   rank_dset : [IN] dataset rank
-*   dims_dset[] : [IN] dataset dimentions
-*   size_datum : [IN] size of a data element in byte
-*   dims_hslab[] : [OUT] calculated hyperslab dimentions
-*   * hslab_nbytes_p : [OUT] total byte of the hyperslab
-*
-* Programmer: Jonathan Kim
-* Date: Feburary, 2012
-* Update:
-*   The hyperslab calucation would be depend on if the dataset is chunked
-*   or not. 
-*
-*   There care 3 conditions to cover:
-*   1. If chunked and a chunk fits in buffer, each chunk would be a unit of
-*      collection and the boundary would be dataset's dims.
-*   2. If chunked but a chunk doesn't fit in buffer, each data element would
-*      be a unit of collection and the boundary would be the chunk itself.
-*   3. If not chunked, each data element would be a unit of collection and
-*      the boundary would be dataset's dims.
-*
-*   The calulation starts from the last dimention (h5dump dims output).
-*
-* Note:
-*   Added for JIRA HDFFV-7862. 
-*-----------------------------------------*/
-
-int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], 
-                   size_t size_datum, 
-                   hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
-{
-    int status = 0;
-    int k;
-    H5D_layout_t dset_layout;
-    int rank_chunk;
-    hsize_t dims_chunk[H5S_MAX_RANK];
-    hsize_t size_chunk=1;
-    hsize_t nchunk_fit;  /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t ndatum_fit;  /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t chunk_dims_map[H5S_MAX_RANK];  /* mapped chunk dimentions */
-    hsize_t hs_dims_map[H5S_MAX_RANK];  /* mapped hyperslab dimentions */
-    hsize_t hslab_nbytes;  /* size of hyperslab in byte */
-
-    /* init to set as size of a data element */
-    hslab_nbytes = size_datum;
-
-    /* get layout of dataset */
-    dset_layout =  H5Pget_layout(dcpl_id);
-
-   /* if dataset is chunked */
-    if ( dset_layout == H5D_CHUNKED )
-    {
-        /* get chunk dims */
-        rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
-        if (rank_chunk < 0)
-        {
-            status = -1;
-            goto out;
-        }
-
-        for (k = rank_dset; k > 0; --k)
-            size_chunk *= dims_chunk[k-1];
-
-        /* figure out how many chunks can fit in the hyperslab buffer */
-        nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
-             
-
-        /* 1. if a chunk fit in hyperslab buffer */
-        if (nchunk_fit >= 1)
-        {
-            /* Calulate a hyperslab that contains as many chunks that can fit
-             * in hyperslab buffer. Hyperslab will be increased starting from 
-             * the last dimention of the dataset (see h5dump's dims output).
-             * The calculation boundary is dataset dims.
-             * In the loop, used mapping from a datum to a chunk to figure out
-             * chunk based hyperslab.
-             */
-            for (k = rank_dset; k > 0; --k)
-            {
-                /* map dataset dimentions with a chunk dims */
-                chunk_dims_map[k-1]= dims_dset[k-1] / dims_chunk[k-1];
-
-                /* if reminder exist, increse by 1 to cover partial edge chunks */
-                if (dims_dset[k-1] % dims_chunk[k-1] > 0)
-                    chunk_dims_map[k-1]++;
-
-                /* get mapped hyperslab dims */
-                hs_dims_map[k-1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
-
-                /* prepare next round */
-                nchunk_fit = nchunk_fit / chunk_dims_map[k-1];
-                /* if a chunk is bigger than the rest of buffer */
-                if (nchunk_fit == 0) 
-                    nchunk_fit=1;
-
-                /* get hyperslab dimentions as unmapping to actual size */
-                dims_hslab[k-1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
-
-                /* calculate total size for the hyperslab */
-                hslab_nbytes *= dims_hslab[k-1];
-            }
-        }
-        /* 2. if a chunk is bigger than hyperslab buffer */
-        else
-        {
-            /* Calulate a hyperslab that contains as many data elements that 
-             * can fit in hyperslab buffer. Hyperslab will be increased 
-             * starting from the last dimention of the chunk (see h5dump's dims
-             * output).
-             * The calculation boundary is a chunk dims.
-             */
-            for (k = rank_dset; k > 0; --k)
-            {
-                ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
-                /* if a datum is bigger than rest of buffer */
-                if ( ndatum_fit == 0)
-                    ndatum_fit = 1;
-                /* get hyperslab dimentions within a chunk boundary */
-                dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
-
-                /* calculate total size for the hyperslab */
-                hslab_nbytes *= dims_hslab[k - 1];
-
-                if (hslab_nbytes <= 0)
-                {
-                     status = -1;
-                     goto out;
-                }
-            }
-        }
-    }
-    /* 3. if dataset is not chunked */
-    else
-    {
-        /* Calulate a hyperslab that contains as many data elements that can
-         * fit in hyperslab buffer. Hyperslab will be increased starting from
-         * the last dimention of the dataset (see h5dump's dims output).
-         * The calculation boundary is dataset dims.
-         */
-        for (k = rank_dset; k > 0; --k)
-        {
-            ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
-            /* if a datum is bigger than rest of buffer */
-            if ( ndatum_fit == 0) 
-                ndatum_fit = 1;
-            /* get hyperslab dimentions within dataset boundary */
-            dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
-
-            /* calculate total size for the hyperslab */
-            hslab_nbytes *= dims_hslab[k - 1];
-
-            if (hslab_nbytes <= 0)
-            {
-                 status = -1;
-                 goto out;
-            }
-        }
-    }
-
-    /* pass out the hyperslab size*/
-    *hslab_nbytes_p = hslab_nbytes;
+ * Function: Get_hyperslab
+ *
+ * Purpose: Calulate a hyperslab from a dataset for higher performance.
+ *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
+ *          Return the hyperslab dimentions and size in byte.
+ *
+ * Return: 0 - SUCCEED, -1 FAILED
+ *
+ * Parameters:
+ *   dcpl_id : [IN] dataset creation property.
+ *   rank_dset : [IN] dataset rank
+ *   dims_dset[] : [IN] dataset dimentions
+ *   size_datum : [IN] size of a data element in byte
+ *   dims_hslab[] : [OUT] calculated hyperslab dimentions
+ *   * hslab_nbytes_p : [OUT] total byte of the hyperslab
+ *
+ * Programmer: Jonathan Kim
+ * Date: Feburary, 2012
+ * Update:
+ *   The hyperslab calucation would be depend on if the dataset is chunked
+ *   or not.
+ *
+ *   There care 3 conditions to cover:
+ *   1. If chunked and a chunk fits in buffer, each chunk would be a unit of
+ *      collection and the boundary would be dataset's dims.
+ *   2. If chunked but a chunk doesn't fit in buffer, each data element would
+ *      be a unit of collection and the boundary would be the chunk itself.
+ *   3. If not chunked, each data element would be a unit of collection and
+ *      the boundary would be dataset's dims.
+ *
+ *   The calulation starts from the last dimention (h5dump dims output).
+ *
+ * Note:
+ *   Added for JIRA HDFFV-7862.
+ *-----------------------------------------*/
+
+int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+		size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) {
+	int status = 0;
+	int k;
+	H5D_layout_t dset_layout;
+	int rank_chunk;
+	hsize_t dims_chunk[H5S_MAX_RANK];
+	hsize_t size_chunk = 1;
+	hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+	hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+	hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
+	hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
+	hsize_t hslab_nbytes; /* size of hyperslab in byte */
+
+	/* init to set as size of a data element */
+	hslab_nbytes = size_datum;
+
+	/* get layout of dataset */
+	dset_layout = H5Pget_layout(dcpl_id);
+
+	/* if dataset is chunked */
+	if (dset_layout == H5D_CHUNKED) {
+		/* get chunk dims */
+		rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
+		if (rank_chunk < 0) {
+			status = -1;
+			goto out;
+		}
+
+		for (k = rank_dset; k > 0; --k)
+			size_chunk *= dims_chunk[k - 1];
+
+		/* figure out how many chunks can fit in the hyperslab buffer */
+		nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
+
+		/* 1. if a chunk fit in hyperslab buffer */
+		if (nchunk_fit >= 1) {
+			/* Calulate a hyperslab that contains as many chunks that can fit
+			 * in hyperslab buffer. Hyperslab will be increased starting from
+			 * the last dimention of the dataset (see h5dump's dims output).
+			 * The calculation boundary is dataset dims.
+			 * In the loop, used mapping from a datum to a chunk to figure out
+			 * chunk based hyperslab.
+			 */
+			for (k = rank_dset; k > 0; --k) {
+				/* map dataset dimentions with a chunk dims */
+				chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
+
+				/* if reminder exist, increse by 1 to cover partial edge chunks */
+				if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
+					chunk_dims_map[k - 1]++;
+
+				/* get mapped hyperslab dims */
+				hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
+
+				/* prepare next round */
+				nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
+				/* if a chunk is bigger than the rest of buffer */
+				if (nchunk_fit == 0)
+					nchunk_fit = 1;
+
+				/* get hyperslab dimentions as unmapping to actual size */
+				dims_hslab[k - 1] =
+						MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
+
+				/* calculate total size for the hyperslab */
+				hslab_nbytes *= dims_hslab[k - 1];
+			}
+		}
+		/* 2. if a chunk is bigger than hyperslab buffer */
+		else {
+			/* Calulate a hyperslab that contains as many data elements that
+			 * can fit in hyperslab buffer. Hyperslab will be increased
+			 * starting from the last dimention of the chunk (see h5dump's dims
+			 * output).
+			 * The calculation boundary is a chunk dims.
+			 */
+			for (k = rank_dset; k > 0; --k) {
+				ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+				/* if a datum is bigger than rest of buffer */
+				if (ndatum_fit == 0)
+					ndatum_fit = 1;
+				/* get hyperslab dimentions within a chunk boundary */
+				dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
+
+				/* calculate total size for the hyperslab */
+				hslab_nbytes *= dims_hslab[k - 1];
+
+				if (hslab_nbytes <= 0) {
+					status = -1;
+					goto out;
+				}
+			}
+		}
+	}
+	/* 3. if dataset is not chunked */
+	else {
+		/* Calulate a hyperslab that contains as many data elements that can
+		 * fit in hyperslab buffer. Hyperslab will be increased starting from
+		 * the last dimention of the dataset (see h5dump's dims output).
+		 * The calculation boundary is dataset dims.
+		 */
+		for (k = rank_dset; k > 0; --k) {
+			ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+			/* if a datum is bigger than rest of buffer */
+			if (ndatum_fit == 0)
+				ndatum_fit = 1;
+			/* get hyperslab dimentions within dataset boundary */
+			dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
+
+			/* calculate total size for the hyperslab */
+			hslab_nbytes *= dims_hslab[k - 1];
+
+			if (hslab_nbytes <= 0) {
+				status = -1;
+				goto out;
+			}
+		}
+	}
+
+	/* pass out the hyperslab size*/
+	*hslab_nbytes_p = hslab_nbytes;
 
 out:
-    return status;
+	return status;
 }
 
 /*-------------------------------------------------------------------------
-* Function: do_copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modifications:
-*
-*  July 2004:     Introduced the extra EC or NN option for SZIP
-*
-*  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
-*                  with the requested filter, use the input one
-*
-*  October 2006:  Read/write using the file type by default.
-*
-*  October 2006:  Read by hyperslabs for big datasets.
-*
-*  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
-*  i.e., if the memory needed to read a dataset is greater than this limit,
-*  then hyperslab I/O is done instead of one operation I/O
-*  For each dataset, the memory needed is calculated according to
-*
-*  memory needed = number of elements * size of each element
-*
-*  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-*  are done
-*
-*  H5Dread( input_dataset1 )
-*  H5Dread( input_dataset2 )
-*
-*  with all elements in the datasets selected. If the memory needed is greater than
-*  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-*  a strip mine is defined for each dimension k (a strip mine is defined as a
-*  hyperslab whose size is memory manageable) according to the formula
-*
-*  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
-*
-*  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
-*  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
-*  mine size k is simply defined as its dimension k, but for larger datasets the
-*  hyperslab size is still memory manageable.
-*  a cycle is done until the number of elements in the dataset is reached. In each
-*  iteration, two parameters are defined for the function H5Sselect_hyperslab,
-*  the start and size of each hyperslab, according to
-*
-*  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
-*
-*  where hyperslab_offset [k] is initially set to zero, and later incremented in
-*  hyperslab_size[k] offsets. The reason for the operation
-*
-*  dimension[k] - hyperslab_offset[k]
-*
-*  in (2) is that, when using the strip mine size, it assures that the "remaining" part
-*  of the dataset that does not fill an entire strip mine is processed.
-*
-*  November 2006:  Use H5Ocopy in the copy of objects. The logic for using
-*   H5Ocopy or not is if a change of filters or layout is requested by the user
-*   then use read/write else use H5Ocopy.
-*
-* May, 1, 2008: Add a printing of the compression ratio of old size / new size
-*
-* Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
-* Programmer: Jonathan Kim
-*
-*  A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
-*  i.e., if the memory needed to read a dataset is greater than this limit,
-*  then hyperslab I/O is done instead of one operation I/O
-*  For each dataset, the memory needed is calculated according to
-*
-*  memory needed = number of elements * size of each element
-*
-*  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-*  are done
-*
-*  H5Dread( input_dataset )
-*  H5Dwrite( output_dataset )
-*
-*  with all elements in the datasets selected. If the memory needed is greater than
-*  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-*  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
-*  2. Calculate the hyperslab selections as the selection is moving forward. 
-*     Selection would be same as the hyperslab except for the remaining edge portion
-*     of the dataset. The code take care of the remaining portion if exist.
-*
-*-------------------------------------------------------------------------
-*/
-
-int do_copy_objects(hid_t fidin,
-                    hid_t fidout,
-                    trav_table_t *travt,
-                    pack_opt_t *options) /* repack options */
+ * Function: do_copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modifications:
+ *
+ *  July 2004:     Introduced the extra EC or NN option for SZIP
+ *
+ *  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
+ *                  with the requested filter, use the input one
+ *
+ *  October 2006:  Read/write using the file type by default.
+ *
+ *  October 2006:  Read by hyperslabs for big datasets.
+ *
+ *  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
+ *  i.e., if the memory needed to read a dataset is greater than this limit,
+ *  then hyperslab I/O is done instead of one operation I/O
+ *  For each dataset, the memory needed is calculated according to
+ *
+ *  memory needed = number of elements * size of each element
+ *
+ *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ *  are done
+ *
+ *  H5Dread( input_dataset1 )
+ *  H5Dread( input_dataset2 )
+ *
+ *  with all elements in the datasets selected. If the memory needed is greater than
+ *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ *  a strip mine is defined for each dimension k (a strip mine is defined as a
+ *  hyperslab whose size is memory manageable) according to the formula
+ *
+ *  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
+ *
+ *  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
+ *  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
+ *  mine size k is simply defined as its dimension k, but for larger datasets the
+ *  hyperslab size is still memory manageable.
+ *  a cycle is done until the number of elements in the dataset is reached. In each
+ *  iteration, two parameters are defined for the function H5Sselect_hyperslab,
+ *  the start and size of each hyperslab, according to
+ *
+ *  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
+ *
+ *  where hyperslab_offset [k] is initially set to zero, and later incremented in
+ *  hyperslab_size[k] offsets. The reason for the operation
+ *
+ *  dimension[k] - hyperslab_offset[k]
+ *
+ *  in (2) is that, when using the strip mine size, it assures that the "remaining" part
+ *  of the dataset that does not fill an entire strip mine is processed.
+ *
+ *  November 2006:  Use H5Ocopy in the copy of objects. The logic for using
+ *   H5Ocopy or not is if a change of filters or layout is requested by the user
+ *   then use read/write else use H5Ocopy.
+ *
+ * May, 1, 2008: Add a printing of the compression ratio of old size / new size
+ *
+ * Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
+ * Programmer: Jonathan Kim
+ *
+ *  A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
+ *  i.e., if the memory needed to read a dataset is greater than this limit,
+ *  then hyperslab I/O is done instead of one operation I/O
+ *  For each dataset, the memory needed is calculated according to
+ *
+ *  memory needed = number of elements * size of each element
+ *
+ *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ *  are done
+ *
+ *  H5Dread( input_dataset )
+ *  H5Dwrite( output_dataset )
+ *
+ *  with all elements in the datasets selected. If the memory needed is greater than
+ *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ *  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
+ *  2. Calculate the hyperslab selections as the selection is moving forward.
+ *     Selection would be same as the hyperslab except for the remaining edge portion
+ *     of the dataset. The code take care of the remaining portion if exist.
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+		pack_opt_t *options) /* repack options */
 {
-    hid_t    grp_in = -1;       /* group ID */
-    hid_t    grp_out = -1;      /* group ID */
-    hid_t    dset_in = -1;      /* read dataset ID */
-    hid_t    dset_out = -1;     /* write dataset ID */
-    hid_t    gcpl_in = -1;      /* group creation property list */
-    hid_t    gcpl_out = -1;     /* group creation property list */
-    hid_t    type_in = -1;      /* named type ID */
-    hid_t    type_out = -1;     /* named type ID */
-    hid_t    dcpl_in = -1;      /* dataset creation property list ID */
-    hid_t    dcpl_out = -1;     /* dataset creation property list ID */
-    hid_t    f_space_id = -1;   /* file space ID */
-    hid_t    ftype_id = -1;     /* file type ID */
-    hid_t    wtype_id = -1;     /* read/write type ID */
-    named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
-    size_t   msize;             /* size of type */
-    hsize_t  nelmts;            /* number of elements in dataset */
-    H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
-    int      rank;              /* rank of dataset */
-    hsize_t  dims[H5S_MAX_RANK];/* dimensions of dataset */
-    hsize_t  dsize_in;          /* input dataset size before filter */
-    hsize_t  dsize_out;         /* output dataset size after filter */
-    int      apply_s;           /* flag for apply filter to small dataset sizes */
-    int      apply_f;           /* flag for apply filter to return error on H5Dcreate */
-    void     *buf=NULL;         /* buffer for raw data */
-    void     *hslab_buf=NULL;   /* hyperslab buffer for raw data */
-    int      has_filter;        /* current object has a filter */
-    int      req_filter;        /* there was a request for a filter */
-    int      req_obj_layout=0;  /* request layout to current object */
-    unsigned crt_order_flags;   /* group creation order flag */
-    unsigned i;
-    unsigned u;
-    int      is_ref=0;
-    htri_t   is_named;
-    hbool_t  limit_maxdims;
-    hsize_t size_dset;
-
-
-    /*-------------------------------------------------------------------------
-    * copy the suppplied object list
-    *-------------------------------------------------------------------------
-    */
-
-    if (options->verbose)
-    {
-        printf("-----------------------------------------\n");
-        printf(" Type     Filter (Compression)     Name\n");
-        printf("-----------------------------------------\n");
-    }
-
-    for ( i = 0; i < travt->nobjs; i++)
-    {
-        /* init variables per obj */
-        buf = NULL;
-        limit_maxdims = FALSE;
-
-        switch ( travt->objs[i].type )
-        {
-
-        case H5TRAV_TYPE_UNKNOWN:
-            HDassert(0);
-            break;
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_GROUP
-            *-------------------------------------------------------------------------
-            */
-        case H5TRAV_TYPE_GROUP:
-
-            if (options->verbose)
-            {
-                printf(FORMAT_OBJ,"group",travt->objs[i].name );
-            }
-
-            /* open input group */
-            if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                goto error;
-
-            /* get input group creation property list */
-            if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
-                goto error;
-
-            /* query and set the group creation properties */
-            if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
-                goto error;
-
-            /* set up group creation property list */
-            if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
-                goto error;
-
-            if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
-                goto error;
-
-
-            /*-------------------------------------------------------------------------
-            * the root is a special case, we get an ID for the root group
-            * and copy its attributes using that ID
-            *-------------------------------------------------------------------------
-            */
-            if(HDstrcmp(travt->objs[i].name, "/") == 0)
-            {
-                if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
-                    goto error;
-            }
-
-            else
-            {
-
-                if (options->grp_compact>0 || options->grp_indexed>0)
-                {
-                    if(H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
-                        goto error;
-                }
-
-                if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
-                    goto error;
-
-            }
-
-            /*-------------------------------------------------------------------------
-            * copy attrs
-            *-------------------------------------------------------------------------
-            */
-            if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
-                goto error;
-
-
-            if(H5Pclose(gcpl_out) < 0)
-                goto error;
-            if(H5Pclose(gcpl_in) < 0)
-                goto error;
-            if(H5Gclose(grp_out) < 0)
-                goto error;
-            if(H5Gclose(grp_in) < 0)
-                goto error;
-
-            break;
-
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_DATASET
-            *-------------------------------------------------------------------------
-            */
-        case H5TRAV_TYPE_DATASET:
-
-            has_filter = 0;
-            req_filter = 0;
-
-            /* check if global filters were requested */
-            if ( options->n_filter_g )
-                req_filter = 1;
-
-            /* check if filters were requested for individual objects */
-            for (u = 0; u < options->op_tbl->nelems; u++) {
-
-                if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
-                        if (options->op_tbl->objs[u].filter->filtn > 0) {
-                            req_filter = 1;
-                        }
-                }
-            }
-
-            /* check if layout change requested individual object */
-            if (options->layout_g != H5D_LAYOUT_ERROR)
-            {
-	            pack_info_t *pckinfo;
-	            /* any dataset is specified */
-	            if (options->op_tbl->nelems > 0)
-	            {
-	                /* check if object exist */
-	                pckinfo = options_get_object (travt->objs[i].name, options->op_tbl);
-	                if (pckinfo)
-	                {
-	                    req_obj_layout = 1;
-	                }
-	            }
-            }
-
-            /* early detection of references */
-            if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                goto error;
-            if((ftype_id = H5Dget_type(dset_in)) < 0)
-                goto error;
-            if(H5T_REFERENCE == H5Tget_class(ftype_id))
-                is_ref = 1;
-
-            /* Check if the datatype is committed */
-            if((is_named = H5Tcommitted(ftype_id)) < 0)
-                goto error;
-            if(is_named)
-                if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
-                    goto error;
-
-            if(H5Tclose(ftype_id) < 0)
-                goto error;
-            if(H5Dclose(dset_in) < 0)
-                goto error;
-
-
-            /*-------------------------------------------------------------------------
-            * check if we should use H5Ocopy or not
-            * if there is a request for filters/layout, we read/write the object
-            * otherwise we do a copy using H5Ocopy
-            *-------------------------------------------------------------------------
-            */
-            if ( options->op_tbl->nelems  ||
-                options->all_filter == 1 ||
-                options->all_layout == 1 ||
-                is_ref ||
-                is_named)
-            {
-
-                int      j;
-
-                if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
-                if((f_space_id = H5Dget_space(dset_in)) < 0)
-                    goto error;
-                if((ftype_id = H5Dget_type(dset_in)) < 0)
-                    goto error;
-                if((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
-                    goto error;
-                if((dcpl_out = H5Pcopy(dcpl_in)) < 0)
-                    goto error;
-                if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
-                    goto error;
-                HDmemset(dims, 0, sizeof dims);
-                if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
-                    goto error;
-
-                if(H5Dget_space_status(dset_in, &space_status) < 0)
-                    goto error;
-
-                nelmts = 1;
-                for(j = 0; j < rank; j++)
-                    nelmts *= dims[j];
-
-                /* wtype_id will have already been set if using a named dtype */
-                if(!is_named) {
-                    if(options->use_native == 1)
-                        wtype_id = h5tools_get_native_type(ftype_id);
-                    else
-                        wtype_id = H5Tcopy(ftype_id);
-                } /* end if */
-
-                if((msize = H5Tget_size(wtype_id)) == 0)
-                    goto error;
-
-                /* size of current dset */
-                size_dset = nelmts * msize;
-
-                /*-------------------------------------------------------------------------
-                * check if the dataset creation property list has filters that
-                * are not registered in the current configuration
-                * 1) the external filters GZIP and SZIP might not be available
-                * 2) the internal filters might be turned off
-                *-------------------------------------------------------------------------
-                */
-                if (h5tools_canreadf((travt->objs[i].name),dcpl_in)==1)
-                {
-                    apply_s=1;
-                    apply_f=1;
-
-                    /*-------------------------------------------------------------------------
-                    * references are a special case
-                    * we cannot just copy the buffers, but instead we recreate the reference
-                    * in a second traversal of the output file
-                    *-------------------------------------------------------------------------
-                    */
-                    if (H5T_REFERENCE!=H5Tget_class(wtype_id))
-                    {
-                        /* get the storage size of the input dataset */
-                        dsize_in=H5Dget_storage_size(dset_in);
-
-                        /* check for small size datasets (less than 1k) except 
-                         * changing to COMPACT. For the reference, COMPACT is limited
-                         * by size 64K by library.
-                         */
-                        if (options->layout_g != H5D_COMPACT)
-                        {
-                            if ( size_dset < options->min_comp )
-                                apply_s=0;
-                        }
-
-                        /* apply the filter */
-                        if (apply_s)
-                        {
-                            if (apply_filters(travt->objs[i].name,
-                                rank,
-                                dims,
-                                msize,
-                                dcpl_out,
-                                options,
-                                &has_filter) < 0)
-                                goto error;
-                        }
-
-                    /* only if layout change requested for entire file or 
-                     * individual obj */
-                    if (options->all_layout > 0 || req_obj_layout == 1)
-                        /*------------------------------------------------- 
-                         * Unset the unlimited max dims if convert to other
-                         * than chunk layouts, because unlimited max dims
-                         * only can be applied to chunk layout. 
-                         * Also perform only for targeted dataset
-                         * Also check for size limit to convert to compact
-                         *-------------------------------------------------*/
-                        if (options->layout_g != H5D_CHUNKED) 
-                        {
-                            /* any dataset is specified */
-                            if (options->op_tbl->nelems > 0)
-                            {
-                                /* if current obj match specified obj */
-                                if (options_get_object (travt->objs[i].name, options->op_tbl))
-                                    limit_maxdims = TRUE;
-                            }
-                            else /* no dataset is specified */
-                            {
-                                limit_maxdims = TRUE;
-                            }
-                        
-                            /* if convert to COMPACT */
-                            if (options->layout_g == H5D_COMPACT)
-                            {
-                                /* should be smaller than 64K */
-                                if ( size_dset > MAX_COMPACT_DSIZE )
-                                    limit_maxdims = FALSE;
-                            }
-                        
-                            /* unset unlimited max dims */
-                            if (limit_maxdims)
-                                H5Sset_extent_simple( f_space_id, rank, dims, NULL );
-                        }
-
-                        /*-------------------------------------------------------------------------
-                        * create the output dataset;
-                        * disable error checking in case the dataset cannot be created with the
-                        * modified dcpl; in that case use the original instead
-                        *-------------------------------------------------------------------------
-                        */
-                        H5E_BEGIN_TRY {
-                            dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
-                        } H5E_END_TRY;
-
-                        if(dset_out == FAIL)
-                        {
-                            if(options->verbose)
-                                printf(" warning: could not create dataset <%s>. Applying original settings\n",
-                                travt->objs[i].name);
-
-                            if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
-                                goto error;
-                            apply_f = 0;
-                        }
-
-                        /*-------------------------------------------------------------------------
-                        * read/write
-                        *-------------------------------------------------------------------------
-                        */
-                        if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED)
-                        {
-                            size_t need = (size_t)(nelmts * msize);  /* bytes needed */
-
-                            /* have to read the whole dataset if there is only one element in the dataset */
-                            if(need < H5TOOLS_MALLOCSIZE)
-                                buf = HDmalloc(need);
-
-                            if(buf != NULL) {
-                               /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-                                CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-                               
-                                /* Check if we have VL data in the dataset's
-                                 * datatype that must be reclaimed */
-                                if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
-                                    if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
-                                        goto error;
-                            }
-                            else /* possibly not enough memory, read/write by hyperslabs */
-                            {
-                                size_t        p_type_nbytes = msize; /*size of memory type */
-                                hsize_t       p_nelmts = nelmts;     /*total elements */
-                                hsize_t       elmtno;                /*counter  */
-                                int           carry;                 /*counter carry value */
-                                unsigned int  vl_data = 0;           /*contains VL datatypes */
-
-                                /* hyperslab info */
-                                hsize_t       hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
-                                hsize_t       hslab_nbytes;             /*bytes per hyperslab */
-                                hsize_t       hslab_nelmts;             /*elements per hyperslab*/
-                                hid_t         hslab_space;              /*hyperslab data space */
-
-                                /* hyperslab selection info */
-                                hsize_t       hs_sel_offset[H5S_MAX_RANK];/* selection offset */
-                                hsize_t       hs_sel_count[H5S_MAX_RANK];  /* selection count */
-                                hsize_t       hs_select_nelmts;    /* selected elements */
-                                hsize_t       zero[8];                /*vector of zeros */
-                                int           k;
-                                H5D_layout_t dset_layout;
-                                hid_t    dcpl_tmp = -1;     /* dataset creation property list ID */
-
-                                /* check if we have VL data in the dataset's datatype */
-                                if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
-                                    vl_data = TRUE;
-
-
-                                /* check first if writing dataset is chunked, 
-                                 * if so use its chunk layout for better performance. */
-                                dset_layout = H5Pget_layout(dcpl_out);
-                                if (dset_layout == H5D_CHUNKED)
-                                   dcpl_tmp = dcpl_out;  /* writing dataset */
-                                else /* if reading dataset is chunked */
-                                {
-                                   dset_layout = H5Pget_layout(dcpl_in);
-                                   if (dset_layout == H5D_CHUNKED)
-                                       dcpl_tmp = dcpl_in;  /* reading dataset */
-                                }
-
-                                /* get hyperslab dims and size in byte */
-                                if(Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
-                                    goto error;
-
-                                hslab_buf = HDmalloc((size_t)hslab_nbytes);
-
-                                hslab_nelmts = hslab_nbytes / p_type_nbytes;
-                                hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
-
-                                /* the hyperslab selection loop */
-                                HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
-                                HDmemset(zero, 0, sizeof zero);
-
-                                for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts)
-                                {
-                                    if (rank > 0)
-                                    {
-                                        /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
-                                         */
-                                        for (k = 0, hs_select_nelmts = 1; k < rank; k++)
-                                        {
-                                            /* MIN() is used to get the remaining edge portion if exist. 
-                                             * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
-                                            hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
-                                            hs_select_nelmts *= hs_sel_count[k];
-                                        }
-
-                                        if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
-                                            goto error;
-                                        if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
-                                            goto error;
-                                    }
-                                    else
-                                    {
-                                        H5Sselect_all(f_space_id);
-                                        H5Sselect_all(hslab_space);
-                                        hs_select_nelmts = 1;
-                                    } /* rank */
-
-                                    /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                    CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-                                    CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-
-                                    /* reclaim any VL memory, if necessary */
-                                    if(vl_data)
-                                        H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
-
-                                    /* calculate the next hyperslab offset */
-                                    for (k = rank, carry = 1; k > 0 && carry; --k)
-                                    {
-                                        hs_sel_offset[k - 1] += hs_sel_count[k - 1];
-                                        /* if reached the end of a dim */
-                                        if (hs_sel_offset[k - 1] == dims[k - 1])
-                                            hs_sel_offset[k - 1] = 0;
-                                        else
-                                            carry = 0;
-                                    } /* k */
-                                } /* elmtno */
-
-                                H5Sclose(hslab_space);
-                                /* free */
-                                if (hslab_buf!=NULL)
-                                {
-                                    HDfree(hslab_buf);
-                                    hslab_buf=NULL;
-                                }
-                            } /* hyperslab read */
-                        } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
-
-                        /*-------------------------------------------------------------------------
-                        * amount of compression used
-                        *-------------------------------------------------------------------------
-                        */
-                        if (options->verbose)
-                        {
-                            double ratio=0;
-
-                            /* only print the compression ration if there was a filter request */
-                            if (apply_s && apply_f && req_filter)
-                            {
-                                /* get the storage size of the output dataset */
-                                dsize_out=H5Dget_storage_size(dset_out);
-
-                                /* compression ratio = uncompressed size /  compressed size */
-                                if (dsize_out!=0)
-                                    ratio = (double) dsize_in / (double) dsize_out;
-
-                                print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
-                            }
-                            else
-                                print_dataset_info(dcpl_in,travt->objs[i].name,ratio,0);
-
-                            /* print a message that the filter was not applied
-                            (in case there was a filter)
-                            */
-                            if ( has_filter && apply_s == 0 )
-                                printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
-                                travt->objs[i].name,
-                                (int)options->min_comp);
-
-                            if ( has_filter && apply_f == 0 )
-                                printf(" <warning: could not apply the filter to %s>\n",
-                                travt->objs[i].name);
-
-                        } /* verbose */
-
-                        /*-------------------------------------------------------------------------
-                        * copy attrs
-                        *-------------------------------------------------------------------------
-                        */
-                        if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
-                            goto error;
-                        /*close */
-                        if (H5Dclose(dset_out) < 0)
-                            goto error;
-
-                    }/*!H5T_REFERENCE*/
-                }/*h5tools_canreadf*/
-
-
-                /*-------------------------------------------------------------------------
-                * close
-                *-------------------------------------------------------------------------
-                */
-                if (H5Tclose(ftype_id) < 0)
-                    goto error;
-                if (H5Tclose(wtype_id) < 0)
-                    goto error;
-                if (H5Pclose(dcpl_in) < 0)
-                    goto error;
-                if (H5Pclose(dcpl_out) < 0)
-                    goto error;
-                if (H5Sclose(f_space_id) < 0)
-                    goto error;
-                if (H5Dclose(dset_in) < 0)
-                    goto error;
-
-            }
-            /*-------------------------------------------------------------------------
-            * we do not have request for filter/chunking use H5Ocopy instead
-            *-------------------------------------------------------------------------
-            */
-            else
-            {
-                hid_t        pid;
-
-                /* create property to pass copy options */
-                if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
-                    goto error;
-
-                /* set options for object copy */
-                if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
-                    goto error;
-
-                /*-------------------------------------------------------------------------
-                * do the copy
-                *-------------------------------------------------------------------------
-                */
-
-                if(H5Ocopy(fidin,          /* Source file or group identifier */
-                    travt->objs[i].name,       /* Name of the source object to be copied */
-                    fidout,                    /* Destination file or group identifier  */
-                    travt->objs[i].name,       /* Name of the destination object  */
-                    pid,                       /* Properties which apply to the copy   */
-                    H5P_DEFAULT) < 0)            /* Properties which apply to the new hard link */
-                    goto error;
-
-                /* close property */
-                if(H5Pclose(pid) < 0)
-                    goto error;
-
-
-                /*-------------------------------------------------------------------------
-                * copy attrs manually
-                *-------------------------------------------------------------------------
-                */
-                if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
-                if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
-                if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
-                    goto error;
-                if(H5Dclose(dset_in) < 0)
-                    goto error;
-                if(H5Dclose(dset_out) < 0)
-                    goto error;
-
-
-                if (options->verbose)
-                    printf(FORMAT_OBJ,"dset",travt->objs[i].name );
-
-
-            } /* end do we have request for filter/chunking */
-
-            break;
-
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_NAMED_DATATYPE
-            *-------------------------------------------------------------------------
-            */
-        case H5TRAV_TYPE_NAMED_DATATYPE:
-
-            if(options->verbose)
-                printf(FORMAT_OBJ, "type", travt->objs[i].name);
-
-            if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                goto error;
-
-            /* Copy the datatype anonymously */
-            if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
-                    travt, options)) < 0)
-                goto error;
-
-            /* Link in to group structure */
-            if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
-                    H5P_DEFAULT, H5P_DEFAULT) < 0)
-                goto error;
-
-            /*-------------------------------------------------------------------------
-            * copy attrs
-            *-------------------------------------------------------------------------
-            */
-            if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
-                goto error;
-
-            if(H5Tclose(type_in) < 0)
-                goto error;
-            if(H5Tclose(type_out) < 0)
-                goto error;
-
-
-
-            break;
-
-
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_LINK
-            * H5TRAV_TYPE_UDLINK
-            *
-            * Only handles external links; H5Lcopy will fail for other UD link types
-            * since we don't have creation or copy callbacks for them.
-            *-------------------------------------------------------------------------
-            */
-
-        case H5TRAV_TYPE_LINK:
-        case H5TRAV_TYPE_UDLINK:
-            {
-
-                if(options->verbose)
-                    printf(FORMAT_OBJ, "link", travt->objs[i].name);
-
-                if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
-                    goto error;
-
-                if (options->verbose)
-                    printf(FORMAT_OBJ,"link",travt->objs[i].name );
-
-            }
-            break;
-
-        default:
-            goto error;
-        } /* switch */
-
-        /* free */
-        if (buf!=NULL)
-        {
-            HDfree(buf);
-            buf=NULL;
-        }
-
-    } /* i */
-
-    /* Finalize (link) the stack of named datatypes (if any) */
-    named_datatype_free(&named_dt_head, 0);
-
-    return 0;
+	hid_t grp_in = -1; /* group ID */
+	hid_t grp_out = -1; /* group ID */
+	hid_t dset_in = -1; /* read dataset ID */
+	hid_t dset_out = -1; /* write dataset ID */
+	hid_t gcpl_in = -1; /* group creation property list */
+	hid_t gcpl_out = -1; /* group creation property list */
+	hid_t type_in = -1; /* named type ID */
+	hid_t type_out = -1; /* named type ID */
+	hid_t dcpl_in = -1; /* dataset creation property list ID */
+	hid_t dcpl_out = -1; /* dataset creation property list ID */
+	hid_t f_space_id = -1; /* file space ID */
+	hid_t ftype_id = -1; /* file type ID */
+	hid_t wtype_id = -1; /* read/write type ID */
+	named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
+	size_t msize; /* size of type */
+	hsize_t nelmts; /* number of elements in dataset */
+	H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
+	int rank; /* rank of dataset */
+	hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+	hsize_t dsize_in; /* input dataset size before filter */
+	hsize_t dsize_out; /* output dataset size after filter */
+	int apply_s; /* flag for apply filter to small dataset sizes */
+	int apply_f; /* flag for apply filter to return error on H5Dcreate */
+	void *buf = NULL; /* buffer for raw data */
+	void *hslab_buf = NULL; /* hyperslab buffer for raw data */
+	int has_filter; /* current object has a filter */
+	int req_filter; /* there was a request for a filter */
+	int req_obj_layout = 0; /* request layout to current object */
+	unsigned crt_order_flags; /* group creation order flag */
+	unsigned i;
+	unsigned u;
+	int is_ref = 0;
+	htri_t is_named;
+	hbool_t limit_maxdims;
+	hsize_t size_dset;
+
+	/*-------------------------------------------------------------------------
+	 * copy the suppplied object list
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (options->verbose) {
+		printf("-----------------------------------------\n");
+		printf(" Type     Filter (Compression)     Name\n");
+		printf("-----------------------------------------\n");
+	}
+
+	for (i = 0; i < travt->nobjs; i++) {
+		/* init variables per obj */
+		buf = NULL;
+		limit_maxdims = FALSE;
+
+		switch (travt->objs[i].type) {
+
+		case H5TRAV_TYPE_UNKNOWN:
+			HDassert(0);
+			break;
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_GROUP
+			 *-------------------------------------------------------------------------
+			 */
+		case H5TRAV_TYPE_GROUP:
+
+			if (options->verbose) {
+				printf(FORMAT_OBJ, "group", travt->objs[i].name);
+			}
+
+			/* open input group */
+			if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+					< 0)
+				goto error;
+
+			/* get input group creation property list */
+			if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+				goto error;
+
+			/* query and set the group creation properties */
+			if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+				goto error;
+
+			/* set up group creation property list */
+			if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+				goto error;
+
+			if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * the root is a special case, we get an ID for the root group
+			 * and copy its attributes using that ID
+			 *-------------------------------------------------------------------------
+			 */
+			if (HDstrcmp(travt->objs[i].name, "/") == 0) {
+				if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+					goto error;
+			}
+			else {
+
+				if (options->grp_compact > 0 || options->grp_indexed > 0) {
+					if (H5Pset_link_phase_change(gcpl_out,
+							(unsigned) options->grp_compact,
+							(unsigned) options->grp_indexed) < 0)
+						goto error;
+				}
+
+				if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name,
+						H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
+					goto error;
+
+			}
+
+			/*-------------------------------------------------------------------------
+			 * copy attrs
+			 *-------------------------------------------------------------------------
+			 */
+			if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
+				goto error;
+
+			if (H5Pclose(gcpl_out) < 0)
+				goto error;
+			if (H5Pclose(gcpl_in) < 0)
+				goto error;
+			if (H5Gclose(grp_out) < 0)
+				goto error;
+			if (H5Gclose(grp_in) < 0)
+				goto error;
+
+			break;
+
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_DATASET
+			 *-------------------------------------------------------------------------
+			 */
+		case H5TRAV_TYPE_DATASET:
+
+			has_filter = 0;
+			req_filter = 0;
+
+			/* check if global filters were requested */
+			if (options->n_filter_g)
+				req_filter = 1;
+
+			/* check if filters were requested for individual objects */
+			for (u = 0; u < options->op_tbl->nelems; u++) {
+
+				if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
+					if (options->op_tbl->objs[u].filter->filtn > 0) {
+						req_filter = 1;
+					}
+				}
+			}
+
+			/* check if layout change requested individual object */
+			if (options->layout_g != H5D_LAYOUT_ERROR) {
+				pack_info_t *pckinfo;
+				/* any dataset is specified */
+				if (options->op_tbl->nelems > 0) {
+					/* check if object exist */
+					pckinfo = options_get_object(travt->objs[i].name,
+							options->op_tbl);
+					if (pckinfo) {
+						req_obj_layout = 1;
+					}
+				}
+			}
+
+			/* early detection of references */
+			if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+					< 0)
+				goto error;
+			if ((ftype_id = H5Dget_type(dset_in)) < 0)
+				goto error;
+			if (H5T_REFERENCE == H5Tget_class(ftype_id))
+				is_ref = 1;
+
+			/* Check if the datatype is committed */
+			if ((is_named = H5Tcommitted(ftype_id)) < 0)
+				goto error;
+			if (is_named)
+				if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+						&named_dt_head, travt, options)) < 0)
+					goto error;
+
+			if (H5Tclose(ftype_id) < 0)
+				goto error;
+			if (H5Dclose(dset_in) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * check if we should use H5Ocopy or not
+			 * if there is a request for filters/layout, we read/write the object
+			 * otherwise we do a copy using H5Ocopy
+			 *-------------------------------------------------------------------------
+			 */
+			if (options->op_tbl->nelems || options->all_filter == 1
+					|| options->all_layout == 1 || is_ref || is_named) {
+
+				int j;
+
+				if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+					goto error;
+				if ((f_space_id = H5Dget_space(dset_in)) < 0)
+					goto error;
+				if ((ftype_id = H5Dget_type(dset_in)) < 0)
+					goto error;
+				if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
+					goto error;
+				if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+					goto error;
+				if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+					goto error;
+				HDmemset(dims, 0, sizeof dims);
+				if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+					goto error;
+
+				if (H5Dget_space_status(dset_in, &space_status) < 0)
+					goto error;
+
+				nelmts = 1;
+				for (j = 0; j < rank; j++)
+					nelmts *= dims[j];
+
+				/* wtype_id will have already been set if using a named dtype */
+				if (!is_named) {
+					if (options->use_native == 1)
+						wtype_id = h5tools_get_native_type(ftype_id);
+					else
+						wtype_id = H5Tcopy(ftype_id);
+				} /* end if */
+
+				if ((msize = H5Tget_size(wtype_id)) == 0)
+					goto error;
+
+				/* size of current dset */
+				size_dset = nelmts * msize;
+
+				/*-------------------------------------------------------------------------
+				 * check if the dataset creation property list has filters that
+				 * are not registered in the current configuration
+				 * 1) the external filters GZIP and SZIP might not be available
+				 * 2) the internal filters might be turned off
+				 *-------------------------------------------------------------------------
+				 */
+				if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
+					apply_s = 1;
+					apply_f = 1;
+
+					/*-------------------------------------------------------------------------
+					 * references are a special case
+					 * we cannot just copy the buffers, but instead we recreate the reference
+					 * in a second traversal of the output file
+					 *-------------------------------------------------------------------------
+					 */
+					if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
+						/* get the storage size of the input dataset */
+						dsize_in = H5Dget_storage_size(dset_in);
+
+						/* check for small size datasets (less than 1k) except
+						 * changing to COMPACT. For the reference, COMPACT is limited
+						 * by size 64K by library.
+						 */
+						if (options->layout_g != H5D_COMPACT) {
+							if (size_dset < options->min_comp)
+								apply_s = 0;
+						}
+
+						/* apply the filter */
+						if (apply_s) {
+							if (apply_filters(travt->objs[i].name, rank, dims,
+									msize, dcpl_out, options, &has_filter) < 0)
+								goto error;
+						}
+
+						/* only if layout change requested for entire file or
+						 * individual obj */
+						if (options->all_layout > 0 || req_obj_layout == 1)
+							/*-------------------------------------------------
+							 * Unset the unlimited max dims if convert to other
+							 * than chunk layouts, because unlimited max dims
+							 * only can be applied to chunk layout.
+							 * Also perform only for targeted dataset
+							 * Also check for size limit to convert to compact
+							 *-------------------------------------------------*/
+							if (options->layout_g != H5D_CHUNKED) {
+								/* any dataset is specified */
+								if (options->op_tbl->nelems > 0) {
+									/* if current obj match specified obj */
+									if (options_get_object(travt->objs[i].name,
+											options->op_tbl))
+										limit_maxdims = TRUE;
+								}
+								else { /* no dataset is specified */
+									limit_maxdims = TRUE;
+								}
+
+								/* if convert to COMPACT */
+								if (options->layout_g == H5D_COMPACT) {
+									/* should be smaller than 64K */
+									if (size_dset > MAX_COMPACT_DSIZE)
+										limit_maxdims = FALSE;
+								}
+
+								/* unset unlimited max dims */
+								if (limit_maxdims)
+									H5Sset_extent_simple(f_space_id, rank, dims,
+											NULL);
+							}
+
+						/*-------------------------------------------------------------------------
+						 * create the output dataset;
+						 * disable error checking in case the dataset cannot be created with the
+						 * modified dcpl; in that case use the original instead
+						 *-------------------------------------------------------------------------
+						 */
+						H5E_BEGIN_TRY
+							{
+								dset_out = H5Dcreate2(fidout,
+										travt->objs[i].name, wtype_id,
+										f_space_id, H5P_DEFAULT, dcpl_out,
+										H5P_DEFAULT);
+							}H5E_END_TRY;
+
+						if (dset_out == FAIL) {
+							if (options->verbose)
+								printf(
+										" warning: could not create dataset <%s>. Applying original settings\n",
+										travt->objs[i].name);
+
+							if ((dset_out = H5Dcreate2(fidout,
+									travt->objs[i].name, wtype_id, f_space_id,
+									H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
+								goto error;
+							apply_f = 0;
+						}
+
+						/*-------------------------------------------------------------------------
+						 * read/write
+						 *-------------------------------------------------------------------------
+						 */
+						if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
+							size_t need = (size_t)(nelmts * msize); /* bytes needed */
+
+							/* have to read the whole dataset if there is only one element in the dataset */
+							if (need < H5TOOLS_MALLOCSIZE)
+								buf = HDmalloc(need);
+
+							if (buf != NULL) {
+								/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+								CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id,
+										H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+								CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id,
+										H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+								/* Check if we have VL data in the dataset's
+								 * datatype that must be reclaimed */
+								if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+									if (H5Dvlen_reclaim(wtype_id, f_space_id,
+											H5P_DEFAULT, buf) < 0)
+										goto error;
+							}
+							else { /* possibly not enough memory, read/write by hyperslabs */
+								size_t p_type_nbytes = msize; /*size of memory type */
+								hsize_t p_nelmts = nelmts; /*total elements */
+								hsize_t elmtno; /*counter  */
+								int carry; /*counter carry value */
+								unsigned int vl_data = 0; /*contains VL datatypes */
+
+								/* hyperslab info */
+								hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
+								hsize_t hslab_nbytes; /*bytes per hyperslab */
+								hsize_t hslab_nelmts; /*elements per hyperslab*/
+								hid_t hslab_space; /*hyperslab data space */
+
+								/* hyperslab selection info */
+								hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
+								hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
+								hsize_t hs_select_nelmts; /* selected elements */
+								hsize_t zero[8]; /*vector of zeros */
+								int k;
+								H5D_layout_t dset_layout;
+								hid_t dcpl_tmp = -1; /* dataset creation property list ID */
+
+								/* check if we have VL data in the dataset's datatype */
+								if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+									vl_data = TRUE;
+
+								/* check first if writing dataset is chunked,
+								 * if so use its chunk layout for better performance. */
+								dset_layout = H5Pget_layout(dcpl_out);
+								if (dset_layout == H5D_CHUNKED)
+									dcpl_tmp = dcpl_out; /* writing dataset */
+								else { /* if reading dataset is chunked */
+									dset_layout = H5Pget_layout(dcpl_in);
+									if (dset_layout == H5D_CHUNKED)
+										dcpl_tmp = dcpl_in; /* reading dataset */
+								}
+
+								/* get hyperslab dims and size in byte */
+								if (Get_hyperslab(dcpl_tmp, rank, dims,
+										p_type_nbytes, hslab_dims,
+										&hslab_nbytes) < 0)
+									goto error;
+
+								hslab_buf = HDmalloc((size_t)hslab_nbytes);
+
+								hslab_nelmts = hslab_nbytes / p_type_nbytes;
+								hslab_space = H5Screate_simple(1, &hslab_nelmts,
+										NULL);
+
+								/* the hyperslab selection loop */
+								HDmemset(hs_sel_offset, 0,
+										sizeof hs_sel_offset);
+								HDmemset(zero, 0, sizeof zero);
+
+								for (elmtno = 0; elmtno < p_nelmts; elmtno +=
+										hs_select_nelmts) {
+									if (rank > 0) {
+										/* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
+										 */
+										for (k = 0, hs_select_nelmts = 1;
+												k < rank; k++) {
+											/* MIN() is used to get the remaining edge portion if exist.
+											 * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+											hs_sel_count[k] =
+													MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
+											hs_select_nelmts *= hs_sel_count[k];
+										}
+
+										if (H5Sselect_hyperslab(f_space_id,
+												H5S_SELECT_SET, hs_sel_offset,
+												NULL, hs_sel_count, NULL) < 0)
+											goto error;
+										if (H5Sselect_hyperslab(hslab_space,
+												H5S_SELECT_SET, zero, NULL,
+												&hs_select_nelmts, NULL) < 0)
+											goto error;
+									}
+									else {
+										H5Sselect_all(f_space_id);
+										H5Sselect_all(hslab_space);
+										hs_select_nelmts = 1;
+									} /* rank */
+
+									/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+									CHECK_H5DRW_ERROR(H5Dread, dset_in,
+											wtype_id, hslab_space, f_space_id,
+											H5P_DEFAULT, hslab_buf);
+									CHECK_H5DRW_ERROR(H5Dwrite, dset_out,
+											wtype_id, hslab_space, f_space_id,
+											H5P_DEFAULT, hslab_buf);
+
+									/* reclaim any VL memory, if necessary */
+									if (vl_data)
+										H5Dvlen_reclaim(wtype_id, hslab_space,
+												H5P_DEFAULT, hslab_buf);
+
+									/* calculate the next hyperslab offset */
+									for (k = rank, carry = 1; k > 0 && carry;
+											--k) {
+										hs_sel_offset[k - 1] += hs_sel_count[k
+												- 1];
+										/* if reached the end of a dim */
+										if (hs_sel_offset[k - 1] == dims[k - 1])
+											hs_sel_offset[k - 1] = 0;
+										else
+											carry = 0;
+									} /* k */
+								} /* elmtno */
+
+								H5Sclose(hslab_space);
+								/* free */
+								if (hslab_buf != NULL) {
+									HDfree(hslab_buf);
+									hslab_buf = NULL;
+								}
+							} /* hyperslab read */
+						} /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+
+						/*-------------------------------------------------------------------------
+						 * amount of compression used
+						 *-------------------------------------------------------------------------
+						 */
+						if (options->verbose) {
+							double ratio = 0;
+
+							/* only print the compression ration if there was a filter request */
+							if (apply_s && apply_f && req_filter) {
+								/* get the storage size of the output dataset */
+								dsize_out = H5Dget_storage_size(dset_out);
+
+								/* compression ratio = uncompressed size /  compressed size */
+								if (dsize_out != 0)
+									ratio = (double) dsize_in
+											/ (double) dsize_out;
+
+								print_dataset_info(dcpl_out,
+										travt->objs[i].name, ratio, 1);
+							}
+							else
+								print_dataset_info(dcpl_in, travt->objs[i].name,
+										ratio, 0);
+
+							/* print a message that the filter was not applied
+							 (in case there was a filter)
+							 */
+							if (has_filter && apply_s == 0)
+								printf(
+										" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+										travt->objs[i].name,
+										(int) options->min_comp);
+
+							if (has_filter && apply_f == 0)
+								printf(
+										" <warning: could not apply the filter to %s>\n",
+										travt->objs[i].name);
+
+						} /* verbose */
+
+						/*-------------------------------------------------------------------------
+						 * copy attrs
+						 *-------------------------------------------------------------------------
+						 */
+						if (copy_attr(dset_in, dset_out, &named_dt_head, travt,
+								options) < 0)
+							goto error;
+						/*close */
+						if (H5Dclose(dset_out) < 0)
+							goto error;
+
+					}/*!H5T_REFERENCE*/
+				}/*h5tools_canreadf*/
+
+				/*-------------------------------------------------------------------------
+				 * close
+				 *-------------------------------------------------------------------------
+				 */
+				if (H5Tclose(ftype_id) < 0)
+					goto error;
+				if (H5Tclose(wtype_id) < 0)
+					goto error;
+				if (H5Pclose(dcpl_in) < 0)
+					goto error;
+				if (H5Pclose(dcpl_out) < 0)
+					goto error;
+				if (H5Sclose(f_space_id) < 0)
+					goto error;
+				if (H5Dclose(dset_in) < 0)
+					goto error;
+
+			}
+			/*-------------------------------------------------------------------------
+			 * we do not have request for filter/chunking use H5Ocopy instead
+			 *-------------------------------------------------------------------------
+			 */
+			else {
+				hid_t pid;
+
+				/* create property to pass copy options */
+				if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
+					goto error;
+
+				/* set options for object copy */
+				if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
+					goto error;
+
+				/*-------------------------------------------------------------------------
+				 * do the copy
+				 *-------------------------------------------------------------------------
+				 */
+
+				if (H5Ocopy(fidin, /* Source file or group identifier */
+				travt->objs[i].name, /* Name of the source object to be copied */
+				fidout, /* Destination file or group identifier  */
+				travt->objs[i].name, /* Name of the destination object  */
+				pid, /* Properties which apply to the copy   */
+				H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
+					goto error;
+
+				/* close property */
+				if (H5Pclose(pid) < 0)
+					goto error;
+
+				/*-------------------------------------------------------------------------
+				 * copy attrs manually
+				 *-------------------------------------------------------------------------
+				 */
+				if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+						< 0)
+					goto error;
+				if ((dset_out = H5Dopen2(fidout, travt->objs[i].name,
+						H5P_DEFAULT)) < 0)
+					goto error;
+				if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options)
+						< 0)
+					goto error;
+				if (H5Dclose(dset_in) < 0)
+					goto error;
+				if (H5Dclose(dset_out) < 0)
+					goto error;
+
+				if (options->verbose)
+					printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+
+			} /* end do we have request for filter/chunking */
+
+			break;
+
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_NAMED_DATATYPE
+			 *-------------------------------------------------------------------------
+			 */
+		case H5TRAV_TYPE_NAMED_DATATYPE:
+
+			if (options->verbose)
+				printf(FORMAT_OBJ, "type", travt->objs[i].name);
+
+			if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+					< 0)
+				goto error;
+
+			/* Copy the datatype anonymously */
+			if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
+					travt, options)) < 0)
+				goto error;
+
+			/* Link in to group structure */
+			if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
+			H5P_DEFAULT, H5P_DEFAULT) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * copy attrs
+			 *-------------------------------------------------------------------------
+			 */
+			if (copy_attr(type_in, type_out, &named_dt_head, travt, options)
+					< 0)
+				goto error;
+
+			if (H5Tclose(type_in) < 0)
+				goto error;
+			if (H5Tclose(type_out) < 0)
+				goto error;
+
+			break;
+
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_LINK
+			 * H5TRAV_TYPE_UDLINK
+			 *
+			 * Only handles external links; H5Lcopy will fail for other UD link types
+			 * since we don't have creation or copy callbacks for them.
+			 *-------------------------------------------------------------------------
+			 */
+
+		case H5TRAV_TYPE_LINK:
+		case H5TRAV_TYPE_UDLINK: {
+
+			if (options->verbose)
+				printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+			if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
+					H5P_DEFAULT, H5P_DEFAULT) < 0)
+				goto error;
+
+			if (options->verbose)
+				printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+		}
+			break;
+
+		default:
+			goto error;
+		} /* switch */
+
+		/* free */
+		if (buf != NULL) {
+			HDfree(buf);
+			buf = NULL;
+		}
+
+	} /* i */
+
+	/* Finalize (link) the stack of named datatypes (if any) */
+	named_datatype_free(&named_dt_head, 0);
+
+	return 0;
 
 error:
-    H5E_BEGIN_TRY {
-        H5Gclose(grp_in);
-        H5Gclose(grp_out);
-        H5Pclose(dcpl_in);
-        H5Pclose(gcpl_in);
-        H5Pclose(gcpl_out);
-        H5Sclose(f_space_id);
-        H5Dclose(dset_in);
-        H5Dclose(dset_out);
-        H5Tclose(ftype_id);
-        H5Tclose(wtype_id);
-        H5Tclose(type_in);
-        H5Tclose(type_out);
-        named_datatype_free(&named_dt_head, 1);
-    } H5E_END_TRY;
-    /* free */
-    if (buf!=NULL)
-        HDfree(buf);
-    if (hslab_buf!=NULL)
-        HDfree(hslab_buf);
-    return -1;
+	H5E_BEGIN_TRY
+		{
+			H5Gclose(grp_in);
+			H5Gclose(grp_out);
+			H5Pclose(dcpl_in);
+			H5Pclose(gcpl_in);
+			H5Pclose(gcpl_out);
+			H5Sclose(f_space_id);
+			H5Dclose(dset_in);
+			H5Dclose(dset_out);
+			H5Tclose(ftype_id);
+			H5Tclose(wtype_id);
+			H5Tclose(type_in);
+			H5Tclose(type_out);
+			named_datatype_free(&named_dt_head, 1);
+		}H5E_END_TRY;
+	/* free */
+	if (buf != NULL)
+		HDfree(buf);
+	if (hslab_buf != NULL)
+		HDfree(hslab_buf);
+	return -1;
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: print_dataset_info
-*
-* Purpose: print name, filters, percentage compression of a dataset
-*
-*-------------------------------------------------------------------------
-*/
-static void print_dataset_info(hid_t dcpl_id,
-                               char *objname,
-                               double ratio,
-                               int pr)
-{
-    char         strfilter[255];
+ * Function: print_dataset_info
+ *
+ * Purpose: print name, filters, percentage compression of a dataset
+ *
+ *-------------------------------------------------------------------------
+ */
+static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
+		int pr) {
+	char strfilter[255];
 #if defined (PRINT_DEBUG )
-    char         temp[255];
+	char temp[255];
 #endif
-    int          nfilters;       /* number of filters */
-    unsigned     filt_flags;     /* filter flags */
-    H5Z_filter_t filtn;          /* filter identification number */
-    unsigned     cd_values[20];  /* filter client data values */
-    size_t       cd_nelmts;      /* filter client number of values */
-    char         f_objname[256];    /* filter objname */
-    int          i;
+	int nfilters; /* number of filters */
+	unsigned filt_flags; /* filter flags */
+	H5Z_filter_t filtn; /* filter identification number */
+	unsigned cd_values[20]; /* filter client data values */
+	size_t cd_nelmts; /* filter client number of values */
+	char f_objname[256]; /* filter objname */
+	int i;
 
+	HDstrcpy(strfilter, "\0");
 
-    HDstrcpy(strfilter,"\0");
+	/* get information about input filters */
+	if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
+		return;
 
-    /* get information about input filters */
-    if((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
-        return;
+	for (i = 0; i < nfilters; i++) {
+		cd_nelmts = NELMTS(cd_values);
 
-    for(i = 0; i < nfilters; i++) {
-        cd_nelmts = NELMTS(cd_values);
+		filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+				cd_values, sizeof(f_objname), f_objname, NULL);
 
-        filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
-            cd_values, sizeof(f_objname), f_objname, NULL);
+		switch (filtn) {
 
-        switch(filtn) {
-        default:
-            break;
+		case H5Z_FILTER_NONE:
+			HDstrcat(strfilter, "NONE ");
+			break;
 
-        case H5Z_FILTER_DEFLATE:
-            HDstrcat(strfilter,"GZIP ");
+		case H5Z_FILTER_DEFLATE:
+			HDstrcat(strfilter, "GZIP ");
 
 #if defined (PRINT_DEBUG)
-            {
-                unsigned level=cd_values[0];
-                sprintf(temp,"(%d)",level);
-                HDstrcat(strfilter,temp);
-            }
+			{
+				unsigned level=cd_values[0];
+				sprintf(temp,"(%d)",level);
+				HDstrcat(strfilter,temp);
+			}
 #endif
-            break;
+			break;
 
-        case H5Z_FILTER_SZIP:
-            HDstrcat(strfilter,"SZIP ");
+		case H5Z_FILTER_SZIP:
+			HDstrcat(strfilter, "SZIP ");
 
 #if defined (PRINT_DEBUG)
-            {
-                unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
-                unsigned ppb=cd_values[1];
-                sprintf(temp,"(%d,",ppb);
-                HDstrcat(strfilter,temp);
-                if (options_mask & H5_SZIP_EC_OPTION_MASK)
-                    HDstrcpy(temp,"EC) ");
-                else if (options_mask & H5_SZIP_NN_OPTION_MASK)
-                    HDstrcpy(temp,"NN) ");
-            }
-            HDstrcat(strfilter,temp);
+			{
+				unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
+				unsigned ppb=cd_values[1];
+				sprintf(temp,"(%d,",ppb);
+				HDstrcat(strfilter,temp);
+				if (options_mask & H5_SZIP_EC_OPTION_MASK)
+				HDstrcpy(temp,"EC) ");
+				else if (options_mask & H5_SZIP_NN_OPTION_MASK)
+				HDstrcpy(temp,"NN) ");
+			}
+			HDstrcat(strfilter,temp);
 
 #endif
 
-            break;
-
-        case H5Z_FILTER_SHUFFLE:
-            HDstrcat(strfilter,"SHUF ");
-            break;
-
-        case H5Z_FILTER_FLETCHER32:
-            HDstrcat(strfilter,"FLET ");
-            break;
-
-        case H5Z_FILTER_NBIT:
-            HDstrcat(strfilter,"NBIT ");
-            break;
-
-        case H5Z_FILTER_SCALEOFFSET:
-            HDstrcat(strfilter,"SCALEOFFSET ");
-            break;
-        } /* switch */
-    }/*i*/
-
-    if(!pr)
-        printf(FORMAT_OBJ,"dset",objname );
-    else
-    {
-        char str[255], temp[28];
-        HDstrcpy(str,"dset     ");
-        HDstrcat(str,strfilter);
-        sprintf(temp,"  (%.3f:1)",ratio);
-        HDstrcat(str,temp);
-        printf(FORMAT_OBJ,str,objname);
-    }
+			break;
+
+		case H5Z_FILTER_SHUFFLE:
+			HDstrcat(strfilter, "SHUF ");
+			break;
+
+		case H5Z_FILTER_FLETCHER32:
+			HDstrcat(strfilter, "FLET ");
+			break;
+
+		case H5Z_FILTER_NBIT:
+			HDstrcat(strfilter, "NBIT ");
+			break;
+
+		case H5Z_FILTER_SCALEOFFSET:
+			HDstrcat(strfilter, "SCALEOFFSET ");
+			break;
+
+		default:
+			HDstrcat(strfilter, "UD ");
+			break;
+		} /* switch */
+	}/*i*/
+
+	if (!pr)
+		printf(FORMAT_OBJ, "dset", objname);
+	else {
+		char str[255], temp[28];
+		HDstrcpy(str, "dset     ");
+		HDstrcat(str, strfilter);
+		sprintf(temp, "  (%.3f:1)", ratio);
+		HDstrcat(str, temp);
+		printf(FORMAT_OBJ, str, objname);
+	}
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: copy_user_block
-*
-* Purpose: copy user block from one file to another
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Peter Cao
-*
-* Date: October, 25, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int
-copy_user_block(const char *infile, const char *outfile, hsize_t size)
-{
-    int infid = -1, outfid = -1;        /* File descriptors */
-    int status = 0;                     /* Return value */
-
-    /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
-    HDassert(size > 0);
-
-    /* Open files */
-    if((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
-        status = -1;
-        goto done;
-    }
-    if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
-        status = -1;
-        goto done;
-    }
-
-    /* Copy the userblock from the input file to the output file */
-    while(size > 0) {
-        ssize_t nread, nbytes;                  /* # of bytes transfered, etc. */
-        char rbuf[USERBLOCK_XFER_SIZE];         /* Buffer for reading */
-        const char *wbuf;                       /* Pointer into buffer, for writing */
-
-        /* Read buffer from source file */
-        if(size > USERBLOCK_XFER_SIZE)
-            nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
-        else
-            nread = HDread(infid, rbuf, (size_t)size);
-        if(nread < 0) {
-            status = -1;
-            goto done;
-        } /* end if */
-
-        /* Write buffer to destination file */
-        /* (compensating for interrupted writes & checking for errors, etc.) */
-        nbytes = nread;
-        wbuf = rbuf;
-        while(nbytes > 0) {
-            ssize_t nwritten;        /* # of bytes written */
-
-            do {
-                nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
-            } while(-1 == nwritten && EINTR == errno);
-            if(-1 == nwritten) { /* error */
-                status = -1;
-                goto done;
-            } /* end if */
-            HDassert(nwritten > 0);
-            HDassert(nwritten <= nbytes);
-
-            /* Update # of bytes left & offset in buffer */
-            nbytes -= nwritten;
-            wbuf += nwritten;
-            HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
-        } /* end while */
-
-        /* Update size of userblock left to transfer */
-        size = size - (hsize_t)nread;
-    } /* end while */
+ * Function: copy_user_block
+ *
+ * Purpose: copy user block from one file to another
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Peter Cao
+ *
+ * Date: October, 25, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int copy_user_block(const char *infile, const char *outfile,
+		hsize_t size) {
+	int infid = -1, outfid = -1; /* File descriptors */
+	int status = 0; /* Return value */
+
+	/* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
+	HDassert(size > 0);
+
+	/* Open files */
+	if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
+		status = -1;
+		goto done;
+	}
+	if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
+		status = -1;
+		goto done;
+	}
+
+	/* Copy the userblock from the input file to the output file */
+	while (size > 0) {
+		ssize_t nread, nbytes; /* # of bytes transfered, etc. */
+		char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
+		const char *wbuf; /* Pointer into buffer, for writing */
+
+		/* Read buffer from source file */
+		if (size > USERBLOCK_XFER_SIZE)
+			nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+		else
+			nread = HDread(infid, rbuf, (size_t)size);
+		if (nread < 0) {
+			status = -1;
+			goto done;
+		} /* end if */
+
+		/* Write buffer to destination file */
+		/* (compensating for interrupted writes & checking for errors, etc.) */
+		nbytes = nread;
+		wbuf = rbuf;
+		while (nbytes > 0) {
+			ssize_t nwritten; /* # of bytes written */
+
+			do {
+				nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
+			} while (-1 == nwritten && EINTR == errno);
+			if (-1 == nwritten) { /* error */
+				status = -1;
+				goto done;
+			} /* end if */
+			HDassert(nwritten > 0);
+			HDassert(nwritten <= nbytes);
+
+			/* Update # of bytes left & offset in buffer */
+			nbytes -= nwritten;
+			wbuf += nwritten;
+			HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
+		} /* end while */
+
+		/* Update size of userblock left to transfer */
+		size = size - (hsize_t) nread;
+	} /* end while */
 
 done:
-    if(infid > 0)
-        HDclose(infid);
-    if(outfid > 0)
-        HDclose(outfid);
+	if (infid > 0)
+		HDclose(infid);
+	if (outfid > 0)
+		HDclose(outfid);
 
-    return status;
+	return status;
 }
 
-
-
 /*-------------------------------------------------------------------------
-* Function: print_user_block
-*
-* Purpose: print user block
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente
-*
-* Date: August, 20, 2008
-*
-*-------------------------------------------------------------------------
-*/
+ * Function: print_user_block
+ *
+ * Purpose: print user block
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente
+ *
+ * Date: August, 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
 static
 void print_user_block(const char *filename, hid_t fid)
 {
-    int     fh;      /* file handle  */
-    hsize_t ub_size; /* user block size */
-    hsize_t size;    /* size read */
-    hid_t   fcpl;    /* file creation property list ID for HDF5 file */
-    int     i;
-
-    /* get user block size */
-    if(( fcpl = H5Fget_create_plist(fid)) < 0)
-    {
-        error_msg("failed to retrieve file creation property list\n");
-        goto done;
-    }
-
-    if(H5Pget_userblock(fcpl, &ub_size) < 0)
-    {
-        error_msg("failed to retrieve userblock size\n");
-        goto done;
-    }
-
-    if(H5Pclose(fcpl) < 0)
-    {
-        error_msg("failed to close property list\n");
-        goto done;
-    }
-
-    /* open file */
-    if((fh = HDopen(filename, O_RDONLY, 0)) < 0)
-    {
-        goto done;
-    }
-
-    size = ub_size;
-
-    /* read file */
-    while(size > 0)
-    {
-        ssize_t nread;                  /* # of bytes read */
-        char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
-
-        /* read buffer */
-        if(size > USERBLOCK_XFER_SIZE)
-            nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
-        else
-            nread = HDread(fh, rbuf, (size_t)size);
-
-        for(i = 0; i < nread; i++)
-        {
-
-            printf("%c ", rbuf[i]);
-
-        }
-        printf("\n");
-
-        if(nread < 0)
-        {
-            goto done;
-        }
-
-
-        /* update size of userblock left to transfer */
-        size -= nread;
-    }
+	int fh; /* file handle  */
+	hsize_t ub_size; /* user block size */
+	hsize_t size; /* size read */
+	hid_t fcpl; /* file creation property list ID for HDF5 file */
+	int i;
 
-done:
-    if(fh > 0)
-        HDclose(fh);
+	/* get user block size */
+	if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+		error_msg("failed to retrieve file creation property list\n");
+		goto done;
+	}
+
+	if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+		error_msg("failed to retrieve userblock size\n");
+		goto done;
+	}
+
+	if(H5Pclose(fcpl) < 0) {
+		error_msg("failed to close property list\n");
+		goto done;
+	}
+
+	/* open file */
+	if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
+		goto done;
+	}
 
+	size = ub_size;
+
+	/* read file */
+	while(size > 0) {
+		ssize_t nread; /* # of bytes read */
+		char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+
+		/* read buffer */
+		if(size > USERBLOCK_XFER_SIZE)
+			nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+		else
+			nread = HDread(fh, rbuf, (size_t)size);
+
+		for(i = 0; i < nread; i++) {
+
+			printf("%c ", rbuf[i]);
+
+		}
+		printf("\n");
+
+		if(nread < 0) {
+			goto done;
+		}
+
+		/* update size of userblock left to transfer */
+		size -= nread;
+	}
+
+done:
+	if(fh > 0)
+		HDclose(fh);
 
-    return;
+	return;
 }
 #endif
 
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index 7edeed2..56e08ef 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -19,12 +19,12 @@
 
 /* number of members in an array */
 #ifndef NELMTS
-#    define NELMTS(X)		(sizeof(X)/sizeof(X[0]))
+#    define NELMTS(X)    (sizeof(X)/sizeof(X[0]))
 #endif
 
 /* minimum of two values */
 #undef MIN
-#define MIN(a,b)		(((a)<(b)) ? (a) : (b))
+#define MIN(a,b)    (((a)<(b)) ? (a) : (b))
 
 /*-------------------------------------------------------------------------
  * Function: aux_find_obj
@@ -345,8 +345,13 @@ int apply_filters(const char* name,    /* object name from traverse list */
         {
             switch (obj.filter[i].filtn)
             {
-            default:
-                break;
+
+            /*-------------------------------------------------------------------------
+             * H5Z_FILTER_NONE       0 , uncompress if compressed
+             *-------------------------------------------------------------------------
+             */
+            case H5Z_FILTER_NONE:
+            	break;
 
            /*-------------------------------------------------------------------------
             * H5Z_FILTER_DEFLATE       1 , deflation like gzip
@@ -436,6 +441,14 @@ int apply_filters(const char* name,    /* object name from traverse list */
                         return -1;
                 }
                 break;
+            default:
+            	{
+            		if (H5Pset_filter (dcpl_id, obj.filter[i].filtn, H5Z_FLAG_MANDATORY, obj.filter[i].cd_nelmts, obj.filter[i].cd_values)<0)
+                		return -1;
+            		if(H5Pset_chunk(dcpl_id, obj.chunk.rank, obj.chunk.chunk_lengths)<0)
+            			return -1;
+            	}
+                break;
             } /* switch */
         }/*i*/
 
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index b6ad0f5..c25b7ea 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -20,16 +20,12 @@
 /* Name of tool */
 #define PROGRAMNAME "h5repack"
 
-static void usage(const char *prog);
-static void parse_command_line(int argc, const char **argv, pack_opt_t* options);
-static void read_info(const char *filename,pack_opt_t *options);
-
+static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
 
 /* module-scoped variables */
-static int  has_i_o = 0;
-const char  *infile  = NULL;
-const char  *outfile = NULL;
-
+static int has_i_o = 0;
+const char *infile = NULL;
+const char *outfile = NULL;
 
 /*
  * Command-line options: The user can specify short or long-named
@@ -37,221 +33,289 @@ const char  *outfile = NULL;
  */
 static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:";
 static struct long_options l_opts[] = {
-    { "help", no_arg, 'h' },
-    { "version", no_arg, 'V' },
-    { "verbose", no_arg, 'v' },
-    { "filter", require_arg, 'f' },
-    { "layout", require_arg, 'l' },
-    { "minimum", require_arg, 'm' },
-    { "file", require_arg, 'e' },
-    { "native", no_arg, 'n' },
-    { "latest", no_arg, 'L' },
-    { "compact", require_arg, 'c' },
-    { "indexed", require_arg, 'd' },
-    { "ssize", require_arg, 's' },
-    { "ublock", require_arg, 'u' },
-    { "block", require_arg, 'b' },
-    { "metadata_block_size", require_arg, 'M' },
-    { "threshold", require_arg, 't' },
-    { "alignment", require_arg, 'a' },
-    { "infile", require_arg, 'i' },   /* -i for backward compability */
-    { "outfile", require_arg, 'o' },  /* -o for backward compability */
-    { NULL, 0, '\0' }
+	{ "help", no_arg, 'h' },
+	{ "version", no_arg, 'V' },
+	{ "verbose", no_arg, 'v' },
+	{ "filter", require_arg, 'f' },
+	{ "layout", require_arg, 'l' },
+	{ "minimum", require_arg, 'm' },
+	{ "file", require_arg, 'e' },
+	{ "native", no_arg, 'n' },
+	{ "latest", no_arg, 'L' },
+	{ "compact", require_arg, 'c' },
+	{ "indexed", require_arg, 'd' },
+	{ "ssize", require_arg, 's' },
+	{ "ublock", require_arg, 'u' },
+	{ "block", require_arg, 'b' },
+	{ "metadata_block_size", require_arg, 'M' },
+	{ "threshold", require_arg, 't' },
+	{ "alignment", require_arg, 'a' },
+	{ "infile", require_arg, 'i' }, /* -i for backward compability */
+	{ "outfile", require_arg, 'o' }, /* -o for backward compability */
+	{ NULL, 0, '\0' }
 };
 
-
-
-
 /*-------------------------------------------------------------------------
- * Function: main
+ * Function: usage
  *
- * Purpose: h5repack main program
+ * Purpose: print usage
  *
- * Return: Success: EXIT_SUCCESS(0)
+ * Return: void
  *
- * Failure: EXIT_FAILURE(1)
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog) {
+	printf("usage: %s [OPTIONS] file1 file2\n", prog);
+	printf("  file1                    Input HDF5 File\n");
+	printf("  file2                    Output HDF5 File\n");
+	printf("  OPTIONS\n");
+	printf("   -h, --help              Print a usage message and exit\n");
+	printf("   -v, --verbose           Verbose mode, print object information\n");
+	printf("   -V, --version           Print version number and exit\n");
+	printf("   -n, --native            Use a native HDF5 type when repacking\n");
+	printf("   -L, --latest            Use latest version of file format\n");
+	printf("   -c L1, --compact=L1     Maximum number of links in header messages\n");
+	printf("   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
+	printf("   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
+	printf("   -m M, --minimum=M       Do not apply the filter to datasets smaller than M\n");
+	printf("   -e E, --file=E          Name of file E with the -f and -l options\n");
+	printf("   -u U, --ublock=U        Name of file U with user block data to be added\n");
+	printf("   -b B, --block=B         Size of user block to be added\n");
+	printf("   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
+	printf("   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
+	printf("   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
+	printf("   -f FILT, --filter=FILT  Filter type\n");
+	printf("   -l LAYT, --layout=LAYT  Layout type\n");
+	printf("\n");
+	printf("    M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
+	printf("    E - is a filename.\n");
+	printf("    S - is an integer\n");
+	printf("    U - is a filename.\n");
+	printf("    T - is an integer\n");
+	printf("    A - is an integer greater than zero\n");
+	printf("    B - is the user block size, any value that is 512 or greater and is\n");
+	printf("        a power of 2 (1024 default)\n");
+	printf("    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
+	printf("        pline|attr>. If F is not specified, S applies to all messages\n");
+	printf("\n");
+	printf("    FILT - is a string with the format:\n");
+	printf("\n");
+	printf("      <list of objects>:<name of filter>=<filter parameters>\n");
+	printf("\n");
+	printf("      <list of objects> is a comma separated list of object names, meaning apply\n");
+	printf("        compression only to those objects. If no names are specified, the filter\n");
+	printf("        is applied to all objects\n");
+	printf("      <name of filter> can be:\n");
+	printf("        GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+	printf("        SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+	printf("        SHUF, to apply the HDF5 shuffle filter\n");
+	printf("        FLET, to apply the HDF5 checksum filter\n");
+	printf("        NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+	printf("        SOFF, to apply the HDF5 Scale/Offset filter\n");
+	printf("        UD,   to apply a user defined filter\n");
+	printf("        NONE, to remove all filters\n");
+	printf("      <filter parameters> is optional filter parameter information\n");
+	printf("        GZIP=<deflation level> from 1-9\n");
+	printf("        SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+	printf("            2-32 and coding method is either EC or NN\n");
+	printf("        SHUF (no parameter)\n");
+	printf("        FLET (no parameter)\n");
+	printf("        NBIT (no parameter)\n");
+	printf("        SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
+	printf("            is either IN or DS\n");
+	printf("        UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
+	printf("            required values for filter_number,cd_value_count,value_1\n");
+	printf("            optional values for value_2 to value_N\n");
+	printf("        NONE (no parameter)\n");
+	printf("\n");
+	printf("    LAYT - is a string with the format:\n");
+	printf("\n");
+	printf("      <list of objects>:<layout type>=<layout parameters>\n");
+	printf("\n");
+	printf("      <list of objects> is a comma separated list of object names, meaning that\n");
+	printf("        layout information is supplied for those objects. If no names are\n");
+	printf("        specified, the layout type is applied to all objects\n");
+	printf("      <layout type> can be:\n");
+	printf("        CHUNK, to apply chunking layout\n");
+	printf("        COMPA, to apply compact layout\n");
+	printf("        CONTI, to apply contiguous layout\n");
+	printf("      <layout parameters> is optional layout information\n");
+	printf("        CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+	printf("        COMPA (no parameter)\n");
+	printf("        CONTI (no parameter)\n");
+	printf("\n");
+	printf("Examples of use:\n");
+	printf("\n");
+	printf("1) h5repack -v -f GZIP=1 file1 file2\n");
+	printf("\n");
+	printf("   GZIP compression with level 1 to all objects\n");
+	printf("\n");
+	printf("2) h5repack -v -f dset1:SZIP=8,NN file1 file2\n");
+	printf("\n");
+	printf("   SZIP compression with 8 pixels per block and NN coding method to object dset1\n");
+	printf("\n");
+	printf("3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2\n");
+	printf("\n");
+	printf("   Chunked layout, with a layout size of 20x10, to objects dset1 and dset2\n");
+	printf("   and remove filters to objects dset3, dset4, dset5\n");
+	printf("\n");
+	printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
+	printf("\n");
+	printf("   Using latest file format with maximum compact group size of 10 and\n");
+	printf("   and minimum shared datatype size of 20\n");
+	printf("\n");
+	printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
+	printf("\n");
+	printf("   Add both filters SHUF and GZIP in this order to all datasets\n");
+	printf("\n");
+	printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
+	printf("\n");
+	printf("   Add bzip2 filter to all datasets\n");
+	printf("\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    leave
  *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Purpose:     Shutdown MPI & HDF5 and call exit()
  *
- * Date: May 9, 2003
+ * Return:      Does not return
  *
- * Comments:
+ * Programmer:  Quincey Koziol
+ *              Saturday, 31. January 2004
+ *
+ * Modifications:
  *
  *-------------------------------------------------------------------------
  */
-int main(int argc, const char **argv)
-{
-
-    pack_opt_t    options;            /*the global options */
-    int           ret=-1;
-
-    h5tools_setprogname(PROGRAMNAME);
-    h5tools_setstatus(EXIT_SUCCESS);
-
-    /* Initialize h5tools lib */
-    h5tools_init();
-
-    /* initialize options  */
-    h5repack_init(&options,0);
-
-    parse_command_line(argc, argv, &options);
-
-    /* get file names if they were not yet got */
-    if ( has_i_o == 0 )
-    {
-
-        if ( argv[ opt_ind ] != NULL && argv[ opt_ind + 1 ] != NULL )
-        {
-            infile = argv[ opt_ind ];
-            outfile = argv[ opt_ind + 1 ];
-
-            if ( HDstrcmp( infile, outfile ) == 0 )
-            {
-                error_msg("file names cannot be the same\n");
-                usage(h5tools_getprogname());
-                HDexit(EXIT_FAILURE);
-
-            }
-        }
-
-        else
-        {
-            error_msg("file names missing\n");
-            usage(h5tools_getprogname());
-            HDexit(EXIT_FAILURE);
-        }
-    }
-
-
-    /* pack it */
-    ret=h5repack(infile,outfile,&options);
-
-    /* free tables */
-    h5repack_end(&options);
+static void leave(int ret) {
+	h5tools_close();
 
-    if (ret==-1)
-        return 1;
-    else
-        return 0;
+	HDexit(ret);
 }
 
-
-
 /*-------------------------------------------------------------------------
- * Function: usage
+ * Function: read_info
  *
- * Purpose: print usage
+ * Purpose: read comp and chunk options from a file
  *
- * Return: void
+ * Return: void, exit on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
  *
  *-------------------------------------------------------------------------
  */
-static void usage(const char *prog)
-{
- printf("usage: %s [OPTIONS] file1 file2\n", prog);
- printf("  file1                    Input HDF5 File\n");
- printf("  file2                    Output HDF5 File\n");
- printf("  OPTIONS\n");
- printf("   -h, --help              Print a usage message and exit\n");
- printf("   -v, --verbose           Verbose mode, print object information\n");
- printf("   -V, --version           Print version number and exit\n");
- printf("   -n, --native            Use a native HDF5 type when repacking\n");
- printf("   -L, --latest            Use latest version of file format\n");
- printf("   -c L1, --compact=L1     Maximum number of links in header messages\n");
- printf("   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
- printf("   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
- printf("   -m M, --minimum=M       Do not apply the filter to datasets smaller than M\n");
- printf("   -e E, --file=E          Name of file E with the -f and -l options\n");
- printf("   -u U, --ublock=U        Name of file U with user block data to be added\n");
- printf("   -b B, --block=B         Size of user block to be added\n");
- printf("   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
- printf("   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
- printf("   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
- printf("   -f FILT, --filter=FILT  Filter type\n");
- printf("   -l LAYT, --layout=LAYT  Layout type\n");
-
- printf("\n");
-
- printf("    M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
- printf("    E - is a filename.\n");
- printf("    S - is an integer\n");
- printf("    U - is a filename.\n");
- printf("    T - is an integer\n");
- printf("    A - is an integer greater than zero\n");
- printf("    B - is the user block size, any value that is 512 or greater and is\n");
- printf("        a power of 2 (1024 default)\n");
- printf("    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
- printf("        pline|attr>. If F is not specified, S applies to all messages\n");
- printf("\n");
-
- printf("    FILT - is a string with the format:\n");
- printf("\n");
- printf("      <list of objects>:<name of filter>=<filter parameters>\n");
- printf("\n");
- printf("      <list of objects> is a comma separated list of object names, meaning apply\n");
- printf("        compression only to those objects. If no names are specified, the filter\n");
- printf("        is applied to all objects\n");
- printf("      <name of filter> can be:\n");
- printf("        GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
- printf("        SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
- printf("        SHUF, to apply the HDF5 shuffle filter\n");
- printf("        FLET, to apply the HDF5 checksum filter\n");
- printf("        NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
- printf("        SOFF, to apply the HDF5 Scale/Offset filter\n");
- printf("        NONE, to remove all filters\n");
- printf("      <filter parameters> is optional filter parameter information\n");
- printf("        GZIP=<deflation level> from 1-9\n");
- printf("        SZIP=<pixels per block,coding> pixels per block is a even number in\n");
- printf("            2-32 and coding method is either EC or NN\n");
- printf("        SHUF (no parameter)\n");
- printf("        FLET (no parameter)\n");
- printf("        NBIT (no parameter)\n");
- printf("        SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
- printf("            is either IN or DS\n");
- printf("        NONE (no parameter)\n");
- printf("\n");
- printf("    LAYT - is a string with the format:\n");
- printf("\n");
- printf("      <list of objects>:<layout type>=<layout parameters>\n");
- printf("\n");
- printf("      <list of objects> is a comma separated list of object names, meaning that\n");
- printf("        layout information is supplied for those objects. If no names are\n");
- printf("        specified, the layout type is applied to all objects\n");
- printf("      <layout type> can be:\n");
- printf("        CHUNK, to apply chunking layout\n");
- printf("        COMPA, to apply compact layout\n");
- printf("        CONTI, to apply contiguous layout\n");
- printf("      <layout parameters> is optional layout information\n");
- printf("        CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
- printf("        COMPA (no parameter)\n");
- printf("        CONTI (no parameter)\n");
- printf("\n");
- printf("Examples of use:\n");
- printf("\n");
- printf("1) h5repack -v -f GZIP=1 file1 file2\n");
- printf("\n");
- printf("   GZIP compression with level 1 to all objects\n");
- printf("\n");
- printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
- printf("\n");
- printf("   SZIP compression with 8 pixels per block and NN coding method to object A\n");
- printf("\n");
- printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
- printf("\n");
- printf("   Chunked layout, with a layout size of 20x10, to objects A and B\n");
- printf("   and remove filters to objects C, D, F\n");
- printf("\n");
- printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
- printf("\n");
- printf("   Using latest file format with maximum compact group size of 10 and\n");
- printf("   and minimum shared datatype size of 20\n");
- printf("\n");
- printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
- printf("\n");
- printf("   Add both filters SHUF and GZIP in this order to all datasets\n");
- printf("\n");
-}
 
+static
+int read_info(const char *filename, pack_opt_t *options) {
+
+	char stype[10];
+	char comp_info[1024];
+	FILE *fp = NULL;
+	char c;
+	int i, rc = 1;
+	int ret_value = EXIT_SUCCESS;
+
+	if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+		error_msg("cannot open options file %s\n", filename);
+		h5tools_setstatus(EXIT_FAILURE);
+		ret_value = EXIT_FAILURE;
+		goto done;
+	}
+
+	/* cycle until end of file reached */
+	while (1) {
+		rc = fscanf(fp, "%s", stype);
+		if (rc == -1)
+			break;
+
+		/*-------------------------------------------------------------------------
+		 * filter
+		 *-------------------------------------------------------------------------
+		 */
+		if (HDstrcmp(stype,"-f") == 0) {
+			/* find begining of info */
+			i = 0;
+			c = '0';
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				if (HDfeof(fp))
+					break;
+			}
+			c = '0';
+			/* go until end */
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				comp_info[i] = c;
+				i++;
+				if (HDfeof(fp))
+					break;
+				if (c == 10 /*eol*/)
+					break;
+			}
+			comp_info[i - 1] = '\0'; /*cut the last " */
+
+			if (h5repack_addfilter(comp_info, options) == -1) {
+				error_msg("could not add compression option\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = EXIT_FAILURE;
+				goto done;
+			}
+		}
+		/*-------------------------------------------------------------------------
+		 * layout
+		 *-------------------------------------------------------------------------
+		 */
+		else if (HDstrcmp(stype,"-l") == 0) {
+
+			/* find begining of info */
+			i = 0;
+			c = '0';
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				if (HDfeof(fp))
+					break;
+			}
+			c = '0';
+			/* go until end */
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				comp_info[i] = c;
+				i++;
+				if (HDfeof(fp))
+					break;
+				if (c == 10 /*eol*/)
+					break;
+			}
+			comp_info[i - 1] = '\0'; /*cut the last " */
+
+			if (h5repack_addlayout(comp_info, options) == -1) {
+				error_msg("could not add chunck option\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = EXIT_FAILURE;
+				goto done;
+			}
+		}
+		/*-------------------------------------------------------------------------
+		 * not valid
+		 *-------------------------------------------------------------------------
+		 */
+		else {
+			error_msg("bad file format for %s", filename);
+			h5tools_setstatus(EXIT_FAILURE);
+			ret_value = EXIT_FAILURE;
+			goto done;
+		}
+	}
+
+done:
+	if (fp)
+		HDfclose(fp);
+
+	return ret_value;
+}
 
 /*-------------------------------------------------------------------------
  * Function: parse_command_line
@@ -262,301 +326,249 @@ static void usage(const char *prog)
  */
 
 static
-void parse_command_line(int argc, const char **argv, pack_opt_t* options)
-{
-
-    int opt;
-
-    /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
-    {
-        switch ((char)opt)
-        {
-
-        /* -i for backward compability */
-        case 'i':
-            infile = opt_arg;
-            has_i_o = 1;
-            break;
-        /* -o for backward compability */
-        case 'o':
-            outfile = opt_arg;
-            has_i_o = 1;
-            break;
-
-
-        case 'h':
-            usage(h5tools_getprogname());
-            HDexit(EXIT_SUCCESS);
-        case 'V':
-            print_version(h5tools_getprogname());
-            HDexit(EXIT_SUCCESS);
-        case 'v':
-            options->verbose = 1;
-            break;
-        case 'f':
-
-            /* parse the -f filter option */
-            if (h5repack_addfilter( opt_arg, options)<0)
-            {
-                error_msg("in parsing filter\n");
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-        case 'l':
-
-            /* parse the -l layout option */
-            if (h5repack_addlayout( opt_arg, options)<0)
-            {
-                error_msg("in parsing layout\n");
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-
-
-        case 'm':
-
-            options->min_comp = HDatoi( opt_arg );
-            if ((int)options->min_comp<=0)
-            {
-                error_msg("invalid minimum compress size <%s>\n", opt_arg );
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-
-        case 'e':
-            read_info( opt_arg, options);
-            break;
-
-        case 'n':
-            options->use_native = 1;
-            break;
-
-        case 'L':
-            options->latest = 1;
-            break;
-
-        case 'c':
-
-            options->grp_compact = HDatoi( opt_arg );
-            if (options->grp_compact>0)
-                options->latest = 1; /* must use latest format */
-            break;
-
-
-        case 'd':
-
-            options->grp_indexed = HDatoi( opt_arg );
-            if (options->grp_indexed>0)
-                options->latest = 1; /* must use latest format */
-            break;
-
-        case 's':
-
-            {
-
-                int idx = 0;
-                int ssize = 0;
-                char *msgPtr = HDstrchr( opt_arg, ':');
-                options->latest = 1; /* must use latest format */
-                if (msgPtr == NULL)
-                {
-                    ssize = HDatoi( opt_arg );
-                    for (idx=0; idx<5; idx++)
-                        options->msg_size[idx] = ssize;
-                }
-                else
-                {
-                    char msgType[10];
-                    HDstrcpy(msgType, msgPtr+1);
-                    msgPtr[0] = '\0';
-                    ssize = HDatoi( opt_arg );
-                    if (HDstrncmp(msgType, "dspace",6) == 0) {
-                        options->msg_size[0] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "dtype", 5) == 0) {
-                        options->msg_size[1] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "fill", 4) == 0) {
-                        options->msg_size[2] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "pline", 5) == 0) {
-                        options->msg_size[3] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "attr", 4) == 0) {
-                        options->msg_size[4] = ssize;
-                    }
-                }
-            }
-
-            break;
-
-        case 'u':
-
-            options->ublock_filename = opt_arg;
-            break;
-
-        case 'b':
-
-            options->ublock_size = (hsize_t)HDatol( opt_arg );
-            break;
-
-        case 'M':
-
-            options->meta_block_size = (hsize_t)HDatol( opt_arg );
-            break;
-
-        case 't':
-
-            options->threshold = (hsize_t)HDatol( opt_arg );
-            break;
-
-        case 'a':
-
-            options->alignment = HDatol( opt_arg );
-            if ( options->alignment < 1 )
-            {
-                error_msg("invalid alignment size\n", opt_arg );
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-        default:
-            break;
-        } /* switch */
-
-
-    } /* while */
-
-    if ( has_i_o == 0 )
-    {
-        /* check for file names to be processed */
-        if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL)
-        {
-            error_msg("missing file names\n");
-            usage(h5tools_getprogname());
-            HDexit(EXIT_FAILURE);
-        }
-    }
-
+int parse_command_line(int argc, const char **argv, pack_opt_t* options) {
+
+	int opt;
+	int ret_value = 0;
+
+	/* parse command line options */
+	while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+		switch ((char) opt) {
+
+		/* -i for backward compability */
+		case 'i':
+			infile = opt_arg;
+			has_i_o = 1;
+			break;
+
+			/* -o for backward compability */
+		case 'o':
+			outfile = opt_arg;
+			has_i_o = 1;
+			break;
+
+		case 'h':
+			usage(h5tools_getprogname());
+			h5tools_setstatus(EXIT_SUCCESS);
+			ret_value = -1;
+			goto done;
+
+		case 'V':
+			print_version(h5tools_getprogname());
+			h5tools_setstatus(EXIT_SUCCESS);
+			ret_value = -1;
+			goto done;
+
+		case 'v':
+			options->verbose = 1;
+			break;
+
+		case 'f':
+			/* parse the -f filter option */
+			if (h5repack_addfilter(opt_arg, options) < 0) {
+				error_msg("in parsing filter\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'l':
+			/* parse the -l layout option */
+			if (h5repack_addlayout(opt_arg, options) < 0) {
+				error_msg("in parsing layout\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'm':
+			options->min_comp = HDatoi( opt_arg );
+			if ((int) options->min_comp <= 0) {
+				error_msg("invalid minimum compress size <%s>\n", opt_arg);
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'e':
+			ret_value = read_info(opt_arg, options);
+			if (ret_value < 0)
+				goto done;
+			break;
+
+		case 'n':
+			options->use_native = 1;
+			break;
+
+		case 'L':
+			options->latest = 1;
+			break;
+
+		case 'c':
+			options->grp_compact = HDatoi( opt_arg );
+			if (options->grp_compact > 0)
+				options->latest = 1; /* must use latest format */
+			break;
+
+		case 'd':
+			options->grp_indexed = HDatoi( opt_arg );
+			if (options->grp_indexed > 0)
+				options->latest = 1; /* must use latest format */
+			break;
+
+		case 's':
+			{
+				int idx = 0;
+				int ssize = 0;
+				char *msgPtr = HDstrchr( opt_arg, ':');
+				options->latest = 1; /* must use latest format */
+				if (msgPtr == NULL) {
+					ssize = HDatoi( opt_arg );
+					for (idx = 0; idx < 5; idx++)
+						options->msg_size[idx] = ssize;
+				}
+				else {
+					char msgType[10];
+					HDstrcpy(msgType, msgPtr + 1);
+					msgPtr[0] = '\0';
+					ssize = HDatoi( opt_arg );
+					if (HDstrncmp(msgType, "dspace",6) == 0) {
+						options->msg_size[0] = ssize;
+					}
+					else if (HDstrncmp(msgType, "dtype", 5) == 0) {
+						options->msg_size[1] = ssize;
+					}
+					else if (HDstrncmp(msgType, "fill", 4) == 0) {
+						options->msg_size[2] = ssize;
+					}
+					else if (HDstrncmp(msgType, "pline", 5) == 0) {
+						options->msg_size[3] = ssize;
+					}
+					else if (HDstrncmp(msgType, "attr", 4) == 0) {
+						options->msg_size[4] = ssize;
+					}
+				}
+			}
+			break;
+
+		case 'u':
+			options->ublock_filename = opt_arg;
+			break;
+
+		case 'b':
+			options->ublock_size = (hsize_t) HDatol( opt_arg );
+			break;
+
+		case 'M':
+			options->meta_block_size = (hsize_t) HDatol( opt_arg );
+			break;
+
+		case 't':
+			options->threshold = (hsize_t) HDatol( opt_arg );
+			break;
+
+		case 'a':
+			options->alignment = HDatol( opt_arg );
+			if (options->alignment < 1) {
+				error_msg("invalid alignment size\n", opt_arg);
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		default:
+			break;
+		} /* switch */
+
+	} /* while */
+
+	if (has_i_o == 0) {
+		/* check for file names to be processed */
+		if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+			error_msg("missing file names\n");
+			usage(h5tools_getprogname());
+			h5tools_setstatus(EXIT_FAILURE);
+			ret_value = -1;
+		}
+	}
+
+done:
+	return ret_value;
 }
 
 /*-------------------------------------------------------------------------
- * Function: read_info
+ * Function: main
  *
- * Purpose: read comp and chunk options from a file
+ * Purpose: h5repack main program
  *
- * Return: void, exit on error
+ * Return: Success: EXIT_SUCCESS(0)
  *
- * Programmer: pvn@ncsa.uiuc.edu
+ * Failure: EXIT_FAILURE(1)
  *
- * Date: September, 22, 2003
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
  *
  *-------------------------------------------------------------------------
  */
-
-static
-void read_info(const char *filename,
-               pack_opt_t *options)
-{
-
-    char stype[10];
-    char comp_info[1024];
-    FILE *fp;
-    char c;
-    int  i, rc=1;
-    char  *srcdir = getenv("srcdir"); /* the source directory */
-    char  data_file[512]="";          /* buffer to hold name of existing file */
-
-    /* compose the name of the file to open, using the srcdir, if appropriate */
-    if (srcdir){
-        HDstrcpy(data_file,srcdir);
-        HDstrcat(data_file,"/");
-    }
-    HDstrcat(data_file,filename);
-
-
-    if ((fp = HDfopen(data_file, "r")) == (FILE *)NULL) {
-        error_msg("cannot open options file %s\n", filename);
-        HDexit(EXIT_FAILURE);
-    }
-
-    /* cycle until end of file reached */
-    while( 1 )
-    {
-        rc=fscanf(fp, "%s", stype);
-        if (rc==-1)
-            break;
-
-       /*-------------------------------------------------------------------------
-        * filter
-        *-------------------------------------------------------------------------
-        */
-        if (HDstrcmp(stype,"-f") == 0) {
-
-            /* find begining of info */
-            i=0; c='0';
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                if (HDfeof(fp)) break;
-            }
-            c='0';
-            /* go until end */
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                comp_info[i]=c;
-                i++;
-                if (HDfeof(fp)) break;
-                if (c==10 /*eol*/) break;
-            }
-            comp_info[i-1]='\0'; /*cut the last " */
-
-            if (h5repack_addfilter(comp_info,options)==-1){
-                error_msg("could not add compression option\n");
-                HDexit(EXIT_FAILURE);
-            }
-        }
-        /*-------------------------------------------------------------------------
-        * layout
-        *-------------------------------------------------------------------------
-        */
-        else if (HDstrcmp(stype,"-l") == 0) {
-
-            /* find begining of info */
-            i=0; c='0';
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                if (HDfeof(fp)) break;
-            }
-            c='0';
-            /* go until end */
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                comp_info[i]=c;
-                i++;
-                if (HDfeof(fp)) break;
-                if (c==10 /*eol*/) break;
-            }
-            comp_info[i-1]='\0'; /*cut the last " */
-
-            if (h5repack_addlayout(comp_info,options)==-1){
-                error_msg("could not add chunck option\n");
-                HDexit(EXIT_FAILURE);
-            }
-        }
-        /*-------------------------------------------------------------------------
-        * not valid
-        *-------------------------------------------------------------------------
-        */
-        else {
-            error_msg("bad file format for %s", filename);
-            HDexit(EXIT_FAILURE);
-        }
-    }
-
-    HDfclose(fp);
-    return;
+int main(int argc, const char **argv) {
+
+	pack_opt_t options; /*the global options */
+	int ret = -1;
+
+	h5tools_setprogname(PROGRAMNAME);
+	h5tools_setstatus(EXIT_SUCCESS);
+
+	/* Initialize h5tools lib */
+	h5tools_init();
+
+	/* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
+	if (h5tools_getenv_update_hyperslab_bufsize() < 0) {
+		h5tools_setstatus(EXIT_FAILURE);
+		goto done;
+	}
+
+	/* initialize options  */
+	h5repack_init(&options, 0);
+
+	if (parse_command_line(argc, argv, &options) < 0)
+		goto done;
+
+	/* get file names if they were not yet got */
+	if (has_i_o == 0) {
+
+		if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
+			infile = argv[opt_ind];
+			outfile = argv[opt_ind + 1];
+
+			if ( HDstrcmp( infile, outfile ) == 0) {
+				error_msg("file names cannot be the same\n");
+				usage(h5tools_getprogname());
+				h5tools_setstatus(EXIT_FAILURE);
+				goto done;
+			}
+		}
+		else {
+			error_msg("file names missing\n");
+			usage(h5tools_getprogname());
+			h5tools_setstatus(EXIT_FAILURE);
+			goto done;
+		}
+	}
+
+	/* pack it */
+	h5tools_setstatus(h5repack(infile, outfile, &options));
+
+done:
+	/* free tables */
+	h5repack_end(&options);
+
+	leave(h5tools_getstatus());
 }
+
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index bcddbb9..b54e887 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -1,4 +1,4 @@
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
  * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
@@ -27,21 +27,19 @@
  *-------------------------------------------------------------------------
  */
 
-void init_packobject(pack_info_t *obj)
-{
-    int j, k;
-
-    HDstrcpy(obj->path,"\0");
-    for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
-    {
-        obj->filter[j].filtn        = -1;
-        for ( k=0; k<CD_VALUES; k++)
-            obj->filter[j].cd_values[k] = 0;
-    }
-    obj->chunk.rank = -1;
-    obj->refobj_id = -1;
-    obj->layout = H5D_LAYOUT_ERROR;
-    obj->nfilters = 0;
+void init_packobject(pack_info_t *obj) {
+	int j, k;
+
+	HDstrcpy(obj->path, "\0");
+	for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) {
+		obj->filter[j].filtn = -1;
+		for (k = 0; k < CD_VALUES; k++)
+			obj->filter[j].cd_values[k] = 0;
+	}
+	obj->chunk.rank = -1;
+	obj->refobj_id = -1;
+	obj->layout = H5D_LAYOUT_ERROR;
+	obj->nfilters = 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -54,19 +52,16 @@ void init_packobject(pack_info_t *obj)
  *-------------------------------------------------------------------------
  */
 
-static void aux_tblinsert_filter(pack_opttbl_t *table,
-                                 unsigned int I,
-                                 filter_info_t filt)
-{
-    if (table->objs[ I ].nfilters<H5_REPACK_MAX_NFILTERS)
-    {
-        table->objs[ I ].filter[ table->objs[ I ].nfilters++ ] = filt;
-    }
-    else
-    {
-    error_msg("cannot insert the filter in this object.\
+static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I,
+		filter_info_t filt) {
+	if (table->objs[I].nfilters < H5_REPACK_MAX_NFILTERS) {
+		table->objs[I].filter[table->objs[I].nfilters++] = filt;
+	}
+	else {
+		error_msg(
+				"cannot insert the filter in this object.\
         Maximum capacity exceeded\n");
-    }
+	}
 }
 
 /*-------------------------------------------------------------------------
@@ -79,33 +74,28 @@ static void aux_tblinsert_filter(pack_opttbl_t *table,
  *-------------------------------------------------------------------------
  */
 
-static void aux_tblinsert_layout(pack_opttbl_t *table,
-                                 unsigned int I,
-                                 pack_info_t *pack)
-{
-    int k;
-
-    table->objs[I].layout = pack->layout;
-    if (H5D_CHUNKED==pack->layout)
-    {
-    /* -2 means the NONE option, remove chunking
-        and set the layout to contiguous */
-        if (pack->chunk.rank==-2)
-        {
-            table->objs[I].layout = H5D_CONTIGUOUS;
-            table->objs[I].chunk.rank = -2;
-        }
-        /* otherwise set the chunking type */
-        else
-        {
-            table->objs[I].chunk.rank = pack->chunk.rank;
-            for (k = 0; k < pack->chunk.rank; k++)
-                table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k];
-        }
-    }
+static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I,
+		pack_info_t *pack) {
+	int k;
+
+	table->objs[I].layout = pack->layout;
+	if (H5D_CHUNKED == pack->layout) {
+		/* -2 means the NONE option, remove chunking
+		 and set the layout to contiguous */
+		if (pack->chunk.rank == -2) {
+			table->objs[I].layout = H5D_CONTIGUOUS;
+			table->objs[I].chunk.rank = -2;
+		}
+		/* otherwise set the chunking type */
+		else {
+			table->objs[I].chunk.rank = pack->chunk.rank;
+			for (k = 0; k < pack->chunk.rank; k++)
+				table->objs[I].chunk.chunk_lengths[k] =
+						pack->chunk.chunk_lengths[k];
+		}
+	}
 }
 
-
 /*-------------------------------------------------------------------------
  * Function: aux_inctable
  *
@@ -116,21 +106,20 @@ static void aux_tblinsert_layout(pack_opttbl_t *table,
  *-------------------------------------------------------------------------
  */
 
-static int aux_inctable(pack_opttbl_t *table, int n_objs )
-{
-    unsigned int i;
-
-    table->size += n_objs;
-    table->objs = (pack_info_t*)HDrealloc(table->objs, table->size * sizeof(pack_info_t));
-    if (table->objs==NULL) {
-        error_msg("not enough memory for options table\n");
-        return -1;
-    }
-    for (i = table->nelems; i < table->size; i++)
-    {
-        init_packobject(&table->objs[i]);
-    }
-    return 0;
+static int aux_inctable(pack_opttbl_t *table, int n_objs) {
+	unsigned int i;
+
+	table->size += n_objs;
+	table->objs =
+			(pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t));
+	if (table->objs == NULL) {
+		error_msg("not enough memory for options table\n");
+		return -1;
+	}
+	for (i = table->nelems; i < table->size; i++) {
+		init_packobject(&table->objs[i]);
+	}
+	return 0;
 }
 
 
@@ -143,31 +132,29 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
  *
  *-------------------------------------------------------------------------
  */
-int options_table_init( pack_opttbl_t **tbl )
-{
-    unsigned int i;
-    pack_opttbl_t *table;
-
-    if(NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t))))
-    {
-        error_msg("not enough memory for options table\n");
-        return -1;
-    }
-
-    table->size   = 30;
-    table->nelems = 0;
-    if(NULL == (table->objs = (pack_info_t*)HDmalloc(table->size * sizeof(pack_info_t))))
-    {
-        error_msg("not enough memory for options table\n");
-        HDfree(table);
-        return -1;
-    }
-
-    for(i = 0; i < table->size; i++)
-        init_packobject(&table->objs[i]);
-
-    *tbl = table;
-    return 0;
+int options_table_init(pack_opttbl_t **tbl) {
+	unsigned int i;
+	pack_opttbl_t *table;
+
+	if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) {
+		error_msg("not enough memory for options table\n");
+		return -1;
+	}
+
+	table->size = 30;
+	table->nelems = 0;
+	if (NULL == (table->objs =
+			(pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) {
+		error_msg("not enough memory for options table\n");
+		HDfree(table);
+		return -1;
+	}
+
+	for (i = 0; i < table->size; i++)
+		init_packobject(&table->objs[i]);
+
+	*tbl = table;
+	return 0;
 }
 
 
@@ -181,11 +168,10 @@ int options_table_init( pack_opttbl_t **tbl )
  *-------------------------------------------------------------------------
  */
 
-int options_table_free( pack_opttbl_t *table )
-{
-    HDfree(table->objs);
-    HDfree(table);
-    return 0;
+int options_table_free(pack_opttbl_t *table) {
+	HDfree(table->objs);
+	HDfree(table);
+	return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -198,95 +184,81 @@ int options_table_free( pack_opttbl_t *table )
  *-------------------------------------------------------------------------
  */
 
-
-int options_add_layout( obj_list_t *obj_list,
-                        int n_objs,
-                        pack_info_t *pack,
-                        pack_opttbl_t *table )
-{
-    unsigned int i, I;
-    int          j, added=0, found=0;
-
-    /* increase the size of the collection by N_OBJS if necessary */
-    if (table->nelems+n_objs >= table->size)
-    {
-        if (aux_inctable(table,n_objs)<0)
-            return -1;
-    }
-
-    /* search if this object is already in the table; "path" is the key */
-    if (table->nelems>0)
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            /* linear table search */
-            for (i = 0; i < table->nelems; i++)
-            {
-                /*already on the table */
-                if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
-                {
-                    /* already chunk info inserted for this one; exit */
-                    if (table->objs[i].chunk.rank>0)
-                    {
-                        error_msg("chunk information already inserted for <%s>\n",obj_list[j].obj);
-                        HDexit(EXIT_FAILURE);
-                    }
-                    /* insert the layout info */
-                    else
-                    {
-                        aux_tblinsert_layout(table,i,pack);
-                        found=1;
-                        break;
-                    }
-                } /* if */
-            } /* i */
-
-            if (found==0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_layout(table,I,pack);
-            }
-            /* cases where we have an already inserted name but there is a new name also
-            example:
-            -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
-            dset1 is already inserted, but dset2 must also be
-            */
-            else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_layout(table,I,pack);
-            }
-        } /* j */
-    }
-
-    /* first time insertion */
-    else
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            I = table->nelems + added;
-            added++;
-            HDstrcpy(table->objs[I].path,obj_list[j].obj);
-            aux_tblinsert_layout(table,I,pack);
-
-        }
-    }
-
-    table->nelems+= added;
-
-    return 0;
+int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack,
+		pack_opttbl_t *table) {
+	unsigned int i, I;
+	int j, added = 0, found = 0;
+
+	/* increase the size of the collection by N_OBJS if necessary */
+	if (table->nelems + n_objs >= table->size) {
+		if (aux_inctable(table, n_objs) < 0)
+			return -1;
+	}
+
+	/* search if this object is already in the table; "path" is the key */
+	if (table->nelems > 0) {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			/* linear table search */
+			for (i = 0; i < table->nelems; i++) {
+				/*already on the table */
+				if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+					/* already chunk info inserted for this one; exit */
+					if (table->objs[i].chunk.rank > 0) {
+						error_msg(
+								"chunk information already inserted for <%s>\n",
+								obj_list[j].obj);
+						HDexit(EXIT_FAILURE);
+					}
+					/* insert the layout info */
+					else {
+						aux_tblinsert_layout(table, i, pack);
+						found = 1;
+						break;
+					}
+				} /* if */
+			} /* i */
+
+			if (found == 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_layout(table, I, pack);
+			}
+			/* cases where we have an already inserted name but there is a new name also
+			 example:
+			 -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
+			 dset1 is already inserted, but dset2 must also be
+			 */
+			else if (found == 1
+					&& HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_layout(table, I, pack);
+			}
+		} /* j */
+	}
+
+	/* first time insertion */
+	else {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			I = table->nelems + added;
+			added++;
+			HDstrcpy(table->objs[I].path, obj_list[j].obj);
+			aux_tblinsert_layout(table, I, pack);
+
+		}
+	}
+
+	table->nelems += added;
+
+	return 0;
 }
 
-
-
 /*-------------------------------------------------------------------------
  * Function: options_add_filter
  *
@@ -297,81 +269,70 @@ int options_add_layout( obj_list_t *obj_list,
  *-------------------------------------------------------------------------
  */
 
-int options_add_filter(obj_list_t *obj_list,
-                       int n_objs,
-                       filter_info_t filt,
-                       pack_opttbl_t *table )
-{
-
-    unsigned int i, I;
-    int          j, added=0, found=0;
-
-    /* increase the size of the collection by N_OBJS if necessary */
-    if (table->nelems+n_objs >= table->size)
-    {
-        if (aux_inctable(table,n_objs)<0)
-            return -1;
-    }
-
-    /* search if this object is already in the table; "path" is the key */
-    if (table->nelems>0)
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            /* linear table search */
-            for (i = 0; i < table->nelems; i++)
-            {
-                /*already on the table */
-                if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
-                {
-                    /* insert */
-                    aux_tblinsert_filter(table,i,filt);
-                    found=1;
-                    break;
-                } /* if */
-            } /* i */
-
-            if (found==0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_filter(table,I,filt);
-            }
-            /* cases where we have an already inserted name but there is a new name also
-            example:
-            -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
-            dset1 is already inserted, but dset2 must also be
-            */
-            else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_filter(table,I,filt);
-            }
-        } /* j */
-    }
-
-    /* first time insertion */
-    else
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            I = table->nelems + added;
-            added++;
-            HDstrcpy(table->objs[I].path,obj_list[j].obj);
-            aux_tblinsert_filter(table,I,filt);
-        }
-    }
-
-    table->nelems+= added;
-
-    return 0;
+int options_add_filter(obj_list_t *obj_list, int n_objs, filter_info_t filt,
+		pack_opttbl_t *table) {
+
+	unsigned int i, I;
+	int j, added = 0, found = 0;
+
+	/* increase the size of the collection by N_OBJS if necessary */
+	if (table->nelems + n_objs >= table->size) {
+		if (aux_inctable(table, n_objs) < 0)
+			return -1;
+	}
+
+	/* search if this object is already in the table; "path" is the key */
+	if (table->nelems > 0) {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			/* linear table search */
+			for (i = 0; i < table->nelems; i++) {
+				/*already on the table */
+				if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+					/* insert */
+					aux_tblinsert_filter(table, i, filt);
+					found = 1;
+					break;
+				} /* if */
+			} /* i */
+
+			if (found == 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_filter(table, I, filt);
+			}
+			/* cases where we have an already inserted name but there is a new name also
+			 example:
+			 -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
+			 dset1 is already inserted, but dset2 must also be
+			 */
+			else if (found == 1
+					&& HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_filter(table, I, filt);
+			}
+		} /* j */
+	}
+
+	/* first time insertion */
+	else {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			I = table->nelems + added;
+			added++;
+			HDstrcpy(table->objs[I].path, obj_list[j].obj);
+			aux_tblinsert_filter(table, I, filt);
+		}
+	}
+
+	table->nelems += added;
+
+	return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -384,34 +345,25 @@ int options_add_filter(obj_list_t *obj_list,
  *-------------------------------------------------------------------------
  */
 
-pack_info_t* options_get_object( const char *path,
-                                 pack_opttbl_t *table )
-{
-    unsigned int i;
-    char tbl_path[MAX_NC_NAME+1]; /* +1 for start with "/" case */
-
-
-    for ( i = 0; i < table->nelems; i++)
-    {
-        /* make full path (start with "/") to compare correctly  */
-        if (HDstrncmp(table->objs[i].path, "/", 1))
-        {
-            HDstrcpy(tbl_path, "/");
-            HDstrcat(tbl_path, table->objs[i].path);
-        }
-        else
-            HDstrcpy(tbl_path, table->objs[i].path);
-
-        /* found it */
-        if (HDstrcmp(tbl_path, path)==0)
-        {
-            return (&table->objs[i]);
-        }
-    }
-
-    return NULL;
+pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) {
+	unsigned int i;
+	char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */
+
+	for (i = 0; i < table->nelems; i++) {
+		/* make full path (start with "/") to compare correctly  */
+		if (HDstrncmp(table->objs[i].path, "/", 1)) {
+			HDstrcpy(tbl_path, "/");
+			HDstrcat(tbl_path, table->objs[i].path);
+		}
+		else
+			HDstrcpy(tbl_path, table->objs[i].path);
+
+		/* found it */
+		if (HDstrcmp(tbl_path, path) == 0) {
+			return (&table->objs[i]);
+		}
+	}
+
+	return NULL;
 }
 
-
-
-
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index 9f798e9..8a297a7 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -31,6 +31,7 @@
  *  FLET, to apply the HDF5 checksum filter
  *  NBIT, to apply the HDF5 NBIT filter (NBIT compression)
  *  SOFF, to apply the HDF5 scale+offset filter (compression)
+ *  UD, to apply a User Defined filter k, m, n1[,…,nm]
  *  NONE, to remove the filter
  *
  * Examples:
@@ -51,402 +52,468 @@ obj_list_t* parse_filter(const char *str,
                          pack_opt_t *options,
                          int *is_glb)
 {
-    unsigned    i, u;
-    char        c;
-    size_t      len=HDstrlen(str);
-    int         j, m, n, k, l, end_obj=-1, no_param=0;
-    char        sobj[MAX_NC_NAME];
-    char        scomp[10];
-    char        stype[5];
-    char        smask[3];
-    obj_list_t* obj_list=NULL;
-    unsigned    pixels_per_block;
-
-
-    /* initialize compression  info */
-    HDmemset(filt,0,sizeof(filter_info_t));
-    *is_glb = 0;
-
-    /* check for the end of object list and number of objects */
-    for ( i = 0, n = 0; i < len; i++)
-    {
-        c = str[i];
-        if ( c==':' )
-        {
-            end_obj=i;
-        }
-        if ( c==',' )
-        {
-            n++;
-        }
-    }
-
-    if (end_obj==-1) /* missing : */
-    {
-        /* apply to all objects */
-        options->all_filter=1;
-        *is_glb = 1;
-    }
-
-    n++;
-    obj_list = (obj_list_t*) HDmalloc(n*sizeof(obj_list_t));
-    if (obj_list==NULL)
-    {
-        error_msg("could not allocate object list\n");
-        return NULL;
-    }
-    *n_objs=n;
-
-    /* get object list */
-    for ( j = 0, k = 0, n = 0; j < end_obj; j++, k++)
-    {
-        c = str[j];
-        sobj[k] = c;
-        if ( c==',' || j==end_obj-1)
-        {
-            if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
-            HDstrcpy(obj_list[n].obj,sobj);
-            HDmemset(sobj,0,sizeof(sobj));
-            n++;
-            k=-1;
-        }
-    }
-    /* nothing after : */
-    if (end_obj+1==(int)len)
-    {
-        if (obj_list) HDfree(obj_list);
-        error_msg("input Error: Invalid compression type in <%s>\n",str);
-        HDexit(EXIT_FAILURE);
-    }
-
-
-    /* get filter additional parameters */
-    m=0;
-    for ( i=end_obj+1, k=0, j=0; i<len; i++,k++)
-    {
-        c = str[i];
-        scomp[k]=c;
-        if ( c=='=' || i==len-1)
-        {
-            if ( c=='=') /*one more parameter */
-            {
-                scomp[k]='\0';     /*cut space */
-
-               /*-------------------------------------------------------------------------
-                * H5Z_FILTER_SZIP
-                * szip has the format SZIP=<pixels per block,coding>
-                * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
-                * example SZIP=8,NN
-                *-------------------------------------------------------------------------
-                */
-                if (HDstrcmp(scomp,"SZIP")==0)
-                {
-                    l=-1; /* mask index check */
-                    for ( m=0,u=i+1; u<len; u++,m++)
-                    {
-                        if (str[u]==',')
-                        {
-                            stype[m]='\0'; /* end digit of szip */
-                            l=0;  /* start EC or NN search */
-                            u++;  /* skip ',' */
-                        }
-                        c = str[u];
-                        if (!isdigit(c) && l==-1){
-                            if (obj_list) HDfree(obj_list);
-                            error_msg("compression parameter not digit in <%s>\n",str);
-                            HDexit(EXIT_FAILURE);
-                        }
-                        if (l==-1)
-                            stype[m]=c;
-                        else
-                        {
-                            smask[l]=c;
-                            l++;
-                            if (l==2)
-                            {
-                                smask[l]='\0';
-                                i=len-1; /* end */
-                                (*n_objs)--; /* we counted an extra ',' */
-                                if (HDstrcmp(smask,"NN")==0)
-                                    filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
-                                else if (HDstrcmp(smask,"EC")==0)
-                                    filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
-                                else
-                                {
-                                    error_msg("szip mask must be 'NN' or 'EC' \n");
-                                    HDexit(EXIT_FAILURE);
-                                }
-
-
-                            }
-                        }
-
-                    }  /* u */
-                } /*if */
-
-                  /*-------------------------------------------------------------------------
-                  * H5Z_FILTER_SCALEOFFSET
-                  * scaleoffset has the format SOFF=<scale_factor,scale_type>
-                  * scale_type can be
-                  *   integer datatype, H5Z_SO_INT (IN)
-                  *   float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE  (DS)
-                  *   float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE  (ES) , not yet implemented
-                  * for integer datatypes, scale_factor denotes Minimum Bits
-                  * for float datatypes, scale_factor denotes decimal scale factor
-                  *  examples
-                  *  SOFF=31,IN
-                  *  SOFF=3,DF
-                  *-------------------------------------------------------------------------
-                */
-
-                else if (HDstrcmp(scomp,"SOFF")==0)
-                {
-                    l=-1; /* mask index check */
-                    for ( m=0,u=i+1; u<len; u++,m++)
-                    {
-                        if (str[u]==',')
-                        {
-                            stype[m]='\0'; /* end digit */
-                            l=0;  /* start 'IN' , 'DS', or 'ES' search */
-                            u++;  /* skip ',' */
-                        }
-                        c = str[u];
-                        if (!isdigit(c) && l==-1){
-                            if (obj_list) HDfree(obj_list);
-                            error_msg("compression parameter is not a digit in <%s>\n",str);
-                            HDexit(EXIT_FAILURE);
-                        }
-                        if (l==-1)
-                            stype[m]=c;
-                        else
-                        {
-                            smask[l]=c;
-                            l++;
-                            if (l==2)
-                            {
-                                smask[l]='\0';
-                                i=len-1; /* end */
-                                (*n_objs)--; /* we counted an extra ',' */
-                                if (HDstrcmp(smask,"IN")==0)
-                                    filt->cd_values[j++]=H5Z_SO_INT;
-                                else if (HDstrcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
-                                    filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE;
-                                else
-                                {
-                                    error_msg("scale type must be 'IN' or 'DS' \n");
-                                    HDexit(EXIT_FAILURE);
-                                }
-
-                            }
-                        }
-
-                    }  /* u */
-                } /*if */
-
-
-               /*-------------------------------------------------------------------------
-                * all other filters
-                *-------------------------------------------------------------------------
-                */
-
-                else
-                {
-                    /* here we could have 1 or 2 digits  */
-                    for ( m=0,u=i+1; u<len; u++,m++)
-                    {
-                        c = str[u];
-                        if (!isdigit(c)){
-                            if (obj_list) HDfree(obj_list);
-                            error_msg("compression parameter is not a digit in <%s>\n",str);
-                            HDexit(EXIT_FAILURE);
-                        }
-                        stype[m]=c;
-                    } /* u */
-
-                    stype[m]='\0';
-                } /*if */
-
-
-
-                filt->cd_values[j++]=atoi(stype);
-                i+=m; /* jump */
-   }
-   else if (i==len-1)
-   { /*no more parameters */
-       scomp[k+1]='\0';
-       no_param=1;
-   }
-
-  /*-------------------------------------------------------------------------
-   * translate from string to filter symbol
-   *-------------------------------------------------------------------------
-   */
-
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_NONE
-   *-------------------------------------------------------------------------
-   */
-   if (HDstrcmp(scomp,"NONE")==0)
-   {
-       filt->filtn=H5Z_FILTER_NONE;
-       filt->cd_nelmts = 0;
-   }
-
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_DEFLATE
-   *-------------------------------------------------------------------------
-   */
-   else if (HDstrcmp(scomp,"GZIP")==0)
-   {
-       filt->filtn=H5Z_FILTER_DEFLATE;
-       filt->cd_nelmts = 1;
-       if (no_param)
-       { /*no more parameters, GZIP must have parameter */
-           if (obj_list) HDfree(obj_list);
-           error_msg("missing compression parameter in <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-   }
-
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_SZIP
-   *-------------------------------------------------------------------------
-   */
-   else if (HDstrcmp(scomp,"SZIP")==0)
-   {
-       filt->filtn=H5Z_FILTER_SZIP;
-       filt->cd_nelmts = 2;
-       if (no_param)
-       { /*no more parameters, SZIP must have parameter */
-           if (obj_list) HDfree(obj_list);
-           error_msg("missing compression parameter in <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-   }
-
-   /*-------------------------------------------------------------------------
-   * H5Z_FILTER_SHUFFLE
-   *-------------------------------------------------------------------------
-   */
-   else if (HDstrcmp(scomp,"SHUF")==0)
-   {
-       filt->filtn=H5Z_FILTER_SHUFFLE;
-       filt->cd_nelmts = 0;
-       if (m>0)
-       { /*shuffle does not have parameter */
-           if (obj_list) HDfree(obj_list);
-           error_msg("extra parameter in SHUF <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-   }
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_FLETCHER32
-   *-------------------------------------------------------------------------
-   */
-   else if (HDstrcmp(scomp,"FLET")==0)
-   {
-       filt->filtn=H5Z_FILTER_FLETCHER32;
-       filt->cd_nelmts = 0;
-       if (m>0)
-       { /*shuffle does not have parameter */
-           if (obj_list) HDfree(obj_list);
-           error_msg("extra parameter in FLET <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-   }
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_NBIT
-   *-------------------------------------------------------------------------
-   */
-   else if (HDstrcmp(scomp,"NBIT")==0)
-   {
-       filt->filtn=H5Z_FILTER_NBIT;
-       filt->cd_nelmts = 0;
-       if (m>0)
-       { /*nbit does not have parameter */
-           if (obj_list) HDfree(obj_list);
-           error_msg("extra parameter in NBIT <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-   }
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_SCALEOFFSET
-   *-------------------------------------------------------------------------
-   */
-   else if (HDstrcmp(scomp,"SOFF")==0)
-   {
-       filt->filtn=H5Z_FILTER_SCALEOFFSET;
-       filt->cd_nelmts = 2;
-       if (no_param)
-       { /*no more parameters, SOFF must have parameter */
-           if (obj_list) HDfree(obj_list);
-           error_msg("missing compression parameter in <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-   }
-   else {
-       if (obj_list) HDfree(obj_list);
-       error_msg("invalid filter type in <%s>\n",str);
-       HDexit(EXIT_FAILURE);
-   }
-  }
- } /*i*/
-
-  /*-------------------------------------------------------------------------
-   * check valid parameters
-   *-------------------------------------------------------------------------
-   */
-
-   switch (filt->filtn)
-   {
-
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_DEFLATE
-   *-------------------------------------------------------------------------
-   */
-
-   case H5Z_FILTER_DEFLATE:
-       if (filt->cd_values[0]>9 )
-       {
-           if (obj_list) HDfree(obj_list);
-           error_msg("invalid compression parameter in <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-       break;
-
-  /*-------------------------------------------------------------------------
-   * H5Z_FILTER_SZIP
-   *-------------------------------------------------------------------------
-   */
-
-   case H5Z_FILTER_SZIP:
-       pixels_per_block=filt->cd_values[0];
-       if ((pixels_per_block%2)==1)
-       {
-           if (obj_list) HDfree(obj_list);
-           error_msg("pixels_per_block is not even in <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-       if (pixels_per_block>H5_SZIP_MAX_PIXELS_PER_BLOCK)
-       {
-           if (obj_list) HDfree(obj_list);
-           error_msg("pixels_per_block is too large in <%s>\n",str);
-           HDexit(EXIT_FAILURE);
-       }
-       if ( (HDstrcmp(smask,"NN")!=0) && (HDstrcmp(smask,"EC")!=0) )
-       {
-           if (obj_list) HDfree(obj_list);
-           error_msg("szip mask must be 'NN' or 'EC' \n");
-           HDexit(EXIT_FAILURE);
-       }
-       break;
-   default:
-       break;
-
-
-   };
-
-   return obj_list;
+	unsigned    i, u;
+	char        c;
+	size_t      len=HDstrlen(str);
+	int         j, m, n, k, l, p, r, q, end_obj=-1, no_param=0;
+	char        sobj[MAX_NC_NAME];
+	char        scomp[10];
+	char        stype[5];
+	char        smask[3];
+	obj_list_t* obj_list=NULL;
+	unsigned    pixels_per_block;
+
+
+	/* initialize compression  info */
+	HDmemset(filt,0,sizeof(filter_info_t));
+	*is_glb = 0;
+
+	/* check for the end of object list and number of objects */
+	for ( i = 0, n = 0; i < len; i++)
+	{
+		c = str[i];
+		if ( c==':' )
+		{
+			end_obj=i;
+		}
+		if ( c==',' )
+		{
+			n++;
+		}
+	}
+
+	if (end_obj==-1) /* missing : */
+	{
+		/* apply to all objects */
+		options->all_filter=1;
+		*is_glb = 1;
+	}
+
+	n++;
+	obj_list = (obj_list_t*) HDmalloc(n*sizeof(obj_list_t));
+	if (obj_list==NULL)
+	{
+		error_msg("could not allocate object list\n");
+		return NULL;
+	}
+	*n_objs=n;
+
+	/* get object list */
+	for ( j = 0, k = 0, n = 0; j < end_obj; j++, k++)
+	{
+		c = str[j];
+		sobj[k] = c;
+		if ( c==',' || j==end_obj-1)
+		{
+			if ( c==',') sobj[k]='\0'; else sobj[k+1]='\0';
+			HDstrcpy(obj_list[n].obj,sobj);
+			HDmemset(sobj,0,sizeof(sobj));
+			n++;
+			k=-1;
+		}
+	}
+	/* nothing after : */
+	if (end_obj+1==(int)len)
+	{
+		if (obj_list) HDfree(obj_list);
+		error_msg("input Error: Invalid compression type in <%s>\n",str);
+		HDexit(EXIT_FAILURE);
+	}
+
+
+	/* get filter additional parameters */
+	m=0;
+	for ( i=end_obj+1, k=0, j=0; i<len; i++,k++)
+	{
+		c = str[i];
+		scomp[k]=c;
+		if ( c=='=' || i==len-1)
+		{
+			if ( c=='=') /*one more parameter */
+			{
+				scomp[k]='\0';     /*cut space */
+
+				/*-------------------------------------------------------------------------
+				 * H5Z_FILTER_SZIP
+				 * szip has the format SZIP=<pixels per block,coding>
+				 * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
+				 * example SZIP=8,NN
+				 *-------------------------------------------------------------------------
+				 */
+				if (HDstrcmp(scomp,"SZIP")==0)
+				{
+					l=-1; /* mask index check */
+					for ( m=0,u=i+1; u<len; u++,m++)
+					{
+						if (str[u]==',')
+						{
+							stype[m]='\0'; /* end digit of szip */
+							l=0;  /* start EC or NN search */
+							u++;  /* skip ',' */
+						}
+						c = str[u];
+						if (!isdigit(c) && l==-1)
+						{
+							if (obj_list) HDfree(obj_list);
+							error_msg("compression parameter not digit in <%s>\n",str);
+							HDexit(EXIT_FAILURE);
+						}
+						if (l==-1)
+							stype[m]=c;
+						else
+						{
+							smask[l]=c;
+							l++;
+							if (l==2)
+							{
+								smask[l]='\0';
+								i=len-1; /* end */
+								(*n_objs)--; /* we counted an extra ',' */
+								if (HDstrcmp(smask,"NN")==0)
+									filt->cd_values[j++]=H5_SZIP_NN_OPTION_MASK;
+								else if (HDstrcmp(smask,"EC")==0)
+									filt->cd_values[j++]=H5_SZIP_EC_OPTION_MASK;
+								else
+								{
+									error_msg("szip mask must be 'NN' or 'EC' \n");
+									HDexit(EXIT_FAILURE);
+								}
+
+
+							}
+						}
+
+					}  /* u */
+				} /*if */
+
+				/*-------------------------------------------------------------------------
+				 * H5Z_FILTER_SCALEOFFSET
+				 * scaleoffset has the format SOFF=<scale_factor,scale_type>
+				 * scale_type can be
+				 *   integer datatype, H5Z_SO_INT (IN)
+				 *   float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE  (DS)
+				 *   float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE  (ES) , not yet implemented
+				 * for integer datatypes, scale_factor denotes Minimum Bits
+				 * for float datatypes, scale_factor denotes decimal scale factor
+				 *  examples
+				 *  SOFF=31,IN
+				 *  SOFF=3,DF
+				 *-------------------------------------------------------------------------
+				 */
+
+				else if (HDstrcmp(scomp,"SOFF")==0)
+				{
+					l=-1; /* mask index check */
+					for ( m=0,u=i+1; u<len; u++,m++)
+					{
+						if (str[u]==',')
+						{
+							stype[m]='\0'; /* end digit */
+							l=0;  /* start 'IN' , 'DS', or 'ES' search */
+							u++;  /* skip ',' */
+						}
+						c = str[u];
+						if (!isdigit(c) && l==-1)
+						{
+							if (obj_list) HDfree(obj_list);
+							error_msg("compression parameter is not a digit in <%s>\n",str);
+							HDexit(EXIT_FAILURE);
+						}
+						if (l==-1)
+							stype[m]=c;
+						else
+						{
+							smask[l]=c;
+							l++;
+							if (l==2)
+							{
+								smask[l]='\0';
+								i=len-1; /* end */
+								(*n_objs)--; /* we counted an extra ',' */
+								if (HDstrcmp(smask,"IN")==0)
+									filt->cd_values[j++]=H5Z_SO_INT;
+								else if (HDstrcmp(smask,"DS")==H5Z_SO_FLOAT_DSCALE)
+									filt->cd_values[j++]=H5Z_SO_FLOAT_DSCALE;
+								else
+								{
+									error_msg("scale type must be 'IN' or 'DS' \n");
+									HDexit(EXIT_FAILURE);
+								}
+
+							}
+						}
+
+					}  /* u */
+				} /*if */
+				/*-------------------------------------------------------------------------
+				 * User Defined
+				 *   has the format UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
+				 *  BZIP2 example
+				 *  UD=307,1,9
+				 *-------------------------------------------------------------------------
+				 */
+
+				else if (HDstrcmp(scomp,"UD")==0)
+				{
+					l=-1; /* filter number index check */
+					p=-1; /* CD_VAL count check */
+					r=-1; /* CD_VAL check */
+					for ( m=0,q=0,u=i+1; u<len; u++,m++,q++)
+					{
+						if (str[u]==',')
+						{
+							stype[q]='\0'; /* end digit */
+							if (l==-1)
+							{
+								filt->filtn=atoi(stype);
+								l=0;
+							}
+							else if (p==-1)
+							{
+								filt->cd_nelmts=atoi(stype);
+								p=0;
+							}
+							else
+								r=0;
+							q=0;
+							u++;  /* skip ',' */
+						}
+						c = str[u];
+						if (!isdigit(c) && l==-1)
+						{
+							if (obj_list) HDfree(obj_list);
+							error_msg("filter number parameter is not a digit in <%s>\n",str);
+							HDexit(EXIT_FAILURE);
+						}
+						stype[q]=c;
+						if (l==0 && p==0)
+						{
+							if (r==0)
+								filt->cd_values[j++]=atoi(stype);
+						}
+
+					}  /* u */
+
+					stype[q]='\0';
+				} /*if */
+
+
+				/*-------------------------------------------------------------------------
+				 * all other filters
+				 *-------------------------------------------------------------------------
+				 */
+
+				else
+				{
+					/* here we could have 1 or 2 digits  */
+					for ( m=0,u=i+1; u<len; u++,m++)
+					{
+						c = str[u];
+						if (!isdigit(c)){
+							if (obj_list) HDfree(obj_list);
+							error_msg("compression parameter is not a digit in <%s>\n",str);
+							HDexit(EXIT_FAILURE);
+						}
+						stype[m]=c;
+					} /* u */
+
+					stype[m]='\0';
+				} /*if */
+
+
+
+				filt->cd_values[j++]=atoi(stype);
+				i+=m; /* jump */
+			}
+			else if (i==len-1)
+			{ /*no more parameters */
+				scomp[k+1]='\0';
+				no_param=1;
+			}
+
+			/*-------------------------------------------------------------------------
+			 * translate from string to filter symbol
+			 *-------------------------------------------------------------------------
+			 */
+
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_NONE
+			 *-------------------------------------------------------------------------
+			 */
+			if (HDstrcmp(scomp,"NONE")==0)
+			{
+				filt->filtn=H5Z_FILTER_NONE;
+				filt->cd_nelmts = 0;
+			}
+
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_DEFLATE
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"GZIP")==0)
+			{
+				filt->filtn=H5Z_FILTER_DEFLATE;
+				filt->cd_nelmts = 1;
+				if (no_param)
+				{ /*no more parameters, GZIP must have parameter */
+					if (obj_list) HDfree(obj_list);
+					error_msg("missing compression parameter in <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_SZIP
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"SZIP")==0)
+			{
+				filt->filtn=H5Z_FILTER_SZIP;
+				filt->cd_nelmts = 2;
+				if (no_param)
+				{ /*no more parameters, SZIP must have parameter */
+					if (obj_list) HDfree(obj_list);
+					error_msg("missing compression parameter in <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_SHUFFLE
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"SHUF")==0)
+			{
+				filt->filtn=H5Z_FILTER_SHUFFLE;
+				filt->cd_nelmts = 0;
+				if (m>0)
+				{ /*shuffle does not have parameter */
+					if (obj_list) HDfree(obj_list);
+					error_msg("extra parameter in SHUF <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_FLETCHER32
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"FLET")==0)
+			{
+				filt->filtn=H5Z_FILTER_FLETCHER32;
+				filt->cd_nelmts = 0;
+				if (m>0)
+				{ /*shuffle does not have parameter */
+					if (obj_list) HDfree(obj_list);
+					error_msg("extra parameter in FLET <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_NBIT
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"NBIT")==0)
+			{
+				filt->filtn=H5Z_FILTER_NBIT;
+				filt->cd_nelmts = 0;
+				if (m>0)
+				{ /*nbit does not have parameter */
+					if (obj_list) HDfree(obj_list);
+					error_msg("extra parameter in NBIT <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+			/*-------------------------------------------------------------------------
+			 * H5Z_FILTER_SCALEOFFSET
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"SOFF")==0)
+			{
+				filt->filtn=H5Z_FILTER_SCALEOFFSET;
+				filt->cd_nelmts = 2;
+				if (no_param)
+				{ /*no more parameters, SOFF must have parameter */
+					if (obj_list) HDfree(obj_list);
+					error_msg("missing compression parameter in <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+			/*-------------------------------------------------------------------------
+			 * User Defined Filter
+			 *-------------------------------------------------------------------------
+			 */
+			else if (HDstrcmp(scomp,"UD")==0)
+			{
+				if (filt->cd_nelmts != j)
+				{ /* parameters does not match count */
+					if (obj_list) HDfree(obj_list);
+					error_msg("incorrect number of compression parameters in <%s>\n",str);
+					HDexit(EXIT_FAILURE);
+				}
+			}
+			else {
+				if (obj_list) HDfree(obj_list);
+				error_msg("invalid filter type in <%s>\n",str);
+				HDexit(EXIT_FAILURE);
+			}
+		}
+	} /*i*/
+
+	/*-------------------------------------------------------------------------
+	 * check valid parameters
+	 *-------------------------------------------------------------------------
+	 */
+
+	switch (filt->filtn)
+	{
+
+	/*-------------------------------------------------------------------------
+	 * H5Z_FILTER_DEFLATE
+	 *-------------------------------------------------------------------------
+	 */
+
+	case H5Z_FILTER_DEFLATE:
+		if (filt->cd_values[0]>9 )
+		{
+			if (obj_list) HDfree(obj_list);
+			error_msg("invalid compression parameter in <%s>\n",str);
+			HDexit(EXIT_FAILURE);
+		}
+		break;
+
+		/*-------------------------------------------------------------------------
+		 * H5Z_FILTER_SZIP
+		 *-------------------------------------------------------------------------
+		 */
+
+	case H5Z_FILTER_SZIP:
+		pixels_per_block=filt->cd_values[0];
+		if ((pixels_per_block%2)==1)
+		{
+			if (obj_list) HDfree(obj_list);
+			error_msg("pixels_per_block is not even in <%s>\n",str);
+			HDexit(EXIT_FAILURE);
+		}
+		if (pixels_per_block>H5_SZIP_MAX_PIXELS_PER_BLOCK)
+		{
+			if (obj_list) HDfree(obj_list);
+			error_msg("pixels_per_block is too large in <%s>\n",str);
+			HDexit(EXIT_FAILURE);
+		}
+		if ( (HDstrcmp(smask,"NN")!=0) && (HDstrcmp(smask,"EC")!=0) )
+		{
+			if (obj_list) HDfree(obj_list);
+			error_msg("szip mask must be 'NN' or 'EC' \n");
+			HDexit(EXIT_FAILURE);
+		}
+		break;
+	default:
+		break;
+
+
+	};
+
+	return obj_list;
 }
 
 
diff --git a/tools/h5repack/h5repack_plugin.sh.in b/tools/h5repack/h5repack_plugin.sh.in
new file mode 100644
index 0000000..a45d1fe
--- /dev/null
+++ b/tools/h5repack/h5repack_plugin.sh.in
@@ -0,0 +1,238 @@
+#! /bin/sh
+#
+# Copyright by The HDF Group.                                              
+# All rights reserved.                                                     
+#                                                                          
+# This file is part of HDF5. The full HDF5 copyright notice, including     
+# terms governing use, modification, and redistribution, is contained in   
+# the files COPYING and Copyright.html.  COPYING can be found at the root  
+# of the source code distribution tree; Copyright.html can be found at the 
+# root level of an installed copy of the electronic document set and is    
+# linked from the top-level documents page.  It can also be found at       
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have access  
+# to either file, you may request a copy from help@hdfgroup.org.           
+#
+srcdir=@srcdir@
+TOP_BUILDDIR=@top_builddir@
+
+# Determine backward compatibility options enabled
+DEPRECATED_SYMBOLS="@DEPRECATED_SYMBOLS@"
+
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+H5REPACK=h5repack               # The tool name
+H5REPACK_BIN=`pwd`/$H5REPACK    # The path of the tool binary
+
+H5DUMP=../h5dump/h5dump         # The h5dump tool name
+H5DUMP_BIN=`pwd`/$H5DUMP        # The path of the h5dump tool binary
+
+nerrors=0
+verbose=yes
+exit_code=$EXIT_SUCCESS
+
+TEST_NAME=ud_plugin
+FROM_DIR=`pwd`/.libs
+PLUGIN_LIB="$FROM_DIR/libdynlibadd.*"
+PLUGIN_LIBDIR=testdir3
+RM="rm -rf"
+
+GREP='grep'
+CP='cp'
+DIRNAME='dirname'
+LS='ls'
+AWK='awk'
+
+# source dirs
+SRC_TOOLS="$srcdir/.."
+
+# testfiles source dirs for tools
+SRC_H5REPACK_TESTFILES="$SRC_TOOLS/h5repack/testfiles"
+
+TESTDIR=testfiles
+test -d $TESTDIR || mkdir $TESTDIR
+
+######################################################################
+# test files
+# --------------------------------------------------------------------
+# All the test files copy from source directory to test directory
+# NOTE: Keep this framework to add/remove test files.
+#       Any test files from other tools can be used in this framework.
+#       This list are also used for checking exist.
+#       Comment '#' without space can be used.
+# --------------------------------------------------------------------
+LIST_HDF5_TEST_FILES="
+$SRC_H5REPACK_TESTFILES/h5repack_layout.h5
+$SRC_H5REPACK_TESTFILES/h5repack_layout.h5-plugin_test.ddl
+$SRC_H5REPACK_TESTFILES/plugin_test.h5repack_layout.h5.tst
+"
+
+#
+# copy test files and expected output files from source dirs to test dir
+#
+COPY_TESTFILES="$LIST_HDF5_TEST_FILES"
+
+# Main Body
+# Create test directories if not exists yet.
+test -d $PLUGIN_LIBDIR || mkdir -p $PLUGIN_LIBDIR
+if [ $? != 0 ]; then
+    echo "Failed to create test directory($PLUGIN_LIBDIR)"
+    exit $EXIT_FAILURE
+fi
+
+# copy plugin library for test
+$CP $PLUGIN_LIB $PLUGIN_LIBDIR
+if [ $? != 0 ]; then
+    echo "Failed to copy plugin library ($PLUGIN_LIB) for test."
+    exit $EXIT_FAILURE
+fi
+
+# setup plugin path
+ENVCMD="env HDF5_PLUGIN_PATH=${PLUGIN_LIBDIR}"
+
+COPY_TESTFILES_TO_TESTDIR()
+{
+    # copy test files. Used -f to make sure get a new copy
+    for tstfile in $COPY_TESTFILES
+    do
+        # ignore '#' comment
+        echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+        RET=$?
+        if [ $RET -eq 1 ]; then
+            # skip cp if srcdir is same as destdir
+            # this occurs when build/test performed in source dir and
+            # make cp fail
+            SDIR=`$DIRNAME $tstfile`
+            INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
+            if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+                $CP -f $tstfile $TESTDIR
+                if [ $? -ne 0 ]; then
+                    echo "Error: FAILED to copy $tstfile ."
+                
+                    # Comment out this to CREATE expected file
+                    exit $EXIT_FAILURE
+                fi
+            fi
+        fi
+    done
+}
+
+# Print a $* message left justified in a field of 70 characters
+#
+MESSAGE() {
+   SPACES="                                                               "
+   echo "$* $SPACES" | cut -c1-70 | tr -d '\012'
+}
+
+# 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'
+}
+
+# Print a line-line message left justified in a field of 70 characters
+# beginning with the word "Verifying".
+#
+VERIFY() {
+    MESSAGE "Verifying $*"
+}
+
+# This is different from $srcdir/../../bin/output_filter.sh
+STDOUT_FILTER() {
+    result_file=$1
+    tmp_file=/tmp/h5test_tmp_$$
+    # Filter name of files.
+    cp $result_file $tmp_file
+    sed -e '/^Opening file/d' -e '/^Making file/d' \
+    < $tmp_file > $result_file
+    # cleanup
+    rm -f $tmp_file
+}
+          
+# This runs h5repack comparing output with h5dump output
+# from -pH option
+#
+TOOLTEST_DUMP() 
+{
+    echo $@
+    infile=$TESTDIR/$2
+    outfile=$TESTDIR/out-$1.$2
+    expect1="$TESTDIR/$1.$2.tst"
+    actual1="$TESTDIR/$1.$2.out"
+    actual1_err="$TESTDIR/$1.$2.err"
+    expect2="$TESTDIR/$2-$1.ddl"
+    actual2="$TESTDIR/$2-$1.out"
+    actual2_err="$TESTDIR/$2-$1.err"
+
+    shift
+    shift
+    
+    # Run test.
+    TESTING $H5REPACK $@
+    (
+        $ENVCMD $H5REPACK_BIN "$@" $infile $outfile
+    ) >$actual1 2>$actual1_err
+    RET=$?
+    STDOUT_FILTER $actual1
+    cat $actual1_err >> $actual1
+    if [ $RET != 0 ] ; then
+     echo "*FAILED*"
+     nerrors="`expr $nerrors + 1`"
+    else
+     echo " PASSED"
+     if cmp -s $expect1 $actual1; then
+      echo " PASSED"
+     else
+      echo "*FAILED*"
+      echo "    Expected result (*.tst) differs from actual result (*.out)"
+      nerrors="`expr $nerrors + 1`"
+      test yes = "$verbose" && diff -c $expect1 $actual1 |sed 's/^/    /'
+     fi
+     VERIFY h5dump output -pH $outfile 
+     (
+        $ENVCMD $H5DUMP_BIN -pH $outfile 
+     ) >$actual2 2>$actual2_err
+     RET=$?
+     cat $actual2_err >> $actual2
+
+     if cmp -s $expect2 $actual2; then
+      echo " PASSED"
+     else
+      echo "*FAILED*"
+      echo "    Expected result (*.ddl) differs from actual result (*.out)"
+      nerrors="`expr $nerrors + 1`"
+      test yes = "$verbose" && diff -c $expect2 $actual2 |sed 's/^/    /'
+     fi
+          
+    fi
+
+    
+   rm -f $actual1 $actual1_err $actual2 $actual2_err
+   rm -f $outfile
+}
+
+##############################################################################
+###           T H E   T E S T S                               
+##############################################################################
+# prepare for test
+COPY_TESTFILES_TO_TESTDIR
+
+# Run the test
+arg="h5repack_layout.h5 -v -f UD=257,1,9"
+TOOLTEST_DUMP plugin_test $arg 
+
+# print results
+if test $nerrors -ne 0 ; then
+    echo "$nerrors errors encountered"
+    exit_code=$EXIT_FAILURE
+else
+    echo "All Plugin API tests passed."
+    exit_code=$EXIT_SUCCESS
+fi
+
+# Clean up temporary files/directories and leave
+$RM $PLUGIN_LIBDIR
+exit $exit_code
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 3b2a95b..71615f2 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -859,8 +859,8 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
 	hid_t space_id=-1, ref_obj_id=-1;
 
     ref_obj_id = H5Rdereference(obj_id, ref_type, ref_in);
-	if (ref_obj_id<0)
-		goto done;
+    if (ref_obj_id<0)
+       goto done;
 
 	ref_obj_name = MapIdToName(ref_obj_id, travt);
 	if (ref_obj_name == NULL)
@@ -881,8 +881,8 @@ static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
 
 done:
     H5E_BEGIN_TRY {
-    	H5Sclose(space_id);
-    	H5Oclose(ref_obj_id);
+      H5Sclose(space_id);
+      H5Oclose(ref_obj_id);
     } H5E_END_TRY;
 
 	return ret;
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index ed70fa6..cec9c86 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -48,20 +48,20 @@ static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *fil
  *-------------------------------------------------------------------------
  */
 
-int h5repack_verify(const char *fname,
-                    pack_opt_t *options)
+int
+h5repack_verify(const char *out_fname, pack_opt_t *options)
 {
-    hid_t        fid;  /* file ID */
-    hid_t        did;  /* dataset ID */
-    hid_t        pid;  /* dataset creation property list ID */
-    hid_t        sid;  /* space ID */
-    hid_t        tid;  /* type ID */
+    hid_t        fidout; /* file ID for output file*/
+    hid_t        did;    /* dataset ID */
+    hid_t        pid;    /* dataset creation property list ID */
+    hid_t        sid;    /* space ID */
+    hid_t        tid;    /* type ID */
     unsigned int i;
     trav_table_t *travt = NULL;
     int          ok = 1;
 
-    /* open the file */
-    if((fid = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
+    /* open the output file */
+    if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
         return -1;
 
     for(i = 0; i < options->op_tbl->nelems; i++)
@@ -73,7 +73,7 @@ int h5repack_verify(const char *fname,
         * open
         *-------------------------------------------------------------------------
         */
-        if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+        if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0)
             goto error;
         if((sid = H5Dget_space(did)) < 0)
             goto error;
@@ -125,7 +125,7 @@ int h5repack_verify(const char *fname,
         trav_table_init(&travt);
 
         /* get the list of objects in the file */
-        if(h5trav_gettable(fid, travt) < 0)
+        if(h5trav_gettable(fidout, travt) < 0)
             goto error;
 
         for(i = 0; i < travt->nobjs; i++)
@@ -139,7 +139,7 @@ int h5repack_verify(const char *fname,
                 * open
                 *-------------------------------------------------------------------------
                 */
-                if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+                if((did = H5Dopen2(fidout, name, H5P_DEFAULT)) < 0)
                     goto error;
                 if((sid = H5Dget_space(did)) < 0)
                     goto error;
@@ -199,8 +199,8 @@ int h5repack_verify(const char *fname,
     *-------------------------------------------------------------------------
     */
 
-    if (H5Fclose(fid) < 0)
-        return -1;
+    if (H5Fclose(fidout) < 0)
+	goto error;
 
     return ok;
 
@@ -209,7 +209,7 @@ error:
         H5Pclose(pid);
         H5Sclose(sid);
         H5Dclose(did);
-        H5Fclose(fid);
+        H5Fclose(fidout);
         if (travt)
             trav_table_free(travt);
     } H5E_END_TRY;
@@ -522,6 +522,9 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
         switch (filtn)
         {
 
+        case H5Z_FILTER_NONE:
+        	break;
+
         case H5Z_FILTER_SHUFFLE:
 
             /* 1 private client value is returned by DCPL */
@@ -598,7 +601,17 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
             break;
 
         default:
-            /* filter has no local values */
+			if ( cd_nelmts != filter[i].cd_nelmts)
+				return 0;
+
+			for( j = 0; j < cd_nelmts; j++)
+			{
+				if (cd_values[j] != filter[i].cd_values[j])
+				{
+					return 0;
+				}
+
+			}
             break;
 
         } /* switch */
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index a22b0fe..4510bd5 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -84,6 +84,9 @@
 /* obj and region references */
 #define FNAME_REF   "h5repack_refs.h5"
 
+/* obj and region references in attr of compound and vlen type */
+#define FNAME_ATTR_REF   "h5repack_attr_refs.h5"
+
 const char *H5REPACK_FILENAMES[] = {
     "h5repack_big_out",
     NULL
@@ -146,6 +149,7 @@ static int verify_userblock( const char* filename);
 static int make_userblock_file(void);
 static int make_named_dtype(hid_t loc_id);
 static int make_references(hid_t loc_id);
+static int make_complex_attr_references(hid_t loc_id);
 
 
 /*-------------------------------------------------------------------------
@@ -1857,6 +1861,17 @@ int make_testfiles(void)
     if(H5Fclose(fid) < 0)
         return -1;
 
+    /*-------------------------------------------------------------------------
+    * create a file with obj and region references in attribute of compound and 
+    * vlen datatype
+    *-------------------------------------------------------------------------*/
+    if((fid = H5Fcreate(FNAME_ATTR_REF,H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT)) < 0)
+        return -1;
+    if (make_complex_attr_references(fid) < 0)
+        goto out;
+    if(H5Fclose(fid) < 0)
+        return -1;
+
     return 0;
 
 out:
@@ -2995,31 +3010,31 @@ out:
  *
  * Purpose: create datasets with contiguous and chunked layouts:
  *
- *	contig_small: < 1k, fixed dims datspace
- *	chunked_small_fixed: < 1k, fixed dims dataspace
+ *  contig_small: < 1k, fixed dims datspace
+ *  chunked_small_fixed: < 1k, fixed dims dataspace
  *
  *-------------------------------------------------------------------------
  */
-#define S_DIM1	4
-#define S_DIM2	10
-#define CONTIG_S	"contig_small"
-#define CHUNKED_S_FIX	"chunked_small_fixed"
+#define S_DIM1  4
+#define S_DIM2  10
+#define CONTIG_S  "contig_small"
+#define CHUNKED_S_FIX  "chunked_small_fixed"
 
 static
 int make_layout2(hid_t loc_id)
 {
 
-    hid_t    contig_dcpl = -1; 	/* dataset creation property list */
+    hid_t    contig_dcpl = -1;   /* dataset creation property list */
     hid_t    chunked_dcpl = -1; /* dataset creation property list */
 
-    int      i, j, n;		/* Local index variables */
-    int	     ret_value = -1;	/* Return value */
-    hid_t    s_sid = -1;	/* dataspace ID */
+    int      i, j, n;    /* Local index variables */
+    int       ret_value = -1;  /* Return value */
+    hid_t    s_sid = -1;  /* dataspace ID */
 
-    hsize_t  s_dims[RANK] = {S_DIM1,S_DIM2};	/* Dataspace (< 1 k) */
-    hsize_t  chunk_dims[RANK] = {S_DIM1/2, S_DIM2/2};	/* Dimension sizes for chunks */
+    hsize_t  s_dims[RANK] = {S_DIM1,S_DIM2};  /* Dataspace (< 1 k) */
+    hsize_t  chunk_dims[RANK] = {S_DIM1/2, S_DIM2/2};  /* Dimension sizes for chunks */
 
-    int      s_buf[S_DIM1][S_DIM2];	/* Temporary buffer */
+    int      s_buf[S_DIM1][S_DIM2];  /* Temporary buffer */
 
     for(i = n = 0; i < S_DIM1; i++) {
         for (j = 0; j < S_DIM2; j++) {
@@ -3355,8 +3370,8 @@ int make_external(hid_t loc_id)
     hid_t   sid=-1;
     hid_t   dcpl;
     int     buf[2]={1,2};
-    hsize_t cur_size[1];		/* data space current size	*/
-    hsize_t max_size[1];		/* data space maximum size	*/
+    hsize_t cur_size[1];    /* data space current size  */
+    hsize_t max_size[1];    /* data space maximum size  */
     hsize_t size;
 
     cur_size[0] = max_size[0] = 2;
@@ -5916,7 +5931,6 @@ static herr_t add_attr_with_objref(hid_t file_id, hid_t obj_id)
 {
     int ret = SUCCEED;
     int status;
-    int data_attr_int[2] = {10,20}; 
     /* attr obj ref */
     hsize_t dim_attr_objref[1]={3};
     hobj_ref_t data_attr_objref[3];
@@ -6460,3 +6474,436 @@ static herr_t make_references(hid_t loc_id)
     return ret;
 }
 
+/*-------------------------------------------------------------------------
+* Function: make_complex_attr_references
+*
+* Purpose: 
+*   create a file with :
+*   1. obj ref in attribute of compound type
+*   2. region ref in attribute of compound type
+*   3. obj ref in attribute of vlen type
+*   4. region ref in attribute of vlen type
+*
+* Programmer: Jonathan (March 25, 2010)
+*-------------------------------------------------------------------------
+*/
+/* obj dset */
+#define RANK_OBJ 2
+#define DIM0_OBJ 6
+#define DIM1_OBJ 10
+/* container dset */
+#define RANK_DSET 1
+#define DIM_DSET 4
+/* 1. obj references in compound attr */
+#define RANK_COMP_OBJREF 1
+#define DIM_COMP_OBJREF 3   /* for dataset, group, datatype */
+/* 2. region references in compound attr */
+#define RANK_COMP_REGREF 1
+#define DIM_COMP_REGREF 1   /* for element region */
+/* 3. obj references in vlen attr */
+#define RANK_VLEN_OBJREF 1
+#define DIM_VLEN_OBJREF 3   /* for dataset, group, datatype */
+#define LEN0_VLEN_OBJREF 1  /* dataset */
+#define LEN1_VLEN_OBJREF 1  /* group */
+#define LEN2_VLEN_OBJREF 1  /* datatype */
+/* 4. region references in vlen attr */
+#define RANK_VLEN_REGREF 1
+#define DIM_VLEN_REGREF 1   /*  for element region */
+#define LEN0_VLEN_REGREF 1  /* element region  */ 
+
+static herr_t make_complex_attr_references(hid_t loc_id)
+{
+    herr_t ret = SUCCEED;
+    herr_t status; 
+    /* 
+     * for objects 
+     */
+    hid_t objgid=0, objdid=0, objtid=0, objsid=0;
+    hsize_t obj_dims[RANK_OBJ] = {DIM0_OBJ, DIM1_OBJ};
+    int obj_data[DIM0_OBJ][DIM1_OBJ]=
+        {{ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9},
+         {10,11,12,13,14,15,16,17,18,19},
+         {20,21,22,23,24,25,26,27,28,29},
+         {30,31,32,33,34,35,36,37,38,39},
+         {40,41,42,43,44,45,46,47,48,49},
+         {50,51,52,53,54,55,56,57,58,59}};
+
+    /*
+     * group main
+     */
+    hid_t main_gid=0;
+    /*
+     * dataset which the attribute will be attached to
+     */
+    hsize_t main_dset_dims[RANK_DSET] = {DIM_DSET};
+    hid_t main_sid=0, main_did=0;
+    /* 
+     * 1. obj references in compound attr 
+     */
+    hid_t comp_objref_tid=0, comp_objref_aid=0;
+    typedef struct comp_objref_t {
+        hobj_ref_t val_objref;
+        int val_int;
+    } comp_objref_t;
+    comp_objref_t comp_objref_data[DIM_COMP_OBJREF];
+    hid_t comp_objref_attr_sid=0;
+    hsize_t comp_objref_dim[RANK_COMP_OBJREF] = {DIM_COMP_OBJREF};
+
+    /* 
+     * 2. region references in compound attr 
+     */
+    hid_t comp_regref_tid=0, comp_regref_aid=0;
+    typedef struct comp_regref_t {
+        hdset_reg_ref_t val_regref;
+        int val_int;
+    } comp_regref_t;
+    comp_regref_t comp_regref_data[DIM_COMP_REGREF];
+    hid_t comp_regref_attr_sid=0;
+    hsize_t comp_regref_dim[RANK_COMP_REGREF] = {DIM_COMP_REGREF};
+    hsize_t coords[4][2] = { {0,1}, {2,3}, {3,4}, {4,5} };
+    
+    /* 
+     * 3. obj references in vlen attr 
+     */
+    hid_t vlen_objref_attr_tid=0, vlen_objref_attr_sid=0;
+    hid_t vlen_objref_attr_id=0;
+    hvl_t vlen_objref_data[DIM_VLEN_OBJREF];
+    hsize_t vlen_objref_dims[RANK_VLEN_OBJREF] = {DIM_VLEN_OBJREF};
+
+    /* 
+     * 4. region references in vlen attr
+     */
+    hid_t vlen_regref_attr_tid=0, vlen_regref_attr_sid=0;
+    hid_t vlen_regref_attr_id=0;
+    hvl_t vlen_regref_data[DIM_VLEN_REGREF];
+    hsize_t vlen_regref_dim[RANK_VLEN_REGREF] = {DIM_VLEN_REGREF};
+
+
+    /* ---------------------------------------
+     * create objects which to be referenced 
+     */
+    /* object1 group */
+    objgid = H5Gcreate2(loc_id, NAME_OBJ_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+    /* object2 dataset */
+    objsid = H5Screate_simple(RANK_OBJ, obj_dims, NULL);
+    objdid = H5Dcreate2(loc_id, NAME_OBJ_DS1, H5T_NATIVE_INT, objsid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    status = H5Dwrite(objdid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_data[0]);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* object3 named datatype */
+    objtid = H5Tcopy(H5T_NATIVE_INT);
+    status = H5Tcommit2(loc_id, NAME_OBJ_NDTYPE, objtid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Tcommit2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+
+    /* ---------------------------------------------
+     *  Put testing objs in this group 
+     * create group contain dataset with attribute and the attribute has
+     * compound type which contain obj and region reference */
+    main_gid = H5Gcreate2(loc_id, "group_main", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    if (main_gid < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /*----------------------------------------------------------
+     * create dataset which the attribute will be attached to
+     */
+    main_sid = H5Screate_simple(RANK_DSET, main_dset_dims, NULL);
+
+    main_did = H5Dcreate2(main_gid, "dset_main", H5T_NATIVE_INT, main_sid, H5P_DEFAULT,H5P_DEFAULT, H5P_DEFAULT);
+    
+    status = H5Dwrite(main_did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, obj_data[0]);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /*-------------------------------------------------------------------
+     * 1. create obj references in a attribute of compound type
+     */
+
+    /* 
+     * create compound type for attribute 
+     */
+    comp_objref_tid = H5Tcreate (H5T_COMPOUND, sizeof(comp_objref_t));
+
+    H5Tinsert(comp_objref_tid, "value_objref", HOFFSET(comp_objref_t, val_objref), H5T_STD_REF_OBJ);
+    H5Tinsert(comp_objref_tid, "value_int", HOFFSET(comp_objref_t, val_int), H5T_NATIVE_INT);
+
+    /*
+     * Create the object references into compound type
+     */
+     /* references to dataset */
+    status = H5Rcreate (&(comp_objref_data[0].val_objref), loc_id, NAME_OBJ_DS1, H5R_OBJECT,-1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    comp_objref_data[0].val_int = 0;
+
+     /* references to group */
+    status = H5Rcreate (&(comp_objref_data[1].val_objref), loc_id, NAME_OBJ_GRP, H5R_OBJECT,-1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    comp_objref_data[1].val_int = 10;
+
+     /* references to datatype */
+    status = H5Rcreate (&(comp_objref_data[2].val_objref), loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT,-1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    comp_objref_data[2].val_int = 20;
+    
+    /* 
+     * create attribute and write the object ref
+     */
+    comp_objref_attr_sid = H5Screate_simple (RANK_COMP_OBJREF, comp_objref_dim, NULL);
+    comp_objref_aid = H5Acreate2 (main_did, "Comp_OBJREF", comp_objref_tid, comp_objref_attr_sid, H5P_DEFAULT, H5P_DEFAULT);
+    status = H5Awrite (comp_objref_aid, comp_objref_tid, comp_objref_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Awrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /*-------------------------------------------------------------------
+     * 2. create region references in attribute of compound type
+     */
+    /*
+     * create compound type for attribute
+     */
+    comp_regref_tid = H5Tcreate (H5T_COMPOUND, sizeof(comp_regref_t));
+
+    H5Tinsert(comp_regref_tid, "value_regref", HOFFSET(comp_regref_t, val_regref), H5T_STD_REF_DSETREG);
+    H5Tinsert(comp_regref_tid, "value_int", HOFFSET(comp_regref_t, val_int), H5T_NATIVE_INT);
+
+    /*
+     * create the region reference 
+     */
+    status = H5Sselect_elements (objsid, H5S_SELECT_SET, (size_t)4, coords[0]);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    status = H5Rcreate (&(comp_regref_data[0].val_regref), loc_id, NAME_OBJ_DS1, H5R_DATASET_REGION, objsid);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    comp_regref_data[0].val_int = 10;
+
+    /*
+     * create attribute and write the region ref
+     */
+    comp_regref_attr_sid = H5Screate_simple (RANK_COMP_REGREF, comp_regref_dim, NULL);
+    comp_regref_aid = H5Acreate2 (main_did, "Comp_REGREF", comp_regref_tid, comp_regref_attr_sid, H5P_DEFAULT, H5P_DEFAULT);
+    status = H5Awrite (comp_regref_aid, comp_regref_tid, comp_regref_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Awrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+
+    /*-------------------------------------------------------------------
+     * 3. create obj references in attribute of vlen type
+     */
+    /*
+     * prepare vlen data
+     */
+     vlen_objref_data[0].len = LEN0_VLEN_OBJREF;
+     vlen_objref_data[0].p = malloc (vlen_objref_data[0].len * sizeof(hobj_ref_t));
+     vlen_objref_data[1].len = LEN1_VLEN_OBJREF;
+     vlen_objref_data[1].p = malloc (vlen_objref_data[1].len * sizeof(hobj_ref_t));
+     vlen_objref_data[2].len = LEN2_VLEN_OBJREF;
+     vlen_objref_data[2].p = malloc (vlen_objref_data[2].len * sizeof(hobj_ref_t));
+
+     /* 
+      * create obj references 
+      */
+     /* reference to dataset */
+     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[0].p)[0], loc_id, NAME_OBJ_DS1, H5R_OBJECT, -1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+     /* reference to group */
+     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[1].p)[0], loc_id, NAME_OBJ_GRP, H5R_OBJECT, -1); 
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+     /* reference to datatype */
+     status = H5Rcreate (&((hobj_ref_t*)vlen_objref_data[2].p)[0], loc_id, NAME_OBJ_NDTYPE, H5R_OBJECT, -1);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+     
+     /* 
+      * create vlen type with obj reference
+      */
+     vlen_objref_attr_tid = H5Tvlen_create (H5T_STD_REF_OBJ);
+     vlen_objref_attr_sid = H5Screate_simple (RANK_VLEN_OBJREF, vlen_objref_dims, NULL);
+
+     /*
+     * create attribute and write the object reference 
+     */
+     vlen_objref_attr_id = H5Acreate2(main_did, "Vlen_OBJREF", vlen_objref_attr_tid, vlen_objref_attr_sid, H5P_DEFAULT, H5P_DEFAULT);
+     status = H5Awrite (vlen_objref_attr_id, vlen_objref_attr_tid, vlen_objref_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Awrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /* close resource for vlen data */
+    status = H5Dvlen_reclaim (vlen_objref_attr_tid, vlen_objref_attr_sid, H5P_DEFAULT, vlen_objref_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dvlen_reclaim failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+    /*-------------------------------------------------------------------
+     * 4. create region references in a attribute of vlen type
+     */
+     
+    /*
+     * prepare vlen data
+     */
+    vlen_regref_data[0].len = LEN0_VLEN_REGREF;
+    vlen_regref_data[0].p = malloc (vlen_regref_data[0].len * sizeof(hdset_reg_ref_t));
+
+    /*
+     * create region reference 
+     */
+    status = H5Sselect_elements(objsid, H5S_SELECT_SET, (size_t)4, coords[0]);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    status = H5Rcreate (&((hdset_reg_ref_t*)vlen_regref_data[0].p)[0], loc_id, NAME_OBJ_DS1, H5R_DATASET_REGION, objsid);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    
+    /* 
+     * create vlen type with region reference
+     */
+    vlen_regref_attr_tid = H5Tvlen_create(H5T_STD_REF_DSETREG);
+    vlen_regref_attr_sid = H5Screate_simple(RANK_VLEN_REGREF, vlen_regref_dim, NULL);
+    
+    /*
+     * create attribute and write the region reference 
+     */
+    vlen_regref_attr_id = H5Acreate2(main_did, "Vlen_REGREF", vlen_regref_attr_tid, vlen_regref_attr_sid, H5P_DEFAULT, H5P_DEFAULT);
+    status = H5Awrite(vlen_regref_attr_id, vlen_regref_attr_tid, vlen_regref_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Awrite failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+    
+    /* close resource for vlen data */
+    status = H5Dvlen_reclaim (vlen_regref_attr_tid, vlen_regref_attr_sid, H5P_DEFAULT, vlen_regref_data);
+    if (status < 0)
+    {
+        fprintf(stderr, "Error: %s %d> H5Dvlen_reclaim failed.\n", FUNC, __LINE__);
+        ret = FAIL;
+        goto out;
+    }
+
+out:
+    /* release resources */
+    if (objgid > 0)
+        H5Gclose(objgid);
+    if (objsid > 0)
+        H5Sclose(objsid);
+    if (objdid > 0)
+        H5Dclose(objdid);
+    if (objtid > 0)
+        H5Tclose(objtid);
+
+    if (main_gid > 0)
+        H5Gclose(main_gid);
+    if (main_sid > 0)
+        H5Sclose(main_sid);
+    if (main_did > 0)
+        H5Dclose(main_did);
+    /* comp obj ref */
+    if (comp_objref_tid > 0)
+        H5Tclose(comp_objref_tid);
+    if (comp_objref_aid > 0)
+        H5Aclose(comp_objref_aid);
+    if (comp_objref_attr_sid > 0)
+        H5Sclose(comp_objref_attr_sid);
+    /* comp region ref */
+    if (comp_regref_tid > 0)
+        H5Tclose(comp_regref_tid);
+    if (comp_regref_aid > 0)
+        H5Aclose(comp_regref_aid);
+    if (comp_regref_attr_sid > 0)
+        H5Sclose(comp_regref_attr_sid);
+    /* vlen obj ref */
+    if (vlen_objref_attr_id > 0)
+        H5Aclose(vlen_objref_attr_id);
+    if (vlen_objref_attr_sid > 0)
+        H5Sclose(vlen_objref_attr_sid);
+    if (vlen_objref_attr_tid > 0)
+        H5Tclose(vlen_objref_attr_tid);
+    /* vlen region ref */
+    if (vlen_regref_attr_id > 0)
+        H5Aclose(vlen_regref_attr_id);
+    if (vlen_regref_attr_sid > 0)
+        H5Sclose(vlen_regref_attr_sid);
+    if (vlen_regref_attr_tid > 0)
+        H5Tclose(vlen_regref_attr_tid);
+
+    return ret;
+}
diff --git a/tools/h5repack/testfiles/h5repack-help.txt b/tools/h5repack/testfiles/h5repack-help.txt
index 67e31fe..ba58bc6 100644
--- a/tools/h5repack/testfiles/h5repack-help.txt
+++ b/tools/h5repack/testfiles/h5repack-help.txt
@@ -45,6 +45,7 @@ usage: h5repack [OPTIONS] file1 file2
         FLET, to apply the HDF5 checksum filter
         NBIT, to apply the HDF5 NBIT filter (NBIT compression)
         SOFF, to apply the HDF5 Scale/Offset filter
+        UD,   to apply a user defined filter
         NONE, to remove all filters
       <filter parameters> is optional filter parameter information
         GZIP=<deflation level> from 1-9
@@ -55,6 +56,9 @@ usage: h5repack [OPTIONS] file1 file2
         NBIT (no parameter)
         SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type
             is either IN or DS
+        UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
+            required values for filter_number,cd_value_count,value_1
+            optional values for value_2 to value_N
         NONE (no parameter)
 
     LAYT - is a string with the format:
@@ -79,14 +83,14 @@ Examples of use:
 
    GZIP compression with level 1 to all objects
 
-2) h5repack -v -f A:SZIP=8,NN file1 file2
+2) h5repack -v -f dset1:SZIP=8,NN file1 file2
 
-   SZIP compression with 8 pixels per block and NN coding method to object A
+   SZIP compression with 8 pixels per block and NN coding method to object dset1
 
-3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2
+3) h5repack -v -l dset1,dset2:CHUNK=20x10 -f dset3,dset4,dset5:NONE file1 file2
 
-   Chunked layout, with a layout size of 20x10, to objects A and B
-   and remove filters to objects C, D, F
+   Chunked layout, with a layout size of 20x10, to objects dset1 and dset2
+   and remove filters to objects dset3, dset4, dset5
 
 4) h5repack -L -c 10 -s 20:dtype file1 file2 
 
@@ -97,3 +101,7 @@ Examples of use:
 
    Add both filters SHUF and GZIP in this order to all datasets
 
+6) h5repack -f UD=307,1,9 file1 file2 
+
+   Add bzip2 filter to all datasets
+
diff --git a/tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl
new file mode 100644
index 0000000..a7ba967
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl
@@ -0,0 +1,158 @@
+HDF5 "testfiles/out-plugin_test.h5repack_layout.h5" {
+GROUP "/" {
+   DATASET "dset1" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 40, 20 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset2" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 40, 20 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset3" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 40, 20 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset4" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 40, 20 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset_chunk" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, H5S_UNLIMITED ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 20, 10 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset_compact" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 40, 20 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset_contiguous" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 40, 20 ) / ( 40, 20 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 40, 20 )
+         SIZE 3200 (1.000:1 COMPRESSION)
+      }
+      FILTERS {
+         USER_DEFINED_FILTER {
+            FILTER_ID 257
+            COMMENT dynlib1
+            PARAMS { 9 }
+         }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+}
+}
diff --git a/tools/h5repack/testfiles/h5repack_objs.h5 b/tools/h5repack/testfiles/h5repack_objs.h5
index 061b1cd..16d55da 100644
--- a/tools/h5repack/testfiles/h5repack_objs.h5
+++ b/tools/h5repack/testfiles/h5repack_objs.h5
diff --git a/tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst b/tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst
new file mode 100644
index 0000000..7f9bd6e
--- /dev/null
+++ b/tools/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst
@@ -0,0 +1,14 @@
+Objects to modify layout are...
+Objects to apply filter are...
+ User Defined 257
+-----------------------------------------
+ Type     Filter (Compression)     Name
+-----------------------------------------
+ group                       /
+ dset     UD   (1.000:1)     /dset1
+ dset     UD   (1.000:1)     /dset2
+ dset     UD   (1.000:1)     /dset3
+ dset     UD   (1.000:1)     /dset4
+ dset     UD   (1.000:1)     /dset_chunk
+ dset     UD   (1.000:1)     /dset_compact
+ dset     UD   (1.000:1)     /dset_contiguous