Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit '6428a637752753cc8a9007c0c3c38b9ea9cc97fd': (165 commits)
  Skip HDFFV-10160 filenotclosed test for split/multi driver Temporary skip this test for split/multi driver. Further investigation to resolve the failure is needed. Please enter the commit message for your changes. Lines starting
  More minor whitespace cleanup
  Fixed a minor comment typo in H5R.c
  * Reverted removal of H5I_REFERENCE to avoid breaking binary   compatibility. * Added a quick H5I_REFERENCE smoke check to test_misc19()   in tmisc.c.
  Added missing free() call to test_misc19().
  Purged the unused H5I_REFERENCE from the library.
  Added a test for VFD IDs to testhdf5.
  Revert "Partial removal of NDEBUG ifdefs from the library."
  Partial removal of NDEBUG ifdefs from the library.
  Removed compiler flag cleanup since Solaris chokes on it.
  Fix for HDFFV-10160 Modifications to fix the assertion/abort failure when the application does not close the file.
  Fixed a bug in autotools Fortran processing where a test for the presence of a C long double type always returned true.
  Updated the --enable-debug/production handling in configure.ac so that it more reliably indicates that the configure option can no longer be used. Previously, using --enable-debug="", etc. would not trigger an error (even though such usage is unlikely).
  Added awk processing to remove extraneous whitespace from H5_ flags in configure.
  Fixed a comment in configure.ac
  HDFFV-10219 another mode change
  HDFFV-10219 change subset to use BINARY mode for h5dump
  HDFFV-10219 default input binary to NATIVE
  Set default of var to NATIVE
  HDFFV-10219 - disable h5dump tests until h5import NATIVE is fixed
  ...

10 files changed, 733 insertions, 665 deletions

diff --git a/tools/src/h5repack/Makefile.am b/tools/src/h5repack/Makefile.am
index 31d368d..c71e65b 100644
--- a/tools/src/h5repack/Makefile.am
+++ b/tools/src/h5repack/Makefile.am
@@ -5,12 +5,10 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
 ##
 ## Makefile.am
 ## Run automake to generate a Makefile.in from this file.
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index c09dee6..bc8527b 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include <stdlib.h>
@@ -53,19 +51,19 @@ static int have_request(pack_opt_t *options);
  *-------------------------------------------------------------------------
  */
 int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
-	/* check input */
-	if (check_options(options) < 0)
-		return -1;
+    /* check input */
+    if (check_options(options) < 0)
+        return -1;
 
-	/* check for objects in input that are in the file */
-	if (check_objects(infile, options) < 0)
-		return -1;
+    /* check for objects in input that are in the file */
+    if (check_objects(infile, options) < 0)
+        return -1;
 
-	/* copy the objects  */
-	if (copy_objects(infile, outfile, options) < 0)
-		return -1;
+    /* copy the objects  */
+    if (copy_objects(infile, outfile, options) < 0)
+        return -1;
 
-	return 0;
+    return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -107,7 +105,7 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
  */
 
 int h5repack_end(pack_opt_t *options) {
-	return options_table_free(options->op_tbl);
+    return options_table_free(options->op_tbl);
 }
 
 /*-------------------------------------------------------------------------
@@ -123,10 +121,10 @@ int h5repack_end(pack_opt_t *options) {
 int
 h5repack_addfilter(const char* str, pack_opt_t *options)
 {
-    obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
-    filter_info_t filter;       /* filter info for the current -f option entry */
-    unsigned n_objs;    /* number of objects in the current -f or -l option entry */
-    int is_glb;         /* is the filter global */
+    obj_list_t   *obj_list = NULL; /* one object list for the -f and -l option entry */
+    filter_info_t filter;          /* filter info for the current -f option entry */
+    unsigned      n_objs;          /* number of objects in the current -f or -l option entry */
+    int           is_glb;          /* is the filter global */
 
     /* parse the -f option */
     if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
@@ -165,10 +163,10 @@ int
 h5repack_addlayout(const char* str, pack_opt_t *options)
 {
     obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
-    unsigned n_objs; /*number of objects in the current -t or -c option entry */
-    pack_info_t pack; /*info about layout to extract from parse */
-    int j;
-    int ret_value = -1;
+    unsigned    n_objs;          /*number of objects in the current -t or -c option entry */
+    pack_info_t pack;            /*info about layout to extract from parse */
+    int         j;
+    int         ret_value = -1;
 
     init_packobject(&pack);
 
@@ -234,87 +232,84 @@ h5repack_addlayout(const char* str, pack_opt_t *options)
  *-------------------------------------------------------------------------
  */
 hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
-		named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
-	named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
-	named_dt_t *dt_ret = NULL; /* Datatype to return */
-	H5O_info_t oinfo; /* Object info of input dtype */
-	hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
-
-	if (H5Oget_info(type_in, &oinfo) < 0)
-		goto done;
-
-	if (*named_dt_head_p) {
-		/* Stack already exists, search for the datatype */
-		while (dt && dt->addr_in != oinfo.addr)
-			dt = dt->next;
-
-		dt_ret = dt;
-	}
-	else {
-		/* Create the stack */
-		size_t i;
-
-		for (i = 0; i < travt->nobjs; i++) {
-			if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
-				/* Push onto the stack */
-				if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
-					goto done;
-				}
-				dt->next = *named_dt_head_p;
-				*named_dt_head_p = dt;
-
-				/* Update the address and id */
-				dt->addr_in = travt->objs[i].objno;
-				dt->id_out = -1;
-
-				/* Check if this type is the one requested */
-				if (oinfo.addr == dt->addr_in) {
-					HDassert(!dt_ret);
-					dt_ret = dt;
-				} /* end if */
-			} /* end if */
-		} /* end for */
-	} /* end else */
-
-	/* Handle the case that the requested datatype was not found.  This is
-	 * possible if the datatype was committed anonymously in the input file. */
-	if (!dt_ret) {
-		/* Push the new datatype onto the stack */
-		if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
-			goto done;
-		}
-		dt_ret->next = *named_dt_head_p;
-		*named_dt_head_p = dt_ret;
-
-		/* Update the address and id */
-		dt_ret->addr_in = oinfo.addr;
-		dt_ret->id_out = -1;
-	} /* end if */
-
-	/* If the requested datatype does not yet exist in the output file, copy it
-	 * anonymously */
-	if (dt_ret->id_out < 0) {
-		if (options->use_native == 1)
-			dt_ret->id_out = h5tools_get_native_type(type_in);
-		else
-			dt_ret->id_out = H5Tcopy(type_in);
-		if (dt_ret->id_out < 0)
-			goto done;
-		if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
-			goto done;
-	} /* end if */
-
-	/* Set return value */
-	ret_value = dt_ret->id_out;
-
-	/* Increment the ref count on id_out, because the calling function will try
-	 * to close it */
-	if(H5Iinc_ref(ret_value) < 0) {
-		ret_value = -1;
-	}
+        named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+    named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+    named_dt_t *dt_ret = NULL;         /* Datatype to return */
+    H5O_info_t  oinfo;                 /* Object info of input dtype */
+    hid_t       ret_value = -1;        /* The identifier of the named dtype in the out file */
+
+    if (H5Oget_info(type_in, &oinfo) < 0)
+        goto done;
+
+    if (*named_dt_head_p) {
+        /* Stack already exists, search for the datatype */
+        while (dt && dt->addr_in != oinfo.addr)
+            dt = dt->next;
+
+        dt_ret = dt;
+    }
+    else {
+        /* Create the stack */
+        size_t i;
+
+        for (i = 0; i < travt->nobjs; i++) {
+            if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+                /* Push onto the stack */
+                if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
+                    goto done;
+                dt->next = *named_dt_head_p;
+                *named_dt_head_p = dt;
+
+                /* Update the address and id */
+                dt->addr_in = travt->objs[i].objno;
+                dt->id_out = -1;
+
+                /* Check if this type is the one requested */
+                if (oinfo.addr == dt->addr_in) {
+                    HDassert(!dt_ret);
+                    dt_ret = dt;
+                } /* end if */
+            } /* end if */
+        } /* end for */
+    } /* end else */
+
+    /* Handle the case that the requested datatype was not found.  This is
+    * possible if the datatype was committed anonymously in the input file. */
+    if (!dt_ret) {
+        /* Push the new datatype onto the stack */
+        if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
+            goto done;
+        dt_ret->next = *named_dt_head_p;
+        *named_dt_head_p = dt_ret;
+
+        /* Update the address and id */
+        dt_ret->addr_in = oinfo.addr;
+        dt_ret->id_out = -1;
+    } /* end if */
+
+    /* If the requested datatype does not yet exist in the output file, copy it
+    * anonymously */
+    if (dt_ret->id_out < 0) {
+        if (options->use_native == 1)
+            dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT);
+        else
+            dt_ret->id_out = H5Tcopy(type_in);
+        if (dt_ret->id_out < 0)
+            goto done;
+        if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+            goto done;
+    } /* end if */
+
+    /* Set return value */
+    ret_value = dt_ret->id_out;
+
+    /* Increment the ref count on id_out, because the calling function will try
+    * to close it */
+    if(H5Iinc_ref(ret_value) < 0)
+        ret_value = -1;
 
 done:
-	return (ret_value);
+    return (ret_value);
 } /* end copy_named_datatype */
 
 /*-------------------------------------------------------------------------
@@ -329,22 +324,22 @@ done:
  *-------------------------------------------------------------------------
  */
 int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
-	named_dt_t *dt = *named_dt_head_p;
-	int ret_value = -1;
+    named_dt_t *dt = *named_dt_head_p;
+    int         ret_value = -1;
 
-	while (dt) {
-		/* Pop the datatype off the stack and free it */
-		if (H5Tclose(dt->id_out) < 0 && !ignore_err)
-			goto done;
-		dt = dt->next;
-		HDfree(*named_dt_head_p);
-		*named_dt_head_p = dt;
-	} /* end while */
+    while (dt) {
+        /* Pop the datatype off the stack and free it */
+        if (H5Tclose(dt->id_out) < 0 && !ignore_err)
+            goto done;
+        dt = dt->next;
+        HDfree(*named_dt_head_p);
+        *named_dt_head_p = dt;
+    } /* end while */
 
-	ret_value = 0;
+    ret_value = 0;
 
 done:
-	return (ret_value);
+    return (ret_value);
 } /* end named_datatype_free */
 
 /*-------------------------------------------------------------------------
@@ -365,25 +360,25 @@ done:
  */
 int
 copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
-		trav_table_t *travt, pack_opt_t *options)
+        trav_table_t *travt, pack_opt_t *options)
 {
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t attr_id = -1; /* attr ID */
-    hid_t attr_out = -1; /* attr ID */
-    hid_t space_id = -1; /* space ID */
-    hid_t ftype_id = -1; /* file type ID */
-    hid_t wtype_id = -1; /* read/write type ID */
-    size_t msize; /* size of type */
-    void *buf = NULL; /* data buffer */
-    hsize_t nelmts; /* number of elements in dataset */
-    int rank; /* rank of dataset */
-    htri_t is_named; /* Whether the datatype is named */
-    hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
-    char name[255];
-    H5O_info_t oinfo; /* object info */
-    int j;
-    unsigned u;
-    hbool_t is_ref = 0;
+    int         ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    hid_t       attr_id = -1;  /* attr ID */
+    hid_t       attr_out = -1; /* attr ID */
+    hid_t       space_id = -1; /* space ID */
+    hid_t       ftype_id = -1; /* file type ID */
+    hid_t       wtype_id = -1; /* read/write type ID */
+    size_t      msize;         /* size of type */
+    void       *buf = NULL;    /* data buffer */
+    hsize_t     nelmts;        /* number of elements in dataset */
+    int         rank;          /* rank of dataset */
+    htri_t      is_named;      /* Whether the datatype is named */
+    hsize_t     dims[H5S_MAX_RANK];/* dimensions of dataset */
+    char        name[255];
+    H5O_info_t  oinfo;         /* object info */
+    int         j;
+    unsigned    u;
+    hbool_t     is_ref = 0;
     H5T_class_t type_class = -1;
 
     if (H5Oget_info(loc_in, &oinfo) < 0)
@@ -427,7 +422,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
         } /* end if */
         else {
             if (options->use_native == 1)
-                wtype_id = h5tools_get_native_type(ftype_id);
+                wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
             else
                 wtype_id = H5Tcopy(ftype_id);
         } /* end else */
@@ -468,7 +463,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
             int nmembers = H5Tget_nmembers(wtype_id);
 
             for (j = 0; j < nmembers; j++) {
-                hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+                hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j);
                 H5T_class_t mtclass = H5Tget_class(mtid);
                 H5Tclose(mtid);
 
@@ -479,16 +474,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
             } /* for (j=0; i<nmembers; j++) */
         } /* if (type_class == H5T_COMPOUND) */
 
-        if (is_ref) {
-            ; /* handled by copy_refs_attr() */
-        }
-        else {
+        if (!is_ref) {
             /*-------------------------------------------------------------------------
              * read to memory
              *-------------------------------------------------------------------------
              */
 
-            buf = (void *) HDmalloc((size_t)(nelmts * msize));
+            buf = (void *)HDmalloc((size_t)(nelmts * msize));
             if (buf == NULL) {
                 error_msg("h5repack", "cannot read into memory\n");
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
@@ -570,193 +562,188 @@ done:
  * Programmer: pvn@ncsa.uiuc.edu
  *
  * Date: September, 22, 2003
- *
- * Modification:
- *   Peter Cao, July 9, 2007
- *   Add "-L, --latest" and other options to pack a file with the latest file format
- *
  *-------------------------------------------------------------------------
  */
 static int check_options(pack_opt_t *options) {
-	unsigned int i;
-	int k, j, has_cp = 0, has_ck = 0;
-	char slayout[30];
-
-	/*-------------------------------------------------------------------------
-	 * objects to layout
-	 *-------------------------------------------------------------------------
-	 */
-	if (options->verbose && have_request(options) /* only print if requested */) {
-		printf("Objects to modify layout are...\n");
-		if (options->all_layout == 1) {
-			switch (options->layout_g) {
-			case H5D_COMPACT:
-				strcpy(slayout, "compact");
-				break;
-			case H5D_CONTIGUOUS:
-				strcpy(slayout, "contiguous");
-				break;
-			case H5D_CHUNKED:
-				strcpy(slayout, "chunked");
-				break;
-			case H5D_VIRTUAL:
-				strcpy(slayout, "virtual");
-				break;
-			case H5D_LAYOUT_ERROR:
-			case H5D_NLAYOUTS:
-				error_msg("invalid layout\n");
-				return -1;
-			default:
-				strcpy(slayout, "invalid layout\n");
-				return -1;
-			}
-			printf(" Apply %s layout to all\n", slayout);
-			if (H5D_CHUNKED == options->layout_g) {
-				printf("with dimension [");
-				for (j = 0; j < options->chunk_g.rank; j++)
-					printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
-				printf("]\n");
-			}
-		}
-	}/* verbose */
-
-	for (i = 0; i < options->op_tbl->nelems; i++) {
-		char* name = options->op_tbl->objs[i].path;
-
-		if (options->op_tbl->objs[i].chunk.rank > 0) {
-			if (options->verbose) {
-				printf(" <%s> with chunk size ", name);
-				for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
-					printf("%d ",
-							(int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
-				printf("\n");
-			}
-			has_ck = 1;
-		}
-		else if (options->op_tbl->objs[i].chunk.rank == -2) {
-			if (options->verbose)
-				printf(" <%s> %s\n", name, "NONE (contigous)");
-			has_ck = 1;
-		}
-	}
-
-	if (options->all_layout == 1 && has_ck) {
-		error_msg(
-				"invalid chunking input: 'all' option\
+    unsigned int i;
+    int          k, j, has_cp = 0, has_ck = 0;
+    char         slayout[30];
+
+    /*-------------------------------------------------------------------------
+    * objects to layout
+    *-------------------------------------------------------------------------
+    */
+    if (options->verbose && have_request(options) /* only print if requested */) {
+        printf("Objects to modify layout are...\n");
+        if (options->all_layout == 1) {
+            switch (options->layout_g) {
+            case H5D_COMPACT:
+                strcpy(slayout, "compact");
+                break;
+            case H5D_CONTIGUOUS:
+                strcpy(slayout, "contiguous");
+                break;
+            case H5D_CHUNKED:
+                strcpy(slayout, "chunked");
+                break;
+            case H5D_VIRTUAL:
+                strcpy(slayout, "virtual");
+                break;
+            case H5D_LAYOUT_ERROR:
+            case H5D_NLAYOUTS:
+                error_msg("invalid layout\n");
+                return -1;
+            default:
+                strcpy(slayout, "invalid layout\n");
+                return -1;
+            }
+            printf(" Apply %s layout to all\n", slayout);
+            if (H5D_CHUNKED == options->layout_g) {
+                printf("with dimension [");
+                for (j = 0; j < options->chunk_g.rank; j++)
+                    printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+                printf("]\n");
+            }
+        }
+    }/* verbose */
+
+    for (i = 0; i < options->op_tbl->nelems; i++) {
+        char* name = options->op_tbl->objs[i].path;
+
+        if (options->op_tbl->objs[i].chunk.rank > 0) {
+            if (options->verbose) {
+                printf(" <%s> with chunk size ", name);
+                for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
+                    printf("%d ",
+                            (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+                printf("\n");
+            }
+            has_ck = 1;
+        }
+        else if (options->op_tbl->objs[i].chunk.rank == -2) {
+            if (options->verbose)
+                printf(" <%s> %s\n", name, "NONE (contigous)");
+            has_ck = 1;
+        }
+    }
+
+    if (options->all_layout == 1 && has_ck) {
+        error_msg(
+                "invalid chunking input: 'all' option\
                             is present with other objects\n");
-		return -1;
-	}
-
-	/*-------------------------------------------------------------------------
-	 * objects to filter
-	 *-------------------------------------------------------------------------
-	 */
-
-	if (options->verbose && have_request(options) /* only print if requested */) {
-		printf("Objects to apply filter are...\n");
-		if (options->all_filter == 1) {
-			for (k = 0; k < options->n_filter_g; k++) {
-				H5Z_filter_t filtn = options->filter_g[k].filtn;
-				switch (filtn) {
-				case H5Z_FILTER_NONE:
-					printf(" Uncompress all\n");
-					break;
-				case H5Z_FILTER_SHUFFLE:
-				case H5Z_FILTER_FLETCHER32:
-					printf(" All with %s\n", get_sfilter(filtn));
-					break;
-				case H5Z_FILTER_SZIP:
-				case H5Z_FILTER_DEFLATE:
-					printf(" All with %s, parameter %d\n", get_sfilter(filtn),
-							options->filter_g[k].cd_values[0]);
-					break;
-				default:
-					printf(" User Defined %d\n", filtn);
-					break;
-				} /* k */
-			};
-		}
-	} /* verbose */
-
-	for (i = 0; i < options->op_tbl->nelems; i++) {
-		pack_info_t pack = options->op_tbl->objs[i];
-		char* name = pack.path;
-
-		for (j = 0; j < pack.nfilters; j++) {
-			if (options->verbose) {
-				printf(" <%s> with %s filter\n", name,
-						get_sfilter(pack.filter[j].filtn));
-			}
-
-			has_cp = 1;
-
-		} /* j */
-	} /* i */
-
-	if (options->all_filter == 1 && has_cp) {
-		error_msg(
-				"invalid compression input: 'all' option\
+        return -1;
+    }
+
+    /*-------------------------------------------------------------------------
+    * objects to filter
+    *-------------------------------------------------------------------------
+    */
+
+    if (options->verbose && have_request(options) /* only print if requested */) {
+        printf("Objects to apply filter are...\n");
+        if (options->all_filter == 1) {
+            for (k = 0; k < options->n_filter_g; k++) {
+                H5Z_filter_t filtn = options->filter_g[k].filtn;
+                switch (filtn) {
+                case H5Z_FILTER_NONE:
+                    printf(" Uncompress all\n");
+                    break;
+                case H5Z_FILTER_SHUFFLE:
+                case H5Z_FILTER_FLETCHER32:
+                    printf(" All with %s\n", get_sfilter(filtn));
+                    break;
+                case H5Z_FILTER_SZIP:
+                case H5Z_FILTER_DEFLATE:
+                    printf(" All with %s, parameter %d\n", get_sfilter(filtn),
+                            options->filter_g[k].cd_values[0]);
+                    break;
+                default:
+                    printf(" User Defined %d\n", filtn);
+                    break;
+                } /* k */
+            };
+        }
+    } /* verbose */
+
+    for (i = 0; i < options->op_tbl->nelems; i++) {
+        pack_info_t pack = options->op_tbl->objs[i];
+        char* name = pack.path;
+
+        for (j = 0; j < pack.nfilters; j++) {
+            if (options->verbose) {
+                printf(" <%s> with %s filter\n", name,
+                        get_sfilter(pack.filter[j].filtn));
+            }
+
+            has_cp = 1;
+
+        } /* j */
+    } /* i */
+
+    if (options->all_filter == 1 && has_cp) {
+        error_msg(
+                "invalid compression input: 'all' option\
                             is present with other objects\n");
-		return -1;
-	}
-
-	/*-------------------------------------------------------------------------
-	 * check options for the latest format
-	 *-------------------------------------------------------------------------
-	 */
-
-	if (options->grp_compact < 0) {
-		error_msg(
-				"invalid maximum number of links to store as header messages\n");
-		return -1;
-	}
-	if (options->grp_indexed < 0) {
-		error_msg(
-				"invalid minimum number of links to store in the indexed format\n");
-		return -1;
-	}
-	if (options->grp_indexed > options->grp_compact) {
-		error_msg(
-				"minimum indexed size is greater than the maximum compact size\n");
-		return -1;
-	}
-	for (i = 0; i < 8; i++) {
-		if (options->msg_size[i] < 0) {
-			error_msg("invalid shared message size\n");
-			return -1;
-		}
-	}
-
-	/*--------------------------------------------------------------------------------
-	 * verify new user userblock options; file name must be present
-	 *---------------------------------------------------------------------------------
-	 */
-	if (options->ublock_filename != NULL && options->ublock_size == 0) {
-		if (options->verbose) {
-			printf(
-					"Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
-					options->ublock_filename);
-			options->ublock_size = 1024;
-		}
-	}
-
-	if (options->ublock_filename == NULL && options->ublock_size != 0) {
-		error_msg("file name missing for user block\n",
-				options->ublock_filename);
-		return -1;
-	}
-
-	/*--------------------------------------------------------------------------------
-	 * verify alignment options; threshold is zero default but alignment not
-	 *---------------------------------------------------------------------------------
-	 */
-
-	if (options->alignment == 0 && options->threshold != 0) {
-		error_msg("alignment for H5Pset_alignment missing\n");
-		return -1;
-	}
-
-	return 0;
+        return -1;
+    }
+
+    /*-------------------------------------------------------------------------
+    * check options for the latest format
+    *-------------------------------------------------------------------------
+    */
+
+    if (options->grp_compact < 0) {
+        error_msg(
+                "invalid maximum number of links to store as header messages\n");
+        return -1;
+    }
+    if (options->grp_indexed < 0) {
+        error_msg(
+                "invalid minimum number of links to store in the indexed format\n");
+        return -1;
+    }
+    if (options->grp_indexed > options->grp_compact) {
+        error_msg(
+                "minimum indexed size is greater than the maximum compact size\n");
+        return -1;
+    }
+    for (i = 0; i < 8; i++) {
+        if (options->msg_size[i] < 0) {
+            error_msg("invalid shared message size\n");
+            return -1;
+        }
+    }
+
+    /*--------------------------------------------------------------------------------
+    * verify new user userblock options; file name must be present
+    *---------------------------------------------------------------------------------
+    */
+    if (options->ublock_filename != NULL && options->ublock_size == 0) {
+        if (options->verbose) {
+            printf(
+                    "Warning: user block size missing for file %s. Assigning a default size of 1024...\n",
+                    options->ublock_filename);
+            options->ublock_size = 1024;
+        }
+    }
+
+    if (options->ublock_filename == NULL && options->ublock_size != 0) {
+        error_msg("file name missing for user block\n",
+                options->ublock_filename);
+        return -1;
+    }
+
+    /*--------------------------------------------------------------------------------
+    * verify alignment options; threshold is zero default but alignment not
+    *---------------------------------------------------------------------------------
+    */
+
+    if (options->alignment == 0 && options->threshold != 0) {
+        error_msg("alignment for H5Pset_alignment missing\n");
+        return -1;
+    }
+
+    return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -774,119 +761,121 @@ static int check_options(pack_opt_t *options) {
  *-------------------------------------------------------------------------
  */
 static int check_objects(const char* fname, pack_opt_t *options) {
-	hid_t fid;
-	unsigned int i;
-	trav_table_t *travt = NULL;
-
-	/* nothing to do */
-	if (options->op_tbl->nelems == 0)
-		return 0;
-
-	/*-------------------------------------------------------------------------
-	 * open the file
-	 *-------------------------------------------------------------------------
-	 */
-	if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
-			< 0) {
-		printf("<%s>: %s\n", fname, H5FOPENERROR);
-		return -1;
-	}
-
-	/*-------------------------------------------------------------------------
-	 * get the list of objects in the file
-	 *-------------------------------------------------------------------------
-	 */
-
-	/* init table */
-	trav_table_init(&travt);
-
-	/* get the list of objects in the file */
-	if (h5trav_gettable(fid, travt) < 0)
-		goto out;
-
-	/*-------------------------------------------------------------------------
-	 * compare with user supplied list
-	 *-------------------------------------------------------------------------
-	 */
-
-	if (options->verbose)
-		printf("Opening file <%s>. Searching for objects to modify...\n",
-				fname);
-
-	for (i = 0; i < options->op_tbl->nelems; i++) {
-		char* name = options->op_tbl->objs[i].path;
-		if (options->verbose)
-			printf(" <%s>", name);
-
-		/* the input object names are present in the file and are valid */
-		if (h5trav_getindext(name, travt) < 0) {
-			error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
-					(options->verbose ? "\n" : ""), name, fname);
-			goto out;
-		}
-		if (options->verbose)
-			printf("...Found\n");
-
-		/* check for extra filter conditions */
-		switch (options->op_tbl->objs[i].filter->filtn) {
-		/* chunk size must be smaller than pixels per block */
-		case H5Z_FILTER_SZIP:
-			{
-				int j;
-				hsize_t csize = 1;
-				unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
-				hsize_t dims[H5S_MAX_RANK];
-				int rank;
-				hid_t did;
-				hid_t sid;
-
-				if (options->op_tbl->objs[i].chunk.rank > 0) {
-					rank = options->op_tbl->objs[i].chunk.rank;
-					for (j = 0; j < rank; j++)
-						csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
-				}
-				else {
-					if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
-						goto out;
-					if ((sid = H5Dget_space(did)) < 0)
-						goto out;
-					if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
-						goto out;
-					HDmemset(dims, 0, sizeof dims);
-					if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
-						goto out;
-					for (j = 0; j < rank; j++)
-						csize *= dims[j];
-					if (H5Sclose(sid) < 0)
-						goto out;
-					if (H5Dclose(did) < 0)
-						goto out;
-				}
-
-				if (csize < ppb) {
-					printf(
-							" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
-					goto out;
-				}
-			}
-			break;
-		default:
-			break;
-		}
-	} /* i */
-
-	/*-------------------------------------------------------------------------
-	 * close
-	 *-------------------------------------------------------------------------
-	 */
-	H5Fclose(fid);
-	trav_table_free(travt);
-	return 0;
+    hid_t         fid;
+    unsigned int  i;
+    trav_table_t *travt = NULL;
+
+    /* nothing to do */
+    if (options->op_tbl->nelems == 0)
+        return 0;
+
+    /*-------------------------------------------------------------------------
+    * open the file
+    *-------------------------------------------------------------------------
+    */
+    if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
+            < 0) {
+        printf("<%s>: %s\n", fname, H5FOPENERROR);
+        return -1;
+    }
+
+    /*-------------------------------------------------------------------------
+    * get the list of objects in the file
+    *-------------------------------------------------------------------------
+    */
+
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
+    /* init table */
+    trav_table_init(&travt);
+
+    /* get the list of objects in the file */
+    if (h5trav_gettable(fid, travt) < 0)
+        goto out;
+
+    /*-------------------------------------------------------------------------
+    * compare with user supplied list
+    *-------------------------------------------------------------------------
+    */
+
+    if (options->verbose)
+        printf("Opening file <%s>. Searching for objects to modify...\n",
+                fname);
+
+    for (i = 0; i < options->op_tbl->nelems; i++) {
+        char* name = options->op_tbl->objs[i].path;
+        if (options->verbose)
+            printf(" <%s>", name);
+
+        /* the input object names are present in the file and are valid */
+        if (h5trav_getindext(name, travt) < 0) {
+            error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
+                    (options->verbose ? "\n" : ""), name, fname);
+            goto out;
+        }
+        if (options->verbose)
+            printf("...Found\n");
+
+        /* check for extra filter conditions */
+        switch (options->op_tbl->objs[i].filter->filtn) {
+        /* chunk size must be smaller than pixels per block */
+        case H5Z_FILTER_SZIP:
+            {
+                int j;
+                hsize_t csize = 1;
+                unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
+                hsize_t dims[H5S_MAX_RANK];
+                int rank;
+                hid_t did;
+                hid_t sid;
+
+                if (options->op_tbl->objs[i].chunk.rank > 0) {
+                    rank = options->op_tbl->objs[i].chunk.rank;
+                    for (j = 0; j < rank; j++)
+                        csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+                }
+                else {
+                    if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+                        goto out;
+                    if ((sid = H5Dget_space(did)) < 0)
+                        goto out;
+                    if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
+                        goto out;
+                    HDmemset(dims, 0, sizeof dims);
+                    if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+                        goto out;
+                    for (j = 0; j < rank; j++)
+                        csize *= dims[j];
+                    if (H5Sclose(sid) < 0)
+                        goto out;
+                    if (H5Dclose(did) < 0)
+                        goto out;
+                }
+
+                if (csize < ppb) {
+                    printf(
+                            " <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
+                    goto out;
+                }
+            }
+            break;
+        default:
+            break;
+        }
+    } /* i */
+
+    /*-------------------------------------------------------------------------
+    * close
+    *-------------------------------------------------------------------------
+    */
+    H5Fclose(fid);
+    trav_table_free(travt);
+    return 0;
 
 out:
-	H5Fclose(fid);
-	trav_table_free(travt);
-	return -1;
+    H5Fclose(fid);
+    trav_table_free(travt);
+    return -1;
 }
 
 /*-------------------------------------------------------------------------
@@ -902,10 +891,10 @@ out:
  */
 static int have_request(pack_opt_t *options) {
 
-	if (options->all_filter || options->all_layout || options->op_tbl->nelems)
-		return 1;
+    if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+        return 1;
 
-	return 0;
+    return 0;
 
 }
 
@@ -920,21 +909,21 @@ static int have_request(pack_opt_t *options) {
  */
 
 static const char* get_sfilter(H5Z_filter_t filtn) {
-	if (filtn == H5Z_FILTER_NONE)
-		return "NONE";
-	else if (filtn == H5Z_FILTER_DEFLATE)
-		return "GZIP";
-	else if (filtn == H5Z_FILTER_SZIP)
-		return "SZIP";
-	else if (filtn == H5Z_FILTER_SHUFFLE)
-		return "SHUFFLE";
-	else if (filtn == H5Z_FILTER_FLETCHER32)
-		return "FLETCHER32";
-	else if (filtn == H5Z_FILTER_NBIT)
-		return "NBIT";
-	else if (filtn == H5Z_FILTER_SCALEOFFSET)
-		return "SOFF";
-	else
-		return "UD";
+    if (filtn == H5Z_FILTER_NONE)
+        return "NONE";
+    else if (filtn == H5Z_FILTER_DEFLATE)
+        return "GZIP";
+    else if (filtn == H5Z_FILTER_SZIP)
+        return "SZIP";
+    else if (filtn == H5Z_FILTER_SHUFFLE)
+        return "SHUFFLE";
+    else if (filtn == H5Z_FILTER_FLETCHER32)
+        return "FLETCHER32";
+    else if (filtn == H5Z_FILTER_NBIT)
+        return "NBIT";
+    else if (filtn == H5Z_FILTER_SCALEOFFSET)
+        return "SOFF";
+    else
+        return "UD";
 }
 
diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h
index 5ad0b80..e5ae03f 100644
--- a/tools/src/h5repack/h5repack.h
+++ b/tools/src/h5repack/h5repack.h
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 
@@ -31,10 +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
 
 
 /*-------------------------------------------------------------------------
@@ -122,10 +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;
 
 
@@ -152,10 +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 45d52bf..946f5ad 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
@@ -33,7 +31,7 @@
  */
 
 /* size of buffer/# of bytes to xfer at a time when copying userblock */
-#define USERBLOCK_XFER_SIZE     512     
+#define USERBLOCK_XFER_SIZE     512
 
 /* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
 #define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf)  {  \
@@ -54,12 +52,12 @@
  *-------------------------------------------------------------------------
  */
 static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
-		size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
+        size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
 static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
 static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
-		pack_opt_t *options);
+        pack_opt_t *options);
 static int copy_user_block(const char *infile, const char *outfile,
-		hsize_t size);
+        hsize_t size);
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
 static void print_user_block(const char *filename, hid_t fid);
 #endif
@@ -67,18 +65,19 @@ static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void
 
 /* get the major number from the error stack. */
 static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
-	if (err_desc)
-		*((hid_t *) udata) = err_desc->maj_num;
+    if (err_desc)
+        *((hid_t *) udata) = err_desc->maj_num;
 
-	return 0;
+    return 0;
 }
 
 /*-------------------------------------------------------------------------
  * Function: copy_objects
  *
- * Purpose: duplicate all HDF5 objects in the file
+ * Purpose:  duplicate all HDF5 objects in the file
  *
- * Return: 0, ok, -1 no
+ * Return:   0, ok,
+ *          -1 no
  *
  * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
@@ -89,21 +88,22 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
 
 int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
 {
-    int   	  ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int           ret_value = 0;          /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
     hid_t         fidin;
     hid_t         fidout = -1;
     trav_table_t  *travt = NULL;
-    hsize_t       ub_size = 0;        	/* size of user block */
-    hid_t         fcpl = H5P_DEFAULT; 	/* file creation property list ID */
-    hid_t         fapl = H5P_DEFAULT; 	/* file access property list ID */
-    H5F_fspace_strategy_t set_strategy;	/* Strategy to be set in outupt file */
-    hbool_t	  set_persist;		/* Persist free-space status to be set in output file */
-    hsize_t	  set_threshold;	/* Free-space section threshold to be set in output file */
-    hsize_t	  set_pagesize;		/* File space page size to be set in output file */
-    H5F_fspace_strategy_t in_strategy;	/* Strategy from input file */
-    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 */
+    hsize_t       ub_size = 0;            /* size of user block */
+    hid_t         fcpl = H5P_DEFAULT;     /* file creation property list ID */
+    hid_t         fapl = H5P_DEFAULT;     /* file access property list ID */
+    H5F_fspace_strategy_t set_strategy;   /* Strategy to be set in outupt file */
+    hbool_t       set_persist;            /* Persist free-space status to be set in output file */
+    hsize_t       set_threshold;          /* Free-space section threshold to be set in output file */
+    hsize_t       set_pagesize;           /* File space page size to be set in output file */
+    H5F_fspace_strategy_t in_strategy;    /* Strategy from input file */
+    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
@@ -117,6 +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");
@@ -128,17 +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");
+        /* 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");
         }
+        /* open root group */
+        if ((grp_in = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 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");
-	}
+        /* 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");
@@ -297,9 +310,9 @@ print_user_block(fnamein, fidin);
     }
 
     /*-------------------------------------------------------------------------
-    * Set file space information
-    *-------------------------------------------------------------------------
-    */
+     * Set file space information
+     *-------------------------------------------------------------------------
+     */
 
     /* either use the FCPL already created or create a new one */
     if (fcpl == H5P_DEFAULT) {
@@ -310,6 +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;
@@ -325,7 +341,7 @@ print_user_block(fnamein, fidin);
         set_persist = FS_PERSIST_DEF;
     else if(options->fs_persist != 0) /* Set "persist" as specified by user */
         set_persist = (hbool_t)options->fs_persist;
-    
+
     if(options->fs_threshold == -1) /* A "0" threshold is specified by user */
         set_threshold = (hsize_t)0;
     else if(options->fs_threshold != 0) /* Set threshold as specified by user */
@@ -333,7 +349,7 @@ print_user_block(fnamein, fidin);
 
     /* Set file space information as specified */
     if(H5Pset_file_space_strategy(fcpl, set_strategy, set_persist, set_threshold) < 0) {
-	error_msg("failed to set file space strategy\n");
+        error_msg("failed to set file space strategy\n");
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
     }
 
@@ -345,7 +361,7 @@ print_user_block(fnamein, fidin);
     if(set_pagesize != FS_PAGESIZE_DEF) /* Set non-default file space page size as specified */
         if(H5Pset_file_space_page_size(fcpl, set_pagesize) < 0) {
             error_msg("failed to set file space page size\n");
-	    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
         }
 
     /*-------------------------------------------------------------------------
@@ -376,6 +392,8 @@ print_user_block(fnamein, fidin);
      *-------------------------------------------------------------------------
      */
 
+    /* Initialize indexing options */
+    h5trav_set_index(sort_by, sort_order);
     /* init table */
     trav_table_init(&travt);
 
@@ -492,10 +510,10 @@ done:
 int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
         size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
 {
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    int k;
+    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int     k;
     H5D_layout_t dset_layout;
-    int rank_chunk;
+    int     rank_chunk;
     hsize_t dims_chunk[H5S_MAX_RANK];
     hsize_t size_chunk = 1;
     hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
@@ -707,36 +725,36 @@ done:
  */
 
 int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
-		pack_opt_t *options) /* repack options */
+        pack_opt_t *options) /* repack options */
 {
     int   ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t grp_in = -1; /* group ID */
-    hid_t grp_out = -1; /* group ID */
-    hid_t dset_in = -1; /* read dataset ID */
+    hid_t grp_in = -1;   /* group ID */
+    hid_t grp_out = -1;  /* group ID */
+    hid_t dset_in = -1;  /* read dataset ID */
     hid_t dset_out = -1; /* write dataset ID */
-    hid_t gcpl_in = -1; /* group creation property list */
+    hid_t gcpl_in = -1;  /* group creation property list */
     hid_t gcpl_out = -1; /* group creation property list */
-    hid_t type_in = -1; /* named type ID */
+    hid_t type_in = -1;  /* named type ID */
     hid_t type_out = -1; /* named type ID */
-    hid_t dcpl_in = -1; /* dataset creation property list ID */
+    hid_t dcpl_in = -1;  /* dataset creation property list ID */
     hid_t dcpl_out = -1; /* dataset creation property list ID */
     hid_t f_space_id = -1; /* file space ID */
     hid_t ftype_id = -1; /* file type ID */
     hid_t wtype_id = -1; /* read/write type ID */
     named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
-    size_t msize; /* size of type */
-    hsize_t nelmts; /* number of elements in dataset */
+    size_t msize;        /* size of type */
+    hsize_t nelmts;      /* number of elements in dataset */
     H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
-    int rank; /* rank of dataset */
+    int rank;            /* rank of dataset */
     hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
-    hsize_t dsize_in; /* input dataset size before filter */
-    hsize_t dsize_out; /* output dataset size after filter */
-    int apply_s; /* flag for apply filter to small dataset sizes */
-    int apply_f; /* flag for apply filter to return error on H5Dcreate */
-    void *buf = NULL; /* buffer for raw data */
+    hsize_t dsize_in;    /* input dataset size before filter */
+    hsize_t dsize_out;   /* output dataset size after filter */
+    int apply_s;         /* flag for apply filter to small dataset sizes */
+    int apply_f;         /* flag for apply filter to return error on H5Dcreate */
+    void *buf = NULL;    /* buffer for raw data */
     void *hslab_buf = NULL; /* hyperslab buffer for raw data */
-    int has_filter; /* current object has a filter */
-    int req_filter; /* there was a request for a filter */
+    int has_filter;      /* current object has a filter */
+    int req_filter;      /* there was a request for a filter */
     int req_obj_layout = 0; /* request layout to current object */
     unsigned crt_order_flags; /* group creation order flag */
     unsigned i;
@@ -917,7 +935,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                     /* wtype_id will have already been set if using a named dtype */
                     if (!is_named) {
                         if (options->use_native == 1)
-                            wtype_id = h5tools_get_native_type(ftype_id);
+                            wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
                         else
                             wtype_id = H5Tcopy(ftype_id);
                     } /* end if */
@@ -1351,20 +1369,19 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
-    int pr)
+static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
 {
-    char strfilter[255];
+    char     strfilter[255];
 #if defined (PRINT_DEBUG )
-    char temp[255];
+    char     temp[255];
 #endif
-    int nfilters; /* number of filters */
-    unsigned filt_flags; /* filter flags */
-    H5Z_filter_t filtn; /* filter identification number */
-    unsigned cd_values[20]; /* filter client data values */
-    size_t cd_nelmts; /* filter client number of values */
-    char f_objname[256]; /* filter objname */
-    int i;
+    int      nfilters;       /* number of filters */
+    unsigned filt_flags;     /* filter flags */
+    H5Z_filter_t filtn;      /* filter identification number */
+    unsigned cd_values[20];  /* filter client data values */
+    size_t   cd_nelmts;      /* filter client number of values */
+    char     f_objname[256]; /* filter objname */
+    int     i;
 
     HDstrcpy(strfilter, "\0");
 
@@ -1463,19 +1480,18 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
  *
  *-------------------------------------------------------------------------
  */
-static int copy_user_block(const char *infile, const char *outfile,
-    hsize_t size)
+static int copy_user_block(const char *infile, const char *outfile, hsize_t size)
 {
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int ret_value = 0;           /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
     int infid = -1, outfid = -1; /* File descriptors */
 
     /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
     HDassert(size > 0);
 
     /* Open files */
-    if ((infid = HDopen(infile, O_RDONLY, 0)) < 0)
+    if ((infid = HDopen(infile, O_RDONLY)) < 0)
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
-    if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
+    if ((outfid = HDopen(outfile, O_WRONLY)) < 0)
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
 
     /* Copy the userblock from the input file to the output file */
@@ -1543,67 +1559,68 @@ done:
 static
 void print_user_block(const char *filename, hid_t fid)
 {
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    int fh; /* file handle  */
-	hsize_t ub_size; /* user block size */
-	hsize_t size; /* size read */
-	hid_t fcpl; /* file creation property list ID for HDF5 file */
-	int i;
-
-	/* get user block size */
-	if(( fcpl = H5Fget_create_plist(fid)) < 0) {
-		error_msg("failed to retrieve file creation property list\n");
+    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int     fh;   /* file handle  */
+    hsize_t ub_size; /* user block size */
+    hsize_t size; /* size read */
+    hid_t   fcpl; /* file creation property list ID for HDF5 file */
+    int     i;
+
+    /* get user block size */
+    if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+        error_msg("failed to retrieve file creation property list\n");
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
     }
 
-	if(H5Pget_userblock(fcpl, &ub_size) < 0) {
-		error_msg("failed to retrieve userblock size\n");
+    if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+        error_msg("failed to retrieve userblock size\n");
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed");
     }
 
-	if(H5Pclose(fcpl) < 0) {
-		error_msg("failed to close property list\n");
+    if(H5Pclose(fcpl) < 0) {
+        error_msg("failed to close property list\n");
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
     }
 
-	/* open file */
-	if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
+    /* open file */
+    if((fh = HDopen(filename, O_RDONLY)) < 0) {
+        error_msg("failed to open file\n");
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
     }
 
-	size = ub_size;
+    size = ub_size;
 
-	/* read file */
-	while(size > 0) {
-		ssize_t nread; /* # of bytes read */
-		char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+    /* read file */
+    while(size > 0) {
+        ssize_t nread; /* # of bytes read */
+        char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
 
-		/* read buffer */
-		if(size > USERBLOCK_XFER_SIZE)
-			nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
-		else
-			nread = HDread(fh, rbuf, (size_t)size);
+        /* read buffer */
+        if(size > USERBLOCK_XFER_SIZE)
+            nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+        else
+            nread = HDread(fh, rbuf, (size_t)size);
 
-		for(i = 0; i < nread; i++) {
+        for(i = 0; i < nread; i++) {
 
-			printf("%c ", rbuf[i]);
+            printf("%c ", rbuf[i]);
 
-		}
-		printf("\n");
+        }
+        printf("\n");
 
-		if(nread < 0) {
+        if(nread < 0) {
             HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
         }
 
-		/* update size of userblock left to transfer */
-		size -= nread;
-	}
+        /* update size of userblock left to transfer */
+        size -= nread;
+    }
 
 done:
-	if(fh > 0)
-		HDclose(fh);
+    if(fh > 0)
+        HDclose(fh);
 
-	return;
+    return;
 }
 #endif
 
diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c
index e21b829..804727b 100644
--- a/tools/src/h5repack/h5repack_filters.c
+++ b/tools/src/h5repack/h5repack_filters.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 07c2b7d..31b1e14 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5tools.h"
@@ -33,7 +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' },
@@ -58,6 +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' }
 };
@@ -92,6 +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");
@@ -105,6 +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");
@@ -372,6 +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
@@ -555,14 +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;
@@ -572,12 +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;
@@ -646,6 +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_opttable.c b/tools/src/h5repack/h5repack_opttable.c
index 8c98b76..93e34b3 100644
--- a/tools/src/h5repack/h5repack_opttable.c
+++ b/tools/src/h5repack/h5repack_opttable.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
diff --git a/tools/src/h5repack/h5repack_parse.c b/tools/src/h5repack/h5repack_parse.c
index 6759169..a9a890d 100644
--- a/tools/src/h5repack/h5repack_parse.c
+++ b/tools/src/h5repack/h5repack_parse.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
index f0f32c3..408142c 100644
--- a/tools/src/h5repack/h5repack_refs.c
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
@@ -27,7 +25,7 @@ static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
 static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
                           trav_table_t *travt, hid_t fidout);
 static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
-		hid_t fid_out, void *ref_out, trav_table_t *travt);
+        hid_t fid_out, void *ref_out, trav_table_t *travt);
 
 /*-------------------------------------------------------------------------
  * Function: do_copy_refobjs
@@ -128,8 +126,8 @@ int do_copy_refobjs(hid_t fidin,
                 for(k = 0; k < rank; k++)
                     nelmts *= dims[k];
 
-                if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+                if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0)
+                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed");
 
                 if((msize = H5Tget_size(mtype_id)) == 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
@@ -427,13 +425,13 @@ done:
  * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Modifier: xcao@hdfgroup.org, 9/12/2011
- * 	         Update values of references(object and region) for the following types:
+ *              Update values of references(object and region) for the following types:
  *               1) References,
  *               2) ARRAY of reference,
  *               3) VLEN of references.
  *               4) COMPOUND of references.
  *          This function does not handle references in other complicated structures,
- *		    such as references in nested compound datatypes.
+ *            such as references in nested compound datatypes.
  *
  * Date: October, 28, 2003
  *
@@ -474,7 +472,7 @@ static int copy_refs_attr(hid_t loc_in,
         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
 
     for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
-    	is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
+        is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
 
         /* open attribute */
         if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
@@ -486,8 +484,8 @@ static int copy_refs_attr(hid_t loc_in,
 
         type_class = H5Tget_class(ftype_id);
 
-        if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5tools_get_native_type failed");
+        if((mtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT)) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type failed");
 
         if((msize = H5Tget_size(mtype_id)) == 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
@@ -530,9 +528,9 @@ static int copy_refs_attr(hid_t loc_in,
                 }
                 H5Tclose(mtid);
             }
-            
-            /* if compound don't contain reference type member, free the above 
-             * mallocs. Otherwise there can be memory leaks by the 'continue' 
+
+            /* if compound don't contain reference type member, free the above
+             * mallocs. Otherwise there can be memory leaks by the 'continue'
              * statement below. */
             if (!ref_comp_field_n) {
                 if (ref_comp_index) {
@@ -541,7 +539,7 @@ static int copy_refs_attr(hid_t loc_in,
                 }
 
                 if (ref_comp_size) {
-            	    HDfree(ref_comp_size);
+                    HDfree(ref_comp_size);
                     ref_comp_size = NULL;
                 }
             }
@@ -590,7 +588,7 @@ static int copy_refs_attr(hid_t loc_in,
             array_rank = (unsigned)H5Tget_array_ndims(mtype_id);
             H5Tget_array_dims2(mtype_id, array_dims);
             for(j = 0; j <array_rank; j++)
-            	array_size *= array_dims[j];
+                array_size *= array_dims[j];
             nelmts *= array_size;
         }
 
@@ -650,7 +648,7 @@ static int copy_refs_attr(hid_t loc_in,
                 }
             } /* H5T_STD_REF_DSETREG */
             else if (is_ref_vlen) {
-            	/* handle VLEN of references */
+                /* handle VLEN of references */
 
                 buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
                 refbuf = buf; /* reuse the read buffer for write */
@@ -690,7 +688,7 @@ static int copy_refs_attr(hid_t loc_in,
                 }
             } /* else if (is_ref_vlen) */
             else if (is_ref_comp) {
-            	/* handle ref fields in a compound */
+                /* handle ref fields in a compound */
 
                 buf = HDmalloc((unsigned)(nelmts * msize));
                 refbuf = buf; /* reuse the read buffer for write */
@@ -730,7 +728,7 @@ static int copy_refs_attr(hid_t loc_in,
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
 
             if (is_ref_vlen && buf)
-            	H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
+                H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
         } /* if (nelmts) */
 
         if (refbuf == buf)
@@ -782,10 +780,10 @@ done:
         HDfree(buf);
 
     if (ref_comp_index)
-    	HDfree(ref_comp_index);
+        HDfree(ref_comp_index);
 
     if (ref_comp_size)
-    	HDfree(ref_comp_size);
+        HDfree(ref_comp_size);
 
     H5E_BEGIN_TRY {
         H5Tclose(ftype_id);
@@ -799,9 +797,9 @@ done:
 }
 
 /*-------------------------------------------------------------------------
- * Function:	MapIdToName
+ * Function:    MapIdToName
  *
- * Purpose:	map a ID from a reference to a dataset name
+ * Purpose:    map a ID from a reference to a dataset name
  *
  *-------------------------------------------------------------------------
  */
@@ -834,16 +832,16 @@ out:
 }
 
 /*-------------------------------------------------------------------------
- * Function:	Update_Ref_value
+ * Function:    Update_Ref_value
  *
- * Purpose:	Update a reference value
+ * Purpose:    Update a reference value
  *
  * Programmer: xcao@hdfgroup.org 9/12/2011
  *
  *-------------------------------------------------------------------------
  */
 static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
-		hid_t fid_out, void *ref_out, trav_table_t *travt)
+        hid_t fid_out, void *ref_out, trav_table_t *travt)
 {
     int    ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
     const char* ref_obj_name;
diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c
index 1022d7a..1a0dab7 100644
--- a/tools/src/h5repack/h5repack_verify.c
+++ b/tools/src/h5repack/h5repack_verify.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
@@ -57,11 +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 )
@@ -124,6 +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);
 
@@ -249,7 +249,7 @@ h5repack_verify(const char *in_fname, const char *out_fname, pack_opt_t *options
      * the same as the input file's strategy.
      */
     if(options->fs_strategy) {
-        if(out_strategy != (options->fs_strategy == (-1) ? 0 : options->fs_strategy)) {
+        if(out_strategy != (options->fs_strategy == (H5F_fspace_strategy_t)-1 ? 0 : options->fs_strategy)) {
             error_msg("file space strategy not set as unexpected\n");
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file space strategy not set as unexpected");
         }
@@ -457,6 +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");
@@ -645,7 +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 */