[svn-r24116] Correct indentation and create single exit point.

Tested : local linux

4 files changed, 3270 insertions, 3426 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 5c44e1a..742bb06 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -1,17 +1,17 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* Copyright by The HDF Group.                                               *
-* Copyright by the Board of Trustees of the University of Illinois.         *
-* All rights reserved.                                                      *
-*                                                                           *
-* This file is part of HDF5.  The full HDF5 copyright notice, including     *
-* terms governing use, modification, and redistribution, is contained in    *
-* the files COPYING and Copyright.html.  COPYING can be found at the root   *
-* of the source code distribution tree; Copyright.html can be found at the  *
-* root level of an installed copy of the electronic HDF5 document set and   *
-* is linked from the top-level documents page.  It can also be found at     *
-* http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
-* access to either file, you may request a copy from help@hdfgroup.org.     *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include <stdlib.h>
 #include <string.h>
@@ -23,223 +23,198 @@
 #include "h5tools_utils.h"
 
 /*-------------------------------------------------------------------------
-* File: h5repack.c
-* Purpose: Public API functions
-*-------------------------------------------------------------------------
-*/
+ * File: h5repack.c
+ * Purpose: Public API functions
+ *-------------------------------------------------------------------------
+ */
 
 static int check_options(pack_opt_t *options);
 static int check_objects(const char* fname, pack_opt_t *options);
-static const char* get_sfilter (H5Z_filter_t filtn);
+static const char* get_sfilter(H5Z_filter_t filtn);
 static int have_request(pack_opt_t *options);
 
+/*-------------------------------------------------------------------------
+ * Function: h5repack
+ *
+ * Purpose: locate all high-level HDF5 objects in the file
+ *  and compress/chunk them using options
+ *
+ * Algorithm: 2 traversals are made to the file; the 1st builds a list of
+ *  the objects, the 2nd makes a copy of them, using the options;
+ *  the reason for the 1st traversal is to check for invalid
+ *  object name requests
+ *
+ * Return: 0, ok, -1, fail
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+	/* check input */
+	if (check_options(options) < 0)
+		return -1;
 
+	/* check for objects in input that are in the file */
+	if (check_objects(infile, options) < 0)
+		return -1;
 
-/*-------------------------------------------------------------------------
-* Function: h5repack
-*
-* Purpose: locate all high-level HDF5 objects in the file
-*  and compress/chunk them using options
-*
-* Algorithm: 2 traversals are made to the file; the 1st builds a list of
-*  the objects, the 2nd makes a copy of them, using the options;
-*  the reason for the 1st traversal is to check for invalid
-*  object name requests
-*
-* Return: 0, ok, -1, fail
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack(const char* infile,
-             const char* outfile,
-             pack_opt_t *options)
-{
-    /* check input */
-    if (check_options(options)<0)
-        return -1;
-
-    /* check for objects in input that are in the file */
-    if (check_objects(infile,options) < 0)
-        return -1;
-
-    /* copy the objects  */
-    if (copy_objects(infile,outfile,options) < 0)
-        return -1;
-
-
-    return 0;
+	/* copy the objects  */
+	if (copy_objects(infile, outfile, options) < 0)
+		return -1;
+
+	return 0;
 }
 
+/*-------------------------------------------------------------------------
+ * Function: h5repack_init
+ *
+ * Purpose: initialize options
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
 
+int h5repack_init(pack_opt_t *options, int verbose,
+		H5F_file_space_type_t strategy, hsize_t threshold) {
+	int k, n;
 
-/*-------------------------------------------------------------------------
-* Function: h5repack_init
-*
-* Purpose: initialize options
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-int
-h5repack_init(pack_opt_t *options, int verbose, H5F_file_space_type_t strategy,
-    hsize_t threshold)
-{
-    int k, n;
-
-    HDmemset(options, 0, sizeof(pack_opt_t));
-    options->min_comp = 0;
-    options->verbose  = verbose;
-    options->layout_g = H5D_LAYOUT_ERROR;
-
-    for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
-    {
-        options->filter_g[n].filtn  = -1;
-        options->filter_g[n].cd_nelmts  = 0;
-        for ( k = 0; k < CD_VALUES; k++)
-            options->filter_g[n].cd_values[k] = 0;
-    }
-
-    options->fs_strategy = strategy;
-    options->fs_threshold = threshold;
-
-    return (options_table_init(&(options->op_tbl)));
-}
+	HDmemset(options, 0, sizeof(pack_opt_t));
+	options->min_comp = 0;
+	options->verbose = verbose;
+	options->layout_g = H5D_LAYOUT_ERROR;
 
+	for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
+		options->filter_g[n].filtn = -1;
+		options->filter_g[n].cd_nelmts = 0;
+		for (k = 0; k < CD_VALUES; k++)
+			options->filter_g[n].cd_values[k] = 0;
+	}
 
-/*-------------------------------------------------------------------------
-* Function: h5repack_end
-*
-* Purpose: free options table
-*
-*-------------------------------------------------------------------------
-*/
-
-int h5repack_end  (pack_opt_t *options)
-{
-    return options_table_free(options->op_tbl);
-}
+	options->fs_strategy = strategy;
+	options->fs_threshold = threshold;
 
+	return (options_table_init(&(options->op_tbl)));
+}
 
 /*-------------------------------------------------------------------------
-* Function: h5repack_addfilter
-*
-* Purpose: add a compression -f option to table
-*   Example: -f dset:GZIP=6
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-int h5repack_addfilter(const char* str,
-                       pack_opt_t *options)
-{
-    obj_list_t      *obj_list=NULL; /* one object list for the -f and -l option entry */
-    filter_info_t   filter;         /* filter info for the current -f option entry */
-    int             n_objs;         /* number of objects in the current -f or -l option entry */
-    int             is_glb;         /* is the filter global */
-
-
-
-    /* parse the -f option */
-    if(NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
-        return -1;
-
-    /* if it applies to all objects */
-    if(is_glb)
-    {
-        int n;
-
-        n = options->n_filter_g++; /* increase # of global filters */
-
-        if(options->n_filter_g > H5_REPACK_MAX_NFILTERS)
-        {
-            error_msg("maximum number of filters exceeded for <%s>\n", str);
-            HDfree(obj_list);
-            return -1;
-        }
-
-        options->filter_g[n] = filter;
-    }
-    else
-        options_add_filter(obj_list, n_objs, filter, options->op_tbl);
-
-    HDfree(obj_list);
-    return 0;
+ * Function: h5repack_end
+ *
+ * Purpose: free options table
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_end(pack_opt_t *options) {
+	return options_table_free(options->op_tbl);
 }
 
+/*-------------------------------------------------------------------------
+ * Function: h5repack_addfilter
+ *
+ * Purpose: add a compression -f option to table
+ *   Example: -f dset:GZIP=6
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+int h5repack_addfilter(const char* str, pack_opt_t *options) {
+	obj_list_t *obj_list = NULL; /* one object list for the -f and -l option entry */
+	filter_info_t filter; /* filter info for the current -f option entry */
+	int n_objs; /* number of objects in the current -f or -l option entry */
+	int is_glb; /* is the filter global */
+
+	/* parse the -f option */
+	if (NULL == (obj_list = parse_filter(str, &n_objs, &filter, options, &is_glb)))
+		return -1;
+
+	/* if it applies to all objects */
+	if (is_glb) {
+		int n;
+
+		n = options->n_filter_g++; /* increase # of global filters */
+
+		if (options->n_filter_g > H5_REPACK_MAX_NFILTERS) {
+			error_msg("maximum number of filters exceeded for <%s>\n", str);
+			HDfree(obj_list);
+			return -1;
+		}
+
+		options->filter_g[n] = filter;
+	}
+	else
+		options_add_filter(obj_list, n_objs, filter, options->op_tbl);
+
+	HDfree(obj_list);
+	return 0;
+}
 
 /*-------------------------------------------------------------------------
-* Function: h5repack_addlayout
-*
-* Purpose: add a layout option
-*
-* Return: 0, ok, -1, fail
-*
-*-------------------------------------------------------------------------
-*/
-
-
-int h5repack_addlayout(const char* str,
-                       pack_opt_t *options)
-{
-
-    obj_list_t  *obj_list=NULL;     /*one object list for the -t and -c option entry */
-    int         n_objs;             /*number of objects in the current -t or -c option entry */
-    pack_info_t pack;               /*info about layout to extract from parse */
-    int         j;
-
-    init_packobject(&pack);
-
-    if (options->all_layout==1){
-        error_msg("invalid layout input: 'all' option \
-                            is present with other objects <%s>\n",str);
-        return -1;
-    }
-
-    /* parse the layout option */
-    obj_list=parse_layout(str,&n_objs,&pack,options);
-    if (obj_list==NULL)
-        return -1;
-
-    /* set layout option */
-    options->layout_g = pack.layout;
-
-    /* no individual dataset specified */
-    if (options->all_layout==1 )
-    {
-        if (pack.layout==H5D_CHUNKED)
-        {
-            /* -2 means the NONE option, remove chunking
-            and set the global layout to contiguous */
-            if (pack.chunk.rank==-2)
-            {
-                options->layout_g = H5D_CONTIGUOUS;
-            }
-            /* otherwise set the global chunking type */
-            else
-            {
-                options->chunk_g.rank=pack.chunk.rank;
-                for (j = 0; j < pack.chunk.rank; j++)
-                    options->chunk_g.chunk_lengths[j] = pack.chunk.chunk_lengths[j];
-            }
-        }
-    }
-
-    /* individual dataset specified */
-    if (options->all_layout==0)
-        options_add_layout(obj_list,
-        n_objs,
-        &pack,
-        options->op_tbl);
-
-    HDfree(obj_list);
-    return 0;
+ * Function: h5repack_addlayout
+ *
+ * Purpose: add a layout option
+ *
+ * Return: 0, ok, -1, fail
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int h5repack_addlayout(const char* str, pack_opt_t *options) {
+
+	obj_list_t *obj_list = NULL; /*one object list for the -t and -c option entry */
+	int n_objs; /*number of objects in the current -t or -c option entry */
+	pack_info_t pack; /*info about layout to extract from parse */
+	int j;
+	int ret_value = -1;
+
+	init_packobject(&pack);
+
+	if (options->all_layout == 1) {
+		error_msg(
+				"invalid layout input: 'all' option \
+                            is present with other objects <%s>\n",
+				str);
+		return ret_value;
+	}
+
+	/* parse the layout option */
+	obj_list = parse_layout(str, &n_objs, &pack, options);
+	if (obj_list) {
+
+		/* set layout option */
+		options->layout_g = pack.layout;
+
+		/* no individual dataset specified */
+		if (options->all_layout == 1) {
+			if (pack.layout == H5D_CHUNKED) {
+				/* -2 means the NONE option, remove chunking
+				 and set the global layout to contiguous */
+				if (pack.chunk.rank == -2) {
+					options->layout_g = H5D_CONTIGUOUS;
+				}
+				/* otherwise set the global chunking type */
+				else {
+					options->chunk_g.rank = pack.chunk.rank;
+					for (j = 0; j < pack.chunk.rank; j++)
+						options->chunk_g.chunk_lengths[j] =
+								pack.chunk.chunk_lengths[j];
+				}
+			}
+		}
+
+		/* individual dataset specified */
+		if (options->all_layout == 0)
+			ret_value = options_add_layout(obj_list, n_objs, &pack, options->op_tbl);
+
+		HDfree(obj_list);
+		ret_value = 0;
+	}
+
+	return ret_value;
 }
 
 /* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
@@ -249,765 +224,720 @@ int h5repack_addlayout(const char* str,
  * others to static in h5repack_copy.c.
  */
 /*-------------------------------------------------------------------------
-* Function: copy_named_datatype
-*
-* Purpose: Copies the specified datatype anonymously, and returns an open
-*          id for that datatype in the output file.  The first time this
-*          is called it scans every named datatype in travt into a
-*          private stack, afterwards it simply scans that stack.  The id
-*          returned must be closed after it is no longer needed.
-*          named_datatype_free must be called before the program exits
-*          to free the stack.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
-{
-    named_dt_t  *dt = *named_dt_head_p; /* Stack pointer */
-    named_dt_t  *dt_ret = NULL;     /* Datatype to return */
-    H5O_info_t  oinfo;              /* Object info of input dtype */
-    hid_t       ret_value = -1;     /* The identifier of the named dtype in the out file */
-
-    if(H5Oget_info(type_in, &oinfo) < 0)
-        goto error;
-
-    if(*named_dt_head_p)
-    {
-        /* Stack already exists, search for the datatype */
-        while(dt && dt->addr_in != oinfo.addr)
-            dt = dt->next;
-
-        dt_ret = dt;
-    }
-    else
-    {
-        /* Create the stack */
-        size_t  i;
-
-        for(i=0; i<travt->nobjs; i++)
-            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
-            {
-                /* Push onto the stack */
-                if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
-                    goto error;
-                dt->next = *named_dt_head_p;
-                *named_dt_head_p = dt;
-
-                /* Update the address and id */
-                dt->addr_in = travt->objs[i].objno;
-                dt->id_out = -1;
-
-                /* Check if this type is the one requested */
-                if(oinfo.addr == dt->addr_in)
-                {
-                    HDassert(!dt_ret);
-                    dt_ret = dt;
-                } /* end if */
-            } /* end if */
-    } /* end else */
-
-    /* Handle the case that the requested datatype was not found.  This is
-     * possible if the datatype was committed anonymously in the input file. */
-    if(!dt_ret)
-    {
-        /* Push the new datatype onto the stack */
-        if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
-            goto error;
-        dt_ret->next = *named_dt_head_p;
-        *named_dt_head_p = dt_ret;
-
-        /* Update the address and id */
-        dt_ret->addr_in = oinfo.addr;
-        dt_ret->id_out = -1;
-    } /* end if */
-
-    /* If the requested datatype does not yet exist in the output file, copy it
-     * anonymously */
-    if(dt_ret->id_out < 0)
-    {
-        if (options->use_native==1)
-            dt_ret->id_out = h5tools_get_native_type(type_in);
-        else
-            dt_ret->id_out = H5Tcopy(type_in);
-        if(dt_ret->id_out < 0)
-            goto error;
-        if(H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
-            goto error;
-    } /* end if */
-
-    /* Set return value */
-    ret_value = dt_ret->id_out;
-
-    /* Increment the ref count on id_out, because the calling function will try
-     * to close it */
-    if(H5Iinc_ref(ret_value) < 0)
-        goto error;
-
-    return(ret_value);
-
-error:
-    return(-1);
+ * Function: copy_named_datatype
+ *
+ * Purpose: Copies the specified datatype anonymously, and returns an open
+ *          id for that datatype in the output file.  The first time this
+ *          is called it scans every named datatype in travt into a
+ *          private stack, afterwards it simply scans that stack.  The id
+ *          returned must be closed after it is no longer needed.
+ *          named_datatype_free must be called before the program exits
+ *          to free the stack.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
+		named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+	named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
+	named_dt_t *dt_ret = NULL; /* Datatype to return */
+	H5O_info_t oinfo; /* Object info of input dtype */
+	hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
+
+	if (H5Oget_info(type_in, &oinfo) < 0)
+		goto done;
+
+	if (*named_dt_head_p) {
+		/* Stack already exists, search for the datatype */
+		while (dt && dt->addr_in != oinfo.addr)
+			dt = dt->next;
+
+		dt_ret = dt;
+	}
+	else {
+		/* Create the stack */
+		size_t i;
+
+		for (i = 0; i < travt->nobjs; i++) {
+			if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
+				/* Push onto the stack */
+				if (NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+					goto done;
+				}
+				dt->next = *named_dt_head_p;
+				*named_dt_head_p = dt;
+
+				/* Update the address and id */
+				dt->addr_in = travt->objs[i].objno;
+				dt->id_out = -1;
+
+				/* Check if this type is the one requested */
+				if (oinfo.addr == dt->addr_in) {
+					HDassert(!dt_ret);
+					dt_ret = dt;
+				} /* end if */
+			} /* end if */
+		} /* end for */
+	} /* end else */
+
+	/* Handle the case that the requested datatype was not found.  This is
+	 * possible if the datatype was committed anonymously in the input file. */
+	if (!dt_ret) {
+		/* Push the new datatype onto the stack */
+		if (NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t)))) {
+			goto done;
+		}
+		dt_ret->next = *named_dt_head_p;
+		*named_dt_head_p = dt_ret;
+
+		/* Update the address and id */
+		dt_ret->addr_in = oinfo.addr;
+		dt_ret->id_out = -1;
+	} /* end if */
+
+	/* If the requested datatype does not yet exist in the output file, copy it
+	 * anonymously */
+	if (dt_ret->id_out < 0) {
+		if (options->use_native == 1)
+			dt_ret->id_out = h5tools_get_native_type(type_in);
+		else
+			dt_ret->id_out = H5Tcopy(type_in);
+		if (dt_ret->id_out < 0)
+			goto done;
+		if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
+			goto done;
+	} /* end if */
+
+	/* Set return value */
+	ret_value = dt_ret->id_out;
+
+	/* Increment the ref count on id_out, because the calling function will try
+	 * to close it */
+	if(H5Iinc_ref(ret_value) < 0) {
+		ret_value = -1;
+	}
+
+done:
+	return (ret_value);
 } /* end copy_named_datatype */
 
-
 /*-------------------------------------------------------------------------
-* Function: named_datatype_free
-*
-* Purpose: Frees the stack of named datatypes.
-*
-* Programmer: Neil Fortner
-*
-* Date: April 14, 2009
-*
-*-------------------------------------------------------------------------
-*/
-int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
-{
-    named_dt_t *dt = *named_dt_head_p;
-
-    while(dt)
-    {
-        /* Pop the datatype off the stack and free it */
-        if(H5Tclose(dt->id_out) < 0 && !ignore_err)
-            goto error;
-        dt = dt->next;
-        HDfree(*named_dt_head_p);
-        *named_dt_head_p = dt;
-    } /* end while */
-
-    return 0;
-
-error:
-    return -1;
+ * Function: named_datatype_free
+ *
+ * Purpose: Frees the stack of named datatypes.
+ *
+ * Programmer: Neil Fortner
+ *
+ * Date: April 14, 2009
+ *
+ *-------------------------------------------------------------------------
+ */
+int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
+	named_dt_t *dt = *named_dt_head_p;
+	hid_t ret_value = -1;
+
+	while (dt) {
+		/* Pop the datatype off the stack and free it */
+		if (H5Tclose(dt->id_out) < 0 && !ignore_err)
+			goto done;
+		dt = dt->next;
+		HDfree(*named_dt_head_p);
+		*named_dt_head_p = dt;
+	} /* end while */
+
+	ret_value = 0;
+
+done:
+	return (ret_value);
 } /* end named_datatype_free */
 
 /*-------------------------------------------------------------------------
-* Function: copy_attr
-*
-* Purpose: copy attributes located in LOC_IN, which is obtained either from
-* loc_id = H5Gopen2( fid, name);
-* loc_id = H5Dopen2( fid, name);
-* loc_id = H5Topen2( fid, name);
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 28, 2003
-*
-*-------------------------------------------------------------------------
-*/
-int copy_attr(hid_t loc_in,
-              hid_t loc_out,
-              named_dt_t **named_dt_head_p,
-              trav_table_t *travt,
-              pack_opt_t *options)
-{
-    hid_t      attr_id=-1;        /* attr ID */
-    hid_t      attr_out=-1;       /* attr ID */
-    hid_t      space_id=-1;       /* space ID */
-    hid_t      ftype_id=-1;       /* file type ID */
-    hid_t      wtype_id=-1;       /* read/write type ID */
-    size_t     msize;             /* size of type */
-    void       *buf = NULL;       /* data buffer */
-    hsize_t    nelmts;            /* number of elements in dataset */
-    int        rank;              /* rank of dataset */
-    htri_t     is_named;          /* Whether the datatype is named */
-    hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
-    char       name[255];
-    H5O_info_t oinfo;             /* object info */
-    int        j;
-    unsigned   u;
-    hbool_t    is_ref=0;
-    H5T_class_t type_class = -1;
-
-    if(H5Oget_info(loc_in, &oinfo) < 0)
-        goto error;
-
-    /*-------------------------------------------------------------------------
-    * copy all attributes
-    *-------------------------------------------------------------------------
-    */
-    for(u = 0; u < (unsigned)oinfo.num_attrs; u++) {
-        /* open attribute */
-        if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-            goto error;
-
-        /* get name */
-        if(H5Aget_name(attr_id, (size_t)255, name) < 0)
-            goto error;
-
-        /* get the file datatype  */
-        if((ftype_id = H5Aget_type(attr_id)) < 0 )
-            goto error;
-
-        /* Check if the datatype is committed */
-        if((is_named = H5Tcommitted(ftype_id)) < 0)
-            goto error;
-        if(is_named && travt) {
-            hid_t fidout;
-
-            /* Create out file id */
-            if((fidout = H5Iget_file_id(loc_out)) < 0)
-                goto error;
-
-            /* Copy named dt */
-            if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
-                    travt, options)) < 0)
-            {
-                H5Fclose(fidout);
-                goto error;
-            } /* end if */
-
-            if(H5Fclose(fidout) < 0)
-                goto error;
-        } /* end if */
-        else {
-            if(options->use_native == 1)
-                wtype_id = h5tools_get_native_type(ftype_id);
-            else
-                wtype_id = H5Tcopy(ftype_id);
-        } /* end else */
-
-
-        /* get the dataspace handle  */
-        if((space_id = H5Aget_space(attr_id)) < 0)
-            goto error;
-
-        /* get dimensions  */
-        if((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
-            goto error;
-
-        nelmts = 1;
-        for(j = 0; j < rank; j++)
-            nelmts *= dims[j];
-
-        if((msize = H5Tget_size(wtype_id)) == 0)
-            goto error;
-
-        /*-------------------------------------------------------------------------
-        * object references are a special case. We cannot just copy the buffers,
-        * but instead we recreate the reference.
-        * This is done on a second sweep of the file that just copies the referenced
-        * objects at copy_refs_attr()
-        *-------------------------------------------------------------------------
-        */
-        type_class = H5Tget_class(wtype_id);
-        is_ref = (type_class == H5T_REFERENCE);
-        if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
-        	hid_t base_type = -1;
-        	base_type = H5Tget_super(ftype_id);
-        	is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
-        	H5Tclose(base_type);
-        }
-
-        if (type_class == H5T_COMPOUND) {
-        	int nmembers = H5Tget_nmembers(wtype_id) ;
-        	for (j=0; j<nmembers; j++) {
-        		hid_t mtid = H5Tget_member_type( wtype_id, (unsigned) j );
-        		H5T_class_t mtclass = H5Tget_class(mtid);
-        		H5Tclose(mtid);
-
-        		if (mtclass==H5T_REFERENCE) {
-        			is_ref = 1;
-        			break;
-        		}
-        	} /* for (j=0; i<nmembers; j++) */
-        } /* if (type_class == H5T_COMPOUND) */
-
-        if(is_ref) {
-            ; /* handled by copy_refs_attr() */
-        }
-        else {
-            /*-------------------------------------------------------------------------
-            * read to memory
-            *-------------------------------------------------------------------------
-            */
-
-            buf = (void *)HDmalloc((size_t)(nelmts * msize));
-            if(buf == NULL) {
-                error_msg("h5repack", "cannot read into memory\n" );
-                goto error;
-            } /* end if */
-            if(H5Aread(attr_id, wtype_id, buf) < 0)
-                goto error;
-
-            /*-------------------------------------------------------------------------
-            * copy
-            *-------------------------------------------------------------------------
-            */
-
-            if((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-                goto error;
-            if(H5Awrite(attr_out, wtype_id, buf) < 0)
-                goto error;
-
-            /*close*/
-            if(H5Aclose(attr_out) < 0)
-                goto error;
-
-            /* Check if we have VL data and string in the attribute's  datatype that must
-             * be reclaimed */
-            if (TRUE == h5tools_detect_vlen(wtype_id))
-                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-            HDfree(buf);
-            buf = NULL;
-        } /*H5T_REFERENCE*/
-
-
-        if(options->verbose)
-            printf(FORMAT_OBJ_ATTR, "attr", name);
-
-        /*-------------------------------------------------------------------------
-        * close
-        *-------------------------------------------------------------------------
-        */
-
-        if(H5Tclose(ftype_id) < 0)
-            goto error;
-        if(H5Tclose(wtype_id) < 0)
-            goto error;
-        if(H5Sclose(space_id) < 0)
-            goto error;
-        if(H5Aclose(attr_id) < 0)
-            goto error;
-    } /* u */
-
-    return 0;
+ * Function: copy_attr
+ *
+ * Purpose: copy attributes located in LOC_IN, which is obtained either from
+ * loc_id = H5Gopen2( fid, name);
+ * loc_id = H5Dopen2( fid, name);
+ * loc_id = H5Topen2( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+int copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
+		trav_table_t *travt, pack_opt_t *options) {
+	hid_t attr_id = -1; /* attr ID */
+	hid_t attr_out = -1; /* attr ID */
+	hid_t space_id = -1; /* space ID */
+	hid_t ftype_id = -1; /* file type ID */
+	hid_t wtype_id = -1; /* read/write type ID */
+	size_t msize; /* size of type */
+	void *buf = NULL; /* data buffer */
+	hsize_t nelmts; /* number of elements in dataset */
+	int rank; /* rank of dataset */
+	htri_t is_named; /* Whether the datatype is named */
+	hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+	char name[255];
+	H5O_info_t oinfo; /* object info */
+	int j;
+	unsigned u;
+	hbool_t is_ref = 0;
+	H5T_class_t type_class = -1;
+
+	if (H5Oget_info(loc_in, &oinfo) < 0)
+		goto error;
+
+	/*-------------------------------------------------------------------------
+	 * copy all attributes
+	 *-------------------------------------------------------------------------
+	 */
+	for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
+		/* open attribute */
+		if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER,
+				H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+			goto error;
+
+		/* get name */
+		if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
+			goto error;
+
+		/* get the file datatype  */
+		if ((ftype_id = H5Aget_type(attr_id)) < 0)
+			goto error;
+
+		/* Check if the datatype is committed */
+		if ((is_named = H5Tcommitted(ftype_id)) < 0)
+			goto error;
+		if (is_named && travt) {
+			hid_t fidout;
+
+			/* Create out file id */
+			if ((fidout = H5Iget_file_id(loc_out)) < 0)
+				goto error;
+
+			/* Copy named dt */
+			if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+					named_dt_head_p, travt, options)) < 0) {
+				H5Fclose(fidout);
+				goto error;
+			} /* end if */
+
+			if (H5Fclose(fidout) < 0)
+				goto error;
+		} /* end if */
+		else {
+			if (options->use_native == 1)
+				wtype_id = h5tools_get_native_type(ftype_id);
+			else
+				wtype_id = H5Tcopy(ftype_id);
+		} /* end else */
+
+		/* get the dataspace handle  */
+		if ((space_id = H5Aget_space(attr_id)) < 0)
+			goto error;
+
+		/* get dimensions  */
+		if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
+			goto error;
+
+		nelmts = 1;
+		for (j = 0; j < rank; j++)
+			nelmts *= dims[j];
+
+		if ((msize = H5Tget_size(wtype_id)) == 0)
+			goto error;
+
+		/*-------------------------------------------------------------------------
+		 * object references are a special case. We cannot just copy the buffers,
+		 * but instead we recreate the reference.
+		 * This is done on a second sweep of the file that just copies the referenced
+		 * objects at copy_refs_attr()
+		 *-------------------------------------------------------------------------
+		 */
+		type_class = H5Tget_class(wtype_id);
+		is_ref = (type_class == H5T_REFERENCE);
+		if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
+			hid_t base_type = -1;
+			base_type = H5Tget_super(ftype_id);
+			is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
+			H5Tclose(base_type);
+		}
+
+		if (type_class == H5T_COMPOUND) {
+			int nmembers = H5Tget_nmembers(wtype_id);
+			for (j = 0; j < nmembers; j++) {
+				hid_t mtid = H5Tget_member_type(wtype_id, (unsigned) j);
+				H5T_class_t mtclass = H5Tget_class(mtid);
+				H5Tclose(mtid);
+
+				if (mtclass == H5T_REFERENCE) {
+					is_ref = 1;
+					break;
+				}
+			} /* for (j=0; i<nmembers; j++) */
+		} /* if (type_class == H5T_COMPOUND) */
+
+		if (is_ref) {
+			; /* handled by copy_refs_attr() */
+		}
+		else {
+			/*-------------------------------------------------------------------------
+			 * read to memory
+			 *-------------------------------------------------------------------------
+			 */
+
+			buf = (void *) HDmalloc((size_t)(nelmts * msize));
+			if (buf == NULL) {
+				error_msg("h5repack", "cannot read into memory\n");
+				goto error;
+			} /* end if */
+			if (H5Aread(attr_id, wtype_id, buf) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * copy
+			 *-------------------------------------------------------------------------
+			 */
+
+			if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id,
+					H5P_DEFAULT, H5P_DEFAULT)) < 0)
+				goto error;
+			if (H5Awrite(attr_out, wtype_id, buf) < 0)
+				goto error;
+
+			/*close*/
+			if (H5Aclose(attr_out) < 0)
+				goto error;
+
+			/* Check if we have VL data and string in the attribute's  datatype that must
+			 * be reclaimed */
+			if (TRUE == h5tools_detect_vlen(wtype_id))
+				H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+			HDfree(buf);
+			buf = NULL;
+		} /*H5T_REFERENCE*/
+
+		if (options->verbose)
+			printf(FORMAT_OBJ_ATTR, "attr", name);
+
+		/*-------------------------------------------------------------------------
+		 * close
+		 *-------------------------------------------------------------------------
+		 */
+
+		if (H5Tclose(ftype_id) < 0)
+			goto error;
+		if (H5Tclose(wtype_id) < 0)
+			goto error;
+		if (H5Sclose(space_id) < 0)
+			goto error;
+		if (H5Aclose(attr_id) < 0)
+			goto error;
+	} /* u */
+
+	return 0;
 
 error:
-    H5E_BEGIN_TRY {
-        if(buf) {
-            /* Check if we have VL data and string in the attribute's  datatype that must
-             * be reclaimed */
-            if (TRUE == h5tools_detect_vlen(wtype_id))
-                H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-
-            /* Free buf */
-            HDfree(buf);
-        } /* end if */
-
-        H5Tclose(ftype_id);
-        H5Tclose(wtype_id);
-        H5Sclose(space_id);
-        H5Aclose(attr_id);
-        H5Aclose(attr_out);
-    } H5E_END_TRY;
-
-    return -1;
+	H5E_BEGIN_TRY
+		{
+			if (buf) {
+				/* Check if we have VL data and string in the attribute's  datatype that must
+				 * be reclaimed */
+				if (TRUE == h5tools_detect_vlen(wtype_id))
+					H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
+
+				/* Free buf */
+				HDfree(buf);
+			} /* end if */
+
+			H5Tclose(ftype_id);
+			H5Tclose(wtype_id);
+			H5Sclose(space_id);
+			H5Aclose(attr_id);
+			H5Aclose(attr_out);
+		} H5E_END_TRY;
+
+	return -1;
 } /* end copy_attr() */
 
 /*-------------------------------------------------------------------------
-* Function: check_options
-*
-* Purpose: print options, checks for invalid options
-*
-* Return: void, return -1 on error
-*
-* Programmer: pvn@ncsa.uiuc.edu
-*
-* Date: September, 22, 2003
-*
-* Modification:
-*   Peter Cao, July 9, 2007
-*   Add "-L, --latest" and other options to pack a file with the latest file format
-*
-*-------------------------------------------------------------------------
-*/
-static int check_options(pack_opt_t *options)
-{
-    unsigned int   i;
-    int            k, j, has_cp=0, has_ck=0;
-    char           slayout[30];
-
-    /*-------------------------------------------------------------------------
-    * objects to layout
-    *-------------------------------------------------------------------------
-    */
-    if (options->verbose && have_request(options) /* only print if requested */)
-    {
-        printf("Objects to modify layout are...\n");
-        if (options->all_layout==1)
-        {
-            switch (options->layout_g)
-            {
-            case H5D_COMPACT:
-                strcpy(slayout,"compact");
-                break;
-            case H5D_CONTIGUOUS:
-                strcpy(slayout,"contiguous");
-                break;
-            case H5D_CHUNKED:
-                strcpy(slayout,"chunked");
-                break;
-            case H5D_LAYOUT_ERROR:
-            case H5D_NLAYOUTS:
-                error_msg("invalid layout\n");
-                return -1;
-            default:
-                strcpy(slayout,"invalid layout\n");
-                return -1;
-            }
-            printf(" Apply %s layout to all\n", slayout);
-            if (H5D_CHUNKED==options->layout_g)
-            {
-                printf("with dimension [");
-                for ( j = 0; j < options->chunk_g.rank; j++)
-                    printf("%d ",(int)options->chunk_g.chunk_lengths[j]);
-                printf("]\n");
-            }
-        }
-    }/* verbose */
-
-    for ( i = 0; i < options->op_tbl->nelems; i++)
-    {
-        char* name=options->op_tbl->objs[i].path;
-
-        if (options->op_tbl->objs[i].chunk.rank>0)
-        {
-            if (options->verbose){
-                printf(" <%s> with chunk size ",name);
-                for ( k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
-                    printf("%d ",(int)options->op_tbl->objs[i].chunk.chunk_lengths[k]);
-                printf("\n");
-            }
-            has_ck=1;
-        }
-        else if (options->op_tbl->objs[i].chunk.rank==-2)
-        {
-            if (options->verbose)
-                printf(" <%s> %s\n",name,"NONE (contigous)");
-            has_ck=1;
-        }
-    }
-
-    if (options->all_layout==1 && has_ck)
-    {
-        error_msg("invalid chunking input: 'all' option\
+ * Function: check_options
+ *
+ * Purpose: print options, checks for invalid options
+ *
+ * Return: void, return -1 on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
+ *
+ * Modification:
+ *   Peter Cao, July 9, 2007
+ *   Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_options(pack_opt_t *options) {
+	unsigned int i;
+	int k, j, has_cp = 0, has_ck = 0;
+	char slayout[30];
+
+	/*-------------------------------------------------------------------------
+	 * objects to layout
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->verbose && have_request(options) /* only print if requested */) {
+		printf("Objects to modify layout are...\n");
+		if (options->all_layout == 1) {
+			switch (options->layout_g) {
+			case H5D_COMPACT:
+				strcpy(slayout, "compact");
+				break;
+			case H5D_CONTIGUOUS:
+				strcpy(slayout, "contiguous");
+				break;
+			case H5D_CHUNKED:
+				strcpy(slayout, "chunked");
+				break;
+			case H5D_LAYOUT_ERROR:
+			case H5D_NLAYOUTS:
+				error_msg("invalid layout\n");
+				return -1;
+			default:
+				strcpy(slayout, "invalid layout\n");
+				return -1;
+			}
+			printf(" Apply %s layout to all\n", slayout);
+			if (H5D_CHUNKED == options->layout_g) {
+				printf("with dimension [");
+				for (j = 0; j < options->chunk_g.rank; j++)
+					printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+				printf("]\n");
+			}
+		}
+	}/* verbose */
+
+	for (i = 0; i < options->op_tbl->nelems; i++) {
+		char* name = options->op_tbl->objs[i].path;
+
+		if (options->op_tbl->objs[i].chunk.rank > 0) {
+			if (options->verbose) {
+				printf(" <%s> with chunk size ", name);
+				for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
+					printf("%d ",
+							(int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+				printf("\n");
+			}
+			has_ck = 1;
+		}
+		else if (options->op_tbl->objs[i].chunk.rank == -2) {
+			if (options->verbose)
+				printf(" <%s> %s\n", name, "NONE (contigous)");
+			has_ck = 1;
+		}
+	}
+
+	if (options->all_layout == 1 && has_ck) {
+		error_msg(
+				"invalid chunking input: 'all' option\
                             is present with other objects\n");
-        return -1;
-    }
-
-    /*-------------------------------------------------------------------------
-    * objects to filter
-    *-------------------------------------------------------------------------
-    */
-
-    if (options->verbose && have_request(options) /* only print if requested */)
-    {
-        printf("Objects to apply filter are...\n");
-        if (options->all_filter==1)
-        {
-
-            for (k = 0; k < options->n_filter_g; k++ )
-            {
-                H5Z_filter_t filtn=options->filter_g[k].filtn;
-                switch (filtn)
-                {
-                case H5Z_FILTER_NONE:
-                    printf(" Uncompress all\n");
-                    break;
-                case H5Z_FILTER_SHUFFLE:
-                case H5Z_FILTER_FLETCHER32:
-                    printf(" All with %s\n",get_sfilter(filtn));
-                    break;
-                case H5Z_FILTER_SZIP:
-                case H5Z_FILTER_DEFLATE:
-                    printf(" All with %s, parameter %d\n",
-                        get_sfilter(filtn),
-                        options->filter_g[k].cd_values[0]);
-                    break;
-                default:
-                    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;
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: check_objects
-*
-* Purpose: locate all HDF5 objects in the file and compare with user
-*  supplied list
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: September, 23, 2003
-*
-*-------------------------------------------------------------------------
-*/
-static int check_objects(const char* fname,
-                         pack_opt_t *options)
-{
-    hid_t         fid;
-    unsigned int  i;
-    trav_table_t  *travt = NULL;
-
-    /* nothing to do */
-    if(options->op_tbl->nelems == 0)
-        return 0;
-
-    /*-------------------------------------------------------------------------
-    * open the file
-    *-------------------------------------------------------------------------
-    */
-    if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0)) < 0)
-    {
-        printf("<%s>: %s\n", fname, H5FOPENERROR );
-        return -1;
-    }
-
-    /*-------------------------------------------------------------------------
-    * get the list of objects in the file
-    *-------------------------------------------------------------------------
-    */
-
-    /* init table */
-    trav_table_init(&travt);
-
-    /* get the list of objects in the file */
-    if(h5trav_gettable(fid, travt) < 0)
-        goto out;
-
-    /*-------------------------------------------------------------------------
-    * compare with user supplied list
-    *-------------------------------------------------------------------------
-    */
-
-    if(options->verbose)
-        printf("Opening file <%s>. Searching for objects to modify...\n", fname);
-
-    for(i = 0; i < options->op_tbl->nelems; i++)
-    {
-        char* name=options->op_tbl->objs[i].path;
-        if(options->verbose)
-            printf(" <%s>",name);
-
-        /* the input object names are present in the file and are valid */
-        if(h5trav_getindext(name, travt) < 0)
-        {
-            error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
-                (options->verbose?"\n":""),name,fname);
-            goto out;
-        }
-        if(options->verbose)
-            printf("...Found\n");
-
-        /* check for extra filter conditions */
-        switch(options->op_tbl->objs[i].filter->filtn)
-        {
-            /* chunk size must be smaller than pixels per block */
-        case H5Z_FILTER_SZIP:
-            {
-                int      j;
-                hsize_t  csize = 1;
-                unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
-                hsize_t  dims[H5S_MAX_RANK];
-                int      rank;
-                hid_t    did;
-                hid_t    sid;
-
-                if(options->op_tbl->objs[i].chunk.rank > 0) {
-                    rank = options->op_tbl->objs[i].chunk.rank;
-                    for(j = 0; j < rank; j++)
-                        csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
-                }
-                else {
-                    if((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
-                        goto out;
-                    if((sid = H5Dget_space(did)) < 0)
-                        goto out;
-                    if((rank = H5Sget_simple_extent_ndims(sid)) < 0)
-                        goto out;
-                    HDmemset(dims, 0, sizeof dims);
-                    if(H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
-                        goto out;
-                    for(j = 0; j < rank; j++)
-                        csize *= dims[j];
-                    if(H5Sclose(sid) < 0)
-                        goto out;
-                    if(H5Dclose(did) < 0)
-                        goto out;
-                }
-
-                if (csize < ppb ) {
-                    printf(" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
-                    goto out;
-                }
-            }
-            break;
-        default:
-            break;
-        }
-    } /* i */
-
-    /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-    H5Fclose(fid);
-    trav_table_free(travt);
-    return 0;
+ * Function: check_objects
+ *
+ * Purpose: locate all HDF5 objects in the file and compare with user
+ *  supplied list
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 23, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+static int check_objects(const char* fname, pack_opt_t *options) {
+	hid_t fid;
+	unsigned int i;
+	trav_table_t *travt = NULL;
+
+	/* nothing to do */
+	if (options->op_tbl->nelems == 0)
+		return 0;
+
+	/*-------------------------------------------------------------------------
+	 * open the file
+	 *-------------------------------------------------------------------------
+	 */
+	if ((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))
+			< 0) {
+		printf("<%s>: %s\n", fname, H5FOPENERROR);
+		return -1;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * get the list of objects in the file
+	 *-------------------------------------------------------------------------
+	 */
+
+	/* init table */
+	trav_table_init(&travt);
+
+	/* get the list of objects in the file */
+	if (h5trav_gettable(fid, travt) < 0)
+		goto out;
+
+	/*-------------------------------------------------------------------------
+	 * compare with user supplied list
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (options->verbose)
+		printf("Opening file <%s>. Searching for objects to modify...\n",
+				fname);
+
+	for (i = 0; i < options->op_tbl->nelems; i++) {
+		char* name = options->op_tbl->objs[i].path;
+		if (options->verbose)
+			printf(" <%s>", name);
+
+		/* the input object names are present in the file and are valid */
+		if (h5trav_getindext(name, travt) < 0) {
+			error_msg("%s Could not find <%s> in file <%s>. Exiting...\n",
+					(options->verbose ? "\n" : ""), name, fname);
+			goto out;
+		}
+		if (options->verbose)
+			printf("...Found\n");
+
+		/* check for extra filter conditions */
+		switch (options->op_tbl->objs[i].filter->filtn) {
+		/* chunk size must be smaller than pixels per block */
+		case H5Z_FILTER_SZIP:
+			{
+				int j;
+				hsize_t csize = 1;
+				unsigned ppb = options->op_tbl->objs[i].filter->cd_values[0];
+				hsize_t dims[H5S_MAX_RANK];
+				int rank;
+				hid_t did;
+				hid_t sid;
+
+				if (options->op_tbl->objs[i].chunk.rank > 0) {
+					rank = options->op_tbl->objs[i].chunk.rank;
+					for (j = 0; j < rank; j++)
+						csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+				}
+				else {
+					if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
+						goto out;
+					if ((sid = H5Dget_space(did)) < 0)
+						goto out;
+					if ((rank = H5Sget_simple_extent_ndims(sid)) < 0)
+						goto out;
+					HDmemset(dims, 0, sizeof dims);
+					if (H5Sget_simple_extent_dims(sid, dims, NULL) < 0)
+						goto out;
+					for (j = 0; j < rank; j++)
+						csize *= dims[j];
+					if (H5Sclose(sid) < 0)
+						goto out;
+					if (H5Dclose(did) < 0)
+						goto out;
+				}
+
+				if (csize < ppb) {
+					printf(
+							" <warning: SZIP settins, chunk size is smaller than pixels per block>\n");
+					goto out;
+				}
+			}
+			break;
+		default:
+			break;
+		}
+	} /* i */
+
+	/*-------------------------------------------------------------------------
+	 * close
+	 *-------------------------------------------------------------------------
+	 */
+	H5Fclose(fid);
+	trav_table_free(travt);
+	return 0;
 
 out:
-    H5Fclose(fid);
-    trav_table_free(travt);
-    return -1;
+	H5Fclose(fid);
+	trav_table_free(travt);
+	return -1;
 }
 
+/*-------------------------------------------------------------------------
+ * Function: have_request
+ *
+ * Purpose: check if a filter or layout was requested
+ *
+ * Return: 1 yes, 0 no
+ *
+ * Date: May, 24, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int have_request(pack_opt_t *options) {
 
+	if (options->all_filter || options->all_layout || options->op_tbl->nelems)
+		return 1;
 
-
-
-/*-------------------------------------------------------------------------
-* Function: have_request
-*
-* Purpose: check if a filter or layout was requested
-*
-* Return: 1 yes, 0 no
-*
-* Date: May, 24, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int have_request(pack_opt_t *options)
-{
-
-    if (options->all_filter || options->all_layout || options->op_tbl->nelems)
-        return 1;
-
-    return 0;
+	return 0;
 
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: get_sfilter
-*
-* Purpose: return the filter as a string name
-*
-* Return: name of filter, exit on error
-*
-*-------------------------------------------------------------------------
-*/
-
-static const char* get_sfilter(H5Z_filter_t filtn)
-{
-    if (filtn==H5Z_FILTER_NONE)
-        return "NONE";
-    else if (filtn==H5Z_FILTER_DEFLATE)
-        return "GZIP";
-    else if (filtn==H5Z_FILTER_SZIP)
-        return "SZIP";
-    else if (filtn==H5Z_FILTER_SHUFFLE)
-        return "SHUFFLE";
-    else if (filtn==H5Z_FILTER_FLETCHER32)
-        return "FLETCHER32";
-    else if (filtn==H5Z_FILTER_NBIT)
-        return "NBIT";
-    else if (filtn==H5Z_FILTER_SCALEOFFSET)
-        return "SOFF";
-    else
-        return "UD";
+ * Function: get_sfilter
+ *
+ * Purpose: return the filter as a string name
+ *
+ * Return: name of filter, exit on error
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static const char* get_sfilter(H5Z_filter_t filtn) {
+	if (filtn == H5Z_FILTER_NONE)
+		return "NONE";
+	else if (filtn == H5Z_FILTER_DEFLATE)
+		return "GZIP";
+	else if (filtn == H5Z_FILTER_SZIP)
+		return "SZIP";
+	else if (filtn == H5Z_FILTER_SHUFFLE)
+		return "SHUFFLE";
+	else if (filtn == H5Z_FILTER_FLETCHER32)
+		return "FLETCHER32";
+	else if (filtn == H5Z_FILTER_NBIT)
+		return "NBIT";
+	else if (filtn == H5Z_FILTER_SCALEOFFSET)
+		return "SOFF";
+	else
+		return "UD";
 }
 
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 2133b48..521b9bd 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -1,36 +1,36 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
-* Copyright by The HDF Group.                                               *
-* Copyright by the Board of Trustees of the University of Illinois.         *
-* All rights reserved.                                                      *
-*                                                                           *
-* This file is part of HDF5.  The full HDF5 copyright notice, including     *
-* terms governing use, modification, and redistribution, is contained in    *
-* the files COPYING and Copyright.html.  COPYING can be found at the root   *
-* of the source code distribution tree; Copyright.html can be found at the  *
-* root level of an installed copy of the electronic HDF5 document set and   *
-* is linked from the top-level documents page.  It can also be found at     *
-* http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
-* access to either file, you may request a copy from help@hdfgroup.org.     *
-* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 #include "h5repack.h"
 #include "h5tools.h"
 #include "h5tools_utils.h"
 
 /*-------------------------------------------------------------------------
-* typedefs
-*-------------------------------------------------------------------------
-*/
+ * typedefs
+ *-------------------------------------------------------------------------
+ */
 
 /*-------------------------------------------------------------------------
-* globals
-*-------------------------------------------------------------------------
-*/
+ * globals
+ *-------------------------------------------------------------------------
+ */
 
 /*-------------------------------------------------------------------------
-* macros
-*-------------------------------------------------------------------------
-*/
+ * macros
+ *-------------------------------------------------------------------------
+ */
 
 /* size of buffer/# of bytes to xfer at a time when copying userblock */
 #define USERBLOCK_XFER_SIZE     512     
@@ -48,1705 +48,1630 @@
         } \
     } H5E_END_TRY; \
 }
-   
+
 /*-------------------------------------------------------------------------
-* local functions
-*-------------------------------------------------------------------------
-*/
-static int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
-static void  print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
-static int   do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
-static int   copy_user_block(const char *infile, const char *outfile, hsize_t size);
+ * local functions
+ *-------------------------------------------------------------------------
+ */
+static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+		size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
+static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
+static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+		pack_opt_t *options);
+static int copy_user_block(const char *infile, const char *outfile,
+		hsize_t size);
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
-static void  print_user_block(const char *filename, hid_t fid);
+static void print_user_block(const char *filename, hid_t fid);
 #endif
 static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
 
 /* get the major number from the error stack. */
-static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata)
-{
-    if (err_desc) 
-        *((int *)udata) = err_desc->maj_num;
-        
-    return 0;
+static herr_t walk_error_callback(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
+	if (err_desc)
+		*((int *) udata) = err_desc->maj_num;
+
+	return 0;
 }
 
 /*-------------------------------------------------------------------------
-* Function: copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modification:
-*   Peter Cao, June 13, 2007
-*   Add "-L, --latest" and other options to pack a file with the latest file format
-*
-*   Peter Cao, September 25, 2007
-*   Copy user block when repacking a file
-*
-*   Pedro Vicente, August 20, 2008
-*   Add a user block to file if requested
-*
-*-------------------------------------------------------------------------
-*/
-
-int copy_objects(const char* fnamein,
-                 const char* fnameout,
-                 pack_opt_t *options)
-{
-    hid_t         fidin;
-    hid_t         fidout = -1;
-    trav_table_t  *travt = NULL;
-    hsize_t       ub_size = 0;        /* size of user block */
-    hid_t         fcpl = H5P_DEFAULT; /* file creation property list ID */
-    hid_t         fapl = H5P_DEFAULT; /* file access property list ID */
-
-    /*-------------------------------------------------------------------------
-    * open input file
-    *-------------------------------------------------------------------------
-    */
-    if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0)
-    {
-        error_msg("<%s>: %s\n", fnamein, H5FOPENERROR );
-        goto out;
-    }
-
-    /* get user block size and file space strategy/threshold */
-    {
-        hid_t fcpl_in; /* file creation property list ID for input file */
-
-        if((fcpl_in = H5Fget_create_plist(fidin)) < 0)
-        {
-            error_msg("failed to retrieve file creation property list\n");
-            goto out;
-        }
-
-        if(H5Pget_userblock(fcpl_in, &ub_size) < 0)
-        {
-            error_msg("failed to retrieve userblock size\n");
-            goto out;
-        }
-
-        if(!options->fs_strategy)
-        {
-            if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0)
-            {
-                error_msg("failed to retrieve file space strategy\n");
-                goto out;
-            }
-        }
-
-        if(!options->fs_threshold)
-        {
-            if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0)
-            {
-                error_msg("failed to retrieve file space threshold\n");
-                goto out;
-            }
-        }
-
-        if(H5Pclose(fcpl_in) < 0)
-        {
-            error_msg("failed to close property list\n");
-            goto out;
-        }
-    }
-
-    /* Check if we need to create a non-default file creation property list */
-    if(options->latest || ub_size > 0)
-    {
-        /* Create file creation property list */
-        if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
-        {
-            error_msg("fail to create a file creation property list\n");
-            goto out;
-        }
-
-        if(ub_size > 0)
-        {
-            if(H5Pset_userblock(fcpl, ub_size) < 0)
-            {
-                error_msg("failed to set non-default userblock size\n");
-                goto out;
-            }
-        }
-
-        if(options->latest)
-        {
-            unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
-
-            /* Adjust group creation parameters for root group */
-            /* (So that it is created in "dense storage" form) */
-            if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
-            {
-                error_msg("fail to adjust group creation parameters for root group\n");
-                goto out;
-            }
-
-            for(i = 0; i < 5; i++)
-            {
-                if(options->msg_size[i] > 0)
-                {
-                    switch(i)
-                    {
-                    case 0:
-                        mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
-                        break;
-
-                    case 1:
-                        mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
-                        break;
-
-                    case 2:
-                        mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
-                        break;
-
-                    case 3:
-                        mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
-                        break;
-
-                    case 4:
-                        mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
-                        break;
-                    default:
-                        break;
-                    } /* end switch */
-                    min_mesg_sizes[nindex] = (unsigned)options->msg_size[i];
-
-                    nindex++;
-                } /* end if */
-            } /* end for */
-
-            if(nindex > 0)
-            {
-                if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0)
-                {
-                    error_msg("fail to set the number of shared object header message indexes\n");
-                    goto out;
-                }
-
-                /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
-                for(i = 0; i < (nindex - 1); i++)
-                {
-                    if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
-                        error_msg("fail to configure the specified shared object header message index\n");
-                        goto out;
-                    } /* end if */
-                } /* end for */
-            } /* if (nindex>0) */
-
-            /* Create file access property list */
-            if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-            {
-                error_msg("Could not create file access property list\n");
-                goto out;
-            } /* end if */
-
-            if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
-            {
-                error_msg("Could not set property for using latest version of the format\n");
-                goto out;
-            } /* end if */
-        } /* end if */
-    } /* end if */
+ * Function: copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modification:
+ *   Peter Cao, June 13, 2007
+ *   Add "-L, --latest" and other options to pack a file with the latest file format
+ *
+ *   Peter Cao, September 25, 2007
+ *   Copy user block when repacking a file
+ *
+ *   Pedro Vicente, August 20, 2008
+ *   Add a user block to file if requested
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) {
+	hid_t fidin;
+	hid_t fidout = -1;
+	trav_table_t *travt = NULL;
+	hsize_t ub_size = 0; /* size of user block */
+	hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
+	hid_t fapl = H5P_DEFAULT; /* file access property list ID */
+
+	/*-------------------------------------------------------------------------
+	 * open input file
+	 *-------------------------------------------------------------------------
+	 */
+	if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL,
+			(size_t) 0)) < 0) {
+		error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
+		goto out;
+	}
+
+	/* get user block size and file space strategy/threshold */
+	{
+		hid_t fcpl_in; /* file creation property list ID for input file */
+
+		if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
+			error_msg("failed to retrieve file creation property list\n");
+			goto out;
+		}
+
+		if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
+			error_msg("failed to retrieve userblock size\n");
+			goto out;
+		}
+
+		if (!options->fs_strategy) {
+			if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
+				error_msg("failed to retrieve file space strategy\n");
+				goto out;
+			}
+		}
+
+		if (!options->fs_threshold) {
+			if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
+				error_msg("failed to retrieve file space threshold\n");
+				goto out;
+			}
+		}
+
+		if (H5Pclose(fcpl_in) < 0) {
+			error_msg("failed to close property list\n");
+			goto out;
+		}
+	}
+
+	/* Check if we need to create a non-default file creation property list */
+	if (options->latest || ub_size > 0) {
+		/* Create file creation property list */
+		if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+			error_msg("fail to create a file creation property list\n");
+			goto out;
+		}
+
+		if (ub_size > 0) {
+			if (H5Pset_userblock(fcpl, ub_size) < 0) {
+				error_msg("failed to set non-default userblock size\n");
+				goto out;
+			}
+		}
+
+		if (options->latest) {
+			unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
+
+			/* Adjust group creation parameters for root group */
+			/* (So that it is created in "dense storage" form) */
+			if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
+					(unsigned) options->grp_indexed) < 0) {
+				error_msg(
+						"fail to adjust group creation parameters for root group\n");
+				goto out;
+			}
+
+			for (i = 0; i < 5; i++) {
+				if (options->msg_size[i] > 0) {
+					switch (i) {
+					case 0:
+						mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
+						break;
+
+					case 1:
+						mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
+						break;
+
+					case 2:
+						mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
+						break;
+
+					case 3:
+						mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
+						break;
+
+					case 4:
+						mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
+						break;
+					default:
+						break;
+					} /* end switch */
+					min_mesg_sizes[nindex] = (unsigned) options->msg_size[i];
+
+					nindex++;
+				} /* end if */
+			} /* end for */
+
+			if (nindex > 0) {
+				if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
+					error_msg(
+							"fail to set the number of shared object header message indexes\n");
+					goto out;
+				}
+
+				/* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
+				for (i = 0; i < (nindex - 1); i++) {
+					if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i],
+							min_mesg_sizes[i]) < 0) {
+						error_msg(
+								"fail to configure the specified shared object header message index\n");
+						goto out;
+					} /* end if */
+				} /* end for */
+			} /* if (nindex>0) */
+
+			/* Create file access property list */
+			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+				error_msg("Could not create file access property list\n");
+				goto out;
+			} /* end if */
+
+			if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+				error_msg(
+						"Could not set property for using latest version of the format\n");
+				goto out;
+			} /* end if */
+		} /* end if */
+	} /* end if */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
-    print_user_block(fnamein, fidin);
+	print_user_block(fnamein, fidin);
 #endif
 
-    /*-------------------------------------------------------------------------
-    * set the new user userblock options in the FCPL (before H5Fcreate )
-    *-------------------------------------------------------------------------
-    */
-    if ( options->ublock_size > 0 )
-    {
-        /* either use the FCPL already created or create a new one */
-        if(fcpl == H5P_DEFAULT)
-        {
-            /* create a file creation property list */
-            if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
-            {
-                error_msg("fail to create a file creation property list\n");
-                goto out;
-            }
-        }
-
-        /* set user block size */
-        if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
-        {
-            error_msg("failed to set userblock size\n");
-            goto out;
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * set alignment options
-    *-------------------------------------------------------------------------
-    */
-    if (  options->alignment > 0 )
-    {
-        /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT)
-        {
-            /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-            {
-                error_msg("Could not create file access property list\n");
-                goto out;
-            }
-        }
-
-        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
-        {
-            error_msg("failed to set alignment\n");
-            goto out;
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * set metadata block size option
-    *-------------------------------------------------------------------------
-    */
-    if ( options->meta_block_size > 0 )
-    {
-        /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT)
-        {
-            /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-            {
-                error_msg("Could not create file access property list\n");
-                goto out;
-            }
-        }
-
-        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
-        {
-            error_msg("failed to set metadata block size\n");
-            goto out;
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * set free-space strategy options
-    *-------------------------------------------------------------------------
-    */
-
-    /* either use the FCPL already created or create a new one */
-    if(fcpl == H5P_DEFAULT)
-    {
-        /* create a file creation property list */
-        if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
-        {
-            error_msg("fail to create a file creation property list\n");
-            goto out;
-        }
-    }
-
-    /* set file space strategy and free space threshold */
-    if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0)
-    {
-        error_msg("failed to set file space strategy & threshold \n");
-        goto out;
-    }
-
-    /*-------------------------------------------------------------------------
-    * create the output file
-    *-------------------------------------------------------------------------
-    */
-    if(options->verbose)
-        printf("Making file <%s>...\n",fnameout);
-
-    if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0)
-    {
-        error_msg("<%s>: Could not create file\n", fnameout );
-        goto out;
-    }
-
-
-    /*-------------------------------------------------------------------------
-    * write a new user block if requested
-    *-------------------------------------------------------------------------
-    */
-    if ( options->ublock_size > 0  )
-    {
-        if ( copy_user_block( options->ublock_filename, fnameout, options->ublock_size) < 0 )
-        {
-            error_msg("Could not copy user block. Exiting...\n");
-            goto out;
-
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-    * get list of objects
-    *-------------------------------------------------------------------------
-    */
-
-    /* init table */
-    trav_table_init(&travt);
-
-    /* get the list of objects in the file */
-    if(h5trav_gettable(fidin, travt) < 0)
-        goto out;
-
-    /*-------------------------------------------------------------------------
-    * do the copy
-    *-------------------------------------------------------------------------
-    */
-    if(do_copy_objects(fidin, fidout, travt, options) < 0)
-    {
-        error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        goto out;
-    } /* end if */
-
-    /*-------------------------------------------------------------------------
-    * do the copy of referenced objects
-    * and create hard links
-    *-------------------------------------------------------------------------
-    */
-    if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 )
-    {
-        printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        goto out;
-    }
-
-    /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-
-    if(fapl > 0)
-        H5Pclose(fapl);
-
-    if(fcpl > 0)
-        H5Pclose(fcpl);
-
-    H5Fclose(fidin);
-    H5Fclose(fidout);
-
-    /* free table */
-    trav_table_free(travt);
-    travt = NULL;
-
-    /*-------------------------------------------------------------------------
-    * write only the input file user block if there is no user block file input
-    *-------------------------------------------------------------------------
-    */
-
-    if( ub_size > 0 && options->ublock_size == 0 )
-    {
-        if ( copy_user_block(fnamein, fnameout, ub_size) < 0 )
-        {
-            error_msg("Could not copy user block. Exiting...\n");
-            goto out;
-
-        }
-    }
-
-    return 0;
-
-    /*-------------------------------------------------------------------------
-    * out
-    *-------------------------------------------------------------------------
-    */
+	/*-------------------------------------------------------------------------
+	 * set the new user userblock options in the FCPL (before H5Fcreate )
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->ublock_size > 0) {
+		/* either use the FCPL already created or create a new one */
+		if (fcpl == H5P_DEFAULT) {
+			/* create a file creation property list */
+			if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+				error_msg("fail to create a file creation property list\n");
+				goto out;
+			}
+		}
+
+		/* set user block size */
+		if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
+			error_msg("failed to set userblock size\n");
+			goto out;
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * set alignment options
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->alignment > 0) {
+		/* either use the FAPL already created or create a new one */
+		if (fapl == H5P_DEFAULT) {
+			/* create a file access property list */
+			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+				error_msg("Could not create file access property list\n");
+				goto out;
+			}
+		}
+
+		if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
+			error_msg("failed to set alignment\n");
+			goto out;
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * set metadata block size option
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->meta_block_size > 0) {
+		/* either use the FAPL already created or create a new one */
+		if (fapl == H5P_DEFAULT) {
+			/* create a file access property list */
+			if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+				error_msg("Could not create file access property list\n");
+				goto out;
+			}
+		}
+
+		if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
+			error_msg("failed to set metadata block size\n");
+			goto out;
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * set free-space strategy options
+	 *-------------------------------------------------------------------------
+	 */
+
+	/* either use the FCPL already created or create a new one */
+	if (fcpl == H5P_DEFAULT) {
+		/* create a file creation property list */
+		if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
+			error_msg("fail to create a file creation property list\n");
+			goto out;
+		}
+	}
+
+	/* set file space strategy and free space threshold */
+	if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) {
+		error_msg("failed to set file space strategy & threshold \n");
+		goto out;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * create the output file
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->verbose)
+		printf("Making file <%s>...\n", fnameout);
+
+	if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
+		error_msg("<%s>: Could not create file\n", fnameout);
+		goto out;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * write a new user block if requested
+	 *-------------------------------------------------------------------------
+	 */
+	if (options->ublock_size > 0) {
+		if (copy_user_block(options->ublock_filename, fnameout,
+				options->ublock_size) < 0) {
+			error_msg("Could not copy user block. Exiting...\n");
+			goto out;
+
+		}
+	}
+
+	/*-------------------------------------------------------------------------
+	 * get list of objects
+	 *-------------------------------------------------------------------------
+	 */
+
+	/* init table */
+	trav_table_init(&travt);
+
+	/* get the list of objects in the file */
+	if (h5trav_gettable(fidin, travt) < 0)
+		goto out;
+
+	/*-------------------------------------------------------------------------
+	 * do the copy
+	 *-------------------------------------------------------------------------
+	 */
+	if (do_copy_objects(fidin, fidout, travt, options) < 0) {
+		error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+		goto out;
+	} /* end if */
+
+	/*-------------------------------------------------------------------------
+	 * do the copy of referenced objects
+	 * and create hard links
+	 *-------------------------------------------------------------------------
+	 */
+	if (do_copy_refobjs(fidin, fidout, travt, options) < 0) {
+		printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein,
+				fnameout);
+		goto out;
+	}
+
+	/*-------------------------------------------------------------------------
+	 * close
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (fapl > 0)
+		H5Pclose(fapl);
+
+	if (fcpl > 0)
+		H5Pclose(fcpl);
+
+	H5Fclose(fidin);
+	H5Fclose(fidout);
+
+	/* free table */
+	trav_table_free(travt);
+	travt = NULL;
+
+	/*-------------------------------------------------------------------------
+	 * write only the input file user block if there is no user block file input
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (ub_size > 0 && options->ublock_size == 0) {
+		if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
+			error_msg("Could not copy user block. Exiting...\n");
+			goto out;
+
+		}
+	}
+
+	return 0;
+
+	/*-------------------------------------------------------------------------
+	 * out
+	 *-------------------------------------------------------------------------
+	 */
 
 out:
-    H5E_BEGIN_TRY
-    {
-        H5Pclose(fapl);
-        H5Pclose(fcpl);
-        H5Fclose(fidin);
-        H5Fclose(fidout);
-    } H5E_END_TRY;
-    if(travt)
-        trav_table_free(travt);
-
-    return -1;
+	H5E_BEGIN_TRY
+		{
+			H5Pclose(fapl);
+			H5Pclose(fcpl);
+			H5Fclose(fidin);
+			H5Fclose(fidout);
+		}H5E_END_TRY;
+	if (travt)
+		trav_table_free(travt);
+
+	return -1;
 }
 
 /*-------------------------------------------------------------------------
-* Function: Get_hyperslab
-*
-* Purpose: Calulate a hyperslab from a dataset for higher performance.
-*          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
-*          Return the hyperslab dimentions and size in byte.
-*
-* Return: 0 - SUCCEED, -1 FAILED
-*
-* Parameters:
-*   dcpl_id : [IN] dataset creation property.
-*   rank_dset : [IN] dataset rank
-*   dims_dset[] : [IN] dataset dimentions
-*   size_datum : [IN] size of a data element in byte
-*   dims_hslab[] : [OUT] calculated hyperslab dimentions
-*   * hslab_nbytes_p : [OUT] total byte of the hyperslab
-*
-* Programmer: Jonathan Kim
-* Date: Feburary, 2012
-* Update:
-*   The hyperslab calucation would be depend on if the dataset is chunked
-*   or not. 
-*
-*   There care 3 conditions to cover:
-*   1. If chunked and a chunk fits in buffer, each chunk would be a unit of
-*      collection and the boundary would be dataset's dims.
-*   2. If chunked but a chunk doesn't fit in buffer, each data element would
-*      be a unit of collection and the boundary would be the chunk itself.
-*   3. If not chunked, each data element would be a unit of collection and
-*      the boundary would be dataset's dims.
-*
-*   The calulation starts from the last dimention (h5dump dims output).
-*
-* Note:
-*   Added for JIRA HDFFV-7862. 
-*-----------------------------------------*/
-
-int Get_hyperslab (hid_t dcpl_id, int rank_dset, hsize_t dims_dset[], 
-                   size_t size_datum, 
-                   hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
-{
-    int status = 0;
-    int k;
-    H5D_layout_t dset_layout;
-    int rank_chunk;
-    hsize_t dims_chunk[H5S_MAX_RANK];
-    hsize_t size_chunk=1;
-    hsize_t nchunk_fit;  /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t ndatum_fit;  /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t chunk_dims_map[H5S_MAX_RANK];  /* mapped chunk dimentions */
-    hsize_t hs_dims_map[H5S_MAX_RANK];  /* mapped hyperslab dimentions */
-    hsize_t hslab_nbytes;  /* size of hyperslab in byte */
-
-    /* init to set as size of a data element */
-    hslab_nbytes = size_datum;
-
-    /* get layout of dataset */
-    dset_layout =  H5Pget_layout(dcpl_id);
-
-   /* if dataset is chunked */
-    if ( dset_layout == H5D_CHUNKED )
-    {
-        /* get chunk dims */
-        rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
-        if (rank_chunk < 0)
-        {
-            status = -1;
-            goto out;
-        }
-
-        for (k = rank_dset; k > 0; --k)
-            size_chunk *= dims_chunk[k-1];
-
-        /* figure out how many chunks can fit in the hyperslab buffer */
-        nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
-             
-
-        /* 1. if a chunk fit in hyperslab buffer */
-        if (nchunk_fit >= 1)
-        {
-            /* Calulate a hyperslab that contains as many chunks that can fit
-             * in hyperslab buffer. Hyperslab will be increased starting from 
-             * the last dimention of the dataset (see h5dump's dims output).
-             * The calculation boundary is dataset dims.
-             * In the loop, used mapping from a datum to a chunk to figure out
-             * chunk based hyperslab.
-             */
-            for (k = rank_dset; k > 0; --k)
-            {
-                /* map dataset dimentions with a chunk dims */
-                chunk_dims_map[k-1]= dims_dset[k-1] / dims_chunk[k-1];
-
-                /* if reminder exist, increse by 1 to cover partial edge chunks */
-                if (dims_dset[k-1] % dims_chunk[k-1] > 0)
-                    chunk_dims_map[k-1]++;
-
-                /* get mapped hyperslab dims */
-                hs_dims_map[k-1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
-
-                /* prepare next round */
-                nchunk_fit = nchunk_fit / chunk_dims_map[k-1];
-                /* if a chunk is bigger than the rest of buffer */
-                if (nchunk_fit == 0) 
-                    nchunk_fit=1;
-
-                /* get hyperslab dimentions as unmapping to actual size */
-                dims_hslab[k-1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
-
-                /* calculate total size for the hyperslab */
-                hslab_nbytes *= dims_hslab[k-1];
-            }
-        }
-        /* 2. if a chunk is bigger than hyperslab buffer */
-        else
-        {
-            /* Calulate a hyperslab that contains as many data elements that 
-             * can fit in hyperslab buffer. Hyperslab will be increased 
-             * starting from the last dimention of the chunk (see h5dump's dims
-             * output).
-             * The calculation boundary is a chunk dims.
-             */
-            for (k = rank_dset; k > 0; --k)
-            {
-                ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
-                /* if a datum is bigger than rest of buffer */
-                if ( ndatum_fit == 0)
-                    ndatum_fit = 1;
-                /* get hyperslab dimentions within a chunk boundary */
-                dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
-
-                /* calculate total size for the hyperslab */
-                hslab_nbytes *= dims_hslab[k - 1];
-
-                if (hslab_nbytes <= 0)
-                {
-                     status = -1;
-                     goto out;
-                }
-            }
-        }
-    }
-    /* 3. if dataset is not chunked */
-    else
-    {
-        /* Calulate a hyperslab that contains as many data elements that can
-         * fit in hyperslab buffer. Hyperslab will be increased starting from
-         * the last dimention of the dataset (see h5dump's dims output).
-         * The calculation boundary is dataset dims.
-         */
-        for (k = rank_dset; k > 0; --k)
-        {
-            ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
-            /* if a datum is bigger than rest of buffer */
-            if ( ndatum_fit == 0) 
-                ndatum_fit = 1;
-            /* get hyperslab dimentions within dataset boundary */
-            dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
-
-            /* calculate total size for the hyperslab */
-            hslab_nbytes *= dims_hslab[k - 1];
-
-            if (hslab_nbytes <= 0)
-            {
-                 status = -1;
-                 goto out;
-            }
-        }
-    }
-
-    /* pass out the hyperslab size*/
-    *hslab_nbytes_p = hslab_nbytes;
+ * Function: Get_hyperslab
+ *
+ * Purpose: Calulate a hyperslab from a dataset for higher performance.
+ *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
+ *          Return the hyperslab dimentions and size in byte.
+ *
+ * Return: 0 - SUCCEED, -1 FAILED
+ *
+ * Parameters:
+ *   dcpl_id : [IN] dataset creation property.
+ *   rank_dset : [IN] dataset rank
+ *   dims_dset[] : [IN] dataset dimentions
+ *   size_datum : [IN] size of a data element in byte
+ *   dims_hslab[] : [OUT] calculated hyperslab dimentions
+ *   * hslab_nbytes_p : [OUT] total byte of the hyperslab
+ *
+ * Programmer: Jonathan Kim
+ * Date: Feburary, 2012
+ * Update:
+ *   The hyperslab calucation would be depend on if the dataset is chunked
+ *   or not.
+ *
+ *   There care 3 conditions to cover:
+ *   1. If chunked and a chunk fits in buffer, each chunk would be a unit of
+ *      collection and the boundary would be dataset's dims.
+ *   2. If chunked but a chunk doesn't fit in buffer, each data element would
+ *      be a unit of collection and the boundary would be the chunk itself.
+ *   3. If not chunked, each data element would be a unit of collection and
+ *      the boundary would be dataset's dims.
+ *
+ *   The calulation starts from the last dimention (h5dump dims output).
+ *
+ * Note:
+ *   Added for JIRA HDFFV-7862.
+ *-----------------------------------------*/
+
+int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+		size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p) {
+	int status = 0;
+	int k;
+	H5D_layout_t dset_layout;
+	int rank_chunk;
+	hsize_t dims_chunk[H5S_MAX_RANK];
+	hsize_t size_chunk = 1;
+	hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+	hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
+	hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
+	hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
+	hsize_t hslab_nbytes; /* size of hyperslab in byte */
+
+	/* init to set as size of a data element */
+	hslab_nbytes = size_datum;
+
+	/* get layout of dataset */
+	dset_layout = H5Pget_layout(dcpl_id);
+
+	/* if dataset is chunked */
+	if (dset_layout == H5D_CHUNKED) {
+		/* get chunk dims */
+		rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
+		if (rank_chunk < 0) {
+			status = -1;
+			goto out;
+		}
+
+		for (k = rank_dset; k > 0; --k)
+			size_chunk *= dims_chunk[k - 1];
+
+		/* figure out how many chunks can fit in the hyperslab buffer */
+		nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
+
+		/* 1. if a chunk fit in hyperslab buffer */
+		if (nchunk_fit >= 1) {
+			/* Calulate a hyperslab that contains as many chunks that can fit
+			 * in hyperslab buffer. Hyperslab will be increased starting from
+			 * the last dimention of the dataset (see h5dump's dims output).
+			 * The calculation boundary is dataset dims.
+			 * In the loop, used mapping from a datum to a chunk to figure out
+			 * chunk based hyperslab.
+			 */
+			for (k = rank_dset; k > 0; --k) {
+				/* map dataset dimentions with a chunk dims */
+				chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
+
+				/* if reminder exist, increse by 1 to cover partial edge chunks */
+				if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
+					chunk_dims_map[k - 1]++;
+
+				/* get mapped hyperslab dims */
+				hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
+
+				/* prepare next round */
+				nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
+				/* if a chunk is bigger than the rest of buffer */
+				if (nchunk_fit == 0)
+					nchunk_fit = 1;
+
+				/* get hyperslab dimentions as unmapping to actual size */
+				dims_hslab[k - 1] =
+						MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
+
+				/* calculate total size for the hyperslab */
+				hslab_nbytes *= dims_hslab[k - 1];
+			}
+		}
+		/* 2. if a chunk is bigger than hyperslab buffer */
+		else {
+			/* Calulate a hyperslab that contains as many data elements that
+			 * can fit in hyperslab buffer. Hyperslab will be increased
+			 * starting from the last dimention of the chunk (see h5dump's dims
+			 * output).
+			 * The calculation boundary is a chunk dims.
+			 */
+			for (k = rank_dset; k > 0; --k) {
+				ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+				/* if a datum is bigger than rest of buffer */
+				if (ndatum_fit == 0)
+					ndatum_fit = 1;
+				/* get hyperslab dimentions within a chunk boundary */
+				dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
+
+				/* calculate total size for the hyperslab */
+				hslab_nbytes *= dims_hslab[k - 1];
+
+				if (hslab_nbytes <= 0) {
+					status = -1;
+					goto out;
+				}
+			}
+		}
+	}
+	/* 3. if dataset is not chunked */
+	else {
+		/* Calulate a hyperslab that contains as many data elements that can
+		 * fit in hyperslab buffer. Hyperslab will be increased starting from
+		 * the last dimention of the dataset (see h5dump's dims output).
+		 * The calculation boundary is dataset dims.
+		 */
+		for (k = rank_dset; k > 0; --k) {
+			ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
+
+			/* if a datum is bigger than rest of buffer */
+			if (ndatum_fit == 0)
+				ndatum_fit = 1;
+			/* get hyperslab dimentions within dataset boundary */
+			dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
+
+			/* calculate total size for the hyperslab */
+			hslab_nbytes *= dims_hslab[k - 1];
+
+			if (hslab_nbytes <= 0) {
+				status = -1;
+				goto out;
+			}
+		}
+	}
+
+	/* pass out the hyperslab size*/
+	*hslab_nbytes_p = hslab_nbytes;
 
 out:
-    return status;
+	return status;
 }
 
 /*-------------------------------------------------------------------------
-* Function: do_copy_objects
-*
-* Purpose: duplicate all HDF5 objects in the file
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
-*
-* Date: October, 23, 2003
-*
-* Modifications:
-*
-*  July 2004:     Introduced the extra EC or NN option for SZIP
-*
-*  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
-*                  with the requested filter, use the input one
-*
-*  October 2006:  Read/write using the file type by default.
-*
-*  October 2006:  Read by hyperslabs for big datasets.
-*
-*  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
-*  i.e., if the memory needed to read a dataset is greater than this limit,
-*  then hyperslab I/O is done instead of one operation I/O
-*  For each dataset, the memory needed is calculated according to
-*
-*  memory needed = number of elements * size of each element
-*
-*  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-*  are done
-*
-*  H5Dread( input_dataset1 )
-*  H5Dread( input_dataset2 )
-*
-*  with all elements in the datasets selected. If the memory needed is greater than
-*  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-*  a strip mine is defined for each dimension k (a strip mine is defined as a
-*  hyperslab whose size is memory manageable) according to the formula
-*
-*  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
-*
-*  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
-*  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
-*  mine size k is simply defined as its dimension k, but for larger datasets the
-*  hyperslab size is still memory manageable.
-*  a cycle is done until the number of elements in the dataset is reached. In each
-*  iteration, two parameters are defined for the function H5Sselect_hyperslab,
-*  the start and size of each hyperslab, according to
-*
-*  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
-*
-*  where hyperslab_offset [k] is initially set to zero, and later incremented in
-*  hyperslab_size[k] offsets. The reason for the operation
-*
-*  dimension[k] - hyperslab_offset[k]
-*
-*  in (2) is that, when using the strip mine size, it assures that the "remaining" part
-*  of the dataset that does not fill an entire strip mine is processed.
-*
-*  November 2006:  Use H5Ocopy in the copy of objects. The logic for using
-*   H5Ocopy or not is if a change of filters or layout is requested by the user
-*   then use read/write else use H5Ocopy.
-*
-* May, 1, 2008: Add a printing of the compression ratio of old size / new size
-*
-* Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
-* Programmer: Jonathan Kim
-*
-*  A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
-*  i.e., if the memory needed to read a dataset is greater than this limit,
-*  then hyperslab I/O is done instead of one operation I/O
-*  For each dataset, the memory needed is calculated according to
-*
-*  memory needed = number of elements * size of each element
-*
-*  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
-*  are done
-*
-*  H5Dread( input_dataset )
-*  H5Dwrite( output_dataset )
-*
-*  with all elements in the datasets selected. If the memory needed is greater than
-*  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
-*
-*  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
-*  2. Calculate the hyperslab selections as the selection is moving forward. 
-*     Selection would be same as the hyperslab except for the remaining edge portion
-*     of the dataset. The code take care of the remaining portion if exist.
-*
-*-------------------------------------------------------------------------
-*/
-
-int do_copy_objects(hid_t fidin,
-                    hid_t fidout,
-                    trav_table_t *travt,
-                    pack_opt_t *options) /* repack options */
+ * Function: do_copy_objects
+ *
+ * Purpose: duplicate all HDF5 objects in the file
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 23, 2003
+ *
+ * Modifications:
+ *
+ *  July 2004:     Introduced the extra EC or NN option for SZIP
+ *
+ *  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
+ *                  with the requested filter, use the input one
+ *
+ *  October 2006:  Read/write using the file type by default.
+ *
+ *  October 2006:  Read by hyperslabs for big datasets.
+ *
+ *  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
+ *  i.e., if the memory needed to read a dataset is greater than this limit,
+ *  then hyperslab I/O is done instead of one operation I/O
+ *  For each dataset, the memory needed is calculated according to
+ *
+ *  memory needed = number of elements * size of each element
+ *
+ *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ *  are done
+ *
+ *  H5Dread( input_dataset1 )
+ *  H5Dread( input_dataset2 )
+ *
+ *  with all elements in the datasets selected. If the memory needed is greater than
+ *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ *  a strip mine is defined for each dimension k (a strip mine is defined as a
+ *  hyperslab whose size is memory manageable) according to the formula
+ *
+ *  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
+ *
+ *  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures
+ *  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip
+ *  mine size k is simply defined as its dimension k, but for larger datasets the
+ *  hyperslab size is still memory manageable.
+ *  a cycle is done until the number of elements in the dataset is reached. In each
+ *  iteration, two parameters are defined for the function H5Sselect_hyperslab,
+ *  the start and size of each hyperslab, according to
+ *
+ *  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
+ *
+ *  where hyperslab_offset [k] is initially set to zero, and later incremented in
+ *  hyperslab_size[k] offsets. The reason for the operation
+ *
+ *  dimension[k] - hyperslab_offset[k]
+ *
+ *  in (2) is that, when using the strip mine size, it assures that the "remaining" part
+ *  of the dataset that does not fill an entire strip mine is processed.
+ *
+ *  November 2006:  Use H5Ocopy in the copy of objects. The logic for using
+ *   H5Ocopy or not is if a change of filters or layout is requested by the user
+ *   then use read/write else use H5Ocopy.
+ *
+ * May, 1, 2008: Add a printing of the compression ratio of old size / new size
+ *
+ * Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
+ * Programmer: Jonathan Kim
+ *
+ *  A threshold of H5TOOLS_MALLOCSIZE is the limit upon which I/O hyperslab is done
+ *  i.e., if the memory needed to read a dataset is greater than this limit,
+ *  then hyperslab I/O is done instead of one operation I/O
+ *  For each dataset, the memory needed is calculated according to
+ *
+ *  memory needed = number of elements * size of each element
+ *
+ *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations
+ *  are done
+ *
+ *  H5Dread( input_dataset )
+ *  H5Dwrite( output_dataset )
+ *
+ *  with all elements in the datasets selected. If the memory needed is greater than
+ *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+ *
+ *  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
+ *  2. Calculate the hyperslab selections as the selection is moving forward.
+ *     Selection would be same as the hyperslab except for the remaining edge portion
+ *     of the dataset. The code take care of the remaining portion if exist.
+ *
+ *-------------------------------------------------------------------------
+ */
+
+int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+		pack_opt_t *options) /* repack options */
 {
-    hid_t    grp_in = -1;       /* group ID */
-    hid_t    grp_out = -1;      /* group ID */
-    hid_t    dset_in = -1;      /* read dataset ID */
-    hid_t    dset_out = -1;     /* write dataset ID */
-    hid_t    gcpl_in = -1;      /* group creation property list */
-    hid_t    gcpl_out = -1;     /* group creation property list */
-    hid_t    type_in = -1;      /* named type ID */
-    hid_t    type_out = -1;     /* named type ID */
-    hid_t    dcpl_in = -1;      /* dataset creation property list ID */
-    hid_t    dcpl_out = -1;     /* dataset creation property list ID */
-    hid_t    f_space_id = -1;   /* file space ID */
-    hid_t    ftype_id = -1;     /* file type ID */
-    hid_t    wtype_id = -1;     /* read/write type ID */
-    named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
-    size_t   msize;             /* size of type */
-    hsize_t  nelmts;            /* number of elements in dataset */
-    H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
-    int      rank;              /* rank of dataset */
-    hsize_t  dims[H5S_MAX_RANK];/* dimensions of dataset */
-    hsize_t  dsize_in;          /* input dataset size before filter */
-    hsize_t  dsize_out;         /* output dataset size after filter */
-    int      apply_s;           /* flag for apply filter to small dataset sizes */
-    int      apply_f;           /* flag for apply filter to return error on H5Dcreate */
-    void     *buf=NULL;         /* buffer for raw data */
-    void     *hslab_buf=NULL;   /* hyperslab buffer for raw data */
-    int      has_filter;        /* current object has a filter */
-    int      req_filter;        /* there was a request for a filter */
-    int      req_obj_layout=0;  /* request layout to current object */
-    unsigned crt_order_flags;   /* group creation order flag */
-    unsigned i;
-    unsigned u;
-    int      is_ref=0;
-    htri_t   is_named;
-    hbool_t  limit_maxdims;
-    hsize_t size_dset;
-
-
-    /*-------------------------------------------------------------------------
-    * copy the suppplied object list
-    *-------------------------------------------------------------------------
-    */
-
-    if (options->verbose)
-    {
-        printf("-----------------------------------------\n");
-        printf(" Type     Filter (Compression)     Name\n");
-        printf("-----------------------------------------\n");
-    }
-
-    for ( i = 0; i < travt->nobjs; i++)
-    {
-        /* init variables per obj */
-        buf = NULL;
-        limit_maxdims = FALSE;
-
-        switch ( travt->objs[i].type )
-        {
-
-        case H5TRAV_TYPE_UNKNOWN:
-            HDassert(0);
-            break;
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_GROUP
-            *-------------------------------------------------------------------------
-            */
-        case H5TRAV_TYPE_GROUP:
-
-            if (options->verbose)
-            {
-                printf(FORMAT_OBJ,"group",travt->objs[i].name );
-            }
-
-            /* open input group */
-            if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                goto error;
-
-            /* get input group creation property list */
-            if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
-                goto error;
-
-            /* query and set the group creation properties */
-            if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
-                goto error;
-
-            /* set up group creation property list */
-            if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
-                goto error;
-
-            if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
-                goto error;
-
-
-            /*-------------------------------------------------------------------------
-            * the root is a special case, we get an ID for the root group
-            * and copy its attributes using that ID
-            *-------------------------------------------------------------------------
-            */
-            if(HDstrcmp(travt->objs[i].name, "/") == 0)
-            {
-                if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
-                    goto error;
-            }
-
-            else
-            {
-
-                if (options->grp_compact>0 || options->grp_indexed>0)
-                {
-                    if(H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
-                        goto error;
-                }
-
-                if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
-                    goto error;
-
-            }
-
-            /*-------------------------------------------------------------------------
-            * copy attrs
-            *-------------------------------------------------------------------------
-            */
-            if(copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
-                goto error;
-
-
-            if(H5Pclose(gcpl_out) < 0)
-                goto error;
-            if(H5Pclose(gcpl_in) < 0)
-                goto error;
-            if(H5Gclose(grp_out) < 0)
-                goto error;
-            if(H5Gclose(grp_in) < 0)
-                goto error;
-
-            break;
-
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_DATASET
-            *-------------------------------------------------------------------------
-            */
-        case H5TRAV_TYPE_DATASET:
-
-            has_filter = 0;
-            req_filter = 0;
-
-            /* check if global filters were requested */
-            if ( options->n_filter_g )
-                req_filter = 1;
-
-            /* check if filters were requested for individual objects */
-            for (u = 0; u < options->op_tbl->nelems; u++) {
-
-                if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
-                        if (options->op_tbl->objs[u].filter->filtn > 0) {
-                            req_filter = 1;
-                        }
-                }
-            }
-
-            /* check if layout change requested individual object */
-            if (options->layout_g != H5D_LAYOUT_ERROR)
-            {
-	            pack_info_t *pckinfo;
-	            /* any dataset is specified */
-	            if (options->op_tbl->nelems > 0)
-	            {
-	                /* check if object exist */
-	                pckinfo = options_get_object (travt->objs[i].name, options->op_tbl);
-	                if (pckinfo)
-	                {
-	                    req_obj_layout = 1;
-	                }
-	            }
-            }
-
-            /* early detection of references */
-            if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                goto error;
-            if((ftype_id = H5Dget_type(dset_in)) < 0)
-                goto error;
-            if(H5T_REFERENCE == H5Tget_class(ftype_id))
-                is_ref = 1;
-
-            /* Check if the datatype is committed */
-            if((is_named = H5Tcommitted(ftype_id)) < 0)
-                goto error;
-            if(is_named)
-                if((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
-                    goto error;
-
-            if(H5Tclose(ftype_id) < 0)
-                goto error;
-            if(H5Dclose(dset_in) < 0)
-                goto error;
-
-
-            /*-------------------------------------------------------------------------
-            * check if we should use H5Ocopy or not
-            * if there is a request for filters/layout, we read/write the object
-            * otherwise we do a copy using H5Ocopy
-            *-------------------------------------------------------------------------
-            */
-            if ( options->op_tbl->nelems  ||
-                options->all_filter == 1 ||
-                options->all_layout == 1 ||
-                is_ref ||
-                is_named)
-            {
-
-                int      j;
-
-                if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
-                if((f_space_id = H5Dget_space(dset_in)) < 0)
-                    goto error;
-                if((ftype_id = H5Dget_type(dset_in)) < 0)
-                    goto error;
-                if((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
-                    goto error;
-                if((dcpl_out = H5Pcopy(dcpl_in)) < 0)
-                    goto error;
-                if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
-                    goto error;
-                HDmemset(dims, 0, sizeof dims);
-                if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
-                    goto error;
-
-                if(H5Dget_space_status(dset_in, &space_status) < 0)
-                    goto error;
-
-                nelmts = 1;
-                for(j = 0; j < rank; j++)
-                    nelmts *= dims[j];
-
-                /* wtype_id will have already been set if using a named dtype */
-                if(!is_named) {
-                    if(options->use_native == 1)
-                        wtype_id = h5tools_get_native_type(ftype_id);
-                    else
-                        wtype_id = H5Tcopy(ftype_id);
-                } /* end if */
-
-                if((msize = H5Tget_size(wtype_id)) == 0)
-                    goto error;
-
-                /* size of current dset */
-                size_dset = nelmts * msize;
-
-                /*-------------------------------------------------------------------------
-                * check if the dataset creation property list has filters that
-                * are not registered in the current configuration
-                * 1) the external filters GZIP and SZIP might not be available
-                * 2) the internal filters might be turned off
-                *-------------------------------------------------------------------------
-                */
-                if (h5tools_canreadf((travt->objs[i].name),dcpl_in)==1)
-                {
-                    apply_s=1;
-                    apply_f=1;
-
-                    /*-------------------------------------------------------------------------
-                    * references are a special case
-                    * we cannot just copy the buffers, but instead we recreate the reference
-                    * in a second traversal of the output file
-                    *-------------------------------------------------------------------------
-                    */
-                    if (H5T_REFERENCE!=H5Tget_class(wtype_id))
-                    {
-                        /* get the storage size of the input dataset */
-                        dsize_in=H5Dget_storage_size(dset_in);
-
-                        /* check for small size datasets (less than 1k) except 
-                         * changing to COMPACT. For the reference, COMPACT is limited
-                         * by size 64K by library.
-                         */
-                        if (options->layout_g != H5D_COMPACT)
-                        {
-                            if ( size_dset < options->min_comp )
-                                apply_s=0;
-                        }
-
-                        /* apply the filter */
-                        if (apply_s)
-                        {
-                            if (apply_filters(travt->objs[i].name,
-                                rank,
-                                dims,
-                                msize,
-                                dcpl_out,
-                                options,
-                                &has_filter) < 0)
-                                goto error;
-                        }
-
-                    /* only if layout change requested for entire file or 
-                     * individual obj */
-                    if (options->all_layout > 0 || req_obj_layout == 1)
-                        /*------------------------------------------------- 
-                         * Unset the unlimited max dims if convert to other
-                         * than chunk layouts, because unlimited max dims
-                         * only can be applied to chunk layout. 
-                         * Also perform only for targeted dataset
-                         * Also check for size limit to convert to compact
-                         *-------------------------------------------------*/
-                        if (options->layout_g != H5D_CHUNKED) 
-                        {
-                            /* any dataset is specified */
-                            if (options->op_tbl->nelems > 0)
-                            {
-                                /* if current obj match specified obj */
-                                if (options_get_object (travt->objs[i].name, options->op_tbl))
-                                    limit_maxdims = TRUE;
-                            }
-                            else /* no dataset is specified */
-                            {
-                                limit_maxdims = TRUE;
-                            }
-                        
-                            /* if convert to COMPACT */
-                            if (options->layout_g == H5D_COMPACT)
-                            {
-                                /* should be smaller than 64K */
-                                if ( size_dset > MAX_COMPACT_DSIZE )
-                                    limit_maxdims = FALSE;
-                            }
-                        
-                            /* unset unlimited max dims */
-                            if (limit_maxdims)
-                                H5Sset_extent_simple( f_space_id, rank, dims, NULL );
-                        }
-
-                        /*-------------------------------------------------------------------------
-                        * create the output dataset;
-                        * disable error checking in case the dataset cannot be created with the
-                        * modified dcpl; in that case use the original instead
-                        *-------------------------------------------------------------------------
-                        */
-                        H5E_BEGIN_TRY {
-                            dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
-                        } H5E_END_TRY;
-
-                        if(dset_out == FAIL)
-                        {
-                            if(options->verbose)
-                                printf(" warning: could not create dataset <%s>. Applying original settings\n",
-                                travt->objs[i].name);
-
-                            if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
-                                goto error;
-                            apply_f = 0;
-                        }
-
-                        /*-------------------------------------------------------------------------
-                        * read/write
-                        *-------------------------------------------------------------------------
-                        */
-                        if(nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED)
-                        {
-                            size_t need = (size_t)(nelmts * msize);  /* bytes needed */
-
-                            /* have to read the whole dataset if there is only one element in the dataset */
-                            if(need < H5TOOLS_MALLOCSIZE)
-                                buf = HDmalloc(need);
-
-                            if(buf != NULL) {
-                               /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-                                CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-                               
-                                /* Check if we have VL data in the dataset's
-                                 * datatype that must be reclaimed */
-                                if(TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
-                                    if(H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
-                                        goto error;
-                            }
-                            else /* possibly not enough memory, read/write by hyperslabs */
-                            {
-                                size_t        p_type_nbytes = msize; /*size of memory type */
-                                hsize_t       p_nelmts = nelmts;     /*total elements */
-                                hsize_t       elmtno;                /*counter  */
-                                int           carry;                 /*counter carry value */
-                                unsigned int  vl_data = 0;           /*contains VL datatypes */
-
-                                /* hyperslab info */
-                                hsize_t       hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
-                                hsize_t       hslab_nbytes;             /*bytes per hyperslab */
-                                hsize_t       hslab_nelmts;             /*elements per hyperslab*/
-                                hid_t         hslab_space;              /*hyperslab data space */
-
-                                /* hyperslab selection info */
-                                hsize_t       hs_sel_offset[H5S_MAX_RANK];/* selection offset */
-                                hsize_t       hs_sel_count[H5S_MAX_RANK];  /* selection count */
-                                hsize_t       hs_select_nelmts;    /* selected elements */
-                                hsize_t       zero[8];                /*vector of zeros */
-                                int           k;
-                                H5D_layout_t dset_layout;
-                                hid_t    dcpl_tmp = -1;     /* dataset creation property list ID */
-
-                                /* check if we have VL data in the dataset's datatype */
-                                if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
-                                    vl_data = TRUE;
-
-
-                                /* check first if writing dataset is chunked, 
-                                 * if so use its chunk layout for better performance. */
-                                dset_layout = H5Pget_layout(dcpl_out);
-                                if (dset_layout == H5D_CHUNKED)
-                                   dcpl_tmp = dcpl_out;  /* writing dataset */
-                                else /* if reading dataset is chunked */
-                                {
-                                   dset_layout = H5Pget_layout(dcpl_in);
-                                   if (dset_layout == H5D_CHUNKED)
-                                       dcpl_tmp = dcpl_in;  /* reading dataset */
-                                }
-
-                                /* get hyperslab dims and size in byte */
-                                if(Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
-                                    goto error;
-
-                                hslab_buf = HDmalloc((size_t)hslab_nbytes);
-
-                                hslab_nelmts = hslab_nbytes / p_type_nbytes;
-                                hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
-
-                                /* the hyperslab selection loop */
-                                HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
-                                HDmemset(zero, 0, sizeof zero);
-
-                                for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts)
-                                {
-                                    if (rank > 0)
-                                    {
-                                        /* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
-                                         */
-                                        for (k = 0, hs_select_nelmts = 1; k < rank; k++)
-                                        {
-                                            /* MIN() is used to get the remaining edge portion if exist. 
-                                             * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
-                                            hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
-                                            hs_select_nelmts *= hs_sel_count[k];
-                                        }
-
-                                        if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
-                                            goto error;
-                                        if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
-                                            goto error;
-                                    }
-                                    else
-                                    {
-                                        H5Sselect_all(f_space_id);
-                                        H5Sselect_all(hslab_space);
-                                        hs_select_nelmts = 1;
-                                    } /* rank */
-
-                                    /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                    CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-                                    CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-
-                                    /* reclaim any VL memory, if necessary */
-                                    if(vl_data)
-                                        H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
-
-                                    /* calculate the next hyperslab offset */
-                                    for (k = rank, carry = 1; k > 0 && carry; --k)
-                                    {
-                                        hs_sel_offset[k - 1] += hs_sel_count[k - 1];
-                                        /* if reached the end of a dim */
-                                        if (hs_sel_offset[k - 1] == dims[k - 1])
-                                            hs_sel_offset[k - 1] = 0;
-                                        else
-                                            carry = 0;
-                                    } /* k */
-                                } /* elmtno */
-
-                                H5Sclose(hslab_space);
-                                /* free */
-                                if (hslab_buf!=NULL)
-                                {
-                                    HDfree(hslab_buf);
-                                    hslab_buf=NULL;
-                                }
-                            } /* hyperslab read */
-                        } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
-
-                        /*-------------------------------------------------------------------------
-                        * amount of compression used
-                        *-------------------------------------------------------------------------
-                        */
-                        if (options->verbose)
-                        {
-                            double ratio=0;
-
-                            /* only print the compression ration if there was a filter request */
-                            if (apply_s && apply_f && req_filter)
-                            {
-                                /* get the storage size of the output dataset */
-                                dsize_out=H5Dget_storage_size(dset_out);
-
-                                /* compression ratio = uncompressed size /  compressed size */
-                                if (dsize_out!=0)
-                                    ratio = (double) dsize_in / (double) dsize_out;
-
-                                print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
-                            }
-                            else
-                                print_dataset_info(dcpl_in,travt->objs[i].name,ratio,0);
-
-                            /* print a message that the filter was not applied
-                            (in case there was a filter)
-                            */
-                            if ( has_filter && apply_s == 0 )
-                                printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
-                                travt->objs[i].name,
-                                (int)options->min_comp);
-
-                            if ( has_filter && apply_f == 0 )
-                                printf(" <warning: could not apply the filter to %s>\n",
-                                travt->objs[i].name);
-
-                        } /* verbose */
-
-                        /*-------------------------------------------------------------------------
-                        * copy attrs
-                        *-------------------------------------------------------------------------
-                        */
-                        if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
-                            goto error;
-                        /*close */
-                        if (H5Dclose(dset_out) < 0)
-                            goto error;
-
-                    }/*!H5T_REFERENCE*/
-                }/*h5tools_canreadf*/
-
-
-                /*-------------------------------------------------------------------------
-                * close
-                *-------------------------------------------------------------------------
-                */
-                if (H5Tclose(ftype_id) < 0)
-                    goto error;
-                if (H5Tclose(wtype_id) < 0)
-                    goto error;
-                if (H5Pclose(dcpl_in) < 0)
-                    goto error;
-                if (H5Pclose(dcpl_out) < 0)
-                    goto error;
-                if (H5Sclose(f_space_id) < 0)
-                    goto error;
-                if (H5Dclose(dset_in) < 0)
-                    goto error;
-
-            }
-            /*-------------------------------------------------------------------------
-            * we do not have request for filter/chunking use H5Ocopy instead
-            *-------------------------------------------------------------------------
-            */
-            else
-            {
-                hid_t        pid;
-
-                /* create property to pass copy options */
-                if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
-                    goto error;
-
-                /* set options for object copy */
-                if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
-                    goto error;
-
-                /*-------------------------------------------------------------------------
-                * do the copy
-                *-------------------------------------------------------------------------
-                */
-
-                if(H5Ocopy(fidin,          /* Source file or group identifier */
-                    travt->objs[i].name,       /* Name of the source object to be copied */
-                    fidout,                    /* Destination file or group identifier  */
-                    travt->objs[i].name,       /* Name of the destination object  */
-                    pid,                       /* Properties which apply to the copy   */
-                    H5P_DEFAULT) < 0)            /* Properties which apply to the new hard link */
-                    goto error;
-
-                /* close property */
-                if(H5Pclose(pid) < 0)
-                    goto error;
-
-
-                /*-------------------------------------------------------------------------
-                * copy attrs manually
-                *-------------------------------------------------------------------------
-                */
-                if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
-                if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
-                if(copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
-                    goto error;
-                if(H5Dclose(dset_in) < 0)
-                    goto error;
-                if(H5Dclose(dset_out) < 0)
-                    goto error;
-
-
-                if (options->verbose)
-                    printf(FORMAT_OBJ,"dset",travt->objs[i].name );
-
-
-            } /* end do we have request for filter/chunking */
-
-            break;
-
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_NAMED_DATATYPE
-            *-------------------------------------------------------------------------
-            */
-        case H5TRAV_TYPE_NAMED_DATATYPE:
-
-            if(options->verbose)
-                printf(FORMAT_OBJ, "type", travt->objs[i].name);
-
-            if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                goto error;
-
-            /* Copy the datatype anonymously */
-            if((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
-                    travt, options)) < 0)
-                goto error;
-
-            /* Link in to group structure */
-            if(H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
-                    H5P_DEFAULT, H5P_DEFAULT) < 0)
-                goto error;
-
-            /*-------------------------------------------------------------------------
-            * copy attrs
-            *-------------------------------------------------------------------------
-            */
-            if(copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
-                goto error;
-
-            if(H5Tclose(type_in) < 0)
-                goto error;
-            if(H5Tclose(type_out) < 0)
-                goto error;
-
-
-
-            break;
-
-
-            /*-------------------------------------------------------------------------
-            * H5TRAV_TYPE_LINK
-            * H5TRAV_TYPE_UDLINK
-            *
-            * Only handles external links; H5Lcopy will fail for other UD link types
-            * since we don't have creation or copy callbacks for them.
-            *-------------------------------------------------------------------------
-            */
-
-        case H5TRAV_TYPE_LINK:
-        case H5TRAV_TYPE_UDLINK:
-            {
-
-                if(options->verbose)
-                    printf(FORMAT_OBJ, "link", travt->objs[i].name);
-
-                if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
-                    goto error;
-
-                if (options->verbose)
-                    printf(FORMAT_OBJ,"link",travt->objs[i].name );
-
-            }
-            break;
-
-        default:
-            goto error;
-        } /* switch */
-
-        /* free */
-        if (buf!=NULL)
-        {
-            HDfree(buf);
-            buf=NULL;
-        }
-
-    } /* i */
-
-    /* Finalize (link) the stack of named datatypes (if any) */
-    named_datatype_free(&named_dt_head, 0);
-
-    return 0;
+	hid_t grp_in = -1; /* group ID */
+	hid_t grp_out = -1; /* group ID */
+	hid_t dset_in = -1; /* read dataset ID */
+	hid_t dset_out = -1; /* write dataset ID */
+	hid_t gcpl_in = -1; /* group creation property list */
+	hid_t gcpl_out = -1; /* group creation property list */
+	hid_t type_in = -1; /* named type ID */
+	hid_t type_out = -1; /* named type ID */
+	hid_t dcpl_in = -1; /* dataset creation property list ID */
+	hid_t dcpl_out = -1; /* dataset creation property list ID */
+	hid_t f_space_id = -1; /* file space ID */
+	hid_t ftype_id = -1; /* file type ID */
+	hid_t wtype_id = -1; /* read/write type ID */
+	named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
+	size_t msize; /* size of type */
+	hsize_t nelmts; /* number of elements in dataset */
+	H5D_space_status_t space_status; /* determines whether space has been allocated for the dataset  */
+	int rank; /* rank of dataset */
+	hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
+	hsize_t dsize_in; /* input dataset size before filter */
+	hsize_t dsize_out; /* output dataset size after filter */
+	int apply_s; /* flag for apply filter to small dataset sizes */
+	int apply_f; /* flag for apply filter to return error on H5Dcreate */
+	void *buf = NULL; /* buffer for raw data */
+	void *hslab_buf = NULL; /* hyperslab buffer for raw data */
+	int has_filter; /* current object has a filter */
+	int req_filter; /* there was a request for a filter */
+	int req_obj_layout = 0; /* request layout to current object */
+	unsigned crt_order_flags; /* group creation order flag */
+	unsigned i;
+	unsigned u;
+	int is_ref = 0;
+	htri_t is_named;
+	hbool_t limit_maxdims;
+	hsize_t size_dset;
+
+	/*-------------------------------------------------------------------------
+	 * copy the suppplied object list
+	 *-------------------------------------------------------------------------
+	 */
+
+	if (options->verbose) {
+		printf("-----------------------------------------\n");
+		printf(" Type     Filter (Compression)     Name\n");
+		printf("-----------------------------------------\n");
+	}
+
+	for (i = 0; i < travt->nobjs; i++) {
+		/* init variables per obj */
+		buf = NULL;
+		limit_maxdims = FALSE;
+
+		switch (travt->objs[i].type) {
+
+		case H5TRAV_TYPE_UNKNOWN:
+			HDassert(0);
+			break;
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_GROUP
+			 *-------------------------------------------------------------------------
+			 */
+		case H5TRAV_TYPE_GROUP:
+
+			if (options->verbose) {
+				printf(FORMAT_OBJ, "group", travt->objs[i].name);
+			}
+
+			/* open input group */
+			if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+					< 0)
+				goto error;
+
+			/* get input group creation property list */
+			if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+				goto error;
+
+			/* query and set the group creation properties */
+			if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+				goto error;
+
+			/* set up group creation property list */
+			if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+				goto error;
+
+			if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * the root is a special case, we get an ID for the root group
+			 * and copy its attributes using that ID
+			 *-------------------------------------------------------------------------
+			 */
+			if (HDstrcmp(travt->objs[i].name, "/") == 0) {
+				if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+					goto error;
+			}
+			else {
+
+				if (options->grp_compact > 0 || options->grp_indexed > 0) {
+					if (H5Pset_link_phase_change(gcpl_out,
+							(unsigned) options->grp_compact,
+							(unsigned) options->grp_indexed) < 0)
+						goto error;
+				}
+
+				if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name,
+						H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
+					goto error;
+
+			}
+
+			/*-------------------------------------------------------------------------
+			 * copy attrs
+			 *-------------------------------------------------------------------------
+			 */
+			if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
+				goto error;
+
+			if (H5Pclose(gcpl_out) < 0)
+				goto error;
+			if (H5Pclose(gcpl_in) < 0)
+				goto error;
+			if (H5Gclose(grp_out) < 0)
+				goto error;
+			if (H5Gclose(grp_in) < 0)
+				goto error;
+
+			break;
+
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_DATASET
+			 *-------------------------------------------------------------------------
+			 */
+		case H5TRAV_TYPE_DATASET:
+
+			has_filter = 0;
+			req_filter = 0;
+
+			/* check if global filters were requested */
+			if (options->n_filter_g)
+				req_filter = 1;
+
+			/* check if filters were requested for individual objects */
+			for (u = 0; u < options->op_tbl->nelems; u++) {
+
+				if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0) {
+					if (options->op_tbl->objs[u].filter->filtn > 0) {
+						req_filter = 1;
+					}
+				}
+			}
+
+			/* check if layout change requested individual object */
+			if (options->layout_g != H5D_LAYOUT_ERROR) {
+				pack_info_t *pckinfo;
+				/* any dataset is specified */
+				if (options->op_tbl->nelems > 0) {
+					/* check if object exist */
+					pckinfo = options_get_object(travt->objs[i].name,
+							options->op_tbl);
+					if (pckinfo) {
+						req_obj_layout = 1;
+					}
+				}
+			}
+
+			/* early detection of references */
+			if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+					< 0)
+				goto error;
+			if ((ftype_id = H5Dget_type(dset_in)) < 0)
+				goto error;
+			if (H5T_REFERENCE == H5Tget_class(ftype_id))
+				is_ref = 1;
+
+			/* Check if the datatype is committed */
+			if ((is_named = H5Tcommitted(ftype_id)) < 0)
+				goto error;
+			if (is_named)
+				if ((wtype_id = copy_named_datatype(ftype_id, fidout,
+						&named_dt_head, travt, options)) < 0)
+					goto error;
+
+			if (H5Tclose(ftype_id) < 0)
+				goto error;
+			if (H5Dclose(dset_in) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * check if we should use H5Ocopy or not
+			 * if there is a request for filters/layout, we read/write the object
+			 * otherwise we do a copy using H5Ocopy
+			 *-------------------------------------------------------------------------
+			 */
+			if (options->op_tbl->nelems || options->all_filter == 1
+					|| options->all_layout == 1 || is_ref || is_named) {
+
+				int j;
+
+				if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+					goto error;
+				if ((f_space_id = H5Dget_space(dset_in)) < 0)
+					goto error;
+				if ((ftype_id = H5Dget_type(dset_in)) < 0)
+					goto error;
+				if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
+					goto error;
+				if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
+					goto error;
+				if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+					goto error;
+				HDmemset(dims, 0, sizeof dims);
+				if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+					goto error;
+
+				if (H5Dget_space_status(dset_in, &space_status) < 0)
+					goto error;
+
+				nelmts = 1;
+				for (j = 0; j < rank; j++)
+					nelmts *= dims[j];
+
+				/* wtype_id will have already been set if using a named dtype */
+				if (!is_named) {
+					if (options->use_native == 1)
+						wtype_id = h5tools_get_native_type(ftype_id);
+					else
+						wtype_id = H5Tcopy(ftype_id);
+				} /* end if */
+
+				if ((msize = H5Tget_size(wtype_id)) == 0)
+					goto error;
+
+				/* size of current dset */
+				size_dset = nelmts * msize;
+
+				/*-------------------------------------------------------------------------
+				 * check if the dataset creation property list has filters that
+				 * are not registered in the current configuration
+				 * 1) the external filters GZIP and SZIP might not be available
+				 * 2) the internal filters might be turned off
+				 *-------------------------------------------------------------------------
+				 */
+				if (h5tools_canreadf((travt->objs[i].name), dcpl_in) == 1) {
+					apply_s = 1;
+					apply_f = 1;
+
+					/*-------------------------------------------------------------------------
+					 * references are a special case
+					 * we cannot just copy the buffers, but instead we recreate the reference
+					 * in a second traversal of the output file
+					 *-------------------------------------------------------------------------
+					 */
+					if (H5T_REFERENCE != H5Tget_class(wtype_id)) {
+						/* get the storage size of the input dataset */
+						dsize_in = H5Dget_storage_size(dset_in);
+
+						/* check for small size datasets (less than 1k) except
+						 * changing to COMPACT. For the reference, COMPACT is limited
+						 * by size 64K by library.
+						 */
+						if (options->layout_g != H5D_COMPACT) {
+							if (size_dset < options->min_comp)
+								apply_s = 0;
+						}
+
+						/* apply the filter */
+						if (apply_s) {
+							if (apply_filters(travt->objs[i].name, rank, dims,
+									msize, dcpl_out, options, &has_filter) < 0)
+								goto error;
+						}
+
+						/* only if layout change requested for entire file or
+						 * individual obj */
+						if (options->all_layout > 0 || req_obj_layout == 1)
+							/*-------------------------------------------------
+							 * Unset the unlimited max dims if convert to other
+							 * than chunk layouts, because unlimited max dims
+							 * only can be applied to chunk layout.
+							 * Also perform only for targeted dataset
+							 * Also check for size limit to convert to compact
+							 *-------------------------------------------------*/
+							if (options->layout_g != H5D_CHUNKED) {
+								/* any dataset is specified */
+								if (options->op_tbl->nelems > 0) {
+									/* if current obj match specified obj */
+									if (options_get_object(travt->objs[i].name,
+											options->op_tbl))
+										limit_maxdims = TRUE;
+								}
+								else { /* no dataset is specified */
+									limit_maxdims = TRUE;
+								}
+
+								/* if convert to COMPACT */
+								if (options->layout_g == H5D_COMPACT) {
+									/* should be smaller than 64K */
+									if (size_dset > MAX_COMPACT_DSIZE)
+										limit_maxdims = FALSE;
+								}
+
+								/* unset unlimited max dims */
+								if (limit_maxdims)
+									H5Sset_extent_simple(f_space_id, rank, dims,
+											NULL);
+							}
+
+						/*-------------------------------------------------------------------------
+						 * create the output dataset;
+						 * disable error checking in case the dataset cannot be created with the
+						 * modified dcpl; in that case use the original instead
+						 *-------------------------------------------------------------------------
+						 */
+						H5E_BEGIN_TRY
+							{
+								dset_out = H5Dcreate2(fidout,
+										travt->objs[i].name, wtype_id,
+										f_space_id, H5P_DEFAULT, dcpl_out,
+										H5P_DEFAULT);
+							}H5E_END_TRY;
+
+						if (dset_out == FAIL) {
+							if (options->verbose)
+								printf(
+										" warning: could not create dataset <%s>. Applying original settings\n",
+										travt->objs[i].name);
+
+							if ((dset_out = H5Dcreate2(fidout,
+									travt->objs[i].name, wtype_id, f_space_id,
+									H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
+								goto error;
+							apply_f = 0;
+						}
+
+						/*-------------------------------------------------------------------------
+						 * read/write
+						 *-------------------------------------------------------------------------
+						 */
+						if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
+							size_t need = (size_t)(nelmts * msize); /* bytes needed */
+
+							/* have to read the whole dataset if there is only one element in the dataset */
+							if (need < H5TOOLS_MALLOCSIZE)
+								buf = HDmalloc(need);
+
+							if (buf != NULL) {
+								/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+								CHECK_H5DRW_ERROR(H5Dread, dset_in, wtype_id,
+										H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+								CHECK_H5DRW_ERROR(H5Dwrite, dset_out, wtype_id,
+										H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
+
+								/* Check if we have VL data in the dataset's
+								 * datatype that must be reclaimed */
+								if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
+									if (H5Dvlen_reclaim(wtype_id, f_space_id,
+											H5P_DEFAULT, buf) < 0)
+										goto error;
+							}
+							else { /* possibly not enough memory, read/write by hyperslabs */
+								size_t p_type_nbytes = msize; /*size of memory type */
+								hsize_t p_nelmts = nelmts; /*total elements */
+								hsize_t elmtno; /*counter  */
+								int carry; /*counter carry value */
+								unsigned int vl_data = 0; /*contains VL datatypes */
+
+								/* hyperslab info */
+								hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
+								hsize_t hslab_nbytes; /*bytes per hyperslab */
+								hsize_t hslab_nelmts; /*elements per hyperslab*/
+								hid_t hslab_space; /*hyperslab data space */
+
+								/* hyperslab selection info */
+								hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
+								hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
+								hsize_t hs_select_nelmts; /* selected elements */
+								hsize_t zero[8]; /*vector of zeros */
+								int k;
+								H5D_layout_t dset_layout;
+								hid_t dcpl_tmp = -1; /* dataset creation property list ID */
+
+								/* check if we have VL data in the dataset's datatype */
+								if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+									vl_data = TRUE;
+
+								/* check first if writing dataset is chunked,
+								 * if so use its chunk layout for better performance. */
+								dset_layout = H5Pget_layout(dcpl_out);
+								if (dset_layout == H5D_CHUNKED)
+									dcpl_tmp = dcpl_out; /* writing dataset */
+								else { /* if reading dataset is chunked */
+									dset_layout = H5Pget_layout(dcpl_in);
+									if (dset_layout == H5D_CHUNKED)
+										dcpl_tmp = dcpl_in; /* reading dataset */
+								}
+
+								/* get hyperslab dims and size in byte */
+								if (Get_hyperslab(dcpl_tmp, rank, dims,
+										p_type_nbytes, hslab_dims,
+										&hslab_nbytes) < 0)
+									goto error;
+
+								hslab_buf = HDmalloc((size_t)hslab_nbytes);
+
+								hslab_nelmts = hslab_nbytes / p_type_nbytes;
+								hslab_space = H5Screate_simple(1, &hslab_nelmts,
+										NULL);
+
+								/* the hyperslab selection loop */
+								HDmemset(hs_sel_offset, 0,
+										sizeof hs_sel_offset);
+								HDmemset(zero, 0, sizeof zero);
+
+								for (elmtno = 0; elmtno < p_nelmts; elmtno +=
+										hs_select_nelmts) {
+									if (rank > 0) {
+										/* calculate the hyperslab selections. The selection would be same as the hyperslab except for remaining edge portion of the dataset which is smaller then the hyperslab.
+										 */
+										for (k = 0, hs_select_nelmts = 1;
+												k < rank; k++) {
+											/* MIN() is used to get the remaining edge portion if exist.
+											 * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
+											hs_sel_count[k] =
+													MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
+											hs_select_nelmts *= hs_sel_count[k];
+										}
+
+										if (H5Sselect_hyperslab(f_space_id,
+												H5S_SELECT_SET, hs_sel_offset,
+												NULL, hs_sel_count, NULL) < 0)
+											goto error;
+										if (H5Sselect_hyperslab(hslab_space,
+												H5S_SELECT_SET, zero, NULL,
+												&hs_select_nelmts, NULL) < 0)
+											goto error;
+									}
+									else {
+										H5Sselect_all(f_space_id);
+										H5Sselect_all(hslab_space);
+										hs_select_nelmts = 1;
+									} /* rank */
+
+									/* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
+									CHECK_H5DRW_ERROR(H5Dread, dset_in,
+											wtype_id, hslab_space, f_space_id,
+											H5P_DEFAULT, hslab_buf);
+									CHECK_H5DRW_ERROR(H5Dwrite, dset_out,
+											wtype_id, hslab_space, f_space_id,
+											H5P_DEFAULT, hslab_buf);
+
+									/* reclaim any VL memory, if necessary */
+									if (vl_data)
+										H5Dvlen_reclaim(wtype_id, hslab_space,
+												H5P_DEFAULT, hslab_buf);
+
+									/* calculate the next hyperslab offset */
+									for (k = rank, carry = 1; k > 0 && carry;
+											--k) {
+										hs_sel_offset[k - 1] += hs_sel_count[k
+												- 1];
+										/* if reached the end of a dim */
+										if (hs_sel_offset[k - 1] == dims[k - 1])
+											hs_sel_offset[k - 1] = 0;
+										else
+											carry = 0;
+									} /* k */
+								} /* elmtno */
+
+								H5Sclose(hslab_space);
+								/* free */
+								if (hslab_buf != NULL) {
+									HDfree(hslab_buf);
+									hslab_buf = NULL;
+								}
+							} /* hyperslab read */
+						} /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+
+						/*-------------------------------------------------------------------------
+						 * amount of compression used
+						 *-------------------------------------------------------------------------
+						 */
+						if (options->verbose) {
+							double ratio = 0;
+
+							/* only print the compression ration if there was a filter request */
+							if (apply_s && apply_f && req_filter) {
+								/* get the storage size of the output dataset */
+								dsize_out = H5Dget_storage_size(dset_out);
+
+								/* compression ratio = uncompressed size /  compressed size */
+								if (dsize_out != 0)
+									ratio = (double) dsize_in
+											/ (double) dsize_out;
+
+								print_dataset_info(dcpl_out,
+										travt->objs[i].name, ratio, 1);
+							}
+							else
+								print_dataset_info(dcpl_in, travt->objs[i].name,
+										ratio, 0);
+
+							/* print a message that the filter was not applied
+							 (in case there was a filter)
+							 */
+							if (has_filter && apply_s == 0)
+								printf(
+										" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
+										travt->objs[i].name,
+										(int) options->min_comp);
+
+							if (has_filter && apply_f == 0)
+								printf(
+										" <warning: could not apply the filter to %s>\n",
+										travt->objs[i].name);
+
+						} /* verbose */
+
+						/*-------------------------------------------------------------------------
+						 * copy attrs
+						 *-------------------------------------------------------------------------
+						 */
+						if (copy_attr(dset_in, dset_out, &named_dt_head, travt,
+								options) < 0)
+							goto error;
+						/*close */
+						if (H5Dclose(dset_out) < 0)
+							goto error;
+
+					}/*!H5T_REFERENCE*/
+				}/*h5tools_canreadf*/
+
+				/*-------------------------------------------------------------------------
+				 * close
+				 *-------------------------------------------------------------------------
+				 */
+				if (H5Tclose(ftype_id) < 0)
+					goto error;
+				if (H5Tclose(wtype_id) < 0)
+					goto error;
+				if (H5Pclose(dcpl_in) < 0)
+					goto error;
+				if (H5Pclose(dcpl_out) < 0)
+					goto error;
+				if (H5Sclose(f_space_id) < 0)
+					goto error;
+				if (H5Dclose(dset_in) < 0)
+					goto error;
+
+			}
+			/*-------------------------------------------------------------------------
+			 * we do not have request for filter/chunking use H5Ocopy instead
+			 *-------------------------------------------------------------------------
+			 */
+			else {
+				hid_t pid;
+
+				/* create property to pass copy options */
+				if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
+					goto error;
+
+				/* set options for object copy */
+				if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
+					goto error;
+
+				/*-------------------------------------------------------------------------
+				 * do the copy
+				 *-------------------------------------------------------------------------
+				 */
+
+				if (H5Ocopy(fidin, /* Source file or group identifier */
+				travt->objs[i].name, /* Name of the source object to be copied */
+				fidout, /* Destination file or group identifier  */
+				travt->objs[i].name, /* Name of the destination object  */
+				pid, /* Properties which apply to the copy   */
+				H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
+					goto error;
+
+				/* close property */
+				if (H5Pclose(pid) < 0)
+					goto error;
+
+				/*-------------------------------------------------------------------------
+				 * copy attrs manually
+				 *-------------------------------------------------------------------------
+				 */
+				if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+						< 0)
+					goto error;
+				if ((dset_out = H5Dopen2(fidout, travt->objs[i].name,
+						H5P_DEFAULT)) < 0)
+					goto error;
+				if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options)
+						< 0)
+					goto error;
+				if (H5Dclose(dset_in) < 0)
+					goto error;
+				if (H5Dclose(dset_out) < 0)
+					goto error;
+
+				if (options->verbose)
+					printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+
+			} /* end do we have request for filter/chunking */
+
+			break;
+
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_NAMED_DATATYPE
+			 *-------------------------------------------------------------------------
+			 */
+		case H5TRAV_TYPE_NAMED_DATATYPE:
+
+			if (options->verbose)
+				printf(FORMAT_OBJ, "type", travt->objs[i].name);
+
+			if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT))
+					< 0)
+				goto error;
+
+			/* Copy the datatype anonymously */
+			if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head,
+					travt, options)) < 0)
+				goto error;
+
+			/* Link in to group structure */
+			if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name,
+			H5P_DEFAULT, H5P_DEFAULT) < 0)
+				goto error;
+
+			/*-------------------------------------------------------------------------
+			 * copy attrs
+			 *-------------------------------------------------------------------------
+			 */
+			if (copy_attr(type_in, type_out, &named_dt_head, travt, options)
+					< 0)
+				goto error;
+
+			if (H5Tclose(type_in) < 0)
+				goto error;
+			if (H5Tclose(type_out) < 0)
+				goto error;
+
+			break;
+
+			/*-------------------------------------------------------------------------
+			 * H5TRAV_TYPE_LINK
+			 * H5TRAV_TYPE_UDLINK
+			 *
+			 * Only handles external links; H5Lcopy will fail for other UD link types
+			 * since we don't have creation or copy callbacks for them.
+			 *-------------------------------------------------------------------------
+			 */
+
+		case H5TRAV_TYPE_LINK:
+		case H5TRAV_TYPE_UDLINK: {
+
+			if (options->verbose)
+				printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+			if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name,
+					H5P_DEFAULT, H5P_DEFAULT) < 0)
+				goto error;
+
+			if (options->verbose)
+				printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
+		}
+			break;
+
+		default:
+			goto error;
+		} /* switch */
+
+		/* free */
+		if (buf != NULL) {
+			HDfree(buf);
+			buf = NULL;
+		}
+
+	} /* i */
+
+	/* Finalize (link) the stack of named datatypes (if any) */
+	named_datatype_free(&named_dt_head, 0);
+
+	return 0;
 
 error:
-    H5E_BEGIN_TRY {
-        H5Gclose(grp_in);
-        H5Gclose(grp_out);
-        H5Pclose(dcpl_in);
-        H5Pclose(gcpl_in);
-        H5Pclose(gcpl_out);
-        H5Sclose(f_space_id);
-        H5Dclose(dset_in);
-        H5Dclose(dset_out);
-        H5Tclose(ftype_id);
-        H5Tclose(wtype_id);
-        H5Tclose(type_in);
-        H5Tclose(type_out);
-        named_datatype_free(&named_dt_head, 1);
-    } H5E_END_TRY;
-    /* free */
-    if (buf!=NULL)
-        HDfree(buf);
-    if (hslab_buf!=NULL)
-        HDfree(hslab_buf);
-    return -1;
+	H5E_BEGIN_TRY
+		{
+			H5Gclose(grp_in);
+			H5Gclose(grp_out);
+			H5Pclose(dcpl_in);
+			H5Pclose(gcpl_in);
+			H5Pclose(gcpl_out);
+			H5Sclose(f_space_id);
+			H5Dclose(dset_in);
+			H5Dclose(dset_out);
+			H5Tclose(ftype_id);
+			H5Tclose(wtype_id);
+			H5Tclose(type_in);
+			H5Tclose(type_out);
+			named_datatype_free(&named_dt_head, 1);
+		}H5E_END_TRY;
+	/* free */
+	if (buf != NULL)
+		HDfree(buf);
+	if (hslab_buf != NULL)
+		HDfree(hslab_buf);
+	return -1;
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: print_dataset_info
-*
-* Purpose: print name, filters, percentage compression of a dataset
-*
-*-------------------------------------------------------------------------
-*/
-static void print_dataset_info(hid_t dcpl_id,
-                               char *objname,
-                               double ratio,
-                               int pr)
-{
-    char         strfilter[255];
+ * Function: print_dataset_info
+ *
+ * Purpose: print name, filters, percentage compression of a dataset
+ *
+ *-------------------------------------------------------------------------
+ */
+static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio,
+		int pr) {
+	char strfilter[255];
 #if defined (PRINT_DEBUG )
-    char         temp[255];
+	char temp[255];
 #endif
-    int          nfilters;       /* number of filters */
-    unsigned     filt_flags;     /* filter flags */
-    H5Z_filter_t filtn;          /* filter identification number */
-    unsigned     cd_values[20];  /* filter client data values */
-    size_t       cd_nelmts;      /* filter client number of values */
-    char         f_objname[256];    /* filter objname */
-    int          i;
-
+	int nfilters; /* number of filters */
+	unsigned filt_flags; /* filter flags */
+	H5Z_filter_t filtn; /* filter identification number */
+	unsigned cd_values[20]; /* filter client data values */
+	size_t cd_nelmts; /* filter client number of values */
+	char f_objname[256]; /* filter objname */
+	int i;
 
-    HDstrcpy(strfilter,"\0");
+	HDstrcpy(strfilter, "\0");
 
-    /* get information about input filters */
-    if((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
-        return;
+	/* get information about input filters */
+	if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
+		return;
 
-    for(i = 0; i < nfilters; i++) {
-        cd_nelmts = NELMTS(cd_values);
+	for (i = 0; i < nfilters; i++) {
+		cd_nelmts = NELMTS(cd_values);
 
-        filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
-            cd_values, sizeof(f_objname), f_objname, NULL);
+		filtn = H5Pget_filter2(dcpl_id, (unsigned) i, &filt_flags, &cd_nelmts,
+				cd_values, sizeof(f_objname), f_objname, NULL);
 
-        switch(filtn) {
+		switch (filtn) {
 
-        case H5Z_FILTER_NONE:
-            HDstrcat(strfilter,"NONE ");
-            break;
+		case H5Z_FILTER_NONE:
+			HDstrcat(strfilter, "NONE ");
+			break;
 
-        case H5Z_FILTER_DEFLATE:
-            HDstrcat(strfilter,"GZIP ");
+		case H5Z_FILTER_DEFLATE:
+			HDstrcat(strfilter, "GZIP ");
 
 #if defined (PRINT_DEBUG)
-            {
-                unsigned level=cd_values[0];
-                sprintf(temp,"(%d)",level);
-                HDstrcat(strfilter,temp);
-            }
+			{
+				unsigned level=cd_values[0];
+				sprintf(temp,"(%d)",level);
+				HDstrcat(strfilter,temp);
+			}
 #endif
-            break;
+			break;
 
-        case H5Z_FILTER_SZIP:
-            HDstrcat(strfilter,"SZIP ");
+		case H5Z_FILTER_SZIP:
+			HDstrcat(strfilter, "SZIP ");
 
 #if defined (PRINT_DEBUG)
-            {
-                unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
-                unsigned ppb=cd_values[1];
-                sprintf(temp,"(%d,",ppb);
-                HDstrcat(strfilter,temp);
-                if (options_mask & H5_SZIP_EC_OPTION_MASK)
-                    HDstrcpy(temp,"EC) ");
-                else if (options_mask & H5_SZIP_NN_OPTION_MASK)
-                    HDstrcpy(temp,"NN) ");
-            }
-            HDstrcat(strfilter,temp);
+			{
+				unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
+				unsigned ppb=cd_values[1];
+				sprintf(temp,"(%d,",ppb);
+				HDstrcat(strfilter,temp);
+				if (options_mask & H5_SZIP_EC_OPTION_MASK)
+				HDstrcpy(temp,"EC) ");
+				else if (options_mask & H5_SZIP_NN_OPTION_MASK)
+				HDstrcpy(temp,"NN) ");
+			}
+			HDstrcat(strfilter,temp);
 
 #endif
 
-            break;
-
-        case H5Z_FILTER_SHUFFLE:
-            HDstrcat(strfilter,"SHUF ");
-            break;
-
-        case H5Z_FILTER_FLETCHER32:
-            HDstrcat(strfilter,"FLET ");
-            break;
-
-        case H5Z_FILTER_NBIT:
-            HDstrcat(strfilter,"NBIT ");
-            break;
-
-        case H5Z_FILTER_SCALEOFFSET:
-            HDstrcat(strfilter,"SCALEOFFSET ");
-            break;
-
-        default:
-            HDstrcat(strfilter,"UD ");
-            break;
-        } /* switch */
-    }/*i*/
-
-    if(!pr)
-        printf(FORMAT_OBJ,"dset",objname );
-    else
-    {
-        char str[255], temp[28];
-        HDstrcpy(str,"dset     ");
-        HDstrcat(str,strfilter);
-        sprintf(temp,"  (%.3f:1)",ratio);
-        HDstrcat(str,temp);
-        printf(FORMAT_OBJ,str,objname);
-    }
+			break;
+
+		case H5Z_FILTER_SHUFFLE:
+			HDstrcat(strfilter, "SHUF ");
+			break;
+
+		case H5Z_FILTER_FLETCHER32:
+			HDstrcat(strfilter, "FLET ");
+			break;
+
+		case H5Z_FILTER_NBIT:
+			HDstrcat(strfilter, "NBIT ");
+			break;
+
+		case H5Z_FILTER_SCALEOFFSET:
+			HDstrcat(strfilter, "SCALEOFFSET ");
+			break;
+
+		default:
+			HDstrcat(strfilter, "UD ");
+			break;
+		} /* switch */
+	}/*i*/
+
+	if (!pr)
+		printf(FORMAT_OBJ, "dset", objname);
+	else {
+		char str[255], temp[28];
+		HDstrcpy(str, "dset     ");
+		HDstrcat(str, strfilter);
+		sprintf(temp, "  (%.3f:1)", ratio);
+		HDstrcat(str, temp);
+		printf(FORMAT_OBJ, str, objname);
+	}
 }
 
-
 /*-------------------------------------------------------------------------
-* Function: copy_user_block
-*
-* Purpose: copy user block from one file to another
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Peter Cao
-*
-* Date: October, 25, 2007
-*
-*-------------------------------------------------------------------------
-*/
-static int
-copy_user_block(const char *infile, const char *outfile, hsize_t size)
-{
-    int infid = -1, outfid = -1;        /* File descriptors */
-    int status = 0;                     /* Return value */
-
-    /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
-    HDassert(size > 0);
-
-    /* Open files */
-    if((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
-        status = -1;
-        goto done;
-    }
-    if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
-        status = -1;
-        goto done;
-    }
-
-    /* Copy the userblock from the input file to the output file */
-    while(size > 0) {
-        ssize_t nread, nbytes;                  /* # of bytes transfered, etc. */
-        char rbuf[USERBLOCK_XFER_SIZE];         /* Buffer for reading */
-        const char *wbuf;                       /* Pointer into buffer, for writing */
-
-        /* Read buffer from source file */
-        if(size > USERBLOCK_XFER_SIZE)
-            nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
-        else
-            nread = HDread(infid, rbuf, (size_t)size);
-        if(nread < 0) {
-            status = -1;
-            goto done;
-        } /* end if */
-
-        /* Write buffer to destination file */
-        /* (compensating for interrupted writes & checking for errors, etc.) */
-        nbytes = nread;
-        wbuf = rbuf;
-        while(nbytes > 0) {
-            ssize_t nwritten;        /* # of bytes written */
-
-            do {
-                nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
-            } while(-1 == nwritten && EINTR == errno);
-            if(-1 == nwritten) { /* error */
-                status = -1;
-                goto done;
-            } /* end if */
-            HDassert(nwritten > 0);
-            HDassert(nwritten <= nbytes);
-
-            /* Update # of bytes left & offset in buffer */
-            nbytes -= nwritten;
-            wbuf += nwritten;
-            HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
-        } /* end while */
-
-        /* Update size of userblock left to transfer */
-        size = size - (hsize_t)nread;
-    } /* end while */
+ * Function: copy_user_block
+ *
+ * Purpose: copy user block from one file to another
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Peter Cao
+ *
+ * Date: October, 25, 2007
+ *
+ *-------------------------------------------------------------------------
+ */
+static int copy_user_block(const char *infile, const char *outfile,
+		hsize_t size) {
+	int infid = -1, outfid = -1; /* File descriptors */
+	int status = 0; /* Return value */
+
+	/* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
+	HDassert(size > 0);
+
+	/* Open files */
+	if ((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
+		status = -1;
+		goto done;
+	}
+	if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
+		status = -1;
+		goto done;
+	}
+
+	/* Copy the userblock from the input file to the output file */
+	while (size > 0) {
+		ssize_t nread, nbytes; /* # of bytes transfered, etc. */
+		char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */
+		const char *wbuf; /* Pointer into buffer, for writing */
+
+		/* Read buffer from source file */
+		if (size > USERBLOCK_XFER_SIZE)
+			nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+		else
+			nread = HDread(infid, rbuf, (size_t)size);
+		if (nread < 0) {
+			status = -1;
+			goto done;
+		} /* end if */
+
+		/* Write buffer to destination file */
+		/* (compensating for interrupted writes & checking for errors, etc.) */
+		nbytes = nread;
+		wbuf = rbuf;
+		while (nbytes > 0) {
+			ssize_t nwritten; /* # of bytes written */
+
+			do {
+				nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
+			} while (-1 == nwritten && EINTR == errno);
+			if (-1 == nwritten) { /* error */
+				status = -1;
+				goto done;
+			} /* end if */
+			HDassert(nwritten > 0);
+			HDassert(nwritten <= nbytes);
+
+			/* Update # of bytes left & offset in buffer */
+			nbytes -= nwritten;
+			wbuf += nwritten;
+			HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
+		} /* end while */
+
+		/* Update size of userblock left to transfer */
+		size = size - (hsize_t) nread;
+	} /* end while */
 
 done:
-    if(infid > 0)
-        HDclose(infid);
-    if(outfid > 0)
-        HDclose(outfid);
+	if (infid > 0)
+		HDclose(infid);
+	if (outfid > 0)
+		HDclose(outfid);
 
-    return status;
+	return status;
 }
 
-
-
 /*-------------------------------------------------------------------------
-* Function: print_user_block
-*
-* Purpose: print user block
-*
-* Return: 0, ok, -1 no
-*
-* Programmer: Pedro Vicente
-*
-* Date: August, 20, 2008
-*
-*-------------------------------------------------------------------------
-*/
+ * Function: print_user_block
+ *
+ * Purpose: print user block
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente
+ *
+ * Date: August, 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
 static
 void print_user_block(const char *filename, hid_t fid)
 {
-    int     fh;      /* file handle  */
-    hsize_t ub_size; /* user block size */
-    hsize_t size;    /* size read */
-    hid_t   fcpl;    /* file creation property list ID for HDF5 file */
-    int     i;
-
-    /* get user block size */
-    if(( fcpl = H5Fget_create_plist(fid)) < 0)
-    {
-        error_msg("failed to retrieve file creation property list\n");
-        goto done;
-    }
-
-    if(H5Pget_userblock(fcpl, &ub_size) < 0)
-    {
-        error_msg("failed to retrieve userblock size\n");
-        goto done;
-    }
-
-    if(H5Pclose(fcpl) < 0)
-    {
-        error_msg("failed to close property list\n");
-        goto done;
-    }
-
-    /* open file */
-    if((fh = HDopen(filename, O_RDONLY, 0)) < 0)
-    {
-        goto done;
-    }
-
-    size = ub_size;
-
-    /* read file */
-    while(size > 0)
-    {
-        ssize_t nread;                  /* # of bytes read */
-        char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
-
-        /* read buffer */
-        if(size > USERBLOCK_XFER_SIZE)
-            nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
-        else
-            nread = HDread(fh, rbuf, (size_t)size);
-
-        for(i = 0; i < nread; i++)
-        {
-
-            printf("%c ", rbuf[i]);
-
-        }
-        printf("\n");
-
-        if(nread < 0)
-        {
-            goto done;
-        }
-
-
-        /* update size of userblock left to transfer */
-        size -= nread;
-    }
+	int fh; /* file handle  */
+	hsize_t ub_size; /* user block size */
+	hsize_t size; /* size read */
+	hid_t fcpl; /* file creation property list ID for HDF5 file */
+	int i;
 
-done:
-    if(fh > 0)
-        HDclose(fh);
+	/* get user block size */
+	if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+		error_msg("failed to retrieve file creation property list\n");
+		goto done;
+	}
+
+	if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+		error_msg("failed to retrieve userblock size\n");
+		goto done;
+	}
+
+	if(H5Pclose(fcpl) < 0) {
+		error_msg("failed to close property list\n");
+		goto done;
+	}
+
+	/* open file */
+	if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
+		goto done;
+	}
 
+	size = ub_size;
+
+	/* read file */
+	while(size > 0) {
+		ssize_t nread; /* # of bytes read */
+		char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+
+		/* read buffer */
+		if(size > USERBLOCK_XFER_SIZE)
+			nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+		else
+			nread = HDread(fh, rbuf, (size_t)size);
+
+		for(i = 0; i < nread; i++) {
+
+			printf("%c ", rbuf[i]);
+
+		}
+		printf("\n");
+
+		if(nread < 0) {
+			goto done;
+		}
+
+		/* update size of userblock left to transfer */
+		size -= nread;
+	}
+
+done:
+	if(fh > 0)
+		HDclose(fh);
 
-    return;
+	return;
 }
 #endif
 
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index b5f9d31..7af776d 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -20,267 +20,345 @@
 /* Name of tool */
 #define PROGRAMNAME "h5repack"
 
-static void usage(const char *prog);
-static void parse_command_line(int argc, const char **argv, pack_opt_t* options);
-static void read_info(const char *filename,pack_opt_t *options);
-
+static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
 
 /* module-scoped variables */
-static int  has_i_o = 0;
-const char  *infile  = NULL;
-const char  *outfile = NULL;
-
+static int has_i_o = 0;
+const char *infile = NULL;
+const char *outfile = NULL;
 
 /*
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
 static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:T:";
-static struct long_options l_opts[] = {
-    { "help", no_arg, 'h' },
-    { "version", no_arg, 'V' },
-    { "verbose", no_arg, 'v' },
-    { "filter", require_arg, 'f' },
-    { "layout", require_arg, 'l' },
-    { "minimum", require_arg, 'm' },
-    { "file", require_arg, 'e' },
-    { "native", no_arg, 'n' },
-    { "latest", no_arg, 'L' },
-    { "compact", require_arg, 'c' },
-    { "indexed", require_arg, 'd' },
-    { "ssize", require_arg, 's' },
-    { "ublock", require_arg, 'u' },
-    { "block", require_arg, 'b' },
-    { "metadata_block_size", require_arg, 'M' },
-    { "threshold", require_arg, 't' },
-    { "alignment", require_arg, 'a' },
-    { "infile", require_arg, 'i' },   /* -i for backward compability */
-    { "outfile", require_arg, 'o' },  /* -o for backward compability */
-    { "fs_strategy", require_arg, 'S' },
-    { "fs_threshold", require_arg, 'T' },
-    { NULL, 0, '\0' }
-};
-
-
-
+static struct long_options l_opts[] = { { "help", no_arg, 'h' }, { "version",
+		no_arg, 'V' }, { "verbose", no_arg, 'v' },
+		{ "filter", require_arg, 'f' }, { "layout", require_arg, 'l' }, {
+				"minimum", require_arg, 'm' }, { "file", require_arg, 'e' }, {
+				"native", no_arg, 'n' }, { "latest", no_arg, 'L' }, { "compact",
+				require_arg, 'c' }, { "indexed", require_arg, 'd' }, { "ssize",
+				require_arg, 's' }, { "ublock", require_arg, 'u' }, { "block",
+				require_arg, 'b' }, { "metadata_block_size", require_arg, 'M' },
+		{ "threshold", require_arg, 't' }, { "alignment", require_arg, 'a' }, {
+				"infile", require_arg, 'i' }, /* -i for backward compability */
+		{ "outfile", require_arg, 'o' }, /* -o for backward compability */
+		{ "fs_strategy", require_arg, 'S' },
+		{ "fs_threshold", require_arg, 'T' }, { NULL, 0, '\0' } };
 
 /*-------------------------------------------------------------------------
- * Function: main
+ * Function: usage
  *
- * Purpose: h5repack main program
+ * Purpose: print usage
  *
- * Return: Success: EXIT_SUCCESS(0)
+ * Return: void
  *
- * Failure: EXIT_FAILURE(1)
+ *-------------------------------------------------------------------------
+ */
+static void usage(const char *prog) {
+	printf("usage: %s [OPTIONS] file1 file2\n", prog);
+	printf("  file1                    Input HDF5 File\n");
+	printf("  file2                    Output HDF5 File\n");
+	printf("  OPTIONS\n");
+	printf("   -h, --help              Print a usage message and exit\n");
+	printf(
+			"   -v, --verbose           Verbose mode, print object information\n");
+	printf("   -V, --version           Print version number and exit\n");
+	printf(
+			"   -n, --native            Use a native HDF5 type when repacking\n");
+	printf("   -L, --latest            Use latest version of file format\n");
+	printf(
+			"   -c L1, --compact=L1     Maximum number of links in header messages\n");
+	printf(
+			"   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
+	printf(
+			"   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
+	printf(
+			"   -m M, --minimum=M       Do not apply the filter to datasets smaller than M\n");
+	printf(
+			"   -e E, --file=E          Name of file E with the -f and -l options\n");
+	printf(
+			"   -u U, --ublock=U        Name of file U with user block data to be added\n");
+	printf("   -b B, --block=B         Size of user block to be added\n");
+	printf(
+			"   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
+	printf("   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
+	printf("   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
+	printf("   -f FILT, --filter=FILT  Filter type\n");
+	printf("   -l LAYT, --layout=LAYT  Layout type\n");
+	printf(
+			"   -S FS_STRGY, --fs_strategy=FS_STRGY  File space management strategy\n");
+	printf(
+			"   -T FS_THRD, --fs_threshold=FS_THRD   Free-space section threshold\n");
+
+	printf("\n");
+
+	printf(
+			"    M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
+	printf("    E - is a filename.\n");
+	printf("    S - is an integer\n");
+	printf("    U - is a filename.\n");
+	printf("    T - is an integer\n");
+	printf("    A - is an integer greater than zero\n");
+	printf(
+			"    B - is the user block size, any value that is 512 or greater and is\n");
+	printf("        a power of 2 (1024 default)\n");
+	printf(
+			"    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
+	printf(
+			"        pline|attr>. If F is not specified, S applies to all messages\n");
+	printf("\n");
+	printf(
+			"    FS_STRGY is the file space management strategy to use for the output file.\n");
+	printf("             It is a string as listed below:\n");
+	printf(
+			"        ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
+	printf("                      for file space allocation\n");
+	printf(
+			"        ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
+	printf("              for file space allocation\n");
+	printf(
+			"        AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
+	printf("        VFD - Use virtual file driver for file space allocation\n");
+	printf("\n");
+	printf(
+			"    FS_THRD is the free-space section threshold to use for the output file.\n");
+	printf(
+			"            It is the minimum size (in bytes) of free-space sections to be tracked\n");
+	printf("            by the the library's free-space managers.\n");
+	printf("\n");
+
+	printf("    FILT - is a string with the format:\n");
+	printf("\n");
+	printf("      <list of objects>:<name of filter>=<filter parameters>\n");
+	printf("\n");
+	printf(
+			"      <list of objects> is a comma separated list of object names, meaning apply\n");
+	printf(
+			"        compression only to those objects. If no names are specified, the filter\n");
+	printf("        is applied to all objects\n");
+	printf("      <name of filter> can be:\n");
+	printf("        GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+	printf("        SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+	printf("        SHUF, to apply the HDF5 shuffle filter\n");
+	printf("        FLET, to apply the HDF5 checksum filter\n");
+	printf("        NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+	printf("        SOFF, to apply the HDF5 Scale/Offset filter\n");
+	printf("        UD,   to apply a user defined filter\n");
+	printf("        NONE, to remove all filters\n");
+	printf(
+			"      <filter parameters> is optional filter parameter information\n");
+	printf("        GZIP=<deflation level> from 1-9\n");
+	printf(
+			"        SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+	printf("            2-32 and coding method is either EC or NN\n");
+	printf("        SHUF (no parameter)\n");
+	printf("        FLET (no parameter)\n");
+	printf("        NBIT (no parameter)\n");
+	printf(
+			"        SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
+	printf("            is either IN or DS\n");
+	printf(
+			"        UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
+	printf(
+			"            required values for filter_number,cd_value_count,value_1\n");
+	printf("            optional values for value_2 to value_N\n");
+	printf("        NONE (no parameter)\n");
+	printf("\n");
+	printf("    LAYT - is a string with the format:\n");
+	printf("\n");
+	printf("      <list of objects>:<layout type>=<layout parameters>\n");
+	printf("\n");
+	printf(
+			"      <list of objects> is a comma separated list of object names, meaning that\n");
+	printf(
+			"        layout information is supplied for those objects. If no names are\n");
+	printf("        specified, the layout type is applied to all objects\n");
+	printf("      <layout type> can be:\n");
+	printf("        CHUNK, to apply chunking layout\n");
+	printf("        COMPA, to apply compact layout\n");
+	printf("        CONTI, to apply contiguous layout\n");
+	printf("      <layout parameters> is optional layout information\n");
+	printf(
+			"        CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+	printf("        COMPA (no parameter)\n");
+	printf("        CONTI (no parameter)\n");
+	printf("\n");
+	printf("Examples of use:\n");
+	printf("\n");
+	printf("1) h5repack -v -f GZIP=1 file1 file2\n");
+	printf("\n");
+	printf("   GZIP compression with level 1 to all objects\n");
+	printf("\n");
+	printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
+	printf("\n");
+	printf(
+			"   SZIP compression with 8 pixels per block and NN coding method to object A\n");
+	printf("\n");
+	printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
+	printf("\n");
+	printf(
+			"   Chunked layout, with a layout size of 20x10, to objects A and B\n");
+	printf("   and remove filters to objects C, D, F\n");
+	printf("\n");
+	printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
+	printf("\n");
+	printf(
+			"   Using latest file format with maximum compact group size of 10 and\n");
+	printf("   and minimum shared datatype size of 20\n");
+	printf("\n");
+	printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
+	printf("\n");
+	printf("   Add both filters SHUF and GZIP in this order to all datasets\n");
+	printf("\n");
+	printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
+	printf("\n");
+	printf("   Add bzip2 filter to all datasets\n");
+	printf("\n");
+}
+
+/*-------------------------------------------------------------------------
+ * Function:    leave
  *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ * Purpose:     Shutdown MPI & HDF5 and call exit()
  *
- * Date: May 9, 2003
+ * Return:      Does not return
  *
- * Comments:
+ * Programmer:  Quincey Koziol
+ *              Saturday, 31. January 2004
+ *
+ * Modifications:
  *
  *-------------------------------------------------------------------------
  */
-int main(int argc, const char **argv)
-{
-
-    pack_opt_t    options;            /*the global options */
-    int           ret=-1;
-
-    h5tools_setprogname(PROGRAMNAME);
-    h5tools_setstatus(EXIT_SUCCESS);
-
-    /* Initialize h5tools lib */
-    h5tools_init();
-
-    /* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
-    if ( h5tools_getenv_update_hyperslab_bufsize() < 0)
-        HDexit(EXIT_FAILURE);
-
-    /* initialize options  */
-    h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (hsize_t)0);
-
-    parse_command_line(argc, argv, &options);
-
-    /* get file names if they were not yet got */
-    if ( has_i_o == 0 )
-    {
-
-        if ( argv[ opt_ind ] != NULL && argv[ opt_ind + 1 ] != NULL )
-        {
-            infile = argv[ opt_ind ];
-            outfile = argv[ opt_ind + 1 ];
-
-            if ( HDstrcmp( infile, outfile ) == 0 )
-            {
-                error_msg("file names cannot be the same\n");
-                usage(h5tools_getprogname());
-                HDexit(EXIT_FAILURE);
-
-            }
-        }
-
-        else
-        {
-            error_msg("file names missing\n");
-            usage(h5tools_getprogname());
-            HDexit(EXIT_FAILURE);
-        }
-    }
-
-
-    /* pack it */
-    ret=h5repack(infile,outfile,&options);
+static void leave(int ret) {
+	h5tools_close();
 
-    /* free tables */
-    h5repack_end(&options);
-
-    if (ret==-1)
-        return 1;
-    else
-        return 0;
+	HDexit(ret);
 }
 
-
-
 /*-------------------------------------------------------------------------
- * Function: usage
+ * Function: read_info
  *
- * Purpose: print usage
+ * Purpose: read comp and chunk options from a file
  *
- * Return: void
+ * Return: void, exit on error
+ *
+ * Programmer: pvn@ncsa.uiuc.edu
+ *
+ * Date: September, 22, 2003
  *
  *-------------------------------------------------------------------------
  */
-static void usage(const char *prog)
-{
- printf("usage: %s [OPTIONS] file1 file2\n", prog);
- printf("  file1                    Input HDF5 File\n");
- printf("  file2                    Output HDF5 File\n");
- printf("  OPTIONS\n");
- printf("   -h, --help              Print a usage message and exit\n");
- printf("   -v, --verbose           Verbose mode, print object information\n");
- printf("   -V, --version           Print version number and exit\n");
- printf("   -n, --native            Use a native HDF5 type when repacking\n");
- printf("   -L, --latest            Use latest version of file format\n");
- printf("   -c L1, --compact=L1     Maximum number of links in header messages\n");
- printf("   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
- printf("   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
- printf("   -m M, --minimum=M       Do not apply the filter to datasets smaller than M\n");
- printf("   -e E, --file=E          Name of file E with the -f and -l options\n");
- printf("   -u U, --ublock=U        Name of file U with user block data to be added\n");
- printf("   -b B, --block=B         Size of user block to be added\n");
- printf("   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
- printf("   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
- printf("   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
- printf("   -f FILT, --filter=FILT  Filter type\n");
- printf("   -l LAYT, --layout=LAYT  Layout type\n");
- printf("   -S FS_STRGY, --fs_strategy=FS_STRGY  File space management strategy\n");
- printf("   -T FS_THRD, --fs_threshold=FS_THRD   Free-space section threshold\n");
-
- printf("\n");
-
- printf("    M - is an integer greater than 1, size of dataset in bytes (default is 0) \n");
- printf("    E - is a filename.\n");
- printf("    S - is an integer\n");
- printf("    U - is a filename.\n");
- printf("    T - is an integer\n");
- printf("    A - is an integer greater than zero\n");
- printf("    B - is the user block size, any value that is 512 or greater and is\n");
- printf("        a power of 2 (1024 default)\n");
- printf("    F - is the shared object header message type, any of <dspace|dtype|fill|\n");
- printf("        pline|attr>. If F is not specified, S applies to all messages\n");
- printf("\n");
- printf("    FS_STRGY is the file space management strategy to use for the output file.\n");
- printf("             It is a string as listed below:\n");
- printf("        ALL_PERSIST - Use persistent free-space managers, aggregators and virtual file driver\n");
- printf("                      for file space allocation\n");
- printf("        ALL - Use non-persistent free-space managers, aggregators and virtual file driver\n");
- printf("              for file space allocation\n");
- printf("        AGGR_VFD - Use aggregators and virtual file driver for file space allocation\n");
- printf("        VFD - Use virtual file driver for file space allocation\n");
- printf("\n");
- printf("    FS_THRD is the free-space section threshold to use for the output file.\n");
- printf("            It is the minimum size (in bytes) of free-space sections to be tracked\n");
- printf("            by the the library's free-space managers.\n");
- printf("\n");
-
- printf("    FILT - is a string with the format:\n");
- printf("\n");
- printf("      <list of objects>:<name of filter>=<filter parameters>\n");
- printf("\n");
- printf("      <list of objects> is a comma separated list of object names, meaning apply\n");
- printf("        compression only to those objects. If no names are specified, the filter\n");
- printf("        is applied to all objects\n");
- printf("      <name of filter> can be:\n");
- printf("        GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
- printf("        SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
- printf("        SHUF, to apply the HDF5 shuffle filter\n");
- printf("        FLET, to apply the HDF5 checksum filter\n");
- printf("        NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
- printf("        SOFF, to apply the HDF5 Scale/Offset filter\n");
- printf("        UD,   to apply a user defined filter\n");
- printf("        NONE, to remove all filters\n");
- printf("      <filter parameters> is optional filter parameter information\n");
- printf("        GZIP=<deflation level> from 1-9\n");
- printf("        SZIP=<pixels per block,coding> pixels per block is a even number in\n");
- printf("            2-32 and coding method is either EC or NN\n");
- printf("        SHUF (no parameter)\n");
- printf("        FLET (no parameter)\n");
- printf("        NBIT (no parameter)\n");
- printf("        SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
- printf("            is either IN or DS\n");
- printf("        UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>\n");
- printf("            required values for filter_number,cd_value_count,value_1\n");
- printf("            optional values for value_2 to value_N\n");
- printf("        NONE (no parameter)\n");
- printf("\n");
- printf("    LAYT - is a string with the format:\n");
- printf("\n");
- printf("      <list of objects>:<layout type>=<layout parameters>\n");
- printf("\n");
- printf("      <list of objects> is a comma separated list of object names, meaning that\n");
- printf("        layout information is supplied for those objects. If no names are\n");
- printf("        specified, the layout type is applied to all objects\n");
- printf("      <layout type> can be:\n");
- printf("        CHUNK, to apply chunking layout\n");
- printf("        COMPA, to apply compact layout\n");
- printf("        CONTI, to apply contiguous layout\n");
- printf("      <layout parameters> is optional layout information\n");
- printf("        CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
- printf("        COMPA (no parameter)\n");
- printf("        CONTI (no parameter)\n");
- printf("\n");
- printf("Examples of use:\n");
- printf("\n");
- printf("1) h5repack -v -f GZIP=1 file1 file2\n");
- printf("\n");
- printf("   GZIP compression with level 1 to all objects\n");
- printf("\n");
- printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
- printf("\n");
- printf("   SZIP compression with 8 pixels per block and NN coding method to object A\n");
- printf("\n");
- printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
- printf("\n");
- printf("   Chunked layout, with a layout size of 20x10, to objects A and B\n");
- printf("   and remove filters to objects C, D, F\n");
- printf("\n");
- printf("4) h5repack -L -c 10 -s 20:dtype file1 file2 \n");
- printf("\n");
- printf("   Using latest file format with maximum compact group size of 10 and\n");
- printf("   and minimum shared datatype size of 20\n");
- printf("\n");
- printf("5) h5repack -f SHUF -f GZIP=1 file1 file2 \n");
- printf("\n");
- printf("   Add both filters SHUF and GZIP in this order to all datasets\n");
- printf("\n");
- printf("6) h5repack -f UD=307,1,9 file1 file2 \n");
- printf("\n");
- printf("   Add bzip2 filter to all datasets\n");
- printf("\n");
-}
 
+static
+int read_info(const char *filename, pack_opt_t *options) {
+
+	char stype[10];
+	char comp_info[1024];
+	FILE *fp = NULL;
+	char c;
+	int i, rc = 1;
+	int ret_value = EXIT_SUCCESS;
+
+	if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+		error_msg("cannot open options file %s\n", filename);
+		h5tools_setstatus(EXIT_FAILURE);
+		ret_value = EXIT_FAILURE;
+		goto done;
+	}
+
+	/* cycle until end of file reached */
+	while (1) {
+		rc = fscanf(fp, "%s", stype);
+		if (rc == -1)
+			break;
+
+		/*-------------------------------------------------------------------------
+		 * filter
+		 *-------------------------------------------------------------------------
+		 */
+		if (HDstrcmp(stype,"-f") == 0) {
+			/* find begining of info */
+			i = 0;
+			c = '0';
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				if (HDfeof(fp))
+					break;
+			}
+			c = '0';
+			/* go until end */
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				comp_info[i] = c;
+				i++;
+				if (HDfeof(fp))
+					break;
+				if (c == 10 /*eol*/)
+					break;
+			}
+			comp_info[i - 1] = '\0'; /*cut the last " */
+
+			if (h5repack_addfilter(comp_info, options) == -1) {
+				error_msg("could not add compression option\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = EXIT_FAILURE;
+				goto done;
+			}
+		}
+		/*-------------------------------------------------------------------------
+		 * layout
+		 *-------------------------------------------------------------------------
+		 */
+		else if (HDstrcmp(stype,"-l") == 0) {
+
+			/* find begining of info */
+			i = 0;
+			c = '0';
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				if (HDfeof(fp))
+					break;
+			}
+			c = '0';
+			/* go until end */
+			while (c != ' ') {
+				fscanf(fp, "%c", &c);
+				comp_info[i] = c;
+				i++;
+				if (HDfeof(fp))
+					break;
+				if (c == 10 /*eol*/)
+					break;
+			}
+			comp_info[i - 1] = '\0'; /*cut the last " */
+
+			if (h5repack_addlayout(comp_info, options) == -1) {
+				error_msg("could not add chunck option\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = EXIT_FAILURE;
+				goto done;
+			}
+		}
+		/*-------------------------------------------------------------------------
+		 * not valid
+		 *-------------------------------------------------------------------------
+		 */
+		else {
+			error_msg("bad file format for %s", filename);
+			h5tools_setstatus(EXIT_FAILURE);
+			ret_value = EXIT_FAILURE;
+			goto done;
+		}
+	}
+
+done:
+	if (fp)
+		HDfclose(fp);
+
+	return ret_value;
+}
 
 /*-------------------------------------------------------------------------
  * Function: parse_command_line
@@ -291,316 +369,275 @@ static void usage(const char *prog)
  */
 
 static
-void parse_command_line(int argc, const char **argv, pack_opt_t* options)
-{
-
-    int opt;
-
-    /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
-    {
-        switch ((char)opt)
-        {
-
-        /* -i for backward compability */
-        case 'i':
-            infile = opt_arg;
-            has_i_o = 1;
-            break;
-        /* -o for backward compability */
-        case 'o':
-            outfile = opt_arg;
-            has_i_o = 1;
-            break;
-
-
-        case 'h':
-            usage(h5tools_getprogname());
-            HDexit(EXIT_SUCCESS);
-        case 'V':
-            print_version(h5tools_getprogname());
-            HDexit(EXIT_SUCCESS);
-        case 'v':
-            options->verbose = 1;
-            break;
-        case 'f':
-
-            /* parse the -f filter option */
-            if (h5repack_addfilter( opt_arg, options)<0)
-            {
-                error_msg("in parsing filter\n");
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-        case 'l':
-
-            /* parse the -l layout option */
-            if (h5repack_addlayout( opt_arg, options)<0)
-            {
-                error_msg("in parsing layout\n");
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-
-
-        case 'm':
-
-            options->min_comp = HDatoi( opt_arg );
-            if ((int)options->min_comp<=0)
-            {
-                error_msg("invalid minimum compress size <%s>\n", opt_arg );
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-
-        case 'e':
-            read_info( opt_arg, options);
-            break;
-
-        case 'n':
-            options->use_native = 1;
-            break;
-
-        case 'L':
-            options->latest = 1;
-            break;
-
-        case 'c':
-
-            options->grp_compact = HDatoi( opt_arg );
-            if (options->grp_compact>0)
-                options->latest = 1; /* must use latest format */
-            break;
-
-
-        case 'd':
-
-            options->grp_indexed = HDatoi( opt_arg );
-            if (options->grp_indexed>0)
-                options->latest = 1; /* must use latest format */
-            break;
-
-        case 's':
-
-            {
-
-                int idx = 0;
-                int ssize = 0;
-                char *msgPtr = HDstrchr( opt_arg, ':');
-                options->latest = 1; /* must use latest format */
-                if (msgPtr == NULL)
-                {
-                    ssize = HDatoi( opt_arg );
-                    for (idx=0; idx<5; idx++)
-                        options->msg_size[idx] = ssize;
-                }
-                else
-                {
-                    char msgType[10];
-                    HDstrcpy(msgType, msgPtr+1);
-                    msgPtr[0] = '\0';
-                    ssize = HDatoi( opt_arg );
-                    if (HDstrncmp(msgType, "dspace",6) == 0) {
-                        options->msg_size[0] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "dtype", 5) == 0) {
-                        options->msg_size[1] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "fill", 4) == 0) {
-                        options->msg_size[2] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "pline", 5) == 0) {
-                        options->msg_size[3] = ssize;
-                    }
-                    else if (HDstrncmp(msgType, "attr", 4) == 0) {
-                        options->msg_size[4] = ssize;
-                    }
-                }
-            }
-
-            break;
-
-        case 'u':
-
-            options->ublock_filename = opt_arg;
-            break;
-
-        case 'b':
-
-            options->ublock_size = (hsize_t)HDatol( opt_arg );
-            break;
-
-        case 'M':
-
-            options->meta_block_size = (hsize_t)HDatol( opt_arg );
-            break;
-
-        case 't':
-
-            options->threshold = (hsize_t)HDatol( opt_arg );
-            break;
-
-        case 'a':
-
-            options->alignment = HDatol( opt_arg );
-            if ( options->alignment < 1 )
-            {
-                error_msg("invalid alignment size\n", opt_arg );
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-
-        case 'S':
-            {
-            char strategy[MAX_NC_NAME];
-
-            HDstrcpy(strategy, opt_arg);
-            if(!HDstrcmp(strategy, "ALL_PERSIST"))
-                options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
-            else if(!HDstrcmp(strategy, "ALL"))
-                options->fs_strategy = H5F_FILE_SPACE_ALL;
-            else if(!HDstrcmp(strategy, "AGGR_VFD"))
-                options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
-            else if(!HDstrcmp(strategy, "VFD"))
-                options->fs_strategy = H5F_FILE_SPACE_VFD;
-            else {
-                error_msg("invalid file space management strategy\n", opt_arg );
-                HDexit(EXIT_FAILURE);
-            }
-            break;
-            }
-
-        case 'T':
-
-            options->fs_threshold = (hsize_t)HDatol( opt_arg );
-            break;
-        default:
-            break;
-        } /* switch */
-
-
-    } /* while */
-
-    if ( has_i_o == 0 )
-    {
-        /* check for file names to be processed */
-        if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL)
-        {
-            error_msg("missing file names\n");
-            usage(h5tools_getprogname());
-            HDexit(EXIT_FAILURE);
-        }
-    }
-
+int parse_command_line(int argc, const char **argv, pack_opt_t* options) {
+
+	int opt;
+	int ret_value = 0;
+
+	/* parse command line options */
+	while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+		switch ((char) opt) {
+
+		/* -i for backward compability */
+		case 'i':
+			infile = opt_arg;
+			has_i_o = 1;
+			break;
+
+			/* -o for backward compability */
+		case 'o':
+			outfile = opt_arg;
+			has_i_o = 1;
+			break;
+
+		case 'h':
+			usage(h5tools_getprogname());
+			h5tools_setstatus(EXIT_SUCCESS);
+			ret_value = -1;
+			goto done;
+
+		case 'V':
+			print_version(h5tools_getprogname());
+			h5tools_setstatus(EXIT_SUCCESS);
+			ret_value = -1;
+			goto done;
+
+		case 'v':
+			options->verbose = 1;
+			break;
+
+		case 'f':
+			/* parse the -f filter option */
+			if (h5repack_addfilter(opt_arg, options) < 0) {
+				error_msg("in parsing filter\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'l':
+			/* parse the -l layout option */
+			if (h5repack_addlayout(opt_arg, options) < 0) {
+				error_msg("in parsing layout\n");
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'm':
+			options->min_comp = HDatoi( opt_arg );
+			if ((int) options->min_comp <= 0) {
+				error_msg("invalid minimum compress size <%s>\n", opt_arg);
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'e':
+			ret_value = read_info(opt_arg, options);
+			if (ret_value < 0)
+				goto done;
+			break;
+
+		case 'n':
+			options->use_native = 1;
+			break;
+
+		case 'L':
+			options->latest = 1;
+			break;
+
+		case 'c':
+			options->grp_compact = HDatoi( opt_arg );
+			if (options->grp_compact > 0)
+				options->latest = 1; /* must use latest format */
+			break;
+
+		case 'd':
+			options->grp_indexed = HDatoi( opt_arg );
+			if (options->grp_indexed > 0)
+				options->latest = 1; /* must use latest format */
+			break;
+
+		case 's':
+			{
+				int idx = 0;
+				int ssize = 0;
+				char *msgPtr = HDstrchr( opt_arg, ':');
+				options->latest = 1; /* must use latest format */
+				if (msgPtr == NULL) {
+					ssize = HDatoi( opt_arg );
+					for (idx = 0; idx < 5; idx++)
+						options->msg_size[idx] = ssize;
+				}
+				else {
+					char msgType[10];
+					HDstrcpy(msgType, msgPtr + 1);
+					msgPtr[0] = '\0';
+					ssize = HDatoi( opt_arg );
+					if (HDstrncmp(msgType, "dspace",6) == 0) {
+						options->msg_size[0] = ssize;
+					}
+					else if (HDstrncmp(msgType, "dtype", 5) == 0) {
+						options->msg_size[1] = ssize;
+					}
+					else if (HDstrncmp(msgType, "fill", 4) == 0) {
+						options->msg_size[2] = ssize;
+					}
+					else if (HDstrncmp(msgType, "pline", 5) == 0) {
+						options->msg_size[3] = ssize;
+					}
+					else if (HDstrncmp(msgType, "attr", 4) == 0) {
+						options->msg_size[4] = ssize;
+					}
+				}
+			}
+			break;
+
+		case 'u':
+			options->ublock_filename = opt_arg;
+			break;
+
+		case 'b':
+			options->ublock_size = (hsize_t) HDatol( opt_arg );
+			break;
+
+		case 'M':
+			options->meta_block_size = (hsize_t) HDatol( opt_arg );
+			break;
+
+		case 't':
+			options->threshold = (hsize_t) HDatol( opt_arg );
+			break;
+
+		case 'a':
+			options->alignment = HDatol( opt_arg );
+			if (options->alignment < 1) {
+				error_msg("invalid alignment size\n", opt_arg);
+				h5tools_setstatus(EXIT_FAILURE);
+				ret_value = -1;
+				goto done;
+			}
+			break;
+
+		case 'S':
+			{
+				char strategy[MAX_NC_NAME];
+
+				HDstrcpy(strategy, opt_arg);
+				if (!HDstrcmp(strategy, "ALL_PERSIST"))
+					options->fs_strategy = H5F_FILE_SPACE_ALL_PERSIST;
+				else if (!HDstrcmp(strategy, "ALL"))
+					options->fs_strategy = H5F_FILE_SPACE_ALL;
+				else if (!HDstrcmp(strategy, "AGGR_VFD"))
+					options->fs_strategy = H5F_FILE_SPACE_AGGR_VFD;
+				else if (!HDstrcmp(strategy, "VFD"))
+					options->fs_strategy = H5F_FILE_SPACE_VFD;
+				else {
+					error_msg("invalid file space management strategy\n", opt_arg);
+					h5tools_setstatus(EXIT_FAILURE);
+					ret_value = -1;
+					goto done;
+				}
+			}
+			break;
+
+		case 'T':
+			options->fs_threshold = (hsize_t) HDatol( opt_arg );
+			break;
+
+		default:
+			break;
+		} /* switch */
+
+	} /* while */
+
+	if (has_i_o == 0) {
+		/* check for file names to be processed */
+		if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+			error_msg("missing file names\n");
+			usage(h5tools_getprogname());
+			h5tools_setstatus(EXIT_FAILURE);
+			ret_value = -1;
+		}
+	}
+
+done:
+	return ret_value;
 }
 
 /*-------------------------------------------------------------------------
- * Function: read_info
+ * Function: main
  *
- * Purpose: read comp and chunk options from a file
+ * Purpose: h5repack main program
  *
- * Return: void, exit on error
+ * Return: Success: EXIT_SUCCESS(0)
  *
- * Programmer: pvn@ncsa.uiuc.edu
+ * Failure: EXIT_FAILURE(1)
  *
- * Date: September, 22, 2003
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
  *
  *-------------------------------------------------------------------------
  */
-
-static
-void read_info(const char *filename,
-               pack_opt_t *options)
-{
-
-    char stype[10];
-    char comp_info[1024];
-    FILE *fp;
-    char c;
-    int  i, rc=1;
-
-    if ((fp = HDfopen(filename, "r")) == (FILE *)NULL) {
-        error_msg("cannot open options file %s\n", filename);
-        HDexit(EXIT_FAILURE);
-    }
-
-    /* cycle until end of file reached */
-    while( 1 )
-    {
-        rc=fscanf(fp, "%s", stype);
-        if (rc==-1)
-            break;
-
-       /*-------------------------------------------------------------------------
-        * filter
-        *-------------------------------------------------------------------------
-        */
-        if (HDstrcmp(stype,"-f") == 0) {
-
-            /* find begining of info */
-            i=0; c='0';
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                if (HDfeof(fp)) break;
-            }
-            c='0';
-            /* go until end */
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                comp_info[i]=c;
-                i++;
-                if (HDfeof(fp)) break;
-                if (c==10 /*eol*/) break;
-            }
-            comp_info[i-1]='\0'; /*cut the last " */
-
-            if (h5repack_addfilter(comp_info,options)==-1){
-                error_msg("could not add compression option\n");
-                HDexit(EXIT_FAILURE);
-            }
-        }
-        /*-------------------------------------------------------------------------
-        * layout
-        *-------------------------------------------------------------------------
-        */
-        else if (HDstrcmp(stype,"-l") == 0) {
-
-            /* find begining of info */
-            i=0; c='0';
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                if (HDfeof(fp)) break;
-            }
-            c='0';
-            /* go until end */
-            while( c!=' ' )
-            {
-                fscanf(fp, "%c", &c);
-                comp_info[i]=c;
-                i++;
-                if (HDfeof(fp)) break;
-                if (c==10 /*eol*/) break;
-            }
-            comp_info[i-1]='\0'; /*cut the last " */
-
-            if (h5repack_addlayout(comp_info,options)==-1){
-                error_msg("could not add chunck option\n");
-                HDexit(EXIT_FAILURE);
-            }
-        }
-        /*-------------------------------------------------------------------------
-        * not valid
-        *-------------------------------------------------------------------------
-        */
-        else {
-            error_msg("bad file format for %s", filename);
-            HDexit(EXIT_FAILURE);
-        }
-    }
-
-    HDfclose(fp);
-    return;
+int main(int argc, const char **argv) {
+
+	pack_opt_t options; /*the global options */
+	int ret = -1;
+
+	h5tools_setprogname(PROGRAMNAME);
+	h5tools_setstatus(EXIT_SUCCESS);
+
+	/* Initialize h5tools lib */
+	h5tools_init();
+
+	/* update hyperslab buffer size from H5TOOLS_BUFSIZE env if exist */
+	if (h5tools_getenv_update_hyperslab_bufsize() < 0) {
+		h5tools_setstatus(EXIT_FAILURE);
+		goto done;
+	}
+
+	/* initialize options  */
+	h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (hsize_t) 0);
+
+	if (parse_command_line(argc, argv, &options) < 0)
+		goto done;
+
+	/* get file names if they were not yet got */
+	if (has_i_o == 0) {
+
+		if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
+			infile = argv[opt_ind];
+			outfile = argv[opt_ind + 1];
+
+			if ( HDstrcmp( infile, outfile ) == 0) {
+				error_msg("file names cannot be the same\n");
+				usage(h5tools_getprogname());
+				h5tools_setstatus(EXIT_FAILURE);
+				goto done;
+			}
+		}
+		else {
+			error_msg("file names missing\n");
+			usage(h5tools_getprogname());
+			h5tools_setstatus(EXIT_FAILURE);
+			goto done;
+		}
+	}
+
+	/* pack it */
+	h5tools_setstatus(h5repack(infile, outfile, &options));
+
+done:
+	/* free tables */
+	h5repack_end(&options);
+
+	leave(h5tools_getstatus());
 }
+
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index bcddbb9..b54e887 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -1,4 +1,4 @@
- /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
  * Copyright by The HDF Group.                                               *
  * Copyright by the Board of Trustees of the University of Illinois.         *
  * All rights reserved.                                                      *
@@ -27,21 +27,19 @@
  *-------------------------------------------------------------------------
  */
 
-void init_packobject(pack_info_t *obj)
-{
-    int j, k;
-
-    HDstrcpy(obj->path,"\0");
-    for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
-    {
-        obj->filter[j].filtn        = -1;
-        for ( k=0; k<CD_VALUES; k++)
-            obj->filter[j].cd_values[k] = 0;
-    }
-    obj->chunk.rank = -1;
-    obj->refobj_id = -1;
-    obj->layout = H5D_LAYOUT_ERROR;
-    obj->nfilters = 0;
+void init_packobject(pack_info_t *obj) {
+	int j, k;
+
+	HDstrcpy(obj->path, "\0");
+	for (j = 0; j < H5_REPACK_MAX_NFILTERS; j++) {
+		obj->filter[j].filtn = -1;
+		for (k = 0; k < CD_VALUES; k++)
+			obj->filter[j].cd_values[k] = 0;
+	}
+	obj->chunk.rank = -1;
+	obj->refobj_id = -1;
+	obj->layout = H5D_LAYOUT_ERROR;
+	obj->nfilters = 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -54,19 +52,16 @@ void init_packobject(pack_info_t *obj)
  *-------------------------------------------------------------------------
  */
 
-static void aux_tblinsert_filter(pack_opttbl_t *table,
-                                 unsigned int I,
-                                 filter_info_t filt)
-{
-    if (table->objs[ I ].nfilters<H5_REPACK_MAX_NFILTERS)
-    {
-        table->objs[ I ].filter[ table->objs[ I ].nfilters++ ] = filt;
-    }
-    else
-    {
-    error_msg("cannot insert the filter in this object.\
+static void aux_tblinsert_filter(pack_opttbl_t *table, unsigned int I,
+		filter_info_t filt) {
+	if (table->objs[I].nfilters < H5_REPACK_MAX_NFILTERS) {
+		table->objs[I].filter[table->objs[I].nfilters++] = filt;
+	}
+	else {
+		error_msg(
+				"cannot insert the filter in this object.\
         Maximum capacity exceeded\n");
-    }
+	}
 }
 
 /*-------------------------------------------------------------------------
@@ -79,33 +74,28 @@ static void aux_tblinsert_filter(pack_opttbl_t *table,
  *-------------------------------------------------------------------------
  */
 
-static void aux_tblinsert_layout(pack_opttbl_t *table,
-                                 unsigned int I,
-                                 pack_info_t *pack)
-{
-    int k;
-
-    table->objs[I].layout = pack->layout;
-    if (H5D_CHUNKED==pack->layout)
-    {
-    /* -2 means the NONE option, remove chunking
-        and set the layout to contiguous */
-        if (pack->chunk.rank==-2)
-        {
-            table->objs[I].layout = H5D_CONTIGUOUS;
-            table->objs[I].chunk.rank = -2;
-        }
-        /* otherwise set the chunking type */
-        else
-        {
-            table->objs[I].chunk.rank = pack->chunk.rank;
-            for (k = 0; k < pack->chunk.rank; k++)
-                table->objs[I].chunk.chunk_lengths[k] = pack->chunk.chunk_lengths[k];
-        }
-    }
+static void aux_tblinsert_layout(pack_opttbl_t *table, unsigned int I,
+		pack_info_t *pack) {
+	int k;
+
+	table->objs[I].layout = pack->layout;
+	if (H5D_CHUNKED == pack->layout) {
+		/* -2 means the NONE option, remove chunking
+		 and set the layout to contiguous */
+		if (pack->chunk.rank == -2) {
+			table->objs[I].layout = H5D_CONTIGUOUS;
+			table->objs[I].chunk.rank = -2;
+		}
+		/* otherwise set the chunking type */
+		else {
+			table->objs[I].chunk.rank = pack->chunk.rank;
+			for (k = 0; k < pack->chunk.rank; k++)
+				table->objs[I].chunk.chunk_lengths[k] =
+						pack->chunk.chunk_lengths[k];
+		}
+	}
 }
 
-
 /*-------------------------------------------------------------------------
  * Function: aux_inctable
  *
@@ -116,21 +106,20 @@ static void aux_tblinsert_layout(pack_opttbl_t *table,
  *-------------------------------------------------------------------------
  */
 
-static int aux_inctable(pack_opttbl_t *table, int n_objs )
-{
-    unsigned int i;
-
-    table->size += n_objs;
-    table->objs = (pack_info_t*)HDrealloc(table->objs, table->size * sizeof(pack_info_t));
-    if (table->objs==NULL) {
-        error_msg("not enough memory for options table\n");
-        return -1;
-    }
-    for (i = table->nelems; i < table->size; i++)
-    {
-        init_packobject(&table->objs[i]);
-    }
-    return 0;
+static int aux_inctable(pack_opttbl_t *table, int n_objs) {
+	unsigned int i;
+
+	table->size += n_objs;
+	table->objs =
+			(pack_info_t*) HDrealloc(table->objs, table->size * sizeof(pack_info_t));
+	if (table->objs == NULL) {
+		error_msg("not enough memory for options table\n");
+		return -1;
+	}
+	for (i = table->nelems; i < table->size; i++) {
+		init_packobject(&table->objs[i]);
+	}
+	return 0;
 }
 
 
@@ -143,31 +132,29 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
  *
  *-------------------------------------------------------------------------
  */
-int options_table_init( pack_opttbl_t **tbl )
-{
-    unsigned int i;
-    pack_opttbl_t *table;
-
-    if(NULL == (table = (pack_opttbl_t *)HDmalloc(sizeof(pack_opttbl_t))))
-    {
-        error_msg("not enough memory for options table\n");
-        return -1;
-    }
-
-    table->size   = 30;
-    table->nelems = 0;
-    if(NULL == (table->objs = (pack_info_t*)HDmalloc(table->size * sizeof(pack_info_t))))
-    {
-        error_msg("not enough memory for options table\n");
-        HDfree(table);
-        return -1;
-    }
-
-    for(i = 0; i < table->size; i++)
-        init_packobject(&table->objs[i]);
-
-    *tbl = table;
-    return 0;
+int options_table_init(pack_opttbl_t **tbl) {
+	unsigned int i;
+	pack_opttbl_t *table;
+
+	if (NULL == (table = (pack_opttbl_t *) HDmalloc(sizeof(pack_opttbl_t)))) {
+		error_msg("not enough memory for options table\n");
+		return -1;
+	}
+
+	table->size = 30;
+	table->nelems = 0;
+	if (NULL == (table->objs =
+			(pack_info_t*) HDmalloc(table->size * sizeof(pack_info_t)))) {
+		error_msg("not enough memory for options table\n");
+		HDfree(table);
+		return -1;
+	}
+
+	for (i = 0; i < table->size; i++)
+		init_packobject(&table->objs[i]);
+
+	*tbl = table;
+	return 0;
 }
 
 
@@ -181,11 +168,10 @@ int options_table_init( pack_opttbl_t **tbl )
  *-------------------------------------------------------------------------
  */
 
-int options_table_free( pack_opttbl_t *table )
-{
-    HDfree(table->objs);
-    HDfree(table);
-    return 0;
+int options_table_free(pack_opttbl_t *table) {
+	HDfree(table->objs);
+	HDfree(table);
+	return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -198,95 +184,81 @@ int options_table_free( pack_opttbl_t *table )
  *-------------------------------------------------------------------------
  */
 
-
-int options_add_layout( obj_list_t *obj_list,
-                        int n_objs,
-                        pack_info_t *pack,
-                        pack_opttbl_t *table )
-{
-    unsigned int i, I;
-    int          j, added=0, found=0;
-
-    /* increase the size of the collection by N_OBJS if necessary */
-    if (table->nelems+n_objs >= table->size)
-    {
-        if (aux_inctable(table,n_objs)<0)
-            return -1;
-    }
-
-    /* search if this object is already in the table; "path" is the key */
-    if (table->nelems>0)
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            /* linear table search */
-            for (i = 0; i < table->nelems; i++)
-            {
-                /*already on the table */
-                if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
-                {
-                    /* already chunk info inserted for this one; exit */
-                    if (table->objs[i].chunk.rank>0)
-                    {
-                        error_msg("chunk information already inserted for <%s>\n",obj_list[j].obj);
-                        HDexit(EXIT_FAILURE);
-                    }
-                    /* insert the layout info */
-                    else
-                    {
-                        aux_tblinsert_layout(table,i,pack);
-                        found=1;
-                        break;
-                    }
-                } /* if */
-            } /* i */
-
-            if (found==0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_layout(table,I,pack);
-            }
-            /* cases where we have an already inserted name but there is a new name also
-            example:
-            -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
-            dset1 is already inserted, but dset2 must also be
-            */
-            else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_layout(table,I,pack);
-            }
-        } /* j */
-    }
-
-    /* first time insertion */
-    else
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            I = table->nelems + added;
-            added++;
-            HDstrcpy(table->objs[I].path,obj_list[j].obj);
-            aux_tblinsert_layout(table,I,pack);
-
-        }
-    }
-
-    table->nelems+= added;
-
-    return 0;
+int options_add_layout(obj_list_t *obj_list, int n_objs, pack_info_t *pack,
+		pack_opttbl_t *table) {
+	unsigned int i, I;
+	int j, added = 0, found = 0;
+
+	/* increase the size of the collection by N_OBJS if necessary */
+	if (table->nelems + n_objs >= table->size) {
+		if (aux_inctable(table, n_objs) < 0)
+			return -1;
+	}
+
+	/* search if this object is already in the table; "path" is the key */
+	if (table->nelems > 0) {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			/* linear table search */
+			for (i = 0; i < table->nelems; i++) {
+				/*already on the table */
+				if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+					/* already chunk info inserted for this one; exit */
+					if (table->objs[i].chunk.rank > 0) {
+						error_msg(
+								"chunk information already inserted for <%s>\n",
+								obj_list[j].obj);
+						HDexit(EXIT_FAILURE);
+					}
+					/* insert the layout info */
+					else {
+						aux_tblinsert_layout(table, i, pack);
+						found = 1;
+						break;
+					}
+				} /* if */
+			} /* i */
+
+			if (found == 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_layout(table, I, pack);
+			}
+			/* cases where we have an already inserted name but there is a new name also
+			 example:
+			 -f dset1:GZIP=1 -l dset1,dset2:CHUNK=20x20
+			 dset1 is already inserted, but dset2 must also be
+			 */
+			else if (found == 1
+					&& HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_layout(table, I, pack);
+			}
+		} /* j */
+	}
+
+	/* first time insertion */
+	else {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			I = table->nelems + added;
+			added++;
+			HDstrcpy(table->objs[I].path, obj_list[j].obj);
+			aux_tblinsert_layout(table, I, pack);
+
+		}
+	}
+
+	table->nelems += added;
+
+	return 0;
 }
 
-
-
 /*-------------------------------------------------------------------------
  * Function: options_add_filter
  *
@@ -297,81 +269,70 @@ int options_add_layout( obj_list_t *obj_list,
  *-------------------------------------------------------------------------
  */
 
-int options_add_filter(obj_list_t *obj_list,
-                       int n_objs,
-                       filter_info_t filt,
-                       pack_opttbl_t *table )
-{
-
-    unsigned int i, I;
-    int          j, added=0, found=0;
-
-    /* increase the size of the collection by N_OBJS if necessary */
-    if (table->nelems+n_objs >= table->size)
-    {
-        if (aux_inctable(table,n_objs)<0)
-            return -1;
-    }
-
-    /* search if this object is already in the table; "path" is the key */
-    if (table->nelems>0)
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            /* linear table search */
-            for (i = 0; i < table->nelems; i++)
-            {
-                /*already on the table */
-                if (HDstrcmp(obj_list[j].obj,table->objs[i].path)==0)
-                {
-                    /* insert */
-                    aux_tblinsert_filter(table,i,filt);
-                    found=1;
-                    break;
-                } /* if */
-            } /* i */
-
-            if (found==0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_filter(table,I,filt);
-            }
-            /* cases where we have an already inserted name but there is a new name also
-            example:
-            -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
-            dset1 is already inserted, but dset2 must also be
-            */
-            else if (found==1 && HDstrcmp(obj_list[j].obj,table->objs[i].path)!=0)
-            {
-                /* keep the grow in a temp var */
-                I = table->nelems + added;
-                added++;
-                HDstrcpy(table->objs[I].path,obj_list[j].obj);
-                aux_tblinsert_filter(table,I,filt);
-            }
-        } /* j */
-    }
-
-    /* first time insertion */
-    else
-    {
-        /* go tru the supplied list of names */
-        for (j = 0; j < n_objs; j++)
-        {
-            I = table->nelems + added;
-            added++;
-            HDstrcpy(table->objs[I].path,obj_list[j].obj);
-            aux_tblinsert_filter(table,I,filt);
-        }
-    }
-
-    table->nelems+= added;
-
-    return 0;
+int options_add_filter(obj_list_t *obj_list, int n_objs, filter_info_t filt,
+		pack_opttbl_t *table) {
+
+	unsigned int i, I;
+	int j, added = 0, found = 0;
+
+	/* increase the size of the collection by N_OBJS if necessary */
+	if (table->nelems + n_objs >= table->size) {
+		if (aux_inctable(table, n_objs) < 0)
+			return -1;
+	}
+
+	/* search if this object is already in the table; "path" is the key */
+	if (table->nelems > 0) {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			/* linear table search */
+			for (i = 0; i < table->nelems; i++) {
+				/*already on the table */
+				if (HDstrcmp(obj_list[j].obj,table->objs[i].path) == 0) {
+					/* insert */
+					aux_tblinsert_filter(table, i, filt);
+					found = 1;
+					break;
+				} /* if */
+			} /* i */
+
+			if (found == 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_filter(table, I, filt);
+			}
+			/* cases where we have an already inserted name but there is a new name also
+			 example:
+			 -l dset1:CHUNK=20x20 -f dset1,dset2:GZIP=1
+			 dset1 is already inserted, but dset2 must also be
+			 */
+			else if (found == 1
+					&& HDstrcmp(obj_list[j].obj,table->objs[i].path) != 0) {
+				/* keep the grow in a temp var */
+				I = table->nelems + added;
+				added++;
+				HDstrcpy(table->objs[I].path, obj_list[j].obj);
+				aux_tblinsert_filter(table, I, filt);
+			}
+		} /* j */
+	}
+
+	/* first time insertion */
+	else {
+		/* go tru the supplied list of names */
+		for (j = 0; j < n_objs; j++) {
+			I = table->nelems + added;
+			added++;
+			HDstrcpy(table->objs[I].path, obj_list[j].obj);
+			aux_tblinsert_filter(table, I, filt);
+		}
+	}
+
+	table->nelems += added;
+
+	return 0;
 }
 
 /*-------------------------------------------------------------------------
@@ -384,34 +345,25 @@ int options_add_filter(obj_list_t *obj_list,
  *-------------------------------------------------------------------------
  */
 
-pack_info_t* options_get_object( const char *path,
-                                 pack_opttbl_t *table )
-{
-    unsigned int i;
-    char tbl_path[MAX_NC_NAME+1]; /* +1 for start with "/" case */
-
-
-    for ( i = 0; i < table->nelems; i++)
-    {
-        /* make full path (start with "/") to compare correctly  */
-        if (HDstrncmp(table->objs[i].path, "/", 1))
-        {
-            HDstrcpy(tbl_path, "/");
-            HDstrcat(tbl_path, table->objs[i].path);
-        }
-        else
-            HDstrcpy(tbl_path, table->objs[i].path);
-
-        /* found it */
-        if (HDstrcmp(tbl_path, path)==0)
-        {
-            return (&table->objs[i]);
-        }
-    }
-
-    return NULL;
+pack_info_t* options_get_object(const char *path, pack_opttbl_t *table) {
+	unsigned int i;
+	char tbl_path[MAX_NC_NAME + 1]; /* +1 for start with "/" case */
+
+	for (i = 0; i < table->nelems; i++) {
+		/* make full path (start with "/") to compare correctly  */
+		if (HDstrncmp(table->objs[i].path, "/", 1)) {
+			HDstrcpy(tbl_path, "/");
+			HDstrcat(tbl_path, table->objs[i].path);
+		}
+		else
+			HDstrcpy(tbl_path, table->objs[i].path);
+
+		/* found it */
+		if (HDstrcmp(tbl_path, path) == 0) {
+			return (&table->objs[i]);
+		}
+	}
+
+	return NULL;
 }
 
-
-
-