(1) Merge branch 'develop' into bugfix/version_bounds

(2) Add two new options to h5repack for low and high bounds as in H5Pset_libver_bounds.
(3) Modify message pre_copy callbacks so that H5Ocopy can handle version bounds check.
(4) Add version bounds check for cache image feature.

6 files changed, 209 insertions, 221 deletions

diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index 6b8cf8a..e7f4aae 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -75,6 +75,8 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
     options->verbose = verbose;
     options->latest = latest;
     options->layout_g = H5D_LAYOUT_ERROR;
+    options->low_bound = H5F_LIBVER_EARLIEST;
+    options->high_bound = H5F_LIBVER_LATEST;
 
     for (n = 0; n < H5_REPACK_MAX_NFILTERS; n++) {
         options->filter_g[n].filtn = -1;
@@ -221,13 +223,12 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
     hid_t       ret_value = -1;        /* The identifier of the named dtype in the out file */
 
     if (H5Oget_info(type_in, &oinfo) < 0)
-        goto done;
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
 
     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 {
@@ -238,7 +239,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
             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;
+                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
                 dt->next = *named_dt_head_p;
                 *named_dt_head_p = dt;
 
@@ -259,7 +260,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
     if (!dt_ret) {
         /* Push the new datatype onto the stack */
         if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
-            goto done;
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
         dt_ret->next = *named_dt_head_p;
         *named_dt_head_p = dt_ret;
 
@@ -276,9 +277,9 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
         else
             dt_ret->id_out = H5Tcopy(type_in);
         if (dt_ret->id_out < 0)
-            goto done;
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed");
         if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
-            goto done;
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed");
     } /* end if */
 
     /* Set return value */
@@ -286,7 +287,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
 
     /* 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;
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iinc_ref failed");
 
 done:
     return ret_value;
@@ -305,7 +306,7 @@ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
     while (dt) {
         /* Pop the datatype off the stack and free it */
         if (H5Tclose(dt->id_out) < 0 && !ignore_err)
-            goto done;
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
         dt = dt->next;
         HDfree(*named_dt_head_p);
         *named_dt_head_p = dt;
@@ -332,7 +333,7 @@ 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)
 {
-    int         ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int         ret_value = 0;
     hid_t       attr_id = -1;  /* attr ID */
     hid_t       attr_out = -1; /* attr ID */
     hid_t       space_id = -1; /* space ID */
@@ -375,7 +376,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
         if ((is_named = H5Tcommitted(ftype_id)) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
         if (is_named && travt) {
-            hid_t fidout;
+            hid_t fidout = -1;
 
             /* Create out file id */
             if ((fidout = H5Iget_file_id(loc_out)) < 0)
@@ -426,7 +427,8 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
 
             base_type = H5Tget_super(ftype_id);
             is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
         }
 
         if (type_class == H5T_COMPOUND) {
@@ -435,7 +437,8 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
             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 (H5Tclose(mtid) < 0)
+                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed");
 
                 if (mtclass == H5T_REFERENCE) {
                     is_ref = 1;
@@ -481,7 +484,24 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
 
         if (options->verbose)
             printf(FORMAT_OBJ_ATTR, "attr", name);
-    } /* u */
+
+        /*-------------------------------------------------------------------------
+         * close
+         *-------------------------------------------------------------------------
+         */
+        if (H5Sclose(space_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
+        space_id = -1;
+        if (H5Tclose(wtype_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+        wtype_id = -1;
+        if (H5Tclose(ftype_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+        ftype_id = -1;
+        if (H5Aclose(attr_id) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
+        attr_id = -1;
+    } /* for u */
 
 done:
     H5E_BEGIN_TRY {
@@ -495,11 +515,11 @@ done:
             HDfree(buf);
         } /* end if */
 
-        H5Tclose(ftype_id);
-        H5Tclose(wtype_id);
+        H5Aclose(attr_out);
         H5Sclose(space_id);
+        H5Tclose(wtype_id);
+        H5Tclose(ftype_id);
         H5Aclose(attr_id);
-        H5Aclose(attr_out);
     } H5E_END_TRY;
 
     return ret_value;
@@ -689,9 +709,9 @@ done:
  */
 static int check_objects(const char* fname, pack_opt_t *options) {
     int           ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t         fid;
-    hid_t         did;
-    hid_t         sid;
+    hid_t         fid = -1;
+    hid_t         did = -1;
+    hid_t         sid = -1;
     unsigned int  i;
     unsigned int  uf;
     trav_table_t *travt = NULL;
@@ -792,9 +812,9 @@ static int check_objects(const char* fname, pack_opt_t *options) {
 
 done:
     H5E_BEGIN_TRY {
-        H5Fclose(fid);
         H5Sclose(sid);
         H5Dclose(did);
+        H5Fclose(fid);
     } H5E_END_TRY;
     if (travt)
         trav_table_free(travt);
diff --git a/tools/src/h5repack/h5repack.h b/tools/src/h5repack/h5repack.h
index 0252768..a0e0387 100644
--- a/tools/src/h5repack/h5repack.h
+++ b/tools/src/h5repack/h5repack.h
@@ -101,21 +101,23 @@ typedef struct {
 
 /* all the above, ready to go to the hrepack call */
 typedef struct {
-    pack_opttbl_t   *op_tbl;     /*table with all -c and -f options */
-    int             all_layout;  /*apply the layout to all objects */
-    int             all_filter;  /*apply the filter to all objects */
+    pack_opttbl_t   *op_tbl;        /*table with all -c and -f options */
+    int             all_layout;     /*apply the layout to all objects */
+    int             all_filter;     /*apply the filter to all objects */
     filter_info_t   filter_g[H5_REPACK_MAX_NFILTERS];    /*global filter array for the ALL case */
-    int             n_filter_g;  /*number of global filters */
-    chunk_info_t    chunk_g;     /*global chunk INFO for the ALL case */
-    H5D_layout_t    layout_g;    /*global layout information for the ALL case */
-    int             verbose;     /*verbose mode */
-    hsize_t         min_comp;    /*minimum size to compress, in bytes */
-    int             use_native;  /*use a native type in write */
-    hbool_t         latest;      /*pack file with the latest file format */
-    int             grp_compact; /* Set the maximum number of links to store as header messages in the group */
-    int             grp_indexed; /* Set the minimum number of links to store in the indexed format */
-    int             msg_size[8]; /* Minimum size of shared messages: dataspace,
-                                    datatype, fill value, filter pipleline, attribute */
+    int             n_filter_g;     /*number of global filters */
+    chunk_info_t    chunk_g;        /*global chunk INFO for the ALL case */
+    H5D_layout_t    layout_g;       /*global layout information for the ALL case */
+    int             verbose;        /*verbose mode */
+    hsize_t         min_comp;       /*minimum size to compress, in bytes */
+    int             use_native;     /*use a native type in write */
+    hbool_t         latest;         /*pack file with the latest file format */
+    H5F_libver_t    low_bound;      /* The file's low bound as in H5Fset_libver_bounds() */
+    H5F_libver_t    high_bound;     /* The file's high bound as in H5Fset_libver_bounds() */
+    int             grp_compact;    /* Set the maximum number of links to store as header messages in the group */
+    int             grp_indexed;    /* Set the minimum number of links to store in the indexed format */
+    int             msg_size[8];    /* Minimum size of shared messages: dataspace,
+                                       datatype, fill value, filter pipleline, attribute */
     const char      *ublock_filename;  /* user block file name */
     hsize_t         ublock_size;       /* user block size */
     hsize_t         meta_block_size;   /* metadata aggregation block size (for H5Pset_meta_block_size) */
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 9fcf218..b279cf9 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -78,23 +78,21 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
  *
  * Return:   0, ok,
  *          -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
  *-------------------------------------------------------------------------
  */
 
 int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
 {
-    int           ret_value = 0;          /* no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t         fidin;
+    int           ret_value = 0;
+    hid_t         fidin = -1;
     hid_t         fidout = -1;
-    trav_table_t  *travt = NULL;
-    hsize_t       ub_size = 0;            /* size of user block */
+    hid_t         fcpl_in = -1;  /* file creation property list ID for input file */
+    hid_t         grp_in = -1;   /* group ID */
+    hid_t         gcpl_in = -1;  /* group creation property list */
     hid_t         fcpl = H5P_DEFAULT;     /* file creation property list ID */
     hid_t         fapl = H5P_DEFAULT;     /* file access property list ID */
+    trav_table_t *travt = NULL;
+    hsize_t       ub_size = 0;            /* size of user block */
     H5F_fspace_strategy_t set_strategy;   /* Strategy to be set in outupt file */
     hbool_t       set_persist;            /* Persist free-space status to be set in output file */
     hsize_t       set_threshold;          /* Free-space section threshold to be set in output file */
@@ -114,10 +112,6 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
 
     /* get user block size and file space strategy/persist/threshold */
     {
-        hid_t fcpl_in; /* file creation property list ID for input file */
-        hid_t grp_in = -1;   /* group ID */
-        hid_t gcpl_in = -1;  /* group creation property list */
-
         if ((fcpl_in = H5Fget_create_plist(fidin)) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
 
@@ -148,8 +142,18 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed to close property list");
     }
 
+    if(options->latest)
+        options->low_bound = options->high_bound = H5F_LIBVER_LATEST;
+    /* Create file access property list */
+    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
+
+    /* It can be default, latest or other settings by users */
+    if(H5Pset_libver_bounds(fapl, options->low_bound, options->high_bound) < 0)
+        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set format version bounds");
+
     /* Check if we need to create a non-default file creation property list */
-    if (options->latest || ub_size > 0) {
+    if (options->low_bound >= H5F_LIBVER_V18 || ub_size > 0) {
         /* Create file creation property list */
         if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create a file creation property list");
@@ -158,7 +162,7 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
             if (H5Pset_userblock(fcpl, ub_size) < 0)
                 HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_userblock failed to set non-default userblock size");
 
-        if (options->latest) {
+        if (options->low_bound >= H5F_LIBVER_V18) {
             unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];
 
             /* Adjust group creation parameters for root group */
@@ -209,12 +213,6 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_shared_mesg_index failed to configure the specified shared object header message index");
             } /* if (nindex>0) */
 
-            /* Create file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed to create file access property list");
-
-            if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_libver_bounds failed to set property for using latest version of the format");
         } /* end if */
     } /* end if */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
@@ -343,42 +341,26 @@ print_user_block(fnamein, fidin);
     /* init table */
     trav_table_init(&travt);
 
-    /* get the list of objects in the file */
-    if (h5trav_gettable(fidin, travt) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
-
-    /*-------------------------------------------------------------------------
-     * do the copy
-     *-------------------------------------------------------------------------
-     */
-    if (do_copy_objects(fidin, fidout, travt, options) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout);
-
-    /*-------------------------------------------------------------------------
-     * do the copy of referenced objects
-     * and create hard links
-     *-------------------------------------------------------------------------
-     */
-    if (do_copy_refobjs(fidin, fidout, travt, options) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout);
-
-    /*-------------------------------------------------------------------------
-     * close
-     *-------------------------------------------------------------------------
-     */
-
-    if (fapl > 0)
-        H5Pclose(fapl);
-
-    if (fcpl > 0)
-        H5Pclose(fcpl);
-
-    H5Fclose(fidin);
-    H5Fclose(fidout);
-
-    /* free table */
-    trav_table_free(travt);
-    travt = NULL;
+    if (travt) {
+        /* get the list of objects in the file */
+        if (h5trav_gettable(fidin, travt) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "h5trav_gettable failed");
+
+        /*-------------------------------------------------------------------------
+        * do the copy
+        *-------------------------------------------------------------------------
+        */
+        if (do_copy_objects(fidin, fidout, travt, options) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_objects from <%s> could not copy data to <%s>", fnamein, fnameout);
+
+        /*-------------------------------------------------------------------------
+        * do the copy of referenced objects
+        * and create hard links
+        *-------------------------------------------------------------------------
+        */
+        if (do_copy_refobjs(fidin, fidout, travt, options) < 0)
+            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "do_copy_refobjs from <%s> could not copy data to <%s>", fnamein, fnameout);
+    }
 
     /*-------------------------------------------------------------------------
      * write only the input file user block if there is no user block file input
@@ -389,17 +371,15 @@ print_user_block(fnamein, fidin);
         if (copy_user_block(fnamein, fnameout, ub_size) < 0)
             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Could not copy user block. Exiting...");
 
-    return 0;
-
-    /*-------------------------------------------------------------------------
-     * out
-     *-------------------------------------------------------------------------
-     */
-
 done:
     H5E_BEGIN_TRY {
+        H5Pclose(fcpl_in);
+        H5Pclose(gcpl_in);
         H5Pclose(fapl);
         H5Pclose(fcpl);
+        H5Gclose(grp_in);
+        H5Fclose(fidin);
+        H5Fclose(fidout);
         H5Fclose(fidin);
         H5Fclose(fidout);
     } H5E_END_TRY;
@@ -416,7 +396,7 @@ done:
  *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
  *          Return the hyperslab dimentions and size in byte.
  *
- * Return: 0 - SUCCEED, -1 FAILED
+ * Return:  0 - SUCCEED, -1 FAILED
  *
  * Parameters:
  *   dcpl_id : [IN] dataset creation property.
@@ -426,8 +406,6 @@ done:
  *   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.
@@ -441,25 +419,23 @@ done:
  *      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[],
+int
+Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
         size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
 {
-    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int     ret_value = 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 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 */
+    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;
@@ -572,24 +548,9 @@ done:
 /*-------------------------------------------------------------------------
  * 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.
+ * Purpose:  duplicate all HDF5 objects in the file
  *
- *  October 2006:  Read by hyperslabs for big datasets.
+ * Return:   0, ok, -1 no
  *
  *  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,
@@ -630,31 +591,6 @@ done:
  *  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
@@ -666,7 +602,7 @@ done:
 int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
         pack_opt_t *options) /* repack options */
 {
-    int   ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int   ret_value = 0;
     hid_t grp_in = -1;   /* group ID */
     hid_t grp_out = -1;  /* group ID */
     hid_t dset_in = -1;  /* read dataset ID */
@@ -988,13 +924,18 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                     if(H5Dread(dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
                                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
                                     if(H5Dwrite(dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
-                                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+                                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
 
                                     /* 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)
                                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
+                                    /* free */
+                                    if (buf != NULL) {
+                                        HDfree(buf);
+                                        buf = NULL;
+                                    }
                                 }
                                 else { /* possibly not enough memory, read/write by hyperslabs */
                                     size_t p_type_nbytes = msize; /*size of memory type */
@@ -1074,7 +1015,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                                         if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
                                             HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
                                         if(H5Dwrite(dset_out, wtype_id,  hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
-                                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
+                                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dwrite failed");
 
                                         /* reclaim any VL memory, if necessary */
                                         if (vl_data)
@@ -1165,7 +1106,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                  *-------------------------------------------------------------------------
                  */
                 else {
-                    hid_t pid;
+                    hid_t pid = -1;
 
                     /* create property to pass copy options */
                     if ((pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
@@ -1243,6 +1184,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
                 if (H5Tclose(type_out) < 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
+                type_out = -1; /* named datatypes stack, named_dt_head, manages allocation */
 
                 break;
 
@@ -1273,6 +1215,18 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
     } /* end if */
 
 done:
+
+    /* Finalize (link) the stack of named datatypes (if any) first
+     * because of reference counting */
+    if (0 == ret_value && named_dt_head != NULL) {
+        if (named_datatype_free(&named_dt_head, 0) < 0)
+            H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed");
+    }
+    else
+        H5E_BEGIN_TRY {
+            named_datatype_free(&named_dt_head, 1);
+        } H5E_END_TRY;
+
     H5E_BEGIN_TRY
     {
         H5Gclose(grp_in);
@@ -1295,14 +1249,6 @@ done:
     if (hslab_buf != NULL)
         HDfree(hslab_buf);
 
-    /* Finalize (link) the stack of named datatypes (if any) */
-    if (0 == ret_value && named_dt_head != NULL)
-        named_datatype_free(&named_dt_head, 0);
-    else
-        H5E_BEGIN_TRY {
-            named_datatype_free(&named_dt_head, 1);
-        } H5E_END_TRY;
-
     return ret_value;
 }
 
@@ -1310,10 +1256,10 @@ done:
  * 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)
+static void
+print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
 {
     char     strfilter[255];
 #if defined (PRINT_DEBUG )
@@ -1325,7 +1271,7 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
     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      i;
 
     HDstrcpy(strfilter, "\0");
 
@@ -1417,19 +1363,15 @@ static void print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int p
 /*-------------------------------------------------------------------------
  * 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
+ * Purpose:  copy user block from one file to another
  *
+ * Return:   0, ok, -1 no
  *-------------------------------------------------------------------------
  */
-static int copy_user_block(const char *infile, const char *outfile, hsize_t size)
+static int
+copy_user_block(const char *infile, const char *outfile, hsize_t size)
 {
-    int ret_value = 0;           /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+    int ret_value = 0;
     int infid = -1, outfid = -1; /* File descriptors */
 
     /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
@@ -1491,66 +1433,62 @@ done:
 /*-------------------------------------------------------------------------
  * Function: print_user_block
  *
- * Purpose: print user block
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente
- *
- * Date: August, 20, 2008
+ * Purpose:  print user block
  *
+ * Return:   0, ok, -1 no
  *-------------------------------------------------------------------------
  */
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
 static
-void print_user_block(const char *filename, hid_t fid)
+void
+print_user_block(const char *filename, hid_t fid)
 {
-    int     ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    int     fh;   /* file handle  */
-    hsize_t ub_size; /* user block size */
-    hsize_t size; /* size read */
-    hid_t   fcpl; /* file creation property list ID for HDF5 file */
+    int     ret_value = 0;
+    int     fh = -1;   /* file handle */
+    hsize_t ub_size;   /* user block size */
+    hsize_t size;      /* size read */
+    hid_t   fcpl = -1; /* file creation property list ID for HDF5 file */
     int     i;
 
     /* get user block size */
-    if(( fcpl = H5Fget_create_plist(fid)) < 0) {
+    if ((fcpl = H5Fget_create_plist(fid)) < 0) {
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed to retrieve file creation property list");
     }
 
-    if(H5Pget_userblock(fcpl, &ub_size) < 0) {
+    if (H5Pget_userblock(fcpl, &ub_size) < 0) {
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed to retrieve userblock size");
     }
 
-    if(H5Pclose(fcpl) < 0) {
+    if (H5Pclose(fcpl) < 0) {
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed to close property list");
     }
 
     /* open file */
-    if((fh = HDopen(filename, O_RDONLY)) < 0) {
+    if ((fh = HDopen(filename, O_RDONLY)) < 0) {
         HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed to open file <%s>", filename);
     }
 
     size = ub_size;
 
     /* read file */
-    while(size > 0) {
+    while (size > 0) {
         ssize_t nread; /* # of bytes read */
         char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
 
         /* read buffer */
-        if(size > USERBLOCK_XFER_SIZE)
+        if (size > USERBLOCK_XFER_SIZE)
             nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
         else
             nread = HDread(fh, rbuf, (size_t)size);
 
-        for(i = 0; i < nread; i++) {
+        for (i = 0; i < nread; i++) {
 
             printf("%c ", rbuf[i]);
 
         }
         printf("\n");
 
-        if(nread < 0) {
+        if (nread < 0) {
             HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
         }
 
@@ -1559,7 +1497,7 @@ void print_user_block(const char *filename, hid_t fid)
     }
 
 done:
-    if(fh > 0)
+    if (fh > 0)
         HDclose(fh);
 
     return;
diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c
index e968b3c..067ebad 100644
--- a/tools/src/h5repack/h5repack_filters.c
+++ b/tools/src/h5repack/h5repack_filters.c
@@ -42,7 +42,7 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */
     H5D_layout_t layout;
     int          rank;           /* rank of dataset */
     hsize_t      chsize[64];     /* chunk size in elements */
-    unsigned int i, j;
+    unsigned int i;
 
     /* get information about input filters */
     if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
@@ -240,7 +240,7 @@ int apply_filters(const char* name, /* object name from traverse list */
     int         nfilters;      /* number of filters in DCPL */
     hsize_t     chsize[64];    /* chunk size in elements */
     H5D_layout_t layout;
-    int         i, j;
+    int         i;
     pack_info_t obj;
     pack_info_t filtobj;
 
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index d34c394..037aa4a 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -31,7 +31,7 @@ const char *outfile = NULL;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E";
+static const char *s_opts = "hVvf:l:m:e:nLj:k:c:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "version", no_arg, 'V' },
@@ -42,6 +42,8 @@ static struct long_options l_opts[] = {
     { "file", require_arg, 'e' },
     { "native", no_arg, 'n' },
     { "latest", no_arg, 'L' },
+    { "low", require_arg, 'j' },
+    { "high", require_arg, 'k' },
     { "compact", require_arg, 'c' },
     { "indexed", require_arg, 'd' },
     { "ssize", require_arg, 's' },
@@ -82,6 +84,9 @@ static void usage(const char *prog) {
     PRINTVALSTREAM(rawoutstream, "   -V, --version           Print version number and exit\n");
     PRINTVALSTREAM(rawoutstream, "   -n, --native            Use a native HDF5 type when repacking\n");
     PRINTVALSTREAM(rawoutstream, "   -L, --latest            Use latest version of file format\n");
+    PRINTVALSTREAM(rawoutstream, "                           This option will take precedence over the -j and -k options\n");
+    PRINTVALSTREAM(rawoutstream, "   -j, --low               The low bound as in H5Pset_libver_bounds()\n");
+    PRINTVALSTREAM(rawoutstream, "   -k, --high              The high bound as in H5Pset_libver_bounds()\n");
     PRINTVALSTREAM(rawoutstream, "   -c L1, --compact=L1     Maximum number of links in header messages\n");
     PRINTVALSTREAM(rawoutstream, "   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
     PRINTVALSTREAM(rawoutstream, "   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
@@ -500,6 +505,22 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
                 options->latest = TRUE;
                 break;
 
+            case 'j':
+                options->low_bound = (H5F_libver_t)HDatoi(opt_arg);
+                if(options->low_bound < H5F_LIBVER_EARLIEST || options->low_bound > H5F_LIBVER_LATEST) {
+                    error_msg("in parsing low bound\n");
+                    goto done;
+                }
+                break;
+
+            case 'k':
+                options->high_bound = (H5F_libver_t)HDatoi(opt_arg);
+                if(options->high_bound < H5F_LIBVER_EARLIEST || options->high_bound > H5F_LIBVER_LATEST) {
+                    error_msg("in parsing high bound\n");
+                    goto done;
+                }
+                break;
+
             case 'c':
                 options->grp_compact = HDatoi( opt_arg );
                 if (options->grp_compact > 0)
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
index 376ab92..7b610a3 100644
--- a/tools/src/h5repack/h5repack_refs.c
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -145,7 +145,7 @@ int do_copy_refobjs(hid_t fidin,
                      *-------------------------------------------------------------------------
                      */
                     if(H5Tequal(mtype_id, H5T_STD_REF_OBJ)) {
-                        hid_t            refobj_id;
+                        hid_t            refobj_id = -1;
                         hobj_ref_t       *refbuf = NULL; /* buffer for object references */
                         hobj_ref_t       *buf = NULL;
                         const char*      refname;
@@ -189,7 +189,8 @@ int do_copy_refobjs(hid_t fidin,
                                             refname);
                                     }
                                 } /*refname*/
-                                H5Oclose(refobj_id);
+                                if (H5Oclose(refobj_id) < 0)
+                                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Oclose refob failed");
                             } /* u */
                         } /*nelmts*/
 
@@ -220,7 +221,7 @@ int do_copy_refobjs(hid_t fidin,
                      *-------------------------------------------------------------------------
                      */
                     else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) {
-                        hid_t            refobj_id;
+                        hid_t            refobj_id = -1;
                         hdset_reg_ref_t  *refbuf = NULL; /* input buffer for region references */
                         hdset_reg_ref_t  *buf = NULL;    /* output buffer */
                         const char*      refname;
@@ -259,7 +260,7 @@ int do_copy_refobjs(hid_t fidin,
                                  * in the second traversal of the file
                                  */
                                 if((refname = MapIdToName(refobj_id, travt)) != NULL) {
-                                    hid_t region_id;    /* region id of the referenced dataset */
+                                    hid_t region_id = -1;    /* region id of the referenced dataset */
 
                                     if((region_id = H5Rget_region(dset_in, H5R_DATASET_REGION, &buf[u])) < 0)
                                         HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rget_region failed");
@@ -276,7 +277,8 @@ int do_copy_refobjs(hid_t fidin,
                                             refname);
                                     }
                                 } /*refname*/
-                                H5Oclose(refobj_id);
+                                if (H5Oclose(refobj_id) < 0)
+                                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Oclose refobj_id failed");
                             } /* u */
                         } /*nelmts*/
 
@@ -377,7 +379,8 @@ int do_copy_refobjs(hid_t fidin,
      * This function is paired with copy_named_datatype() which is called
      * in copy_attr(), so need to free.
      */
-    named_datatype_free(&named_dt_head, 0);
+    if (named_datatype_free(&named_dt_head, 0) < 0)
+        H5TOOLS_INFO(H5E_tools_min_id_g, "named_datatype_free failed");
 
     return ret_value;
 
@@ -392,7 +395,7 @@ done:
         H5Tclose(ftype_id);
         H5Tclose(mtype_id);
         H5Tclose(type_in);
-        named_datatype_free(&named_dt_head, 0);
+        named_datatype_free(&named_dt_head, 1);
     } H5E_END_TRY;
 
     return ret_value;
@@ -478,20 +481,20 @@ static int copy_refs_attr(hid_t loc_in,
         is_ref = (type_class == H5T_REFERENCE);
 
         if(type_class == H5T_VLEN ) {
-            hid_t base_type;
+            hid_t base_type = H5Tget_super(ftype_id);
 
-            base_type = H5Tget_super(ftype_id);
             is_ref_vlen = (H5Tget_class(base_type) == H5T_REFERENCE);
             msize = H5Tget_size(base_type);
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
         }
         else if(type_class == H5T_ARRAY ) {
-            hid_t base_type;
+            hid_t base_type = H5Tget_super(ftype_id);
 
-            base_type = H5Tget_super(ftype_id);
             is_ref_array = (H5Tget_class(base_type) == H5T_REFERENCE);
             msize = H5Tget_size(base_type);
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
         }
         else if(type_class == H5T_COMPOUND) {
             int nmembers = H5Tget_nmembers(ftype_id) ;
@@ -511,7 +514,8 @@ static int copy_refs_attr(hid_t loc_in,
                     ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
                     ref_comp_field_n++;
                 }
-                H5Tclose(mtid);
+                if (H5Tclose(mtid) < 0)
+                    H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed");
             }
 
             /* if compound don't contain reference type member, free the above
@@ -533,9 +537,12 @@ static int copy_refs_attr(hid_t loc_in,
         is_ref_comp = (ref_comp_field_n > 0);
 
         if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) {
-            H5Tclose(mtype_id);
-            H5Tclose(ftype_id);
-            H5Aclose(attr_id);
+            if (H5Tclose(mtype_id) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtype_id failed");
+            if (H5Tclose(ftype_id) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose ftype_id failed");
+            if (H5Aclose(attr_id) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Aclose attr_id failed");
             continue;
         }
 
@@ -564,11 +571,11 @@ static int copy_refs_attr(hid_t loc_in,
             unsigned  array_rank = 0;
             hsize_t   array_size = 1;
             hsize_t array_dims[H5S_MAX_RANK];
-            hid_t base_type;
+            hid_t base_type = H5Tget_super(ftype_id);
 
-            base_type = H5Tget_super(ftype_id);
             msize = H5Tget_size(base_type);
-            H5Tclose(base_type);
+            if (H5Tclose(base_type) < 0)
+                H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
 
             array_rank = (unsigned)H5Tget_array_ndims(mtype_id);
             H5Tget_array_dims2(mtype_id, array_dims);