Merge branch 'develop' into gcc_flag_cull

51 files changed, 744 insertions, 539 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ce91052..b84cc7c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -851,6 +851,11 @@ if (EXISTS "${HDF5_SOURCE_DIR}/fortran" AND IS_DIRECTORY "${HDF5_SOURCE_DIR}/for
   option (SKIP_HDF5_FORTRAN_SHARED "Do not build the fortran shared libraries" OFF)
   if (HDF5_BUILD_FORTRAN)
     if (BUILD_SHARED_LIBS AND APPLE)
+      # Tell cmake to do the right thing with COMMON symbols, this fixes 
+      # corrupt values with COMMON and EQUIVALENCE when building shared 
+      # Fortran libraries on OSX with gnu and Intel compilers (HDFFV-2772).
+      # *** NOTE: Fix does not work with Cmake. ***
+      # set (HDF5_LINKER_FLAGS "-Wl,-commons,use_dylibs")
       if (NOT ALLOW_UNSUPPORTED)
         message (STATUS " **** Shared FORTRAN libraries are unsupported **** ")
         set (SKIP_HDF5_FORTRAN_SHARED ON)
diff --git a/MANIFEST b/MANIFEST
index e448a44..c34e614 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -2240,6 +2240,8 @@
 ./tools/test/h5diff/testfiles/h5diff_709.txt
 ./tools/test/h5diff/testfiles/h5diff_710.txt
 ./tools/test/h5diff/testfiles/h5diff_80.txt
+./tools/test/h5diff/testfiles/h5diff_800.txt
+./tools/test/h5diff/testfiles/h5diff_801.txt
 ./tools/test/h5diff/testfiles/h5diff_90.txt
 ./tools/test/h5diff/testfiles/h5diff_100.txt
 ./tools/test/h5diff/testfiles/h5diff_101.txt
@@ -2350,6 +2352,7 @@
 ./tools/test/h5diff/testfiles/h5diff_basic2.h5
 ./tools/test/h5diff/testfiles/h5diff_dset1.h5
 ./tools/test/h5diff/testfiles/h5diff_dset2.h5
+./tools/test/h5diff/testfiles/h5diff_dset3.h5
 ./tools/test/h5diff/testfiles/h5diff_dtypes.h5
 ./tools/test/h5diff/testfiles/h5diff_empty.h5
 ./tools/test/h5diff/testfiles/h5diff_hyper1.h5
@@ -2429,6 +2432,7 @@
 ./tools/test/h5repack/testfiles/h5repack_soffset.h5
 ./tools/test/h5repack/testfiles/h5repack_szip.h5
 ./tools/test/h5repack/testfiles/ublock.bin
+./tools/test/h5repack/testfiles/crtorder.tordergr.h5.ddl
 ./tools/test/h5repack/testfiles/deflate_limit.h5repack_layout.h5.ddl
 ./tools/test/h5repack/testfiles/plugin_none.h5repack_layout.UD.h5.tst
 ./tools/test/h5repack/testfiles/plugin_test.h5repack_layout.h5.tst
diff --git a/configure.ac b/configure.ac
index d0aeda9..9695fe3 100644
--- a/configure.ac
+++ b/configure.ac
@@ -918,14 +918,13 @@ H5_FORTRAN_SHARED="no"
 if test "X${HDF_FORTRAN}" = "Xyes" && test "X${enable_shared}" != "Xno"; then
   AC_MSG_CHECKING([if shared Fortran libraries are supported])
   H5_FORTRAN_SHARED="yes"
-
-  ## Disable fortran shared libraries on Mac. (MAM - 03/30/11)
-
+  ## tell libtool to do the right thing with COMMON symbols, this fixes 
+  ## corrupt values with COMMON and EQUIVALENCE when building shared 
+  ## Fortran libraries on OSX with gnu and Intel compilers (HDFFV-2772).
   case "`uname`" in
     Darwin*)
-    H5_FORTRAN_SHARED="no"
-    CHECK_WARN="Shared Fortran libraries not currently supported on Mac."
-      ;;
+    H5_LDFLAGS="$H5_LDFLAGS -Wl,-commons,use_dylibs"
+    ;;
   esac
 
   ## Report results of check(s)
@@ -3484,6 +3483,14 @@ chmod 755 tools/src/misc/h5cc
 
 if test "X$HDF_FORTRAN" = "Xyes"; then
   chmod 755 fortran/src/h5fc
+  ## libtool does not pass the correct argument linker (wl=) for the Intel Fortran compiler 
+  ## on OS X, which is needed when building shared libraries on OS X.  This script 
+  ## replaces the 3rd occurrence, which is for Fortran, of wl="" with wl="-Wl," (HDFFV-2772)
+  case "`uname`" in
+    Darwin*)
+      cat libtool | awk '/wl=\"/{c++;if(c==3){sub("wl=\"\"","wl=\"-Wl,\"");c=0}}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool
+      ;;
+  esac
 fi
 
 if test "X$HDF_CXX" = "Xyes"; then
diff --git a/fortran/test/fortranlib_test.F90 b/fortran/test/fortranlib_test.F90
index 94b084e..8d5b32b 100644
--- a/fortran/test/fortranlib_test.F90
+++ b/fortran/test/fortranlib_test.F90
@@ -50,11 +50,11 @@ PROGRAM fortranlibtest
   IF(total_error .EQ. 0) THEN
 
      WRITE(*, '(" FORTRANLIB_TEST is linked with HDF5 Library version ")', advance="NO")
-     WRITE(*, '(I1)', advance="NO") majnum
+     WRITE(*, '(I0)', advance="NO") majnum
      WRITE(*, '(".")', advance="NO")
-     WRITE(*, '(I1)', advance="NO") minnum
+     WRITE(*, '(I0)', advance="NO") minnum
      WRITE(*, '(" release ")', advance="NO")
-     WRITE(*, '(I3)') relnum
+     WRITE(*, '(I0)') relnum
   ELSE
      total_error = total_error + 1
   ENDIF
diff --git a/fortran/test/fortranlib_test_1_8.F90 b/fortran/test/fortranlib_test_1_8.F90
index 850cab9..1306da5 100644
--- a/fortran/test/fortranlib_test_1_8.F90
+++ b/fortran/test/fortranlib_test_1_8.F90
@@ -46,11 +46,11 @@ PROGRAM fortranlibtest
   CALL h5get_libversion_f(majnum, minnum, relnum, total_error)
   IF(total_error .EQ. 0) THEN
      WRITE(*, '(" FORTRANLIB_TEST is linked with HDF5 Library version ")', advance="NO")
-     WRITE(*, '(I1)', advance="NO") majnum
+     WRITE(*, '(I0)', advance="NO") majnum
      WRITE(*, '(".")', advance="NO")
-     WRITE(*, '(I1)', advance="NO") minnum
+     WRITE(*, '(I0)', advance="NO") minnum
      WRITE(*, '(" release ")', advance="NO")
-     WRITE(*, '(I3)') relnum
+     WRITE(*, '(I0)') relnum
   ELSE
      total_error = total_error + 1
   ENDIF
diff --git a/fortran/test/fortranlib_test_F03.F90 b/fortran/test/fortranlib_test_F03.F90
index ae12dba..9a74120 100644
--- a/fortran/test/fortranlib_test_F03.F90
+++ b/fortran/test/fortranlib_test_F03.F90
@@ -47,11 +47,11 @@ PROGRAM fortranlibtest_F03
   CALL h5get_libversion_f(majnum, minnum, relnum, total_error)
   IF(total_error .EQ. 0) THEN
      WRITE(*, '(" FORTRANLIB_TEST is linked with HDF5 Library version ")', advance="NO")
-     WRITE(*, '(I1)', advance="NO") majnum
+     WRITE(*, '(I0)', advance="NO") majnum
      WRITE(*, '(".")', advance="NO") 
-     WRITE(*, '(I1)', advance="NO") minnum
+     WRITE(*, '(I0)', advance="NO") minnum
      WRITE(*, '(" release ")', advance="NO")
-     WRITE(*, '(I3)') relnum
+     WRITE(*, '(I0)') relnum
   ELSE
      total_error = total_error + 1
   ENDIF
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index c670066..8fb56cc 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -74,15 +74,15 @@ New Features
 
     Tools:
     ------
-    - 
+    -
 
     High-Level APIs:
     ---------------
-    - 
+    -
 
     C Packet Table API
     ------------------
-    - 
+    -
 
     Internal header file
     --------------------
@@ -105,7 +105,7 @@ Bug Fixes since HDF5-1.10.1 release
 
     Configuration
     -------------
-    - 
+    -
 
     Performance
     -------------
@@ -117,7 +117,9 @@ Bug Fixes since HDF5-1.10.1 release
 
     Tools
     -----
-    - 
+    - Improved h5diff compare of strings and arrays.
+
+      (ADB, 2017/05/18, HDFFV-9055, HDFFV-10128)
 
     High-Level APIs:
     ------
@@ -302,16 +304,16 @@ The following platforms are not supported but have been tested for this release.
                                   (cmake and autotools)
 
     Fedora 24  4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
-                                  gcc, g++ (GCC) 6.1.1 20160621 
+                                  gcc, g++ (GCC) 6.1.1 20160621
                                       (Red Hat 6.1.1-3)
-                                  GNU Fortran (GCC) 6.1.1 20160621 
+                                  GNU Fortran (GCC) 6.1.1 20160621
                                       (Red Hat 6.1.1-3)
                                   (cmake and autotools)
 
     Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux
-                                  gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) 
+                                  gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2)
                                       5.4.0 20160609
-                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 
+                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2)
                                       5.4.0 20160609
                                   (cmake and autotools)
 
diff --git a/src/H5FDmpi.c b/src/H5FDmpi.c
index 16be455..98e1b1a 100644
--- a/src/H5FDmpi.c
+++ b/src/H5FDmpi.c
@@ -315,6 +315,11 @@ H5FD_mpi_comm_info_dup(MPI_Comm comm, MPI_Info info, MPI_Comm *comm_new, MPI_Inf
 	info_dup = info;
     }
 
+    /* Set MPI_ERRORS_RETURN on comm_dup so that MPI failures are not fatal, 
+       and return codes can be checked and handled. May 23, 2017 FTW */
+    if (MPI_SUCCESS != (mpi_code = MPI_Comm_set_errhandler(comm_dup, MPI_ERRORS_RETURN)))
+        HMPI_GOTO_ERROR(FAIL, "MPI_Errhandler_set failed", mpi_code)
+ 
     /* copy them to the return arguments */
     *comm_new = comm_dup;
     *info_new = info_dup;
diff --git a/src/H5S.c b/src/H5S.c
index dd390d9..9ac40a7 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -1544,7 +1544,7 @@ H5Sencode(hid_t obj_id, void *buf, size_t *nalloc)
     H5TRACE3("e", "i*x*z", obj_id, buf, nalloc);
 
     /* Check argument and retrieve object */
-    if (NULL==(dspace=(H5S_t *)H5I_object_verify(obj_id, H5I_DATASPACE)))
+    if (NULL == (dspace = (H5S_t *)H5I_object_verify(obj_id, H5I_DATASPACE)))
 	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
 
     if(H5S_encode(dspace, (unsigned char **)&buf, nalloc)<0)
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index e6e6cff..9263cd8 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -7571,7 +7571,7 @@ H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[],
     H5TRACE6("e", "iSs*h*h*h*h", space_id, op, start, stride, count, block);
 
     /* Check args */
-    if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE)))
+    if (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
     if (H5S_SCALAR==H5S_GET_EXTENT_TYPE(space))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "hyperslab doesn't support H5S_SCALAR space")
@@ -7640,7 +7640,7 @@ H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[],
     H5TRACE6("i", "iSs*h*h*h*h", space_id, op, start, stride, count, block);
 
     /* Check args */
-    if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE)))
+    if (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
     if(start==NULL || count==NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "hyperslab not specified")
@@ -7768,9 +7768,9 @@ H5Scombine_select(hid_t space1_id, H5S_seloper_t op, hid_t space2_id)
     H5TRACE3("i", "iSsi", space1_id, op, space2_id);
 
     /* Check args */
-    if (NULL == (space1=H5I_object_verify(space1_id, H5I_DATASPACE)))
+    if (NULL == (space1 = (H5S_t *)H5I_object_verify(space1_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
-    if (NULL == (space2=H5I_object_verify(space2_id, H5I_DATASPACE)))
+    if (NULL == (space2 = (H5S_t *)H5I_object_verify(space2_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
     if(!(op>H5S_SELECT_NOOP && op<H5S_SELECT_INVALID))
         HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation")
@@ -7896,9 +7896,9 @@ H5Sselect_select(hid_t space1_id, H5S_seloper_t op, hid_t space2_id)
     H5TRACE3("e", "iSsi", space1_id, op, space2_id);
 
     /* Check args */
-    if (NULL == (space1=H5I_object_verify(space1_id, H5I_DATASPACE)))
+    if (NULL == (space1 = (H5S_t *)H5I_object_verify(space1_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
-    if (NULL == (space2=H5I_object_verify(space2_id, H5I_DATASPACE)))
+    if (NULL == (space2 = (H5S_t *)H5I_object_verify(space2_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
     if(!(op>H5S_SELECT_NOOP && op<H5S_SELECT_INVALID))
         HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "invalid selection operation")
diff --git a/src/H5Zszip.c b/src/H5Zszip.c
index dd35859..769011c 100644
--- a/src/H5Zszip.c
+++ b/src/H5Zszip.c
@@ -85,7 +85,7 @@ H5Z_can_apply_szip(hid_t H5_ATTR_UNUSED dcpl_id, hid_t type_id, hid_t H5_ATTR_UN
     FUNC_ENTER_NOAPI(FAIL)
 
     /* Get datatype */
-    if(NULL == (type = H5I_object_verify(type_id, H5I_DATATYPE)))
+    if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE)))
 	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
 
     /* Get datatype's size, for checking the "bits-per-pixel" */
@@ -156,7 +156,7 @@ H5Z_set_local_szip(hid_t dcpl_id, hid_t type_id, hid_t space_id)
         HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
 
     /* Get datatype */
-    if(NULL == (type = H5I_object_verify(type_id, H5I_DATATYPE)))
+    if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE)))
 	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
 
     /* Get the filter's current parameters */
diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index 49f41dc..499d5eb 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -623,6 +623,7 @@ static hsize_t diff_datum(void       *_mem1,
     *-------------------------------------------------------------------------
     */
     case H5T_COMPOUND:
+        h5difftrace("diff_datum H5T_COMPOUND\n");
 
         nmembs = members->n;
 
@@ -655,18 +656,21 @@ static hsize_t diff_datum(void       *_mem1,
     *-------------------------------------------------------------------------
     */
     case H5T_STRING:
-
+        h5difftrace("diff_datum H5T_STRING\n");
         {
-            H5T_str_t pad;
-            char      *s;
-            char *s1;
-            char *s2;
-            size_t size1;
-            size_t size2;
+            char      *s = NULL;
+            char      *sx = NULL;
+            char      *s1 = NULL;
+            char      *s2 = NULL;
+            size_t     size1;
+            size_t     size2;
+            size_t     sizex;
+            size_t     size_mtype = H5Tget_size(m_type);
+            H5T_str_t  pad = H5Tget_strpad(m_type);
 
             /* if variable length string */
-            if(H5Tis_variable_str(m_type))
-            {
+            if(H5Tis_variable_str(m_type)) {
+                h5difftrace("diff_datum H5T_STRING variable\n");
                 /* Get pointer to first string */
                 s1 = *(char**) mem1;
                 size1 = HDstrlen(s1);
@@ -674,14 +678,26 @@ static hsize_t diff_datum(void       *_mem1,
                 s2 = *(char**) mem2;
                 size2 = HDstrlen(s2);
             }
-            else
-            {
+            else if (H5T_STR_NULLTERM == pad) {
+                h5difftrace("diff_datum H5T_STRING null term\n");
+                /* Get pointer to first string */
+                s1 = (char*) mem1;
+                size1 = HDstrlen(s1);
+                if (size1 > size_mtype)
+                    size1 = size_mtype;
+                /* Get pointer to second string */
+                s2 = (char*) mem2;
+                size2 = HDstrlen(s2);
+                if (size2 > size_mtype)
+                    size2 = size_mtype;
+            }
+            else {
                 /* Get pointer to first string */
                 s1 = (char *)mem1;
-                size1 = H5Tget_size(m_type);
+                size1 = size_mtype;
                 /* Get pointer to second string */
                 s2 = (char *)mem2;
-                size2 = H5Tget_size(m_type);
+                size2 = size_mtype;
             }
 
             /*
@@ -692,45 +708,59 @@ static hsize_t diff_datum(void       *_mem1,
              */
             h5diffdebug2("diff_datum string size:%d\n",size1);
             h5diffdebug2("diff_datum string size:%d\n",size2);
-            if(size1 != size2)
-            {
+            if(size1 != size2) {
                 h5difftrace("diff_datum string sizes\n");
                 nfound++;
             }
-            if(size1 < size2)
-            {
+            if(size1 < size2) {
                 size = size1;
                 s = s1;
+                sizex = size2;
+                sx = s2;
             }
-            else
-            {
+            else {
                 size = size2;
                 s = s2;
+                sizex = size1;
+                sx = s1;
             }
 
             /* check for NULL pointer for string */
-            if(s!=NULL)
-            {
+            if(s!=NULL) {
                 /* try fast compare first */
-                if (HDmemcmp(s1, s2, size)==0)
-                    break;
-
-                pad = H5Tget_strpad(m_type);
-
-                for (u=0; u<size; u++)
-                    nfound+=character_compare(
-                        s1 + u,
-                        s2 + u, /* offset */
-                        i,        /* index position */
-                        u,        /* string character position */
-                        rank,
-                        dims,
-                        acc,
-                        pos,
-                        options,
-                        obj1,
-                        obj2,
-                        ph);
+                if(HDmemcmp(s1, s2, size)==0) {
+                    if(size1 != size2)
+                        if(print_data(options))
+                            for (u=size; u<sizex; u++)
+                                character_compare(
+                                    s1 + u,
+                                    s2 + u, /* offset */
+                                    i,        /* index position */
+                                    u,        /* string character position */
+                                    rank,
+                                    dims,
+                                    acc,
+                                    pos,
+                                    options,
+                                    obj1,
+                                    obj2,
+                                    ph);
+                }
+                else
+                    for (u=0; u<size; u++)
+                        nfound+=character_compare(
+                            s1 + u,
+                            s2 + u, /* offset */
+                            i,        /* index position */
+                            u,        /* string character position */
+                            rank,
+                            dims,
+                            acc,
+                            pos,
+                            options,
+                            obj1,
+                            obj2,
+                            ph);
             }
 
         }
@@ -741,6 +771,7 @@ static hsize_t diff_datum(void       *_mem1,
     *-------------------------------------------------------------------------
     */
     case H5T_BITFIELD:
+        h5difftrace("diff_datum H5T_BITFIELD\n");
 
         /* byte-by-byte comparison */
         for (u=0; u<type_size; u++)
@@ -764,7 +795,7 @@ static hsize_t diff_datum(void       *_mem1,
      *-------------------------------------------------------------------------
      */
     case H5T_OPAQUE:
-
+        h5difftrace("diff_datum H5T_OPAQUE\n");
         /* byte-by-byte comparison */
         for (u=0; u<type_size; u++)
             nfound+=character_compare_opt(
@@ -788,6 +819,7 @@ static hsize_t diff_datum(void       *_mem1,
     *-------------------------------------------------------------------------
     */
     case H5T_ENUM:
+        h5difftrace("diff_datum H5T_ENUM\n");
 
     /* For enumeration types we compare the names instead of the
     integer values.  For each pair of elements being
diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c
index 004672e..74607da 100644
--- a/tools/lib/h5diff_attr.c
+++ b/tools/lib/h5diff_attr.c
@@ -91,7 +91,7 @@ static void table_attrs_free( table_attrs_t *table )
 /*-------------------------------------------------------------------------
  * Function: table_attr_mark_exist
  *
- * Purpose: mark given attribute name to table as sign of exsit
+ * Purpose: mark given attribute name to table as sign of exist
  *
  * Parameter:
  *  - exist [IN]
@@ -155,6 +155,7 @@ static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t
     unsigned i;
     table_attrs_t *table_lp = NULL;
 
+    h5difftrace("build_match_list_attrs start\n");
     if(H5Oget_info(loc1_id, &oinfo1) < 0)
         goto error;
     if(H5Oget_info(loc2_id, &oinfo2) < 0)
@@ -162,6 +163,7 @@ static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t
 
     table_attrs_init( &table_lp );
 
+    h5diffdebug3("build_match_list_attrs: %ld - %ld\n", curr1 < oinfo1.num_attrs, curr2 < oinfo2.num_attrs);
 
     /*--------------------------------------------------
      * build the list
@@ -226,6 +228,7 @@ static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t
         /* get name */
         if(H5Aget_name(attr1_id, (size_t)ATTR_NAME_MAX, name1) < 0)
             goto error;
+        h5diffdebug2("build_match_list_attrs #1 name - %s\n", name1);
 
         table_attr_mark_exist(infile, name1, table_lp);
         table_lp->nattrs_only1++;
@@ -247,6 +250,7 @@ static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t
         /* get name */
         if(H5Aget_name(attr2_id, (size_t)ATTR_NAME_MAX, name2) < 0)
             goto error;
+        h5diffdebug2("build_match_list_attrs #2 name - %s\n", name2);
 
         table_attr_mark_exist(infile, name2, table_lp);
         table_lp->nattrs_only2++;
@@ -278,6 +282,7 @@ static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t
 
     *table_out = table_lp;
 
+    h5difftrace("build_match_list_attrs end\n");
     return 0;
 
 error:
@@ -286,6 +291,7 @@ error:
     if (0 < attr2_id)
         H5Aclose(attr2_id);
 
+    h5difftrace("build_match_list_attrs end with error\n");
     return -1;
 }
 
@@ -322,8 +328,8 @@ hsize_t diff_attr(hid_t loc1_id,
     hid_t      space2_id=-1;    /* space ID */
     hid_t      ftype1_id=-1;    /* file data type ID */
     hid_t      ftype2_id=-1;    /* file data type ID */
-    int	       vstrtype1=0;     /* ftype1 is a variable string */
-    int	       vstrtype2=0;     /* ftype2 is a variable string */
+    int           vstrtype1=0;     /* ftype1 is a variable string */
+    int           vstrtype2=0;     /* ftype2 is a variable string */
     hid_t      mtype1_id=-1;    /* memory data type ID */
     hid_t      mtype2_id=-1;    /* memory data type ID */
     size_t     msize1;          /* memory size of memory type */
@@ -346,12 +352,15 @@ hsize_t diff_attr(hid_t loc1_id,
     hsize_t    nfound_total = 0;
     int       j;
 
-    table_attrs_t * match_list_attrs = NULL;
+    table_attrs_t *match_list_attrs = NULL;
+    h5difftrace("diff_attr start\n");
+
     if(build_match_list_attrs(loc1_id, loc2_id, &match_list_attrs, options) < 0)
         goto error;
 
     /* if detect any unique extra attr */
     if(match_list_attrs->nattrs_only1 || match_list_attrs->nattrs_only2) {
+        h5difftrace("diff_attr attributes only in one file\n");
         /* exit will be 1 */
         options->contents = 0;
     }
@@ -359,6 +368,7 @@ hsize_t diff_attr(hid_t loc1_id,
     for(u = 0; u < (unsigned)match_list_attrs->nattrs; u++) {
         if((match_list_attrs->attrs[u].exist[0]) && (match_list_attrs->attrs[u].exist[1])) {
             name1 = name2 = match_list_attrs->attrs[u].name;
+            h5diffdebug2("diff_attr name - %s\n", name1);
 
             /*--------------
             * attribute 1 */
@@ -370,6 +380,7 @@ hsize_t diff_attr(hid_t loc1_id,
             if((attr2_id = H5Aopen(loc2_id, name2, H5P_DEFAULT)) < 0)
                 goto error;
 
+            h5difftrace("diff_attr got attributes\n");
             /* get the datatypes  */
             if((ftype1_id = H5Aget_type(attr1_id)) < 0)
                 goto error;
@@ -556,6 +567,7 @@ hsize_t diff_attr(hid_t loc1_id,
 
     table_attrs_free(match_list_attrs);
 
+    h5difftrace("diff_attr end\n");
     return nfound_total;
 
 error:
@@ -584,6 +596,7 @@ error:
     } H5E_END_TRY;
 
     options->err_stat = 1;
+    h5difftrace("diff_attr end with error\n");
     return nfound_total;
 }
 
diff --git a/tools/lib/h5diff_dset.c b/tools/lib/h5diff_dset.c
index 9f70299..991ef48 100644
--- a/tools/lib/h5diff_dset.c
+++ b/tools/lib/h5diff_dset.c
@@ -44,6 +44,7 @@ hsize_t diff_dataset( hid_t file1_id,
     hid_t   dcpl2 = -1;
     hsize_t nfound = 0;
 
+    h5difftrace("diff_dataset start\n");
     /*-------------------------------------------------------------------------
     * open the handles
     *-------------------------------------------------------------------------
@@ -52,13 +53,11 @@ hsize_t diff_dataset( hid_t file1_id,
     H5E_BEGIN_TRY
     {
         /* Open the datasets */
-        if((did1 = H5Dopen2(file1_id, obj1_name, H5P_DEFAULT)) < 0)
-        {
+        if((did1 = H5Dopen2(file1_id, obj1_name, H5P_DEFAULT)) < 0) {
             parallel_print("Cannot open dataset <%s>\n", obj1_name);
             goto error;
         }
-        if((did2 = H5Dopen2(file2_id, obj2_name, H5P_DEFAULT)) < 0)
-        {
+        if((did2 = H5Dopen2(file2_id, obj2_name, H5P_DEFAULT)) < 0) {
             parallel_print("Cannot open dataset <%s>\n", obj2_name);
             goto error;
         }
@@ -78,15 +77,9 @@ hsize_t diff_dataset( hid_t file1_id,
     * 2) the internal filters might be turned off
     *-------------------------------------------------------------------------
     */
-    if ((h5tools_canreadf((options->m_verbose?obj1_name:NULL),dcpl1)==1) &&
-        (h5tools_canreadf((options->m_verbose?obj2_name:NULL),dcpl2)==1))
-    {
-        nfound=diff_datasetid(did1,
-            did2,
-            obj1_name,
-            obj2_name,
-            options);
-    }
+    if ((h5tools_canreadf((options->m_verbose ? obj1_name : NULL), dcpl1) == 1) &&
+        (h5tools_canreadf((options->m_verbose ? obj2_name : NULL), dcpl2) == 1))
+        nfound = diff_datasetid(did1, did2, obj1_name, obj2_name, options);
     else
         goto error;
 
@@ -94,20 +87,12 @@ hsize_t diff_dataset( hid_t file1_id,
     * close
     *-------------------------------------------------------------------------
     */
-    /* disable error reporting */
-    H5E_BEGIN_TRY {
-        H5Pclose(dcpl1);
-        H5Pclose(dcpl2);
-        H5Dclose(did1);
-        H5Dclose(did2);
-        /* enable error reporting */
-    } H5E_END_TRY;
-
-
-    return nfound;
+    goto done;
 
 error:
-    options->err_stat=1;
+    options->err_stat = 1;
+
+done:
     /* disable error reporting */
     H5E_BEGIN_TRY {
         H5Pclose(dcpl1);
@@ -117,6 +102,7 @@ error:
         /* enable error reporting */
     } H5E_END_TRY;
 
+    h5difftrace("diff_dataset end\n");
     return nfound;
 }
 
@@ -188,20 +174,24 @@ hsize_t diff_datasetid( hid_t did1,
     hid_t      sid2=-1;
     hid_t      f_tid1=-1;
     hid_t      f_tid2=-1;
+    hid_t      dam_tid=-1;               /* m_tid for diff_array function */
     hid_t      m_tid1=-1;
     hid_t      m_tid2=-1;
     hid_t      dcpl1 = -1;
     hid_t      dcpl2 = -1;
     H5D_layout_t     stl1 = -1;
     H5D_layout_t     stl2 = -1;
+    size_t     dam_size;                /* m_size for diff_array function */
     size_t     m_size1;
     size_t     m_size2;
     H5T_sign_t sign1;
     H5T_sign_t sign2;
     int        rank1;
     int        rank2;
+    hsize_t    danelmts;                /* nelmts for diff_array function */
     hsize_t    nelmts1;
     hsize_t    nelmts2;
+    hsize_t    *dadims;                 /* dims for diff_array function */
     hsize_t    dims1[H5S_MAX_RANK];
     hsize_t    dims2[H5S_MAX_RANK];
     hsize_t    maxdim1[H5S_MAX_RANK];
@@ -223,30 +213,29 @@ hsize_t diff_datasetid( hid_t did1,
 
     h5difftrace("diff_datasetid start\n");
     /* Get the dataspace handle */
-    if ( (sid1 = H5Dget_space(did1)) < 0 )
+    if((sid1 = H5Dget_space(did1)) < 0)
         goto error;
 
     /* Get rank */
-    if ( (rank1 = H5Sget_simple_extent_ndims(sid1)) < 0 )
+    if((rank1 = H5Sget_simple_extent_ndims(sid1)) < 0)
         goto error;
 
     /* Get the dataspace handle */
-    if ( (sid2 = H5Dget_space(did2)) < 0 )
+    if((sid2 = H5Dget_space(did2)) < 0 )
         goto error;
 
     /* Get rank */
-    if ( (rank2 = H5Sget_simple_extent_ndims(sid2)) < 0 )
+    if((rank2 = H5Sget_simple_extent_ndims(sid2)) < 0)
         goto error;
 
     /* Get dimensions */
-    if ( H5Sget_simple_extent_dims(sid1,dims1,maxdim1) < 0 )
+    if(H5Sget_simple_extent_dims(sid1, dims1, maxdim1) < 0)
         goto error;
 
     /* Get dimensions */
-    if ( H5Sget_simple_extent_dims(sid2,dims2,maxdim2) < 0 )
-    {
+    if(H5Sget_simple_extent_dims(sid2, dims2, maxdim2) < 0)
         goto error;
-    }
+    h5diffdebug3("rank: %ld - %ld\n", rank1, rank2);
 
     /*-------------------------------------------------------------------------
     * get the file data type
@@ -254,15 +243,12 @@ hsize_t diff_datasetid( hid_t did1,
     */
 
     /* Get the data type */
-    if ( (f_tid1 = H5Dget_type(did1)) < 0 )
+    if((f_tid1 = H5Dget_type(did1)) < 0)
         goto error;
 
     /* Get the data type */
-    if ( (f_tid2 = H5Dget_type(did2)) < 0 )
-    {
+    if((f_tid2 = H5Dget_type(did2)) < 0)
         goto error;
-    }
-
 
     /*-------------------------------------------------------------------------
     * get the storage layout type
@@ -284,22 +270,20 @@ hsize_t diff_datasetid( hid_t did1,
     */
     h5difftrace("check for empty datasets\n");
 
-    storage_size1=H5Dget_storage_size(did1);
-    storage_size2=H5Dget_storage_size(did2);
+    storage_size1 = H5Dget_storage_size(did1);
+    storage_size2 = H5Dget_storage_size(did2);
+    h5diffdebug3("storage size: %ld - %ld\n", storage_size1, storage_size2);
 
-    if (storage_size1==0 || storage_size2==0)
-    {
-        if (stl1==H5D_VIRTUAL || stl2==H5D_VIRTUAL)
-        {
-            if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
+    if(storage_size1 == 0 || storage_size2 == 0) {
+        if(stl1 == H5D_VIRTUAL || stl2 == H5D_VIRTUAL) {
+            if((options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
                 parallel_print("Warning: <%s> or <%s> is a virtual dataset\n", obj1_name, obj2_name);
         }
-        else
-        {
-            if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
+        else {
+            if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name)
                 parallel_print("Not comparable: <%s> or <%s> is an empty dataset\n", obj1_name, obj2_name);
-            can_compare=0;
-            options->not_cmp=1;
+            can_compare = 0;
+            options->not_cmp = 1;
         }
     }
 
@@ -307,71 +291,58 @@ hsize_t diff_datasetid( hid_t did1,
     * check for comparable TYPE and SPACE
     *-------------------------------------------------------------------------
     */
-
-    if (diff_can_type(f_tid1,
-        f_tid2,
-        rank1,
-        rank2,
-        dims1,
-        dims2,
-        maxdim1,
-        maxdim2,
-        obj1_name,
-        obj2_name,
-        options,
-        0)!=1)
-    {
-        can_compare=0;
-    }
+    if (diff_can_type(f_tid1, f_tid2, rank1, rank2,
+            dims1, dims2, maxdim1, maxdim2,
+            obj1_name, obj2_name,
+            options, 0) != 1)
+        can_compare = 0;
 
     /*-------------------------------------------------------------------------
     * memory type and sizes
     *-------------------------------------------------------------------------
     */
     h5difftrace("check for memory type and sizes\n");
-    if ((m_tid1=H5Tget_native_type(f_tid1, H5T_DIR_DEFAULT)) < 0)
+    if((m_tid1 = H5Tget_native_type(f_tid1, H5T_DIR_DEFAULT)) < 0)
         goto error;
 
-    if ((m_tid2=H5Tget_native_type(f_tid2, H5T_DIR_DEFAULT)) < 0)
+    if((m_tid2 = H5Tget_native_type(f_tid2, H5T_DIR_DEFAULT)) < 0)
         goto error;
 
-    m_size1 = H5Tget_size( m_tid1 );
-    m_size2 = H5Tget_size( m_tid2 );
+    m_size1 = H5Tget_size(m_tid1);
+    m_size2 = H5Tget_size(m_tid2);
+    h5diffdebug3("type size: %ld - %ld\n", m_size1, m_size2);
 
     /*-------------------------------------------------------------------------
     * check for different signed/unsigned types
     *-------------------------------------------------------------------------
     */
-    if (can_compare)
-    {
+    if(can_compare) {
         h5difftrace("can_compare for sign\n");
-        sign1=H5Tget_sign(m_tid1);
-        sign2=H5Tget_sign(m_tid2);
-        if ( sign1 != sign2 )
-        {
+        sign1 = H5Tget_sign(m_tid1);
+        sign2 = H5Tget_sign(m_tid2);
+        if(sign1 != sign2) {
             h5difftrace("sign1 != sign2\n");
-            if ((options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
-            {
+            if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
                 parallel_print("Not comparable: <%s> has sign %s ", obj1_name, get_sign(sign1));
                 parallel_print("and <%s> has sign %s\n", obj2_name, get_sign(sign2));
             }
 
-            can_compare=0;
-            options->not_cmp=1;
+            can_compare = 0;
+            options->not_cmp = 1;
         }
     }
 
     /* Check if type is either VLEN-data or VLEN-string to reclaim any
      * VLEN memory buffer later */
-    if( TRUE == h5tools_detect_vlen(m_tid1) )
+    if(TRUE == h5tools_detect_vlen(m_tid1))
         vl_data = TRUE;
 
     /*------------------------------------------------------------------------
     * only attempt to compare if possible
     *-------------------------------------------------------------------------
     */
-    if(can_compare) /* it is possible to compare */
-    {
+    if(can_compare) { /* it is possible to compare */
+        H5T_class_t  tclass = H5Tget_class(f_tid1);
         h5difftrace("can_compare attempt\n");
 
         /*-----------------------------------------------------------------
@@ -386,19 +357,44 @@ hsize_t diff_datasetid( hid_t did1,
         for(i = 0; i < rank2; i++)
             nelmts2 *= dims2[i];
 
+        h5diffdebug3("nelmts: %ld - %ld\n", nelmts1, nelmts2);
         HDassert(nelmts1 == nelmts2);
 
-        /*-----------------------------------------------------------------
-        * "upgrade" the smaller memory size
-        *------------------------------------------------------------------
-        */
-        h5difftrace("upgrade the smaller memory size?\n");
-
-        if (FAIL == match_up_memsize (f_tid1, f_tid2,
-                                      &m_tid1, &m_tid2,
-                                      &m_size1, &m_size2))
-            goto error;
-
+        if(tclass != H5T_ARRAY) {
+            /*-----------------------------------------------------------------
+            * "upgrade" the smaller memory size
+            *------------------------------------------------------------------
+            */
+            h5difftrace("upgrade the smaller memory size?\n");
+            if (FAIL == match_up_memsize (f_tid1, f_tid2,
+                                        &m_tid1, &m_tid2,
+                                        &m_size1, &m_size2))
+                goto error;
+            h5diffdebug3("m_size: %ld - %ld\n", m_size1, m_size2);
+            dadims = dims1;
+            dam_size = m_size1;
+            dam_tid = m_tid1;
+            danelmts = nelmts1;
+            need = (size_t)(nelmts1 * m_size1);  /* bytes needed */
+         }
+        else {
+            h5diffdebug3("Array dims: %d - %d\n", dims1[0], dims2[0]);
+            /* Compare the smallest array, but create the largest buffer */
+            if(m_size1 <= m_size2) {
+                dadims = dims1;
+                dam_size = m_size1;
+                dam_tid = m_tid1;
+                danelmts = nelmts1;
+                need = (size_t)(nelmts2 * m_size2);  /* bytes needed */
+            }
+            else {
+                dadims = dims2;
+                dam_size = m_size2;
+                dam_tid = m_tid2;
+                danelmts = nelmts2;
+                need = (size_t)(nelmts1 * m_size1);  /* bytes needed */
+            }
+        }
         /* print names */
         if(obj1_name)
             name1 = diff_basename(obj1_name);
@@ -410,7 +406,6 @@ hsize_t diff_datasetid( hid_t did1,
         * read/compare
         *-----------------------------------------------------------------
         */
-        need = (size_t)(nelmts1 * m_size1);  /* bytes needed */
         if(need < H5TOOLS_MALLOCSIZE) {
             buf1 = HDmalloc(need);
             buf2 = HDmalloc(need);
@@ -420,12 +415,13 @@ hsize_t diff_datasetid( hid_t did1,
             h5difftrace("buf1 != NULL && buf2 != NULL\n");
             if(H5Dread(did1, m_tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf1) < 0)
                 goto error;
+            h5difftrace("H5Dread did2\n");
             if(H5Dread(did2, m_tid2, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf2) < 0)
                 goto error;
 
             /* array diff */
-            nfound = diff_array(buf1, buf2, nelmts1, (hsize_t)0, rank1, dims1,
-                options, name1, name2, m_tid1, did1, did2);
+            nfound = diff_array(buf1, buf2, danelmts, (hsize_t)0, rank1, dadims,
+                options, name1, name2, dam_tid, did1, did2);
 
             /* reclaim any VL memory, if necessary */
             if(vl_data) {
@@ -433,10 +429,9 @@ hsize_t diff_datasetid( hid_t did1,
                 H5Dvlen_reclaim(m_tid2, sid2, H5P_DEFAULT, buf2);
             } /* end if */
         } /* end if */
-        else /* possibly not enough memory, read/compare by hyperslabs */
-        {
-            size_t        p_type_nbytes = m_size1; /*size of memory type */
-            hsize_t       p_nelmts = nelmts1;      /*total selected elmts */
+        else { /* possibly not enough memory, read/compare by hyperslabs */
+            size_t        p_type_nbytes = dam_size; /*size of memory type */
+            hsize_t       p_nelmts = danelmts;      /*total selected elmts */
             hsize_t       elmtno;                  /*counter  */
             int           carry;                   /*counter carry value */
 
@@ -462,7 +457,7 @@ hsize_t diff_datasetid( hid_t did1,
 
                 if(size == 0) /* datum size > H5TOOLS_BUFSIZE */
                     size = 1;
-                sm_size[i - 1] = MIN(dims1[i - 1], size);
+                sm_size[i - 1] = MIN(dadims[i - 1], size);
                 sm_nbytes *= sm_size[i - 1];
                 HDassert(sm_nbytes > 0);
             } /* end for */
@@ -490,7 +485,7 @@ hsize_t diff_datasetid( hid_t did1,
                 /* calculate the hyperslab size */
                 if(rank1 > 0) {
                     for(i = 0, hs_nelmts = 1; i < rank1; i++) {
-                        hs_size[i] = MIN(dims1[i] - hs_offset[i], sm_size[i]);
+                        hs_size[i] = MIN(dadims[i] - hs_offset[i], sm_size[i]);
                         hs_nelmts *= hs_size[i];
                     } /* end for */
                     if(H5Sselect_hyperslab(sid1, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
@@ -503,15 +498,15 @@ hsize_t diff_datasetid( hid_t did1,
                 else
                     hs_nelmts = 1;
 
-                if(H5Dread(did1,m_tid1,sm_space,sid1,H5P_DEFAULT,sm_buf1) < 0)
+                if(H5Dread(did1, m_tid1, sm_space, sid1, H5P_DEFAULT, sm_buf1) < 0)
                     goto error;
-                if(H5Dread(did2,m_tid2,sm_space,sid2,H5P_DEFAULT,sm_buf2) < 0)
+                if(H5Dread(did2, m_tid2, sm_space, sid2, H5P_DEFAULT, sm_buf2) < 0)
                     goto error;
 
                 /* get array differences. in the case of hyperslab read, increment the number of differences
-                found in each hyperslab and pass the position at the beggining for printing */
+                found in each hyperslab and pass the position at the beginning for printing */
                 nfound += diff_array(sm_buf1, sm_buf2, hs_nelmts, elmtno, rank1,
-                    dims1, options, name1, name2, m_tid1, did1, did2);
+                        dadims, options, name1, name2, dam_tid, did1, did2);
 
                 /* reclaim any VL memory, if necessary */
                 if(vl_data) {
@@ -522,7 +517,7 @@ hsize_t diff_datasetid( hid_t did1,
                 /* calculate the next hyperslab offset */
                 for(i = rank1, carry = 1; i > 0 && carry; --i) {
                     hs_offset[i - 1] += hs_size[i - 1];
-                    if(hs_offset[i - 1] == dims1[i - 1])
+                    if(hs_offset[i - 1] == dadims[i - 1])
                         hs_offset[i - 1] = 0;
                     else
                         carry = 0;
@@ -574,37 +569,33 @@ error:
     options->err_stat=1;
 
     /* free */
-    if (buf1!=NULL)
-    {
+    if(buf1 != NULL) {
         /* reclaim any VL memory, if necessary */
         if(vl_data)
             H5Dvlen_reclaim(m_tid1, sid1, H5P_DEFAULT, buf1);
         HDfree(buf1);
-        buf1=NULL;
+        buf1 = NULL;
     }
-    if (buf2!=NULL)
-    {
+    if(buf2 != NULL) {
         /* reclaim any VL memory, if necessary */
         if(vl_data)
             H5Dvlen_reclaim(m_tid2, sid2, H5P_DEFAULT, buf2);
         HDfree(buf2);
-        buf2=NULL;
+        buf2 = NULL;
     }
-    if (sm_buf1!=NULL)
-    {
+    if(sm_buf1 != NULL) {
         /* reclaim any VL memory, if necessary */
         if(vl_data)
             H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf1);
         HDfree(sm_buf1);
-        sm_buf1=NULL;
+        sm_buf1 = NULL;
     }
-    if (sm_buf2!=NULL)
-    {
+    if(sm_buf2 != NULL) {
         /* reclaim any VL memory, if necessary */
         if(vl_data)
             H5Dvlen_reclaim(m_tid1, sm_space, H5P_DEFAULT, sm_buf2);
         HDfree(sm_buf2);
-        sm_buf2=NULL;
+        sm_buf2 = NULL;
     }
 
     /* disable error reporting */
@@ -652,75 +643,55 @@ int diff_can_type( hid_t       f_tid1, /* file data type */
                    diff_opt_t  *options,
                    int         is_compound)
 {
-
-
     H5T_class_t  tclass1;
     H5T_class_t  tclass2;
-    int          maxdim_diff=0;          /* maximum dimensions are different */
-    int          dim_diff=0;             /* current dimensions are different */
+    int          maxdim_diff = 0;          /* maximum dimensions are different */
+    int          dim_diff = 0;             /* current dimensions are different */
     int          i;
-    int          can_compare = 1;        /* return value */
+    int          can_compare = 1;          /* return value */
 
+    h5difftrace("diff_can_type start\n");
     /*-------------------------------------------------------------------------
     * check for the same class
     *-------------------------------------------------------------------------
     */
-
-    if ((tclass1=H5Tget_class(f_tid1)) < 0)
+    if((tclass1 = H5Tget_class(f_tid1)) < 0)
         return -1;
-
-    if ((tclass2=H5Tget_class(f_tid2)) < 0)
+    if((tclass2 = H5Tget_class(f_tid2)) < 0)
         return -1;
 
-    if ( tclass1 != tclass2 )
-    {
-
-        if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
-        {
-
-            if ( is_compound )
-            {
-
+    if(tclass1 != tclass2) {
+        if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
+            if(is_compound) {
                 parallel_print("Not comparable: <%s> has a class %s and <%s> has a class %s\n",
-                    obj1_name, get_class(tclass1),
-                    obj2_name, get_class(tclass2) );
-
+                        obj1_name, get_class(tclass1),
+                        obj2_name, get_class(tclass2));
             }
-
-            else
-
-            {
-
+            else {
                 parallel_print("Not comparable: <%s> is of class %s and <%s> is of class %s\n",
-                    obj1_name, get_class(tclass1),
-                    obj2_name, get_class(tclass2) );
-
+                        obj1_name, get_class(tclass1),
+                        obj2_name, get_class(tclass2));
             }
-
         }
-
-
         can_compare = 0;
         options->not_cmp = 1;
-        return can_compare;
+        goto done;
     }
 
     /*-------------------------------------------------------------------------
     * check for non supported classes
     *-------------------------------------------------------------------------
     */
-
-    HDassert(tclass1==tclass2);
-    switch (tclass1)
-    {
+    HDassert(tclass1 == tclass2);
+    switch (tclass1) {
         case H5T_TIME:
-            if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name) {
+            if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
                 parallel_print("Not comparable: <%s> and <%s> are of class %s\n",
-                    obj1_name,obj2_name,get_class(tclass2) );
+                        obj1_name, obj2_name, get_class(tclass2));
             } /* end if */
             can_compare = 0;
             options->not_cmp = 1;
-            return can_compare;
+            goto done;
 
         case H5T_INTEGER:
         case H5T_FLOAT:
@@ -735,6 +706,7 @@ int diff_can_type( hid_t       f_tid1, /* file data type */
         case H5T_NO_CLASS:
         case H5T_NCLASSES:
         default:
+            h5diffdebug2("diff_can_type class - %s\n", get_class(tclass1));
             break;
     } /* end switch */
 
@@ -742,17 +714,11 @@ int diff_can_type( hid_t       f_tid1, /* file data type */
     * check for equal file datatype; warning only
     *-------------------------------------------------------------------------
     */
-
-    if ( (H5Tequal(f_tid1, f_tid2)==0) &&
-        (options->m_verbose) && obj1_name && obj2_name)
-    {
-
+    if((H5Tequal(f_tid1, f_tid2) == 0) && (options->m_verbose) && obj1_name && obj2_name) {
         H5T_class_t cl = H5Tget_class(f_tid1);
 
-
         parallel_print("Warning: different storage datatype\n");
-        if ( cl == H5T_INTEGER || cl == H5T_FLOAT )
-        {
+        if(cl == H5T_INTEGER || cl == H5T_FLOAT) {
             parallel_print("<%s> has file datatype ", obj1_name);
             print_type(f_tid1);
             parallel_print("\n");
@@ -760,110 +726,85 @@ int diff_can_type( hid_t       f_tid1, /* file data type */
             print_type(f_tid2);
             parallel_print("\n");
         }
-
-
-
     }
 
     /*-------------------------------------------------------------------------
     * check for the same rank
     *-------------------------------------------------------------------------
     */
-
-
-    if ( rank1 != rank2 )
-    {
-
-        if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
-        {
+    if(rank1 != rank2) {
+        if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
             parallel_print("Not comparable: <%s> has rank %d, dimensions ", obj1_name, rank1);
-            print_dimensions(rank1,dims1);
+            print_dimensions(rank1, dims1);
             parallel_print(", max dimensions ");
-            print_dimensions(rank1,maxdim1);
+            print_dimensions(rank1, maxdim1);
             parallel_print("\n" );
             parallel_print("and <%s> has rank %d, dimensions ", obj2_name, rank2);
-            print_dimensions(rank2,dims2);
+            print_dimensions(rank2, dims2);
             parallel_print(", max dimensions ");
-            print_dimensions(rank2,maxdim2);
+            print_dimensions(rank2, maxdim2);
             parallel_print("\n");
         }
-
         can_compare = 0;
         options->not_cmp = 1;
-        return can_compare;
+        goto done;
     }
 
     /*-------------------------------------------------------------------------
     * check for different dimensions
     *-------------------------------------------------------------------------
     */
-
-    HDassert(rank1==rank2);
-    for ( i=0; i<rank1; i++)
-    {
-        if (maxdim1 && maxdim2)
-        {
-            if ( maxdim1[i] != maxdim2[i] )
-                maxdim_diff=1;
+    HDassert(rank1 == rank2);
+    for(i = 0; i<rank1; i++) {
+        if(maxdim1 && maxdim2) {
+            if(maxdim1[i] != maxdim2[i])
+                maxdim_diff = 1;
         }
-        if ( dims1[i] != dims2[i] )
-            dim_diff=1;
+        if(dims1[i] != dims2[i])
+            dim_diff = 1;
     }
 
     /*-------------------------------------------------------------------------
     * current dimensions
     *-------------------------------------------------------------------------
     */
-
-    if (dim_diff==1)
-    {
-        if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
-        {
+    if(dim_diff == 1) {
+        if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
             parallel_print("Not comparable: <%s> has rank %d, dimensions ", obj1_name, rank1);
-            print_dimensions(rank1,dims1);
-            if (maxdim1 && maxdim2)
-            {
+            print_dimensions(rank1, dims1);
+            if(maxdim1 && maxdim2) {
                 parallel_print(", max dimensions ");
-                print_dimensions(rank1,maxdim1);
+                print_dimensions(rank1, maxdim1);
                 parallel_print("\n" );
                 parallel_print("and <%s> has rank %d, dimensions ", obj2_name, rank2);
-                print_dimensions(rank2,dims2);
+                print_dimensions(rank2, dims2);
                 parallel_print(", max dimensions ");
-                print_dimensions(rank2,maxdim2);
+                print_dimensions(rank2, maxdim2);
                 parallel_print("\n");
             }
         }
-
-
         can_compare = 0;
         options->not_cmp = 1;
-        return can_compare;
-
-
-
+        goto done;
     }
 
     /*-------------------------------------------------------------------------
     * maximum dimensions; just give a warning
     *-------------------------------------------------------------------------
     */
-    if (maxdim1 && maxdim2 && maxdim_diff==1 && obj1_name )
-    {
-        if (options->m_verbose) {
+    if(maxdim1 && maxdim2 && maxdim_diff == 1 && obj1_name) {
+        if(options->m_verbose) {
             parallel_print( "Warning: different maximum dimensions\n");
             parallel_print("<%s> has max dimensions ", obj1_name);
-            print_dimensions(rank1,maxdim1);
+            print_dimensions(rank1, maxdim1);
             parallel_print("\n");
             parallel_print("<%s> has max dimensions ", obj2_name);
-            print_dimensions(rank2,maxdim2);
+            print_dimensions(rank2, maxdim2);
             parallel_print("\n");
         }
     }
 
-
-    if ( tclass1 == H5T_COMPOUND )
-    {
-
+    if(tclass1 == H5T_COMPOUND) {
         int   nmembs1;
         int   nmembs2;
         int   j;
@@ -873,67 +814,40 @@ int diff_can_type( hid_t       f_tid1, /* file data type */
         nmembs1 = H5Tget_nmembers(f_tid1);
         nmembs2 = H5Tget_nmembers(f_tid2);
 
-        if ( nmembs1 != nmembs2 )
-        {
-
-            if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
-            {
+        if(nmembs1 != nmembs2) {
+            if((options->m_verbose || options->m_list_not_cmp) && obj1_name && obj2_name) {
                 parallel_print("Not comparable: <%s> has %d members ", obj1_name, nmembs1);
                 parallel_print("<%s> has %d members ", obj2_name, nmembs2);
                 parallel_print("\n");
             }
-
             can_compare = 0;
             options->not_cmp = 1;
-            return can_compare;
+            goto done;
         }
 
-        for (j = 0; j < nmembs1; j++)
-        {
+        for (j = 0; j < nmembs1; j++) {
             memb_type1 = H5Tget_member_type(f_tid1, (unsigned)j);
             memb_type2 = H5Tget_member_type(f_tid2, (unsigned)j);
 
-            if (diff_can_type(memb_type1,
-                memb_type2,
-                rank1,
-                rank2,
-                dims1,
-                dims2,
-                maxdim1,
-                maxdim2,
-                obj1_name,
-                obj2_name,
-                options,
-                1)!=1)
-            {
+            if (diff_can_type(memb_type1, memb_type2, rank1, rank2,
+                    dims1, dims2, maxdim1, maxdim2, obj1_name, obj2_name,
+                    options, 1) != 1) {
                 can_compare = 0;
                 options->not_cmp = 1;
                 H5Tclose(memb_type1);
                 H5Tclose(memb_type2);
-                return can_compare;
+                goto done;
             }
-
             H5Tclose(memb_type1);
             H5Tclose(memb_type2);
-
         }
-
-
-
-
-
     }
-
-
-
-
-
+done:
+    h5diffdebug2("diff_can_type end - %d\n", can_compare);
     return can_compare;
 }
 
 
-
-
 /*-------------------------------------------------------------------------
 * Function: print_sizes
 *
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index a74fdd2..22fd863 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -51,6 +51,10 @@ unsigned    packed_data_length; /* length of packed bits to display */
 unsigned long long packed_data_mask;  /* mask in which packed bits to display */
 int          enable_error_stack= FALSE; /* re-enable error stack */
 
+/* sort parameters */
+H5_index_t   sort_by           = H5_INDEX_NAME; /*sort_by [creation_order | name]  */
+H5_iter_order_t sort_order     = H5_ITER_INC; /*sort_order [ascending | descending]   */
+
 /* module-scoped variables */
 static int  h5tools_init_g;     /* if h5tools lib has been initialized */
 
diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index c5e750a..3d38dd0 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -568,6 +568,10 @@ H5TOOLS_DLLVAR int     oid_output;          /* oid output */
 H5TOOLS_DLLVAR int     data_output;         /* data output */
 H5TOOLS_DLLVAR int     attr_data_output;    /* attribute data output */
 
+/* sort parameters */
+H5TOOLS_DLLVAR H5_index_t   sort_by;        /*sort_by [creation_order | name]  */
+H5TOOLS_DLLVAR H5_iter_order_t sort_order;  /*sort_order [ascending | descending]   */
+
 /* things to display or which are set via command line parameters */
 H5TOOLS_DLLVAR int     enable_error_stack; /* re-enable error stack */
 
diff --git a/tools/lib/h5tools_type.c b/tools/lib/h5tools_type.c
index b57e274..ae7160b 100644
--- a/tools/lib/h5tools_type.c
+++ b/tools/lib/h5tools_type.c
@@ -15,38 +15,6 @@
 #include "h5tools.h"
 
 /*-------------------------------------------------------------------------
- * Function: h5tools_get_native_type
- *
- * Purpose: Wrapper around H5Tget_native_type() to work around
- *  Problems with bitfields.
- *
- * Return: Success:    datatype ID
- *
- *  Failure:    FAIL
- *
- * Programmer: Quincey Koziol
- *              Tuesday, October  5, 2004
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-hid_t
-h5tools_get_native_type(hid_t type)
-{
-    hid_t p_type;
-    H5T_class_t type_class;
-
-    type_class = H5Tget_class(type);
-    if(type_class==H5T_BITFIELD)
-        p_type=H5Tcopy(type);
-    else
-        p_type = H5Tget_native_type(type,H5T_DIR_DEFAULT);
-
-    return(p_type);
-}
-
-/*-------------------------------------------------------------------------
  * Function: h5tools_get_little_endian_type
  *
  * Purpose: Get a little endian type from a file type
diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index 5437803..0537b9f 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -56,7 +56,7 @@ static struct long_options l_opts[] = {
 static void check_options(diff_opt_t* options)
 {
     /*--------------------------------------------------------------
-     * check for mutually exclusive options 
+     * check for mutually exclusive options
      *--------------------------------------------------------------*/
 
     /* check between -d , -p, --use-system-epsilon.
@@ -127,13 +127,13 @@ void parse_command_line(int argc,
             h5diff_exit(EXIT_SUCCESS);
         case 'v':
             options->m_verbose = 1;
-            /* This for loop is for handling style like 
+            /* This for loop is for handling style like
              * -v, -v1, --verbose, --verbose=1.
              */
             for (i = 1; i < argc; i++)
-            {                
-                /* 
-                 * short opt 
+            {
+                /*
+                 * short opt
                  */
                 if (!strcmp (argv[i], "-v"))  /* no arg */
             {
@@ -145,10 +145,10 @@ void parse_command_line(int argc,
             {
                     options->m_verbose_level = atoi(&argv[i][2]);
                     break;
-            }    
+            }
 
-                /* 
-                 * long opt 
+                /*
+                 * long opt
                  */
                 if (!strcmp (argv[i], "--verbose"))  /* no arg */
             {
@@ -177,7 +177,7 @@ void parse_command_line(int argc,
             break;
         case 'E':
             options->exclude_path = 1;
-            
+
             /* create linked list of excluding objects */
             if( (exclude_node = (struct exclude_path_list*) HDmalloc(sizeof(struct exclude_path_list))) == NULL)
             {
@@ -189,8 +189,8 @@ void parse_command_line(int argc,
             exclude_node->obj_path = (char*)opt_arg;
             exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
             exclude_prev = exclude_head;
-            
-            if (NULL == exclude_head)            
+
+            if (NULL == exclude_head)
             {
                 exclude_head = exclude_node;
                 exclude_head->next = NULL;
@@ -202,7 +202,7 @@ void parse_command_line(int argc,
 
                 exclude_node->next = NULL;
                 exclude_prev->next = exclude_node;
-            }            
+            }
             break;
         case 'd':
             options->d=1;
@@ -458,7 +458,7 @@ check_d_input( const char *str )
 
 void usage(void)
 {
- printf("usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] \n");
+ printf("usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]\n");
  printf("  file1             File name of the first HDF5 file\n");
  printf("  file2             File name of the second HDF5 file\n");
  printf("  [obj1]            Name of an HDF5 object, in absolute path\n");
@@ -519,19 +519,22 @@ void usage(void)
  printf("   -n C, --count=C\n");
  printf("         Print differences up to C. C must be a positive integer.\n");
  printf("   -d D, --delta=D\n");
- printf("         Print difference if (|a-b| > D). D must be a positive number.\n");
+ printf("         Print difference if (|a-b| > D). D must be a positive number. Where a\n");
+ printf("         is the data point value in file1 and b is the data point value in file2.\n");
  printf("         Can not use with '-p' or '--use-system-epsilon'.\n");
  printf("   -p R, --relative=R\n");
- printf("         Print difference if (|(a-b)/b| > R). R must be a positive number.\n");
+ printf("         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a\n");
+ printf("         is the data point value in file1 and b is the data point value in file2.\n");
  printf("         Can not use with '-d' or '--use-system-epsilon'.\n");
  printf("   --use-system-epsilon\n");
- printf("         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.\n");
+ printf("         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a\n");
+ printf("         is the data point value in file1 and b is the data point value in file2.\n");
  printf("         If the system epsilon is not defined,one of the following predefined\n");
  printf("         values will be used:\n");
  printf("           FLT_EPSILON = 1.19209E-07 for floating-point type\n");
  printf("           DBL_EPSILON = 2.22045E-16 for double precision type\n");
  printf("         Can not use with '-p' or '-d'.\n");
- printf("   --exclude-path \"path\" \n");
+ printf("   --exclude-path \"path\"\n");
  printf("         Exclude the specified path to an object when comparing files or groups.\n");
  printf("         If a group is excluded, all member objects will also be excluded.\n");
  printf("         The specified path is excluded wherever it occurs.\n");
@@ -570,15 +573,15 @@ void usage(void)
  printf("\n");
 
  printf(" Object comparison:\n");
- printf("  1) Groups \n");
+ printf("  1) Groups\n");
  printf("      First compares the names of member objects (relative path, from the\n");
  printf("      specified group) and generates a report of objects that appear in only\n");
  printf("      one group or in both groups. Common objects are then compared recursively.\n");
- printf("  2) Datasets \n");
+ printf("  2) Datasets\n");
  printf("      Array rank and dimensions, datatypes, and data values are compared.\n");
- printf("  3) Datatypes \n");
+ printf("  3) Datatypes\n");
  printf("      The comparison is based on the return value of H5Tequal.\n");
- printf("  4) Symbolic links \n");
+ printf("  4) Symbolic links\n");
  printf("      The paths to the target objects are compared.\n");
  printf("      (The option --follow-symlinks overrides the default behavior when\n");
  printf("       symbolic links are compared.).\n");
diff --git a/tools/src/h5dump/h5dump.h b/tools/src/h5dump/h5dump.h
index 211fd14..801f60d 100644
--- a/tools/src/h5dump/h5dump.h
+++ b/tools/src/h5dump/h5dump.h
@@ -78,10 +78,6 @@ int          include_attrs     = TRUE; /* Display attributes */
 int          display_vds_first = FALSE; /* vds display to all by default*/
 int          vds_gap_size       = 0; /* vds skip missing files default is none */
 
-/* sort parameters */
-H5_index_t   sort_by           = H5_INDEX_NAME; /*sort_by [creation_order | name]  */
-H5_iter_order_t sort_order     = H5_ITER_INC; /*sort_order [ascending | descending]   */
-
 #define PACKED_BITS_MAX         8  /* Maximum number of packed-bits to display */
 #define PACKED_BITS_SIZE_MAX    (8*sizeof(long long))  /* Maximum bits size of integer types of packed-bits */
 /* mask list for packed bits */
diff --git a/tools/src/h5dump/h5dump_extern.h b/tools/src/h5dump/h5dump_extern.h
index 22aca73..00d3bd2 100644
--- a/tools/src/h5dump/h5dump_extern.h
+++ b/tools/src/h5dump/h5dump_extern.h
@@ -77,10 +77,6 @@ extern int          include_attrs; /* Display attributes */
 extern int          display_vds_first; /* vds display to first missing */
 extern int          vds_gap_size; /* vds skip missing files */
 
-/* sort parameters */
-extern H5_index_t   sort_by; /*sort_by [creation_order | name]  */
-extern H5_iter_order_t sort_order; /*sort_order [ascending | descending]   */
-
 #define PACKED_BITS_MAX         8  /* Maximum number of packed-bits to display */
 #define PACKED_BITS_SIZE_MAX    8*sizeof(long long)  /* Maximum bits size of integer types of packed-bits */
 /* mask list for packed bits */
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index 3c9ce90..bc8527b 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -784,6 +784,8 @@ static int check_objects(const char* fname, pack_opt_t *options) {
     *-------------------------------------------------------------------------
     */
 
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
     /* init table */
     trav_table_init(&travt);
 
diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h
index e36f0ef..e5ae03f 100644
--- a/tools/src/h5repack/h5repack.h
+++ b/tools/src/h5repack/h5repack.h
@@ -29,10 +29,10 @@
 #define MAX_COMPACT_DSIZE  64512  /* max data size for compact layout. -1k for header size */
 
 /* File space default information */
-#define FS_PAGESIZE_DEF		4096
-#define FS_STRATEGY_DEF        	H5F_FSPACE_STRATEGY_FSM_AGGR
-#define FS_PERSIST_DEF         	FALSE
-#define FS_THRESHOLD_DEF       	1
+#define FS_PAGESIZE_DEF        4096
+#define FS_STRATEGY_DEF            H5F_FSPACE_STRATEGY_FSM_AGGR
+#define FS_PERSIST_DEF             FALSE
+#define FS_THRESHOLD_DEF           1
 
 
 /*-------------------------------------------------------------------------
@@ -120,10 +120,10 @@ typedef struct {
  hsize_t         meta_block_size;  /* metadata aggregation block size (for H5Pset_meta_block_size) */
  hsize_t         threshold;        /* alignment threshold for H5Pset_alignment */
  hsize_t         alignment;        /* alignment for H5Pset_alignment */
- H5F_fspace_strategy_t fs_strategy;	/* File space handling strategy */
- int		fs_persist; 		/* Free space section threshold */
- long		fs_threshold; 		/* Free space section threshold */
- long long 	fs_pagesize;   		/* File space page size */
+ H5F_fspace_strategy_t fs_strategy;    /* File space handling strategy */
+ int        fs_persist;         /* Free space section threshold */
+ long        fs_threshold;         /* Free space section threshold */
+ long long     fs_pagesize;           /* File space page size */
 } pack_opt_t;
 
 
@@ -150,10 +150,10 @@ int h5repack_end(pack_opt_t *options);
 int h5repack_verify(const char *in_fname, 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 
- * bugfix1726. 
- * Made shared functions as copy_attr() was needed in h5repack_refs.c. 
+/* 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
+ * bugfix1726.
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c.
  * However copy_attr() may be obsoleted when H5Acopy is available and put back
  * others to static in h5repack_copy.c.
  */
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index ec3e287..42fedbc 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -103,6 +103,7 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
     hbool_t       in_persist;             /* Persist free-space status from input file */
     hsize_t       in_threshold;           /* Free-space section threshold from input file */
     hsize_t       in_pagesize;            /* File space page size from input file */
+    unsigned      crt_order_flags;        /* group creation order flag */
 
     /*-------------------------------------------------------------------------
      * open input file
@@ -116,6 +117,8 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
     /* get user block size and file space strategy/persist/threshold */
     {
         hid_t fcpl_in; /* file creation property list ID for input file */
+        hid_t grp_in = -1;   /* group ID */
+        hid_t gcpl_in = -1;  /* group creation property list */
 
         if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
             error_msg("failed to retrieve file creation property list\n");
@@ -127,17 +130,28 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
         }
 
-    /* If the -S option is not set, get "strategy" from the input file */
-    if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) {
-        error_msg("failed to retrieve file space strategy\n");
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
+        /* If the -S option is not set, get "strategy" from the input file */
+        if(H5Pget_file_space_strategy(fcpl_in, &in_strategy, &in_persist, &in_threshold) < 0) {
+            error_msg("failed to retrieve file space strategy\n");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+        }
 
-    /* If the -G option is not set, get "pagesize" from the input file */
-    if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) {
-        error_msg("failed to retrieve file space threshold\n");
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
+        /* If the -G option is not set, get "pagesize" from the input file */
+        if(H5Pget_file_space_page_size(fcpl_in, &in_pagesize) < 0) {
+            error_msg("failed to retrieve file space threshold\n");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+        }
+        /* open root group */
+        if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
+
+        /* get root group creation property list */
+        if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
+
+        /* query and set the group creation properties */
+        if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
 
         if (H5Pclose(fcpl_in) < 0) {
             error_msg("failed to close property list\n");
@@ -309,6 +323,9 @@ print_user_block(fnamein, fidin);
         }
     }
 
+    if(H5Pset_link_creation_order(fcpl, crt_order_flags ) < 0)
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
+
     /* Set file space info to those from input file */
     set_strategy = in_strategy;
     set_persist = in_persist;
@@ -375,6 +392,8 @@ print_user_block(fnamein, fidin);
      *-------------------------------------------------------------------------
      */
 
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
     /* init table */
     trav_table_init(&travt);
 
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 339dc83..31b1e14 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -31,7 +31,7 @@ const char *outfile = NULL;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:P:T:G:E";
+static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "version", no_arg, 'V' },
@@ -56,6 +56,8 @@ static struct long_options l_opts[] = {
     { "fs_persist", require_arg, 'P' },
     { "fs_threshold", require_arg, 'T' },
     { "fs_pagesize", require_arg, 'G' },
+    { "sort_by", require_arg, 'q' },
+    { "sort_order", require_arg, 'z' },
     { "enable-error-stack", no_arg, 'E' },
     { NULL, 0, '\0' }
 };
@@ -90,6 +92,8 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
     PRINTVALSTREAM(rawoutstream, "   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
     PRINTVALSTREAM(rawoutstream, "   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
+    PRINTVALSTREAM(rawoutstream, "   -q Q, --sort_by=Q       Sort groups and attributes by index Q\n");
+    PRINTVALSTREAM(rawoutstream, "   -z Z, --sort_order=Z    Sort groups and attributes by order Z\n");
     PRINTVALSTREAM(rawoutstream, "   -f FILT, --filter=FILT  Filter type\n");
     PRINTVALSTREAM(rawoutstream, "   -l LAYT, --layout=LAYT  Layout type\n");
     PRINTVALSTREAM(rawoutstream, "   -S FS_STRATEGY, --fs_strategy=FS_STRATEGY  File space management strategy for H5Pset_file_space_strategy\n");
@@ -103,6 +107,8 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "    U - is a filename.\n");
     PRINTVALSTREAM(rawoutstream, "    T - is an integer\n");
     PRINTVALSTREAM(rawoutstream, "    A - is an integer greater than zero\n");
+    PRINTVALSTREAM(rawoutstream, "    Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n");
+    PRINTVALSTREAM(rawoutstream, "    Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\n");
     PRINTVALSTREAM(rawoutstream, "    B - is the user block size, any value that is 512 or greater and is\n");
     PRINTVALSTREAM(rawoutstream, "        a power of 2 (1024 default)\n");
     PRINTVALSTREAM(rawoutstream, "    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
@@ -370,6 +376,52 @@ done:
 }
 
 /*-------------------------------------------------------------------------
+ * Function:    set_sort_by
+ *
+ * Purpose: set the "by" form of sorting by translating from a string input
+ *          parameter to a H5_index_t return value
+ *          current sort values are [creation_order | name]
+ *
+ * Return: H5_index_t form of sort or H5_INDEX_UNKNOWN if none found
+ *-------------------------------------------------------------------------
+ */
+static H5_index_t
+set_sort_by(const char *form)
+{
+    H5_index_t idx_type = H5_INDEX_UNKNOWN;
+
+    if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */
+        idx_type = H5_INDEX_NAME;
+    else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */
+        idx_type = H5_INDEX_CRT_ORDER;
+
+    return idx_type;
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    set_sort_order
+ *
+ * Purpose: set the order of sorting by translating from a string input
+ *          parameter to a H5_iter_order_t return value
+ *          current order values are [ascending | descending ]
+ *
+ * Return: H5_iter_order_t form of order or H5_ITER_UNKNOWN if none found
+ *-------------------------------------------------------------------------
+ */
+static H5_iter_order_t
+set_sort_order(const char *form)
+{
+    H5_iter_order_t iter_order = H5_ITER_UNKNOWN;
+
+    if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */
+        iter_order = H5_ITER_INC;
+    else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */
+        iter_order = H5_ITER_DEC;
+
+    return iter_order;
+}
+
+/*-------------------------------------------------------------------------
  * Function: parse_command_line
  *
  * Purpose: parse command line input
@@ -553,14 +605,14 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
                 break;
 
             case 'P':
-                options->fs_persist = HDatoi( opt_arg );
+                options->fs_persist = HDatoi(opt_arg);
                 if(options->fs_persist == 0)
                     /* To distinguish the "specified" zero value */
                     options->fs_persist = -1;
                 break;
 
             case 'T':
-                options->fs_threshold = HDatol( opt_arg );
+                options->fs_threshold = HDatol(opt_arg);
                 if(options->fs_threshold == 0)
                     /* To distinguish the "specified" zero value */
                     options->fs_threshold = -1;
@@ -570,12 +622,30 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
                 options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0);
                 if(options->fs_pagesize == 0)
                     /* To distinguish the "specified" zero value */
-                   options->fs_pagesize = -1;	
+                   options->fs_pagesize = -1;
                 break;
 
-	    case 'E':
-		enable_error_stack = TRUE;
-		break;
+            case 'q':
+                if((sort_by = set_sort_by(opt_arg)) < 0) {
+                    error_msg(" failed to set sort by form <%s>\n", opt_arg);
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'z':
+                if((sort_order = set_sort_order(opt_arg)) < 0) {
+                    error_msg(" failed to set sort order form <%s>\n", opt_arg);
+                    h5tools_setstatus(EXIT_FAILURE);
+                    ret_value = -1;
+                    goto done;
+                }
+                break;
+
+            case 'E':
+            enable_error_stack = TRUE;
+            break;
 
             default:
                 break;
@@ -644,6 +714,9 @@ int main(int argc, const char **argv)
     /* initialize options  */
     h5repack_init(&options, 0, FALSE);
 
+    /* Initialize default indexing options */
+    sort_by = H5_INDEX_CRT_ORDER;
+
     if (parse_command_line(argc, argv, &options) < 0)
         goto done;
 
diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c
index 7e79aa7..4ff4875 100644
--- a/tools/src/h5repack/h5repack_verify.c
+++ b/tools/src/h5repack/h5repack_verify.c
@@ -55,11 +55,11 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
     trav_table_t *travt = NULL;
     int          ok = 1;
     hid_t       fcpl_in     = -1;   /* file creation property for input file */
-    hid_t   	fcpl_out    = -1;   /* file creation property for output file */
-    H5F_fspace_strategy_t in_strategy, out_strategy;	/* file space handling strategy for in/output file */
-    hbool_t 	in_persist, out_persist;		/* free-space persist status for in/output file */
-    hsize_t	in_threshold, out_threshold;		/* free-space section threshold for in/output file */
-    hsize_t	in_pagesize, out_pagesize;		/* file space page size for input/output file */
+    hid_t       fcpl_out    = -1;   /* file creation property for output file */
+    H5F_fspace_strategy_t in_strategy, out_strategy;    /* file space handling strategy for in/output file */
+    hbool_t     in_persist, out_persist;        /* free-space persist status for in/output file */
+    hsize_t    in_threshold, out_threshold;        /* free-space section threshold for in/output file */
+    hsize_t    in_pagesize, out_pagesize;        /* file space page size for input/output file */
 
     /* open the output file */
     if((fidout = H5Fopen(out_fname, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
@@ -122,6 +122,8 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
     if(options->all_filter == 1 || options->all_layout == 1)
     {
 
+        /* Initialize indexing options */
+        h5trav_set_index(sort_by, sort_order);
         /* init table */
         trav_table_init(&travt);
 
@@ -455,6 +457,9 @@ int h5repack_cmp_pl(const char *fname1,
     * get file table list of objects
     *-------------------------------------------------------------------------
     */
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
+    /* init table */
     trav_table_init(&trav);
     if(h5trav_gettable(fid1, trav) < 0)
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
@@ -643,7 +648,7 @@ int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter)
         {
 
             case H5Z_FILTER_NONE:
-        	break;
+            break;
 
             case H5Z_FILTER_SHUFFLE:
                 /* 1 private client value is returned by DCPL */
diff --git a/tools/test/h5copy/h5copygentest.c b/tools/test/h5copy/h5copygentest.c
index ed41998..bda0686 100644
--- a/tools/test/h5copy/h5copygentest.c
+++ b/tools/test/h5copy/h5copygentest.c
@@ -33,12 +33,12 @@
 #define DATASET_COMPRESSED      "compressed"
 #define DATASET_NAMED_VL        "named_vl"
 #define DATASET_NESTED_VL       "nested_vl"
-#define DATASET_ATTR		"dset_attr"
-#define ATTR			"attr"
+#define DATASET_ATTR            "dset_attr"
+#define ATTR                    "attr"
 #define GROUP_EMPTY             "grp_empty"
 #define GROUP_DATASETS          "grp_dsets"
 #define GROUP_NESTED            "grp_nested"
-#define GROUP_ATTR		"grp_attr"
+#define GROUP_ATTR              "grp_attr"
 
 /* Obj reference */
 #define OBJ_REF_DS "Dset1"
@@ -327,8 +327,8 @@ static void gent_nested_vl(hid_t loc_id)
  * Function:    gent_att_compound_vlstr
  *
  * Purpose:     Generate a dataset and a group.
- *		Both has an attribute with a compound datatype consisting 
- *		of a variable length string
+ *              Both has an attribute with a compound datatype consisting 
+ *              of a variable length string
  *
  *-------------------------------------------------------------------------
  */
@@ -347,7 +347,7 @@ static void gent_att_compound_vlstr(hid_t loc_id)
     hid_t vl_str_tid = -1;	/* Variable length datatype ID */
     hid_t cmpd_tid = -1;	/* Compound datatype ID */
     hid_t null_sid = -1;	/* Null dataspace ID */
-    s1 buf;			/* Buffer */
+    s1 buf;                 /* Buffer */
 
     buf.i = 9;
     buf.v = "ThisIsAString";
diff --git a/tools/test/h5diff/CMakeTests.cmake b/tools/test/h5diff/CMakeTests.cmake
index f6cd2dd..72dda6b 100644
--- a/tools/test/h5diff/CMakeTests.cmake
+++ b/tools/test/h5diff/CMakeTests.cmake
@@ -28,6 +28,7 @@
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr2.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_dset1.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_dset2.h5
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_dset3.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_hyper1.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_hyper2.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_empty.h5
@@ -275,6 +276,8 @@
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_709.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_710.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_80.txt
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_800.txt
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_801.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_90.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_tmp1.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_tmp2.txt
@@ -464,6 +467,7 @@
   set (FILE6 h5diff_attr2.h5)
   set (FILE7 h5diff_dset1.h5)
   set (FILE8 h5diff_dset2.h5)
+  set (FILE8A h5diff_dset3.h5)
   set (FILE9 h5diff_hyper1.h5)
   set (FILE10 h5diff_hyper2.h5)
   set (FILE11 h5diff_empty.h5)
@@ -872,6 +876,10 @@
           h5diff_710.out.err
           h5diff_80.out
           h5diff_80.out.err
+          h5diff_800.out
+          h5diff_800.out.err
+          h5diff_801.out
+          h5diff_801.out.err
           h5diff_90.out
           h5diff_90.out.err
           h5diff_v1.out
@@ -1478,6 +1486,14 @@ ADD_H5_TEST (h5diff_645 1 -v -p 0.05 --use-system-epsilon ${FILE1} ${FILE2} /g1/
 ADD_H5_TEST (h5diff_646 1 -v --use-system-epsilon -p 0.05 ${FILE1} ${FILE2} /g1/dset3 /g1/dset4)
 
 # ##############################################################################
+# # Test array variances
+# ##############################################################################
+#
+# Test with -d , -p and --use-system-epsilon.
+ADD_H5_TEST (h5diff_800 1 -v ${FILE7} ${FILE8} /g1/array /g1/array)
+ADD_H5_TEST (h5diff_801 1 -v ${FILE7} ${FILE8A} /g1/array /g1/array)
+
+# ##############################################################################
 # VDS tests
 # ##############################################################################
 ADD_H5_TEST (h5diff_v1 0 -v ${FILEV1} ${FILEV2})
diff --git a/tools/test/h5diff/h5diffgentest.c b/tools/test/h5diff/h5diffgentest.c
index cc7b057..708f371 100644
--- a/tools/test/h5diff/h5diffgentest.c
+++ b/tools/test/h5diff/h5diffgentest.c
@@ -48,6 +48,7 @@ size_t H5TOOLS_MALLOCSIZE = (128 * 1024 * 1024);
 #define FILE6    "h5diff_attr2.h5"
 #define FILE7    "h5diff_dset1.h5"
 #define FILE8    "h5diff_dset2.h5"
+#define FILE8A   "h5diff_dset3.h5"
 #define FILE9    "h5diff_hyper1.h5"
 #define FILE10   "h5diff_hyper2.h5"
 #define FILE11   "h5diff_empty.h5"
@@ -197,6 +198,7 @@ int main(void)
     /* generate 2 files, the second call creates a similar file with differences */
     test_datasets(FILE7,0);
     test_datasets(FILE8,1);
+    test_datasets(FILE8A,2);
 
     /* generate 2 files, the second call creates a similar file with differences */
     test_hyperslab(FILE9,0);
@@ -1328,7 +1330,7 @@ int test_datasets(const char *file,
     herr_t  status;
     int     buf[2]={1,2};
 
-    if(make_diffs)
+    if(make_diffs > 0)
         memset(buf, 0, sizeof buf);
 
     /* Create a file  */
@@ -1399,9 +1401,8 @@ int test_special_datasets(const char *file,
 
     /* Create a dataset with zero dimension size in one file but the other one
      * has a dataset with a non-zero dimension size */
-    if(make_diffs) {
+    if(make_diffs)
         dims[1] = SPACE1_DIM2 + 4;
-    }
 
     sid = H5Screate_simple(SPACE1_RANK, dims, NULL);
     did  = H5Dcreate2(fid, "dset2", H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@@ -5466,6 +5467,34 @@ static void test_objs_strings(const char *fname1, const char *fname2)
     H5Sclose(space);
     H5Dclose(dataset);
 
+    /* string 5 : early term long string */
+    string4A[0][10] = 0;
+    string4A[0][11] = 0;
+    string4B[0][10] = 0;
+
+    string4A[1][10] = 0;
+    string4A[1][11] = 'Z';
+    string4B[1][10] = 0;
+    string4B[1][11] = 'x';
+
+    string4A[2][10] = 0;
+    string4B[2][10] = 0;
+    string4B[2][11] = 'a';
+    string4B[2][12] = 'B';
+    string4B[2][13] = 'c';
+    space = H5Screate_simple(1, dims4, NULL);
+    f_type = mkstr(168, H5T_STR_NULLTERM);
+    m_type = mkstr(21, H5T_STR_NULLTERM);
+    dataset = H5Dcreate2(fid1, "/string5", f_type, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    H5Dwrite(dataset, m_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, string4A);
+    H5Dclose(dataset);
+    dataset = H5Dcreate2(fid2, "/string5", f_type, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    H5Dwrite(dataset, m_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, string4B);
+    H5Tclose(m_type);
+    H5Tclose(f_type);
+    H5Sclose(space);
+    H5Dclose(dataset);
+
 out:
     /*-----------------------------------------------------------------------
     * Close IDs
@@ -6613,6 +6642,9 @@ void write_dset_in(hid_t loc_id,
     int        buf73[4][3][2];    /* integer */
     float      buf83[4][3][2];    /* float */
 
+    if(make_diffs == 2) {
+        dimarray[0] = 4;
+    }
 
     /*-------------------------------------------------------------------------
     * H5S_SCALAR
@@ -6621,11 +6653,8 @@ void write_dset_in(hid_t loc_id,
 
 
 
-    if ( make_diffs )
-    {
-
+    if(make_diffs)
         scalar_data = 1;
-    }
 
     /* create a space  */
     sid = H5Screate(H5S_SCALAR);
@@ -7208,7 +7237,7 @@ void write_dset_in(hid_t loc_id,
 
     n=1;
     for (i = 0; i < 24; i++) {
-        for (j = 0; j < (int)dimarray[0]; j++) {
+        for (j = 0; j < 3; j++) {
             if (make_diffs) buf63[i][j]=0;
             else buf63[i][j]=n++;
         }
diff --git a/tools/test/h5diff/testfiles/diff_strings1.h5 b/tools/test/h5diff/testfiles/diff_strings1.h5
index 8839f5a..0f8b380 100644
--- a/tools/test/h5diff/testfiles/diff_strings1.h5
+++ b/tools/test/h5diff/testfiles/diff_strings1.h5
diff --git a/tools/test/h5diff/testfiles/diff_strings2.h5 b/tools/test/h5diff/testfiles/diff_strings2.h5
index 810278c..e8520ae 100644
--- a/tools/test/h5diff/testfiles/diff_strings2.h5
+++ b/tools/test/h5diff/testfiles/diff_strings2.h5
diff --git a/tools/test/h5diff/testfiles/h5diff_10.txt b/tools/test/h5diff/testfiles/h5diff_10.txt
index a699f00..0a0ee22 100644
--- a/tools/test/h5diff/testfiles/h5diff_10.txt
+++ b/tools/test/h5diff/testfiles/h5diff_10.txt
@@ -1,4 +1,4 @@
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -59,19 +59,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -106,15 +109,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_58.txt b/tools/test/h5diff/testfiles/h5diff_58.txt
index 768dd97..d27a0c9 100644
--- a/tools/test/h5diff/testfiles/h5diff_58.txt
+++ b/tools/test/h5diff/testfiles/h5diff_58.txt
@@ -1,5 +1,5 @@
 dataset: </refreg> and </refreg>
-Referenced dataset      10720            10720
+Referenced dataset      10784            10784
 ------------------------------------------------------------
 Region blocks
 block #0           (2,2)-(7,7)           (0,0)-(2,2)
diff --git a/tools/test/h5diff/testfiles/h5diff_600.txt b/tools/test/h5diff/testfiles/h5diff_600.txt
index 3c3ad9f..4362711 100644
--- a/tools/test/h5diff/testfiles/h5diff_600.txt
+++ b/tools/test/h5diff/testfiles/h5diff_600.txt
@@ -1,4 +1,4 @@
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -59,19 +59,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -106,15 +109,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_603.txt b/tools/test/h5diff/testfiles/h5diff_603.txt
index 087764a..9ab3204 100644
--- a/tools/test/h5diff/testfiles/h5diff_603.txt
+++ b/tools/test/h5diff/testfiles/h5diff_603.txt
@@ -1,5 +1,5 @@
 <-d -4> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_606.txt b/tools/test/h5diff/testfiles/h5diff_606.txt
index c31a67e..afe0e72 100644
--- a/tools/test/h5diff/testfiles/h5diff_606.txt
+++ b/tools/test/h5diff/testfiles/h5diff_606.txt
@@ -1,5 +1,5 @@
 <-d 0x1> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_612.txt b/tools/test/h5diff/testfiles/h5diff_612.txt
index 05318bd..97a1747 100644
--- a/tools/test/h5diff/testfiles/h5diff_612.txt
+++ b/tools/test/h5diff/testfiles/h5diff_612.txt
@@ -1,5 +1,5 @@
 <-p -4> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_615.txt b/tools/test/h5diff/testfiles/h5diff_615.txt
index fd756b3..78770f0 100644
--- a/tools/test/h5diff/testfiles/h5diff_615.txt
+++ b/tools/test/h5diff/testfiles/h5diff_615.txt
@@ -1,5 +1,5 @@
 <-p 0x1> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_621.txt b/tools/test/h5diff/testfiles/h5diff_621.txt
index fd8c680..b2a5881 100644
--- a/tools/test/h5diff/testfiles/h5diff_621.txt
+++ b/tools/test/h5diff/testfiles/h5diff_621.txt
@@ -1,5 +1,5 @@
 <-n -4> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_622.txt b/tools/test/h5diff/testfiles/h5diff_622.txt
index f0d38af..66a3025 100644
--- a/tools/test/h5diff/testfiles/h5diff_622.txt
+++ b/tools/test/h5diff/testfiles/h5diff_622.txt
@@ -1,5 +1,5 @@
 <-n 0> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_623.txt b/tools/test/h5diff/testfiles/h5diff_623.txt
index 4ab66a5..f9258d1 100644
--- a/tools/test/h5diff/testfiles/h5diff_623.txt
+++ b/tools/test/h5diff/testfiles/h5diff_623.txt
@@ -1,5 +1,5 @@
 <-n u> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_624.txt b/tools/test/h5diff/testfiles/h5diff_624.txt
index f5e7ee3..57a4ddd 100644
--- a/tools/test/h5diff/testfiles/h5diff_624.txt
+++ b/tools/test/h5diff/testfiles/h5diff_624.txt
@@ -1,5 +1,5 @@
 <-n 0x1> is not a valid option
-usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]] 
+usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   file1             File name of the first HDF5 file
   file2             File name of the second HDF5 file
   [obj1]            Name of an HDF5 object, in absolute path
@@ -60,19 +60,22 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
    -n C, --count=C
          Print differences up to C. C must be a positive integer.
    -d D, --delta=D
-         Print difference if (|a-b| > D). D must be a positive number.
+         Print difference if (|a-b| > D). D must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-p' or '--use-system-epsilon'.
    -p R, --relative=R
-         Print difference if (|(a-b)/b| > R). R must be a positive number.
+         Print difference if (|(a-b)/b| > R). R must be a positive number. Where a
+         is the data point value in file1 and b is the data point value in file2.
          Can not use with '-d' or '--use-system-epsilon'.
    --use-system-epsilon
-         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.
+         Print difference if (|a-b| > EPSILON), EPSILON is system defined value. Where a
+         is the data point value in file1 and b is the data point value in file2.
          If the system epsilon is not defined,one of the following predefined
          values will be used:
            FLT_EPSILON = 1.19209E-07 for floating-point type
            DBL_EPSILON = 2.22045E-16 for double precision type
          Can not use with '-p' or '-d'.
-   --exclude-path "path" 
+   --exclude-path "path"
          Exclude the specified path to an object when comparing files or groups.
          If a group is excluded, all member objects will also be excluded.
          The specified path is excluded wherever it occurs.
@@ -107,15 +110,15 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
   common objects.
 
  Object comparison:
-  1) Groups 
+  1) Groups
       First compares the names of member objects (relative path, from the
       specified group) and generates a report of objects that appear in only
       one group or in both groups. Common objects are then compared recursively.
-  2) Datasets 
+  2) Datasets
       Array rank and dimensions, datatypes, and data values are compared.
-  3) Datatypes 
+  3) Datatypes
       The comparison is based on the return value of H5Tequal.
-  4) Symbolic links 
+  4) Symbolic links
       The paths to the target objects are compared.
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
diff --git a/tools/test/h5diff/testfiles/h5diff_80.txt b/tools/test/h5diff/testfiles/h5diff_80.txt
index 5957d72..836e073 100644
--- a/tools/test/h5diff/testfiles/h5diff_80.txt
+++ b/tools/test/h5diff/testfiles/h5diff_80.txt
@@ -865,7 +865,7 @@ position        vlen3D          vlen3D          difference
 [ 3 2 1 ]          59              0               59             
 59 differences found
 dataset: </refreg> and </refreg>
-Referenced dataset      10720            10720
+Referenced dataset      10784            10784
 ------------------------------------------------------------
 Region blocks
 block #0           (2,2)-(7,7)           (0,0)-(2,2)
diff --git a/tools/test/h5diff/testfiles/h5diff_800.txt b/tools/test/h5diff/testfiles/h5diff_800.txt
new file mode 100644
index 0000000..e43e7b4
--- /dev/null
+++ b/tools/test/h5diff/testfiles/h5diff_800.txt
@@ -0,0 +1,12 @@
+dataset: </g1/array> and </g1/array>
+size:           [2]           [2]
+position        array           array           difference          
+------------------------------------------------------------
+[ 0 ]          1               0               1              
+[ 0 ]          2               0               2              
+[ 0 ]          3               0               3              
+[ 1 ]          4               0               4              
+[ 1 ]          5               0               5              
+[ 1 ]          6               0               6              
+6 differences found
+EXIT CODE: 1
diff --git a/tools/test/h5diff/testfiles/h5diff_801.txt b/tools/test/h5diff/testfiles/h5diff_801.txt
new file mode 100644
index 0000000..043e7e3
--- /dev/null
+++ b/tools/test/h5diff/testfiles/h5diff_801.txt
@@ -0,0 +1,13 @@
+dataset: </g1/array> and </g1/array>
+Warning: different storage datatype
+size:           [2]           [2]
+position        array           array           difference          
+------------------------------------------------------------
+[ 0 ]          1               0               1              
+[ 0 ]          2               0               2              
+[ 0 ]          3               0               3              
+[ 1 ]          4               0               4              
+[ 1 ]          5               0               5              
+[ 1 ]          6               0               6              
+6 differences found
+EXIT CODE: 1
diff --git a/tools/test/h5diff/testfiles/h5diff_dset1.h5 b/tools/test/h5diff/testfiles/h5diff_dset1.h5
index 123e141..fefd86a 100644
--- a/tools/test/h5diff/testfiles/h5diff_dset1.h5
+++ b/tools/test/h5diff/testfiles/h5diff_dset1.h5
diff --git a/tools/test/h5diff/testfiles/h5diff_dset2.h5 b/tools/test/h5diff/testfiles/h5diff_dset2.h5
index 3ae6993..598e481 100644
--- a/tools/test/h5diff/testfiles/h5diff_dset2.h5
+++ b/tools/test/h5diff/testfiles/h5diff_dset2.h5
diff --git a/tools/test/h5diff/testfiles/h5diff_dset3.h5 b/tools/test/h5diff/testfiles/h5diff_dset3.h5
new file mode 100644
index 0000000..893c135
--- /dev/null
+++ b/tools/test/h5diff/testfiles/h5diff_dset3.h5
diff --git a/tools/test/h5repack/CMakeTests.cmake b/tools/test/h5repack/CMakeTests.cmake
index 04e405f..897209c 100644
--- a/tools/test/h5repack/CMakeTests.cmake
+++ b/tools/test/h5repack/CMakeTests.cmake
@@ -90,6 +90,7 @@
       ${HDF5_TOOLS_DIR}/testfiles/tfamily00008.h5
       ${HDF5_TOOLS_DIR}/testfiles/tfamily00009.h5
       ${HDF5_TOOLS_DIR}/testfiles/tfamily00010.h5
+      ${HDF5_TOOLS_DIR}/testfiles/tordergr.h5
       # tools/testfiles/vds
       ${HDF5_TOOLS_DIR}/testfiles/vds/1_a.h5
       ${HDF5_TOOLS_DIR}/testfiles/vds/1_b.h5
@@ -137,6 +138,7 @@
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_compa-v.ddl
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_conti-v.ddl
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.h5-plugin_zero.tst
+      ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/crtorder.tordergr.h5.ddl
   )
 
   foreach (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
@@ -312,7 +314,7 @@
             NAME H5REPACK_DMP-h5dump-${testname}
             COMMAND "${CMAKE_COMMAND}"
                 -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
-                -D "TEST_ARGS:STRING=-pH;out-${testname}.${resultfile}"
+                -D "TEST_ARGS:STRING=-q;creation_order;-pH;out-${testname}.${resultfile}"
                 -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
                 -D "TEST_OUTPUT=${resultfile}-${testname}.out"
                 -D "TEST_EXPECT=${resultcode}"
@@ -965,6 +967,11 @@
   endif ()
   ADD_H5_TEST (deflate_file ${TESTTYPE} ${arg})
 
+#crtorder
+  set (arg tordergr.h5 -L)
+  set (TESTTYPE "TEST")
+  ADD_H5_DMP_TEST (crtorder ${TESTTYPE} 0 ${arg})
+
 #########################################################
 # layout options (these files have no filters)
 #########################################################
diff --git a/tools/test/h5repack/h5repack.sh.in b/tools/test/h5repack/h5repack.sh.in
index e479031..bc6b527 100644
--- a/tools/test/h5repack/h5repack.sh.in
+++ b/tools/test/h5repack/h5repack.sh.in
@@ -113,6 +113,7 @@ $SRC_TOOLS_TESTFILES/tfamily00007.h5
 $SRC_TOOLS_TESTFILES/tfamily00008.h5
 $SRC_TOOLS_TESTFILES/tfamily00009.h5
 $SRC_TOOLS_TESTFILES/tfamily00010.h5
+$SRC_TOOLS_TESTFILES/tordergr.h5
 $SRC_TOOLS_TESTFILES/vds/1_a.h5
 $SRC_TOOLS_TESTFILES/vds/1_b.h5
 $SRC_TOOLS_TESTFILES/vds/1_c.h5
@@ -143,6 +144,7 @@ $SRC_H5REPACK_TESTFILES/h5repack-help.txt
 $SRC_H5REPACK_TESTFILES/h5repack_ext.bin
 $SRC_H5REPACK_TESTFILES/ublock.bin
 $SRC_H5REPACK_TESTFILES/h5repack.info
+$SRC_H5REPACK_TESTFILES/crtorder.tordergr.h5.ddl
 $SRC_H5REPACK_TESTFILES/deflate_limit.h5repack_layout.h5.ddl
 $SRC_H5REPACK_TESTFILES/h5repack_layout.h5.ddl
 $SRC_H5REPACK_TESTFILES/h5repack_filters.h5-gzip_verbose_filters.tst
@@ -684,7 +686,7 @@ TOOLTEST_DUMP()
      VERIFY h5dump output $@
      (
         cd $TESTDIR
-        $RUNSERIAL $H5DUMP_BIN -pH $outfile
+        $RUNSERIAL $H5DUMP_BIN -q creation_order -pH $outfile
      ) >$actual 2>$actual_err
      cat $actual_err >> $actual
 
@@ -1051,6 +1053,10 @@ else
  TOOLTEST deflate_file $arg
 fi
 
+#crtorder
+arg="tordergr.h5 -L"
+TOOLTEST_DUMP crtorder $arg
+
 #########################################################
 # layout options (these files have no filters)
 #########################################################
diff --git a/tools/test/h5repack/testfiles/crtorder.tordergr.h5.ddl b/tools/test/h5repack/testfiles/crtorder.tordergr.h5.ddl
new file mode 100644
index 0000000..870d154
--- /dev/null
+++ b/tools/test/h5repack/testfiles/crtorder.tordergr.h5.ddl
@@ -0,0 +1,36 @@
+HDF5 "out-crtorder.tordergr.h5" {
+GROUP "/" {
+   GROUP "2" {
+      GROUP "a" {
+         GROUP "a1" {
+         }
+         GROUP "a2" {
+            GROUP "a21" {
+            }
+            GROUP "a22" {
+            }
+         }
+      }
+      GROUP "b" {
+      }
+      GROUP "c" {
+      }
+   }
+   GROUP "1" {
+      GROUP "c" {
+      }
+      GROUP "b" {
+      }
+      GROUP "a" {
+         GROUP "a1" {
+         }
+         GROUP "a2" {
+            GROUP "a22" {
+            }
+            GROUP "a21" {
+            }
+         }
+      }
+   }
+}
+}
diff --git a/tools/test/h5repack/testfiles/h5repack-help.txt b/tools/test/h5repack/testfiles/h5repack-help.txt
index 69b1644..65edd89 100644
--- a/tools/test/h5repack/testfiles/h5repack-help.txt
+++ b/tools/test/h5repack/testfiles/h5repack-help.txt
@@ -17,6 +17,8 @@ usage: h5repack [OPTIONS] file1 file2
    -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size
    -t T, --threshold=T     Threshold value for H5Pset_alignment
    -a A, --alignment=A     Alignment value for H5Pset_alignment
+   -q Q, --sort_by=Q       Sort groups and attributes by index Q
+   -z Z, --sort_order=Z    Sort groups and attributes by order Z
    -f FILT, --filter=FILT  Filter type
    -l LAYT, --layout=LAYT  Layout type
    -S FS_STRATEGY, --fs_strategy=FS_STRATEGY  File space management strategy for H5Pset_file_space_strategy
@@ -30,6 +32,8 @@ usage: h5repack [OPTIONS] file1 file2
     U - is a filename.
     T - is an integer
     A - is an integer greater than zero
+    Q - is the sort index type for the input file. It can be "name" or "creation_order" (default)
+    Z - is the sort order type for the input file. It can be "descending" or "ascending" (default)
     B - is the user block size, any value that is 512 or greater and is
         a power of 2 (1024 default)
     F - is the shared object header message type, any of <dspace|dtype|fill|