[svn-r14115] Description:

	Remove all plain calls to H5Gopen() from source, replacing them with
either H5Gopen2().

	Add test for H5Gopen1().

	Reformatted several pieces of code, to clean them up.

Tested on:
	FreeBSD/32 6.2 (duty)
	FreeBSD/64 6.2 (liberty)
	Linux/32 2.6 (kagiso)
	Linux/64 2.6 (smirom)
	Solaris/32 5.10 (linew)
	Mac OS X/32 10.4.10 (amazon)

17 files changed, 1205 insertions, 1298 deletions

diff --git a/tools/h5diff/h5diffgentest.c b/tools/h5diff/h5diffgentest.c
index 12acd77..fa3ec77 100644
--- a/tools/h5diff/h5diffgentest.c
+++ b/tools/h5diff/h5diffgentest.c
@@ -629,7 +629,7 @@ int test_attributes(const char *file,
 
     /* Create groups */
     gid  = H5Gcreate2(fid, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-    root_id   = H5Gopen(fid, "/");
+    root_id   = H5Gopen2(fid, "/", H5P_DEFAULT);
 
     /*-------------------------------------------------------------------------
     * write a series of attributes on the dataset, group, and root group
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index ac4c1d2..ec89210 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -28,10 +28,12 @@ const char  *progname = "h5dump";
 
 /* Macros for displaying objects */
 #define begin_obj(obj,name,begin)                               \
-    if (name)                                                   \
-        printf("%s \"%s\" %s\n", (obj), (name), (begin));       \
-    else                                                        \
-        printf("%s %s\n", (obj), (begin));
+    do {							\
+        if (name)                                               \
+            printf("%s \"%s\" %s\n", (obj), (name), (begin));   \
+        else                                                    \
+            printf("%s %s\n", (obj), (begin));			\
+    } while(0);
 
 #define end_obj(obj,end)                                        \
     if(HDstrlen(end)) {                                         \
@@ -1294,99 +1296,95 @@ dump_selected_attr(hid_t loc_id, const char *name)
           dump_header_format->attributeblockbegin);
     H5Gget_objinfo(loc_id, obj_name, FALSE, &statbuf);
 
-    switch (statbuf.type) {
-    case H5G_GROUP:
-    if ((oid = H5Gopen(loc_id, obj_name)) < 0) {
-        indentation(COL);
-            error_msg(progname, "unable to open group \"%s\"\n", obj_name);
-        end_obj(dump_header_format->attributeend,
-            dump_header_format->attributeblockend);
-        d_status = EXIT_FAILURE;
-        return FAIL;
-    }
-    break;
+    switch(statbuf.type) {
+        case H5G_GROUP:
+            if((oid = H5Gopen2(loc_id, obj_name, H5P_DEFAULT)) < 0) {
+                indentation(COL);
+                error_msg(progname, "unable to open group \"%s\"\n", obj_name);
+                end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend);
+                d_status = EXIT_FAILURE;
+                return FAIL;
+            } /* end if */
+            break;
 
-    case H5G_DATASET:
-    if ((oid = H5Dopen(loc_id, obj_name)) < 0) {
-        indentation(COL);
-            error_msg(progname, "unable to open dataset \"%s\"\n", obj_name);
-        end_obj(dump_header_format->attributeend,
-            dump_header_format->attributeblockend);
-        d_status = EXIT_FAILURE;
-        return FAIL;
-    }
-    break;
+        case H5G_DATASET:
+            if((oid = H5Dopen(loc_id, obj_name)) < 0) {
+                indentation(COL);
+                error_msg(progname, "unable to open dataset \"%s\"\n", obj_name);
+                end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend);
+                d_status = EXIT_FAILURE;
+                return FAIL;
+            } /* end if */
+            break;
 
-    case H5G_TYPE:
-    if ((oid = H5Topen(loc_id, obj_name)) < 0) {
-        indentation(COL);
-            error_msg(progname, "unable to open datatype \"%s\"\n", obj_name);
-        end_obj(dump_header_format->attributeend,
-            dump_header_format->attributeblockend);
-        d_status = EXIT_FAILURE;
-        return FAIL;
-    }
-    break;
+        case H5G_TYPE:
+            if((oid = H5Topen(loc_id, obj_name)) < 0) {
+                indentation(COL);
+                error_msg(progname, "unable to open datatype \"%s\"\n", obj_name);
+                end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend);
+                d_status = EXIT_FAILURE;
+                return FAIL;
+            } /* end if */
+            break;
 
-    default:
-    indentation(COL);
-        error_msg(progname, "unable to open unknown \"%s\"\n", obj_name);
-    end_obj(dump_header_format->attributeend,
-        dump_header_format->attributeblockend);
-    d_status = EXIT_FAILURE;
-    return FAIL;
-    }
+        default:
+            indentation(COL);
+            error_msg(progname, "unable to open unknown \"%s\"\n", obj_name);
+            end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend);
+            d_status = EXIT_FAILURE;
+            return FAIL;
+    } /* end switch */
 
-    if ((attr_id = H5Aopen_name(oid, attr_name)) >= 0) {
-    type = H5Aget_type(attr_id);
-    space = H5Aget_space(attr_id);
-    dump_datatype(type);
-    dump_dataspace(space);
+    if((attr_id = H5Aopen_name(oid, attr_name)) >= 0) {
+        type = H5Aget_type(attr_id);
+        space = H5Aget_space(attr_id);
+        dump_datatype(type);
+        dump_dataspace(space);
 
-    if (display_oid)
-        dump_oid(attr_id);
+        if(display_oid)
+            dump_oid(attr_id);
 
-    if (display_data || display_attr_data)
-        dump_data(attr_id, ATTRIBUTE_DATA, NULL, display_ai);
+        if(display_data || display_attr_data)
+            dump_data(attr_id, ATTRIBUTE_DATA, NULL, display_ai);
 
-    H5Tclose(type);
-    H5Sclose(space);
-    H5Aclose(attr_id);
-    end_obj(dump_header_format->attributeend,
+        H5Tclose(type);
+        H5Sclose(space);
+        H5Aclose(attr_id);
+        end_obj(dump_header_format->attributeend,
         dump_header_format->attributeblockend);
     } else {
-    indentation(COL);
+        indentation(COL);
         error_msg(progname, "unable to open attribute \"%s\"\n", obj_name);
-    end_obj(dump_header_format->attributeend,
-        dump_header_format->attributeblockend);
-    d_status = EXIT_FAILURE;
-    }
-
-    switch (statbuf.type) {
-    case H5G_GROUP:
-    if (H5Gclose(oid) < 0) {
+        end_obj(dump_header_format->attributeend, dump_header_format->attributeblockend);
         d_status = EXIT_FAILURE;
-        return FAIL;
     }
-    break;
 
-    case H5G_DATASET:
-    if (H5Dclose(oid) < 0) {
-        d_status = EXIT_FAILURE;
-        return FAIL;
-    }
-    break;
+    switch(statbuf.type) {
+        case H5G_GROUP:
+            if(H5Gclose(oid) < 0) {
+                d_status = EXIT_FAILURE;
+                return FAIL;
+            } /* end if */
+            break;
 
-    case H5G_TYPE:
-    if (H5Tclose(oid) < 0) {
-        d_status = EXIT_FAILURE;
-        return FAIL;
-    }
-    break;
-    default:
-    d_status = EXIT_FAILURE;
-    return FAIL;
-    }
+        case H5G_DATASET:
+            if(H5Dclose(oid) < 0) {
+                d_status = EXIT_FAILURE;
+                return FAIL;
+            } /* end if */
+            break;
+
+        case H5G_TYPE:
+            if(H5Tclose(oid) < 0) {
+                d_status = EXIT_FAILURE;
+                return FAIL;
+            } /* end if */
+            break;
+
+        default:
+            d_status = EXIT_FAILURE;
+            return FAIL;
+    } /* end switch */
 
     free(obj_name);
     return SUCCEED;
@@ -1542,130 +1540,124 @@ dump_all(hid_t group, const char *name, void * op_data)
             break;
         }
         case H5G_UDLINK:
-        {
             indentation(indent);
             switch(linfo.type) {
-              case H5L_TYPE_EXTERNAL:
-              {
-                char *targbuf;
-
-                targbuf = HDmalloc(statbuf.linklen);
-                HDassert(targbuf);
-                if(!doxml) {
-                    begin_obj(dump_header_format->extlinkbegin, name, dump_header_format->extlinkblockbegin);
-                } /* end if */
+                case H5L_TYPE_EXTERNAL:
+                    {
+                    char *targbuf;
 
-                if(H5Lget_val(group, name, targbuf, statbuf.linklen, H5P_DEFAULT) < 0) {
-                    error_msg(progname, "unable to get external link value\n");
-                    d_status = EXIT_FAILURE;
-                    ret = FAIL;
-                } else {
-                    const char *filename;
-                    const char *targname;
+                    targbuf = HDmalloc(statbuf.linklen);
+                    HDassert(targbuf);
+                    if(!doxml)
+                        begin_obj(dump_header_format->extlinkbegin, name, dump_header_format->extlinkblockbegin);
 
-                    if(H5Lunpack_elink_val(targbuf, statbuf.linklen, NULL, &filename, &targname) < 0) {
-                      error_msg(progname, "unable to unpack external link value\n");
-                      d_status = EXIT_FAILURE;
-                      ret = FAIL;
+                    if(H5Lget_val(group, name, targbuf, statbuf.linklen, H5P_DEFAULT) < 0) {
+                        error_msg(progname, "unable to get external link value\n");
+                        d_status = EXIT_FAILURE;
+                        ret = FAIL;
                     } else {
-                      if (!doxml) {
-                          indentation(indent + COL);
-                          printf("LINKCLASS %d\n", linfo.type);
-                          indentation(indent + COL);
-                          printf("TARGETFILE \"%s\"\n", filename);
-                          indentation(indent + COL);
-                          printf("TARGETPATH \"%s\"\n", targname);
-                      }
-                      else /* XML */
-                      {
-                        char linkxid[100];
-                        char parentxid[100];
-                        char *t_name = xml_escape_the_name(name);
-                        char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
-                        char *t_obj_path = xml_escape_the_name(obj_path);
-                        char *t_filename = xml_escape_the_name(filename);
-                        char *t_targname = xml_escape_the_name(targname);
-
-                        /* Create OBJ-XIDs for the parent and object */
-                        xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1);
-                        xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1);
-
-                            printf("<%sExternalLink LinkName=\"%s\" "
-                                  "OBJ-XID=\"%s\" "
-                                  "H5SourcePath=\"%s\" "
-                                  "TargetFilename=\"%s\"  "
-                                  "TargetPath=\"%s\"  "
-                                  "Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
-                                    xmlnsprefix,
-                                    t_name,         /* LinkName */
-                                    linkxid,        /* OBJ-XID */
-                                    t_obj_path,     /* H5SourcePath */
-                                    filename,       /* TargetFilename */
-                                    targname,       /* TargetPath*/
-                                    parentxid,      /* Parents */
-                                    t_prefix);      /* H5ParentPaths */
-                        HDfree(t_prefix);
-                        HDfree(t_name);
-                        HDfree(t_filename);
-                        HDfree(t_targname);
-                        HDfree(t_obj_path);
-                      }
+                        const char *filename;
+                        const char *targname;
+
+                        if(H5Lunpack_elink_val(targbuf, statbuf.linklen, NULL, &filename, &targname) < 0) {
+                                error_msg(progname, "unable to unpack external link value\n");
+                                d_status = EXIT_FAILURE;
+                                ret = FAIL;
+                        } else {
+                            if (!doxml) {
+                                indentation(indent + COL);
+                                printf("LINKCLASS %d\n", linfo.type);
+                                indentation(indent + COL);
+                                printf("TARGETFILE \"%s\"\n", filename);
+                                indentation(indent + COL);
+                                printf("TARGETPATH \"%s\"\n", targname);
+                            }
+                            /* XML */
+                            else {
+                                char linkxid[100];
+                                char parentxid[100];
+                                char *t_name = xml_escape_the_name(name);
+                                char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
+                                char *t_obj_path = xml_escape_the_name(obj_path);
+                                char *t_filename = xml_escape_the_name(filename);
+                                char *t_targname = xml_escape_the_name(targname);
+
+                                /* Create OBJ-XIDs for the parent and object */
+                                xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1);
+                                xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1);
+
+                                printf("<%sExternalLink LinkName=\"%s\" "
+                                          "OBJ-XID=\"%s\" "
+                                          "H5SourcePath=\"%s\" "
+                                          "TargetFilename=\"%s\"  "
+                                          "TargetPath=\"%s\"  "
+                                          "Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
+                                            xmlnsprefix,
+                                            t_name,         /* LinkName */
+                                            linkxid,        /* OBJ-XID */
+                                            t_obj_path,     /* H5SourcePath */
+                                            filename,       /* TargetFilename */
+                                            targname,       /* TargetPath*/
+                                            parentxid,      /* Parents */
+                                            t_prefix);      /* H5ParentPaths */
+                                HDfree(t_prefix);
+                                HDfree(t_name);
+                                HDfree(t_filename);
+                                HDfree(t_targname);
+                                HDfree(t_obj_path);
+                            }
+                        }
                     }
-                }
-                if (!doxml) {
-                    end_obj(dump_header_format->extlinkend,
-                            dump_header_format->extlinkblockend);
-                }
-                HDfree(targbuf);
-              }
-              break;
+                    if (!doxml)
+                        end_obj(dump_header_format->extlinkend, dump_header_format->extlinkblockend);
+                    HDfree(targbuf);
+                  }
+                  break;
+
               default:
                   if (!doxml) {
-                      begin_obj(dump_header_format->udlinkbegin, name,
-                                dump_header_format->udlinkblockbegin);
+                      begin_obj(dump_header_format->udlinkbegin, name, dump_header_format->udlinkblockbegin);
                       indentation(indent + COL);
                   }
-                  if (!doxml) {
+                  if (!doxml)
                       printf("LINKCLASS %d\n", linfo.type);
-                  }
                   else /* XML */
                   {
-                    char linkxid[100];
-                    char parentxid[100];
-                    char *t_name = xml_escape_the_name(name);
-                    char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
-                    char *t_obj_path = xml_escape_the_name(obj_path);
-
-                    /* Create OBJ-XIDs for the parent and object */
-                    xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1);
-                    xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1);
-
-                        printf("<%sUserDefined LinkName=\"%s\" "
-                               "OBJ-XID=\"%s\" "
-                               "H5SourcePath=\"%s\" "
-                               "LinkClass=\"%d\"  "
-                               "Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
-                                xmlnsprefix,
-                                t_name,             /* LinkName */
-                                linkxid,            /* OBJ-XID */
-                                t_obj_path,         /* H5SourcePath */
-                                linfo.type,    /* LinkClass */
-                                parentxid,          /* Parents */
-                                t_prefix);          /* H5ParentPaths */
-                    HDfree(t_prefix);
-                    HDfree(t_name);
-                    HDfree(t_obj_path);
+                      char linkxid[100];
+                      char parentxid[100];
+                      char *t_name = xml_escape_the_name(name);
+                      char *t_prefix = xml_escape_the_name(HDstrcmp(prefix,"") ? prefix : "/");
+                      char *t_obj_path = xml_escape_the_name(obj_path);
+
+                      /* Create OBJ-XIDs for the parent and object */
+                      xml_name_to_XID(t_obj_path, linkxid, sizeof(linkxid), 1);
+                      xml_name_to_XID(prefix, parentxid, sizeof(parentxid), 1);
+
+                      printf("<%sUserDefined LinkName=\"%s\" "
+                                 "OBJ-XID=\"%s\" "
+                                 "H5SourcePath=\"%s\" "
+                                 "LinkClass=\"%d\"  "
+                                 "Parents=\"%s\" H5ParentPaths=\"%s\" />\n",
+                                  xmlnsprefix,
+                                  t_name,             /* LinkName */
+                                  linkxid,            /* OBJ-XID */
+                                  t_obj_path,         /* H5SourcePath */
+                                  linfo.type,    /* LinkClass */
+                                  parentxid,          /* Parents */
+                                  t_prefix);          /* H5ParentPaths */
+                      HDfree(t_prefix);
+                      HDfree(t_name);
+                      HDfree(t_obj_path);
                   }
                   if (!doxml) {
                       indentation(indent);
-                      end_obj(dump_header_format->udlinkend,
-                              dump_header_format->udlinkblockend);
+                      end_obj(dump_header_format->udlinkend, dump_header_format->udlinkblockend);
                   }
             }
             break;
-          }
+
         case H5G_GROUP:
-            if ((obj = H5Gopen(group, name)) < 0) {
+            if((obj = H5Gopen2(group, name, H5P_DEFAULT)) < 0) {
                 error_msg(progname, "unable to dump group \"%s\"\n", name);
                 d_status = EXIT_FAILURE;
                 ret = FAIL;
@@ -1689,7 +1681,6 @@ dump_all(hid_t group, const char *name, void * op_data)
                 /* Close group */
                 H5Gclose(obj);
             }
-
             break;
 
         case H5G_DATASET:
@@ -3173,29 +3164,27 @@ handle_groups(hid_t fid, char *group, void UNUSED * data)
 {
     hid_t       gid;
 
-    if ((gid = H5Gopen(fid, group)) < 0) {
-        begin_obj(dump_header_format->groupbegin, group,
-                  dump_header_format->groupblockbegin);
+    if((gid = H5Gopen2(fid, group, H5P_DEFAULT)) < 0) {
+        begin_obj(dump_header_format->groupbegin, group, dump_header_format->groupblockbegin);
         indentation(COL);
         error_msg(progname, "unable to open group \"%s\"\n", group);
-        end_obj(dump_header_format->groupend,
-                dump_header_format->groupblockend);
+        end_obj(dump_header_format->groupend, dump_header_format->groupblockend);
         d_status = EXIT_FAILURE;
     } else {
         size_t new_len = HDstrlen(group) + 1;
 
-        if (prefix_len <= new_len) {
+        if(prefix_len <= new_len) {
             prefix_len = new_len;
             prefix = HDrealloc(prefix, prefix_len);
-        }
+        } /* end if */
 
         HDstrcpy(prefix, group);
         dump_group(gid, group);
 
-        if (H5Gclose(gid) < 0)
+        if(H5Gclose(gid) < 0)
             d_status = EXIT_FAILURE;
-    }
-}
+    } /* end else */
+} /* end handle_groups() */
 
 /*-------------------------------------------------------------------------
  * Function:    handle_links
@@ -3797,32 +3786,31 @@ main(int argc, const char *argv[])
     init_ref_path_table(fid);      /* Insert the root group into the ref. path table */
     H5Giterate(fid, (const char *)"/", NULL, fill_ref_path_table, (void *)"");
 
-    if (doxml) {
-    /* initialize XML */
+    if(doxml) {
+        /* initialize XML */
 
-    /* reset prefix! */
-    HDstrcpy(prefix, "");
+        /* reset prefix! */
+        HDstrcpy(prefix, "");
 
-    /* make sure the URI is initialized to something */
-    if (xml_dtd_uri == NULL) {
-        if (useschema) {
-            xml_dtd_uri = DEFAULT_XSD;
+        /* make sure the URI is initialized to something */
+        if (xml_dtd_uri == NULL) {
+            if (useschema) {
+                xml_dtd_uri = DEFAULT_XSD;
+            } else {
+                xml_dtd_uri = DEFAULT_DTD;
+                xmlnsprefix = "";
+            }
         } else {
-            xml_dtd_uri = DEFAULT_DTD;
-            xmlnsprefix = "";
-        }
-    } else {
-        if (useschema && strcmp(xmlnsprefix,"")) {
-        error_msg(progname, "Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n");
-            leave(EXIT_FAILURE);
+            if (useschema && strcmp(xmlnsprefix,"")) {
+                error_msg(progname, "Cannot set Schema URL for a qualified namespace--use -X or -U option with -D \n");
+                leave(EXIT_FAILURE);
+            }
         }
     }
-    }
 
     /* find all shared objects */
     if(init_objs(fid, &info, &group_table, &dset_table, &type_table) < 0) {
-        error_msg(progname, "internal error (file %s:line %d)\n",
-                  __FILE__, __LINE__);
+        error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__);
         d_status = EXIT_FAILURE;
         goto done;
     }
@@ -3882,42 +3870,40 @@ main(int argc, const char *argv[])
             dump_fcpl(fid);
     }
 
-    if (display_all) {
-        if ((gid = H5Gopen(fid, "/")) < 0) {
+    if(display_all) {
+        if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0) {
             error_msg(progname, "unable to open root group\n");
             d_status = EXIT_FAILURE;
         } else {
-        dump_function_table->dump_group_function(gid, "/");
+            dump_function_table->dump_group_function(gid, "/");
         }
 
-        if (H5Gclose(gid) < 0) {
+        if(H5Gclose(gid) < 0) {
             error_msg(progname, "unable to close root group\n");
             d_status = EXIT_FAILURE;
         }
     } else {
-    if (doxml) {
         /* Note: this option is not supported for XML */
-            error_msg(progname, "internal error (file %s:line %d)\n",
-                      __FILE__, __LINE__);
+        if(doxml) {
+            error_msg(progname, "internal error (file %s:line %d)\n", __FILE__, __LINE__);
             d_status = EXIT_FAILURE;
-        goto done;
-    }
+            goto done;
+        } /* end if */
 
-        for (i = 0; i < argc; i++)
-            if (hand[i].func)
+        for(i = 0; i < argc; i++)
+            if(hand[i].func)
                 hand[i].func(fid, hand[i].obj, hand[i].subset_info);
     }
 
     if (!doxml) {
-    end_obj(dump_header_format->fileend,
-        dump_header_format->fileblockend);
+        end_obj(dump_header_format->fileend, dump_header_format->fileblockend);
     } else {
-    printf("</%sHDF5-File>\n", xmlnsprefix);
+        printf("</%sHDF5-File>\n", xmlnsprefix);
     }
 
 done:
     if (H5Fclose(fid) < 0)
-    d_status = EXIT_FAILURE;
+        d_status = EXIT_FAILURE;
 
     free_handler(hand, argc);
 
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c
index 321a15d..38b1f27 100644
--- a/tools/h5dump/h5dumpgentest.c
+++ b/tools/h5dump/h5dumpgentest.c
@@ -225,7 +225,8 @@ typedef struct s1_t {
 /* "File 51" macros */
 #define F51_MAX_NAME_LEN    ((64*1024)+1024)
 
-static void gent_group(void)
+static void
+gent_group(void)
 {
     hid_t fid, group;
 
@@ -270,7 +271,8 @@ static void gent_group(void)
     H5Fclose(fid);
 }
 
-static void gent_dataset(void)
+static void
+gent_dataset(void)
 {
     hid_t fid, dataset, space;
     hsize_t dims[2];
@@ -309,7 +311,8 @@ static void gent_dataset(void)
     H5Fclose(fid);
 }
 
-static void gent_dataset2(void)
+static void
+gent_dataset2(void)
 {
     hid_t fid, dataset, space, create_plist;
     hsize_t dims[2];
@@ -356,7 +359,8 @@ static void gent_dataset2(void)
 }
 
 
-static void gent_attribute(void)
+static void
+gent_attribute(void)
 {
     hid_t fid, root, space, attr, type;
     hsize_t dims[2];
@@ -367,7 +371,7 @@ static void gent_attribute(void)
     int point = 100;
 
     fid = H5Fcreate(FILE3, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    root = H5Gopen (fid, "/");
+    root = H5Gopen2(fid, "/", H5P_DEFAULT);
 
     /* attribute 1 */
     dims[0] = 24;
@@ -426,7 +430,7 @@ static void gent_softlink(void)
     hid_t fid, root;
 
     fid = H5Fcreate(FILE4, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    root = H5Gopen (fid, "/");
+    root = H5Gopen2(fid, "/", H5P_DEFAULT);
     H5Glink (root, H5L_TYPE_SOFT, "somevalue", "slink1");
     H5Glink (root, H5L_TYPE_SOFT, "linkvalue", "slink2");
 
@@ -472,7 +476,7 @@ static void gent_hardlink(void)
     H5Glink (group, H5L_TYPE_HARD, "/dset1", "dset3");
     H5Gclose(group);
 
-    group = H5Gopen(fid, "/g1");
+    group = H5Gopen2(fid, "/g1", H5P_DEFAULT);
     H5Glink (group, H5L_TYPE_HARD, "/g2", "g1.1");
     H5Gclose(group);
 
@@ -921,7 +925,7 @@ static void gent_all(void)
   H5Gclose(group);
 
   /* root attributes */
-  group = H5Gopen (fid, "/");
+  group = H5Gopen2(fid, "/", H5P_DEFAULT);
 
   dims[0] = 10;
   space = H5Screate_simple(1, dims, NULL);
@@ -941,7 +945,7 @@ static void gent_all(void)
 
   H5Gclose(group);
 
-  group = H5Gopen (fid, "/g1/g1.1");
+  group = H5Gopen2(fid, "/g1/g1.1", H5P_DEFAULT);
 
   /* dset1.1.1 */
   dims[0] = 10; dims[1] = 10;
@@ -988,11 +992,11 @@ static void gent_all(void)
   H5Lcreate_external("somefile", "somepath", fid, "/g1/g1.2/extlink", H5P_DEFAULT, H5P_DEFAULT);
 
   /* soft link */
-  group = H5Gopen (fid, "/g1/g1.2/g1.2.1");
+  group = H5Gopen2(fid, "/g1/g1.2/g1.2.1", H5P_DEFAULT);
   H5Glink (group, H5L_TYPE_SOFT, "somevalue", "slink");
   H5Gclose(group);
 
-  group = H5Gopen (fid, "/g2");
+  group = H5Gopen2(fid, "/g2", H5P_DEFAULT);
 
   /* dset2.1 */
   dims[0] = 10;
@@ -1238,7 +1242,7 @@ static void gent_many(void)
   H5Sclose(space);
   H5Gclose(group);
 
-  group = H5Gopen(fid, "/g3");
+  group = H5Gopen2(fid, "/g3", H5P_DEFAULT);
   H5Glink (group, H5L_TYPE_HARD, "/g4/dset2", "link3");
   H5Gclose(group);
 
@@ -1261,7 +1265,7 @@ static void gent_many(void)
   H5Sclose(space);
   H5Gclose(group);
 
-  group = H5Gopen(fid, "/g5");
+  group = H5Gopen2(fid, "/g5", H5P_DEFAULT);
   H5Glink (group, H5L_TYPE_SOFT, "/g6/dset3", "slink4");
   H5Gclose(group);
   H5Pclose(create_plist);
@@ -2937,7 +2941,7 @@ void gent_split_file(void)
     fapl = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_split(fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT);
     fid = H5Fcreate(FILE34, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
-    root = H5Gopen(fid, "/");
+    root = H5Gopen2(fid, "/", H5P_DEFAULT);
 
     atype = H5Tcopy(H5T_C_S1);
     H5Tset_size(atype, strlen(meta) + 1);
@@ -3112,7 +3116,7 @@ static void gent_vlstr(void)
     H5Tcommit(fid1, "vl_string_type", tid1);
 
     /* Create an group attribute of VL string type */
-    root = H5Gopen(fid1, "/");
+    root = H5Gopen2(fid1, "/", H5P_DEFAULT);
     dataspace = H5Screate(H5S_SCALAR);
 
     att = H5Acreate(root, "test_scalar", tid1, dataspace, H5P_DEFAULT);
@@ -4094,7 +4098,7 @@ static void gent_attr_all(void)
     /* Create groups */
     group_id  = H5Gcreate2(fid, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
     group2_id = H5Gcreate2(fid, "g2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-    root_id   = H5Gopen(fid, "/");
+    root_id   = H5Gopen2(fid, "/", H5P_DEFAULT);
 
     /*-------------------------------------------------------------------------
     * write a series of attributes on the dataset, group
@@ -4497,7 +4501,7 @@ static void gent_null_space(void)
     int point = 4;
 
     fid = H5Fcreate(FILE45, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    root = H5Gopen (fid, "/");
+    root = H5Gopen2(fid, "/", H5P_DEFAULT);
 
     /* null space */
     space = H5Screate(H5S_NULL);
@@ -5017,7 +5021,7 @@ static void gent_fcontents(void)
 
 
     /* hard link to "g2" */
-    gid1 = H5Gopen(fid, "/g1");
+    gid1 = H5Gopen2(fid, "/g1", H5P_DEFAULT);
     H5Glink (gid1, H5L_TYPE_HARD, "/g2", "g1.1");
     H5Gclose(gid1);
 
@@ -5626,7 +5630,8 @@ gent_binary(void)
 #define GB4LL    ((unsigned long_long) 4*1024*1024*1024)
 #define DIM_4GB  (GB4LL + 10)
 
-static void gent_bigdims(void)
+static void
+gent_bigdims(void)
 {
     hid_t   fid;
     hid_t   did;
@@ -5727,27 +5732,28 @@ out:
  *
  *-------------------------------------------------------------------------
  */
-static void gent_hyperslab(void)
+static void
+gent_hyperslab(void)
 {
- hid_t    fid;     /* file id */
- hsize_t  dims[2]  = {32,4097}; /* big enough data size to force a second stripmine read */
- double   *buf;
- int      i, ret;
+    hid_t    fid;     /* file id */
+    hsize_t  dims[2]  = {32,4097}; /* big enough data size to force a second stripmine read */
+    double   *buf;
+    int      i, ret;
 
- buf = malloc(32 * 4097 * sizeof(double) );
- for (i = 0; i < 32 * 4097; i++)
-  buf[i] = 1;
+    buf = malloc(32 * 4097 * sizeof(double) );
+    for (i = 0; i < 32 * 4097; i++)
+        buf[i] = 1;
 
- /* create a file */
- fid  = H5Fcreate(FILE57, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
- assert(fid>=0);
+    /* create a file */
+    fid  = H5Fcreate(FILE57, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    assert(fid>=0);
 
- write_dset(fid,2,dims,"stripmine",H5T_NATIVE_DOUBLE,buf);
+    write_dset(fid,2,dims,"stripmine",H5T_NATIVE_DOUBLE,buf);
 
- ret=H5Fclose(fid);
- assert(ret>=0);
+    ret=H5Fclose(fid);
+    assert(ret>=0);
 
- free(buf);
+    free(buf);
 }
 
 
diff --git a/tools/h5import/h5import.c b/tools/h5import/h5import.c
index b494a67..1babd9e 100755
--- a/tools/h5import/h5import.c
+++ b/tools/h5import/h5import.c
@@ -852,7 +852,7 @@ processStrData(FILE **strm, struct Input *in, hid_t file_id)
             j = 0;
             handle = file_id;
             while(j < in->path.count - 1) {
-                if((group_id = H5Gopen(handle, in->path.group[j])) < 0) {
+                if((group_id = H5Gopen2(handle, in->path.group[j], H5P_DEFAULT)) < 0) {
                     group_id = H5Gcreate2(handle, in->path.group[j++], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                     for(; j < in->path.count - 1; j++)
                         group_id = H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@@ -2444,7 +2444,7 @@ process(struct Options *opt)
             j = 0;
             handle = file_id;
             while(j < in->path.count - 1) {
-                if((group_id = H5Gopen(handle, in->path.group[j])) < 0) {
+                if((group_id = H5Gopen2(handle, in->path.group[j], H5P_DEFAULT)) < 0) {
                   group_id = H5Gcreate2(handle, in->path.group[j++], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                   for (; j < in->path.count - 1; j++)
                     group_id = H5Gcreate2(group_id, in->path.group[j], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
diff --git a/tools/h5jam/h5jamgentest.c b/tools/h5jam/h5jamgentest.c
index d0c1283..fe31658 100644
--- a/tools/h5jam/h5jamgentest.c
+++ b/tools/h5jam/h5jamgentest.c
@@ -203,7 +203,7 @@ gent_ub(const char * filename, size_t ub_size, size_t ub_fill)
   H5Gclose(group);
 
   /* root attributes */
-  group = H5Gopen(fid, "/");
+  group = H5Gopen2(fid, "/", H5P_DEFAULT);
 
   dims[0] = 10;
   space = H5Screate_simple(1, dims, NULL);
@@ -223,7 +223,7 @@ gent_ub(const char * filename, size_t ub_size, size_t ub_fill)
 
   H5Gclose(group);
 
-  group = H5Gopen (fid, "/g1/g1.1");
+  group = H5Gopen2(fid, "/g1/g1.1", H5P_DEFAULT);
 
   /* dset1.1.1 */
   dims[0] = 10; dims[1] = 10;
@@ -270,11 +270,11 @@ gent_ub(const char * filename, size_t ub_size, size_t ub_fill)
   H5Lcreate_external("somefile", "somepath", fid, "/g1/g1.2/extlink", H5P_DEFAULT, H5P_DEFAULT);
 
   /* soft link */
-  group = H5Gopen (fid, "/g1/g1.2/g1.2.1");
+  group = H5Gopen2(fid, "/g1/g1.2/g1.2.1", H5P_DEFAULT);
   H5Glink (group, H5L_TYPE_SOFT, "somevalue", "slink");
   H5Gclose(group);
 
-  group = H5Gopen (fid, "/g2");
+  group = H5Gopen2(fid, "/g2", H5P_DEFAULT);
 
   /* dset2.1 */
   dims[0] = 10;
diff --git a/tools/h5ls/h5ls.c b/tools/h5ls/h5ls.c
index a362250..f127f3f 100644
--- a/tools/h5ls/h5ls.c
+++ b/tools/h5ls/h5ls.c
@@ -62,7 +62,7 @@ static struct {
 /* Information about how to display each type of object */
 static struct dispatch_t {
     const char *name;
-    hid_t (*open)(hid_t loc, const char *name);
+    hid_t (*open)(hid_t loc, const char *name, hid_t apl_id);
     herr_t (*close)(hid_t obj);
     herr_t (*list1)(hid_t obj);
     herr_t (*list2)(hid_t obj, const char *name);
@@ -1728,11 +1728,11 @@ datatype_list2(hid_t type, const char UNUSED *name)
  *-------------------------------------------------------------------------
  */
 static hid_t
-slink_open(hid_t location, const char *name)
+slink_open(hid_t location, const char *name, hid_t UNUSED apl_id)
 {
     H5G_stat_t  statbuf;
 
-    if (H5Gget_objinfo(location, name, FALSE, &statbuf) < 0) 
+    if(H5Gget_objinfo(location, name, FALSE, &statbuf) < 0) 
         return -1;
 
     if(statbuf.type == H5G_LINK) {    /* Soft link */
@@ -1771,7 +1771,7 @@ slink_open(hid_t location, const char *name)
  *-------------------------------------------------------------------------
  */
 static hid_t
-udlink_open(hid_t location, const char *name)
+udlink_open(hid_t location, const char *name, hid_t UNUSED apl_id)
 {
     H5L_info_t linfo;
     char * buf = NULL;
@@ -1789,7 +1789,8 @@ udlink_open(hid_t location, const char *name)
             if(H5Lget_val(location, name, buf, linfo.u.val_size, H5P_DEFAULT) < 0)
                 goto error;
 
-            if(H5Lunpack_elink_val(buf, linfo.u.val_size, NULL, &filename, &path) < 0) goto error;
+            if(H5Lunpack_elink_val(buf, linfo.u.val_size, NULL, &filename, &path) < 0)
+                goto error;
             HDfputs("file: ", stdout);
             HDfputs(filename, stdout);
             HDfputs("    path: ", stdout);
@@ -1879,17 +1880,16 @@ list (hid_t group, const char *name, void *_iter)
 
     /* Open the object.  Not all objects can be opened.  If this is the case
      * then return right away. */
-    if (sb.type>=0 &&
-            (NULL==dispatch_g[sb.type].open ||
-            (obj=(dispatch_g[sb.type].open)(group, name))<0)) {
+    if(sb.type >= 0 &&
+            (NULL == dispatch_g[sb.type].open ||
+            (obj = (dispatch_g[sb.type].open)(group, name, H5P_DEFAULT)) < 0)) {
         printf(" *ERROR*\n");
         goto done;
-    }
+    } /* end if */
 
     /* List the first line of information for the object. */
-    if (sb.type>=0 && dispatch_g[sb.type].list1) {
+    if(sb.type >= 0 && dispatch_g[sb.type].list1)
         (dispatch_g[sb.type].list1)(obj);
-    }
     putchar('\n');
 
     /* Show detailed information about the object, beginning with information
@@ -2120,9 +2120,9 @@ main (int argc, const char *argv[])
     h5tools_init();
 
     /* Build display table */
-    DISPATCH(H5G_DATASET, "Dataset", H5Dopen, H5Dclose, dataset_list1, dataset_list2);
-    DISPATCH(H5G_GROUP, "Group", H5Gopen, H5Gclose, NULL, group_list2);
-    DISPATCH(H5G_TYPE, "Type", H5Topen, H5Tclose, NULL, datatype_list2);
+    DISPATCH(H5G_DATASET, "Dataset", H5Dopen2, H5Dclose, dataset_list1, dataset_list2);
+    DISPATCH(H5G_GROUP, "Group", H5Gopen2, H5Gclose, NULL, group_list2);
+    DISPATCH(H5G_TYPE, "Type", H5Topen2, H5Tclose, NULL, datatype_list2);
     DISPATCH(H5G_LINK, "-> ", slink_open, NULL, NULL, NULL);
     DISPATCH(H5G_UDLINK, "-> ", udlink_open, NULL, NULL, NULL);
 
@@ -2317,30 +2317,31 @@ main (int argc, const char *argv[])
             fprintf(stderr, "%s: unable to open file\n", argv[argno-1]);
             continue;
         }
-        if (oname) oname++;
-        if (!oname || !*oname) oname = root_name;
+        if(oname)
+            oname++;
+        if(!oname || !*oname)
+            oname = root_name;
 
         /* Open the object and display it's information */
-        if (H5Gget_objinfo(file, oname, TRUE, &sb)>=0 &&
-                H5G_GROUP==sb.type && !grp_literal_g) {
-            /* Specified name is a group. List the complete contents of the
-             * group. */
+        if(H5Gget_objinfo(file, oname, TRUE, &sb) >= 0 && H5G_GROUP == sb.type && !grp_literal_g) {
+            /* Specified name is a group. List the complete contents of the group. */
             sym_insert(&sb, oname);
-            iter.container = container = fix_name(show_file_name_g?fname:"", oname);
+            iter.container = container = fix_name((show_file_name_g ? fname : ""), oname);
+
             /* list root attributes */
-            if (verbose_g>0)
-            {
-             if ((root=H5Gopen(file, "/"))<0)
-              leave(1);
-             H5Aiterate(root, NULL, list_attr, NULL);
-             if (H5Gclose(root)<0)
-              leave(1);
-            }
+            if(verbose_g > 0) {
+                if((root = H5Gopen2(file, "/", H5P_DEFAULT)) < 0)
+                    leave(1);
+                H5Aiterate(root, NULL, list_attr, NULL);
+                if(H5Gclose(root) < 0)
+                    leave(1);
+            } /* end if */
+
             /* list */
             H5Giterate(file, oname, NULL, list, &iter);
             free(container);
 
-        } else if ((root=H5Gopen(file, "/"))<0) {
+        } else if((root = H5Gopen2(file, "/", H5P_DEFAULT)) < 0) {
             leave(1); /*major problem!*/
 
         } else {
@@ -2348,7 +2349,8 @@ main (int argc, const char *argv[])
             * container for the object is everything up to the base name. */
             iter.container = show_file_name_g ? fname : "/";
             list(root, oname, &iter);
-            if (H5Gclose(root)<0) leave(1);
+            if(H5Gclose(root) < 0)
+                leave(1);
         }
         H5Fclose(file);
         free(fname);
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index f8f642b..d986cc0 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -174,10 +174,6 @@ int apply_filters(const char* name,    /* object name from traverse list */
                   pack_opt_t *options, /* repack options */
                   int *has_filter);     /* (OUT) object NAME has a filter */
 
-int has_filter(hid_t dcpl_id,
-               H5Z_filter_t filtnin);
-
-
 int can_read(const char* name,    /* object name from traverse list */
              hid_t dcpl_id,       /* dataset creation property list */
              pack_opt_t *options); /* repack options */
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index e9a89e2..f32d15d 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -281,566 +281,547 @@ int do_copy_objects(hid_t fidin,
                     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_id=-1;        /* group creation property list */
- hid_t    type_in=-1;        /* named type ID */
- hid_t    type_out=-1;       /* named type ID */
- hid_t    dcpl_id=-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 */
- size_t   msize;             /* size of type */
- hsize_t  nelmts;            /* number of elements in 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 */
- double   per;               /* percent utilization of storage */
- void     *buf=NULL;         /* buffer for raw data */
- void     *sm_buf=NULL;      /* buffer for raw data */
- int      has_filter;        /* current object has a filter */
- unsigned i;
- int      is_ref=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_id=-1;        /* group creation property list */
+    hid_t    type_in=-1;        /* named type ID */
+    hid_t    type_out=-1;       /* named type ID */
+    hid_t    dcpl_id=-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 */
+    size_t   msize;             /* size of type */
+    hsize_t  nelmts;            /* number of elements in 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 */
+    double   per;               /* percent utilization of storage */
+    void     *buf=NULL;         /* buffer for raw data */
+    void     *sm_buf=NULL;      /* buffer for raw data */
+    int      has_filter;        /* current object has a filter */
+    unsigned i;
+    int      is_ref=0;
 
-/*-------------------------------------------------------------------------
- * copy the suppplied object list
- *-------------------------------------------------------------------------
- */
-
- if (options->verbose) {
-  printf("-----------------------------------------\n");
-  printf(" Type     Filter (Ratio)     Name\n");
-  printf("-----------------------------------------\n");
- }
-
- for ( i = 0; i < travt->nobjs; i++)
- {
-
-  buf = NULL;
-
-  switch ( travt->objs[i].type )
-  {
-/*-------------------------------------------------------------------------
- * H5G_GROUP
- *-------------------------------------------------------------------------
- */
-  case H5G_GROUP:
-   if (options->verbose)
-    printf(FORMAT_OBJ,"group",travt->objs[i].name );
-
-   if (options->grp_compact>0 || options->grp_indexed>0) {
-    /* Set up group creation property list */
-    if((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
-      goto error;
-
-     if(H5Pset_link_phase_change(gcpl_id, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
-      goto error;
-
-     if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
-      goto error; 
-   }
-   else {
-    if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-        goto error;
-   }
-
-   if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
-    goto error;
-
-   /*-------------------------------------------------------------------------
-    * copy attrs
+    /*-------------------------------------------------------------------------
+    * copy the suppplied object list
     *-------------------------------------------------------------------------
     */
-   if (copy_attr(grp_in,grp_out,options)<0)
-    goto error;
 
-   if (gcpl_id>0) {
-     if (H5Pclose(gcpl_id)<0)
-      goto error;
-   }
-   if (H5Gclose(grp_out)<0)
-    goto error;
-   if (H5Gclose(grp_in)<0)
-    goto error;
-
-
-   break;
-
-/*-------------------------------------------------------------------------
- * H5G_DATASET
- *-------------------------------------------------------------------------
- */
-  case H5G_DATASET:
+    if (options->verbose) {
+        printf("-----------------------------------------\n");
+        printf(" Type     Filter (Ratio)     Name\n");
+        printf("-----------------------------------------\n");
+    }
 
-   has_filter = 0;
+    for ( i = 0; i < travt->nobjs; i++) {
+
+        buf = NULL;
+        switch ( travt->objs[i].type ) {
+            /*-------------------------------------------------------------------------
+            * H5G_GROUP
+            *-------------------------------------------------------------------------
+            */
+            case H5G_GROUP:
+                if (options->verbose)
+                printf(FORMAT_OBJ,"group",travt->objs[i].name );
+
+                if (options->grp_compact>0 || options->grp_indexed>0) {
+                    /* Set up group creation property list */
+                    if((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+                        goto error;
+
+                    if(H5Pset_link_phase_change(gcpl_id, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
+                        goto error;
+
+                    if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
+                        goto error; 
+                }
+                else {
+                    if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+                        goto error;
+                }
+
+                if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                    goto error;
+
+                /*-------------------------------------------------------------------------
+                * copy attrs
+                *-------------------------------------------------------------------------
+                */
+                if (copy_attr(grp_in,grp_out,options)<0)
+                    goto error;
+
+                if (gcpl_id>0) {
+                    if (H5Pclose(gcpl_id)<0)
+                        goto error;
+                }
+                if (H5Gclose(grp_out)<0)
+                    goto error;
+                if (H5Gclose(grp_in)<0)
+                    goto error;
+
+                break;
+
+            /*-------------------------------------------------------------------------
+            * H5G_DATASET
+            *-------------------------------------------------------------------------
+            */
+            case H5G_DATASET:
+
+                has_filter = 0;
+
+                /* early detection of references */
+                if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
+                    goto error;
+                if ((ftype_id=H5Dget_type (dset_in))<0)
+                    goto error;
+                if (H5T_REFERENCE==H5Tget_class(ftype_id))
+                    is_ref=1;
+                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
+                   )
+                {
+                    int j;
+
+                    if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<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_id=H5Dget_create_plist(dset_in))<0)
+                        goto error;
+                    if ((dcpl_out = H5Pcopy (dcpl_id))<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;
+                    nelmts=1;
+                    for (j=0; j<rank; j++)
+                        nelmts*=dims[j];
+
+                    if (options->use_native==1)
+                        wtype_id = h5tools_get_native_type(ftype_id);
+                    else
+                        wtype_id = H5Tcopy(ftype_id); 
+
+                    if ((msize=H5Tget_size(wtype_id))==0)
+                        goto error;
+                      
+                    /*-------------------------------------------------------------------------
+                     * 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_id)==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 datasets too small */
+                            if (nelmts*msize < options->threshold )
+                                apply_s=0;
+
+                            /* apply the filter */
+                            if (apply_s) {
+                                if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options,&has_filter)<0)
+                                    goto error;
+                            }
+
+                            /*-------------------------------------------------------------------------
+                            * 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=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out);
+                            } H5E_END_TRY;
+                            if (dset_out==FAIL)
+                            {
+                                if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0)
+                                    goto error;
+                                apply_f=0;
+                            }
+
+                            /*-------------------------------------------------------------------------
+                            * read/write
+                            *-------------------------------------------------------------------------
+                            */
+                            if (nelmts)
+                            {
+                                size_t need = (size_t)(nelmts*msize);  /* bytes needed */
+                                if ( need < H5TOOLS_MALLOCSIZE )
+                                    buf = HDmalloc(need);
+
+                                if (buf != NULL )
+                                {
+                                    if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+                                        goto error;
+                                    if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,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 selected elmts */
+                                    hsize_t       elmtno;                /*counter  */
+                                    int           carry;                 /*counter carry value */
+                                    unsigned int  vl_data = 0;           /*contains VL datatypes */
+
+                                    /* stripmine info */
+                                    hsize_t       sm_size[H5S_MAX_RANK]; /*stripmine size */
+                                    hsize_t       sm_nbytes;             /*bytes per stripmine */
+                                    hsize_t       sm_nelmts;             /*elements per stripmine*/
+                                    hid_t         sm_space;              /*stripmine data space */
+
+                                    /* hyperslab info */
+                                    hsize_t       hs_offset[H5S_MAX_RANK];/*starting offset */
+                                    hsize_t       hs_size[H5S_MAX_RANK];  /*size this pass */
+                                    hsize_t       hs_nelmts;              /*elements in request */
+                                    hsize_t       zero[8];                /*vector of zeros */
+                                    int           k;          
+
+                                    /* check if we have VL data in the dataset's datatype */
+                                    if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+                                        vl_data = TRUE;
+
+                                    /*
+                                    * determine the strip mine size and allocate a buffer. The strip mine is
+                                    * a hyperslab whose size is manageable.
+                                    */
+                                    sm_nbytes = p_type_nbytes;
+
+                                    for (k = rank; k > 0; --k) {
+                                        sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes);
+                                        sm_nbytes *= sm_size[k - 1];
+                                        assert(sm_nbytes > 0);
+                                    }
+                                    sm_buf = HDmalloc((size_t)sm_nbytes);
+
+                                    sm_nelmts = sm_nbytes / p_type_nbytes;
+                                    sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
+
+                                    /* the stripmine loop */
+                                    memset(hs_offset, 0, sizeof hs_offset);
+                                    memset(zero, 0, sizeof zero);
+
+                                    for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) 
+                                    {
+                                        /* calculate the hyperslab size */
+                                        if (rank > 0) 
+                                        {
+                                            for (k = 0, hs_nelmts = 1; k < rank; k++) 
+                                            {
+                                                hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
+                                                hs_nelmts *= hs_size[k];
+                                            }
+
+                                            if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0)
+                                                goto error;
+                                            if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0)
+                                                goto error;
+                                        } 
+                                        else 
+                                        {
+                                            H5Sselect_all(f_space_id);
+                                            H5Sselect_all(sm_space);
+                                            hs_nelmts = 1;
+                                        } /* rank */
+
+                                        /* read/write */
+                                        if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
+                                            goto error;
+                                        if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
+                                            goto error;
+
+                                        /* reclaim any VL memory, if necessary */
+                                        if(vl_data)
+                                            H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
+
+                                        /* calculate the next hyperslab offset */
+                                        for (k = rank, carry = 1; k > 0 && carry; --k) 
+                                        {
+                                            hs_offset[k - 1] += hs_size[k - 1];
+                                            if (hs_offset[k - 1] == dims[k - 1])
+                                                hs_offset[k - 1] = 0;
+                                            else
+                                                carry = 0;
+                                        } /* k */
+                                    } /* elmtno */
+
+                                    H5Sclose(sm_space);
+                                    /* free */
+                                    if (sm_buf!=NULL)
+                                    {
+                                        HDfree(sm_buf);
+                                        sm_buf=NULL;
+                                    }
+                                } /* hyperslab read */
+                            }/*nelmts*/
+
+                            /*-------------------------------------------------------------------------
+                            * amount of compression used
+                            *-------------------------------------------------------------------------
+                            */
+                            if (options->verbose) 
+                            {
+                                if (apply_s && apply_f)
+                                {
+                                    /* get the storage size of the input dataset */
+                                    dsize_out=H5Dget_storage_size(dset_out);
+                                    PER((hssize_t)dsize_in,(hssize_t)dsize_out);
+                                    print_dataset_info(dcpl_out,travt->objs[i].name,per*100.0);
+                                }
+                                else
+                                    print_dataset_info(dcpl_id,travt->objs[i].name,0.0);
+
+                                /* 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->threshold);
+
+                                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,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_id)<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=H5Dopen(fidin,travt->objs[i].name))<0)
+                        goto error;
+                    if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
+                        goto error;
+                    if (copy_attr(dset_in,dset_out,options)<0)
+                        goto error;
+                    if (H5Dclose(dset_in)<0)
+                        goto error;
+                    if (H5Dclose(dset_out)<0)
+                        goto error;
+
+                } /* end do we have request for filter/chunking */
+
+
+                break;
+
+            /*-------------------------------------------------------------------------
+            * H5G_TYPE
+            *-------------------------------------------------------------------------
+            */
+            case H5G_TYPE:
+
+                if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
+                    goto error;
+
+                if ((type_out = H5Tcopy(type_in))<0)
+                    goto error;
+
+                if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0)
+                    goto error;
+
+                /*-------------------------------------------------------------------------
+                * copy attrs
+                *-------------------------------------------------------------------------
+                */
+                if (copy_attr(type_in,type_out,options)<0)
+                    goto error;
+
+                if (H5Tclose(type_in)<0)
+                    goto error;
+                if (H5Tclose(type_out)<0)
+                    goto error;
+
+                if (options->verbose)
+                    printf(FORMAT_OBJ,"type",travt->objs[i].name );
+
+                break;
+
+
+            /*-------------------------------------------------------------------------
+            * H5G_LINK
+            * H5G_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 H5G_LINK:
+            case H5G_UDLINK:
+            {
+                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 */
 
-   /* early detection of references */
-   if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
-    goto error;
-   if ((ftype_id=H5Dget_type (dset_in))<0)
-    goto error;
-   if (H5T_REFERENCE==H5Tget_class(ftype_id))
-    {
-     is_ref=1;
-    }
-   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
-       )
-   {       
-    int j;
-
-    if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<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_id=H5Dget_create_plist(dset_in))<0)
-     goto error;
-    if ((dcpl_out = H5Pcopy (dcpl_id))<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;
-    nelmts=1;
-    for (j=0; j<rank; j++)
-     nelmts*=dims[j];
-    
-    if (options->use_native==1)
-     wtype_id = h5tools_get_native_type(ftype_id);
-    else
-     wtype_id = H5Tcopy(ftype_id); 
-    
-    if ((msize=H5Tget_size(wtype_id))==0)
-     goto error;
-      
-    /*-------------------------------------------------------------------------
-     * 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_id)==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))
-     {
-         ;
-     }
-     else /* H5T_REFERENCE */
-     {
-      /* get the storage size of the input dataset */
-      dsize_in=H5Dget_storage_size(dset_in);
-      
-      /* check for datasets too small */
-      if (nelmts*msize < options->threshold )
-       apply_s=0;
-      
-      /* apply the filter */
-      if (apply_s){
-       if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options,&has_filter)<0)
-        goto error;
-      }
-      
-     /*-------------------------------------------------------------------------
-      * 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=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out);
-      } H5E_END_TRY;
-      if (dset_out==FAIL)
-      {
-       if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0)
-        goto error;
-       apply_f=0;
-      }
-      
-     /*-------------------------------------------------------------------------
-      * read/write
-      *-------------------------------------------------------------------------
-      */
-      if (nelmts)
-      {
-       size_t need = (size_t)(nelmts*msize);  /* bytes needed */
-       if ( need < H5TOOLS_MALLOCSIZE )
-        buf = HDmalloc(need);
-       
-       if (buf != NULL )
-       {
-        if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
-         goto error;
-        if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,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 selected elmts */
-        hsize_t       elmtno;                /*counter  */
-        int           carry;                 /*counter carry value */
-        unsigned int  vl_data = 0;           /*contains VL datatypes */
-        
-        /* stripmine info */
-        hsize_t       sm_size[H5S_MAX_RANK]; /*stripmine size */
-        hsize_t       sm_nbytes;             /*bytes per stripmine */
-        hsize_t       sm_nelmts;             /*elements per stripmine*/
-        hid_t         sm_space;              /*stripmine data space */
-        
-        /* hyperslab info */
-        hsize_t       hs_offset[H5S_MAX_RANK];/*starting offset */
-        hsize_t       hs_size[H5S_MAX_RANK];  /*size this pass */
-        hsize_t       hs_nelmts;              /*elements in request */
-        hsize_t       zero[8];                /*vector of zeros */
-        int           k;          
-        
-        /* check if we have VL data in the dataset's datatype */
-        if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
-         vl_data = TRUE;
-        
-        /*
-         * determine the strip mine size and allocate a buffer. The strip mine is
-         * a hyperslab whose size is manageable.
-         */
-        sm_nbytes = p_type_nbytes;
-        
-        for (k = rank; k > 0; --k) {
-         sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes);
-         sm_nbytes *= sm_size[k - 1];
-         assert(sm_nbytes > 0);
-        }
-        sm_buf = HDmalloc((size_t)sm_nbytes);
-        
-        sm_nelmts = sm_nbytes / p_type_nbytes;
-        sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
-        
-        /* the stripmine loop */
-        memset(hs_offset, 0, sizeof hs_offset);
-        memset(zero, 0, sizeof zero);
-        
-        for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) 
-        {
-         /* calculate the hyperslab size */
-         if (rank > 0) 
-         {
-          for (k = 0, hs_nelmts = 1; k < rank; k++) 
-          {
-           hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
-           hs_nelmts *= hs_size[k];
-          }
-          
-          if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL)<0)
-           goto error;
-          if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL)<0)
-           goto error;
-         } 
-         else 
-         {
-          H5Sselect_all(f_space_id);
-          H5Sselect_all(sm_space);
-          hs_nelmts = 1;
-         } /* rank */
-         
-         /* read/write */
-         if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
-          goto error;
-         if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
-          goto error;
-         
-         /* reclaim any VL memory, if necessary */
-         if(vl_data)
-          H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
-         
-         /* calculate the next hyperslab offset */
-         for (k = rank, carry = 1; k > 0 && carry; --k) 
-         {
-          hs_offset[k - 1] += hs_size[k - 1];
-          if (hs_offset[k - 1] == dims[k - 1])
-           hs_offset[k - 1] = 0;
-          else
-           carry = 0;
-         } /* k */
-        } /* elmtno */
-        
-        H5Sclose(sm_space);
         /* free */
-        if (sm_buf!=NULL)
+        if (buf!=NULL)
         {
-         HDfree(sm_buf);
-         sm_buf=NULL;
+            HDfree(buf);
+            buf=NULL;
         }
-       } /* hyperslab read */
-    }/*nelmts*/
-    
+
+    } /* i */
+
     /*-------------------------------------------------------------------------
-     * amount of compression used
-     *-------------------------------------------------------------------------
-     */
-     if (options->verbose) 
-     {
-      if (apply_s && apply_f)
-      {
-       /* get the storage size of the input dataset */
-       dsize_out=H5Dget_storage_size(dset_out);
-       PER((hssize_t)dsize_in,(hssize_t)dsize_out);
-       print_dataset_info(dcpl_out,travt->objs[i].name,per*100.0);
-      }
-      else
-       print_dataset_info(dcpl_id,travt->objs[i].name,0.0);
-     
-      /* 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->threshold);
-     
-      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,options)<0)
-      goto error;
-     
-     /*close */
-     if (H5Dclose(dset_out)<0)
-      goto error;
-     
-    }/*H5T_REFERENCE*/
-   }/*h5tools_canreadf*/
-   
-   
-   /*-------------------------------------------------------------------------
-    * close
+    * the root is a special case, we get an ID for the root group
+    * and copy its attributes using that ID
     *-------------------------------------------------------------------------
     */
-    if (H5Tclose(ftype_id)<0)
-     goto error;
-    if (H5Tclose(wtype_id)<0)
-     goto error;
-    if (H5Pclose(dcpl_id)<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=H5Dopen(fidin,travt->objs[i].name))<0)
-         goto error;
-     if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
-         goto error;
-     if (copy_attr(dset_in,dset_out,options)<0)
-         goto error;
-     if (H5Dclose(dset_in)<0)
-         goto error;
-     if (H5Dclose(dset_out)<0)
-         goto error;
-
-     
-    } /* end do we have request for filter/chunking */
-
-
-   break;
-
-/*-------------------------------------------------------------------------
- * H5G_TYPE
- *-------------------------------------------------------------------------
- */
-  case H5G_TYPE:
-
-   if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
-    goto error;
-
-   if ((type_out = H5Tcopy(type_in))<0)
-    goto error;
-
-   if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<0)
-    goto error;
-
-/*-------------------------------------------------------------------------
- * copy attrs
- *-------------------------------------------------------------------------
- */
-   if (copy_attr(type_in,type_out,options)<0)
-    goto error;
-
-   if (H5Tclose(type_in)<0)
-    goto error;
-   if (H5Tclose(type_out)<0)
-    goto error;
-
-   if (options->verbose)
-    printf(FORMAT_OBJ,"type",travt->objs[i].name );
 
-   break;
-
-
-/*-------------------------------------------------------------------------
- * H5G_LINK
- * H5G_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 H5G_LINK:
-  case H5G_UDLINK:
-   {
-    if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
+    if ((grp_out = H5Gopen2(fidout, "/", 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 */
-
-/*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- *-------------------------------------------------------------------------
- */
-
- if ((grp_out = H5Gopen(fidout,"/"))<0)
-  goto error;
-
- if ((grp_in  = H5Gopen(fidin,"/"))<0)
-  goto error;
+    if ((grp_in  = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+        goto error;
 
- if (copy_attr(grp_in,grp_out,options)<0)
-  goto error;
+    if (copy_attr(grp_in,grp_out,options)<0)
+        goto error;
 
- if (H5Gclose(grp_out)<0)
-  goto error;
- if (H5Gclose(grp_in)<0)
-  goto error;
+    if (H5Gclose(grp_out)<0)
+        goto error;
+    if (H5Gclose(grp_in)<0)
+        goto error;
 
- return 0;
+    return 0;
 
 error:
- H5E_BEGIN_TRY {
-  H5Gclose(grp_in);
-  H5Gclose(grp_out);
-  H5Pclose(dcpl_id);
-  H5Pclose(gcpl_id);
-  H5Sclose(f_space_id);
-  H5Dclose(dset_in);
-  H5Dclose(dset_out);
-  H5Tclose(ftype_id);
-  H5Tclose(wtype_id);
-  H5Tclose(type_in);
-  H5Tclose(type_out);
-  /* free */
-  if (buf!=NULL)
-  {
-   HDfree(buf);
-   buf=NULL;
-  }
-  if (sm_buf!=NULL)
-  {
-   HDfree(sm_buf);
-   sm_buf=NULL;
-  }
- } H5E_END_TRY;
- return -1;
-
+    H5E_BEGIN_TRY {
+        H5Gclose(grp_in);
+        H5Gclose(grp_out);
+        H5Pclose(dcpl_id);
+        H5Pclose(gcpl_id);
+        H5Sclose(f_space_id);
+        H5Dclose(dset_in);
+        H5Dclose(dset_out);
+        H5Tclose(ftype_id);
+        H5Tclose(wtype_id);
+        H5Tclose(type_in);
+        H5Tclose(type_out);
+    } H5E_END_TRY;
+    /* free */
+    if (buf!=NULL)
+        HDfree(buf);
+    if (sm_buf!=NULL)
+        HDfree(sm_buf);
+    return -1;
 }
 
 
@@ -848,9 +829,9 @@ error:
  * Function: copy_attr
  *
  * Purpose: copy attributes located in LOC_IN, which is obtained either from
- * loc_id = H5Gopen( fid, name);
- * loc_id = H5Dopen( fid, name);
- * loc_id = H5Topen( fid, name);
+ * loc_id = H5Gopen2( fid, name);
+ * loc_id = H5Dopen2( fid, name);
+ * loc_id = H5Topen2( fid, name);
  *
  * Return: 0, ok, -1 no
  *
diff --git a/tools/h5repack/h5repack_list.c b/tools/h5repack/h5repack_list.c
index 3de8101..78b8858 100644
--- a/tools/h5repack/h5repack_list.c
+++ b/tools/h5repack/h5repack_list.c
@@ -165,52 +165,3 @@ out:
     return -1;
 }
 
-
-
-/*-------------------------------------------------------------------------
- * Function: print_objlist
- *
- * Purpose: print list of objects in file
- *
- * Return: void
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October 23, 2003
- *
- *-------------------------------------------------------------------------
- */
-void print_objlist(const char *filename,
-                   int nobjects,
-                   trav_info_t *info )
-{
-    int i;
-    
-    printf("File <%s>: # of entries = %d\n", filename, nobjects );
-    for ( i = 0; i < nobjects; i++)
-    {
-        switch ( info[i].type )
-        {
-        case H5G_GROUP:
-            printf(" %-10s %s\n", "group", info[i].name  );
-            break;
-        case H5G_DATASET:
-            printf(" %-10s %s\n", "dataset", info[i].name );
-            break;
-        case H5G_TYPE:
-            printf(" %-10s %s\n", "datatype", info[i].name );
-            break;
-        case H5G_LINK:
-            printf(" %-10s %s\n", "link", info[i].name );
-            break;
-        case H5G_UDLINK:
-            printf(" %-10s %s\n", "User defined link", info[i].name );
-            break;
-        default:
-            printf(" %-10s %s\n", "User defined object", info[i].name );
-            break;
-        }
-    }
-
-}
-
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 538c99f..71e42bb 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -53,406 +53,390 @@ int do_copy_refobjs(hid_t fidin,
                     trav_table_t *travt,
                     pack_opt_t *options) /* repack options */
 {
- hid_t     grp_in=(-1);            /* read group ID */
- hid_t     grp_out=(-1);           /* write group ID */
- hid_t     dset_in=(-1);           /* read dataset ID */
- hid_t     dset_out=(-1);          /* write dataset ID */
- hid_t     type_in=(-1);           /* named type ID */
- hid_t     dcpl_id=(-1);           /* dataset creation property list ID */
- hid_t     space_id=(-1);          /* space ID */
- hid_t     ftype_id=(-1);          /* file data type ID */
- hid_t     mtype_id=(-1);          /* memory data type ID */
- size_t    msize;                  /* memory size of memory type */
- hsize_t   nelmts;                 /* number of elements in dataset */
- int       rank;                   /* rank of dataset */
- hsize_t   dims[H5S_MAX_RANK];     /* dimensions of dataset */
- unsigned int i, j;
- int       k;
+    hid_t     grp_in=(-1);            /* read group ID */
+    hid_t     grp_out=(-1);           /* write group ID */
+    hid_t     dset_in=(-1);           /* read dataset ID */
+    hid_t     dset_out=(-1);          /* write dataset ID */
+    hid_t     type_in=(-1);           /* named type ID */
+    hid_t     dcpl_id=(-1);           /* dataset creation property list ID */
+    hid_t     space_id=(-1);          /* space ID */
+    hid_t     ftype_id=(-1);          /* file data type ID */
+    hid_t     mtype_id=(-1);          /* memory data type ID */
+    size_t    msize;                  /* memory size of memory type */
+    hsize_t   nelmts;                 /* number of elements in dataset */
+    int       rank;                   /* rank of dataset */
+    hsize_t   dims[H5S_MAX_RANK];     /* dimensions of dataset */
+    unsigned int i, j;
+    int       k;
 
-/*-------------------------------------------------------------------------
- * browse
- *-------------------------------------------------------------------------
- */
-
- for ( i = 0; i < travt->nobjs; i++)
- {
-  switch ( travt->objs[i].type )
-  {
- /*-------------------------------------------------------------------------
-  * H5G_GROUP
-  *-------------------------------------------------------------------------
-  */
-  case H5G_GROUP:
-      
-  /*-------------------------------------------------------------------------
-   * copy referenced objects in attributes
-   *-------------------------------------------------------------------------
-   */
-
-      if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0)
-          goto error;
-      
-      if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
-          goto error;
-      
-      if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
-          goto error;
-      
-      if (H5Gclose(grp_out)<0)
-          goto error;
-      if (H5Gclose(grp_in)<0)
-          goto error;
-
-
-
-
-   /*-------------------------------------------------------------------------
-    * check for hard links
+    /*-------------------------------------------------------------------------
+    * browse
     *-------------------------------------------------------------------------
     */
 
-   if (travt->objs[i].nlinks)
-   {
-    for ( j=0; j<travt->objs[i].nlinks; j++)
+    for ( i = 0; i < travt->nobjs; i++)
     {
-      H5Glink(fidout,
-      H5G_LINK_HARD,
-      travt->objs[i].name,
-      travt->objs[i].links[j].new_name);
+        switch ( travt->objs[i].type )
+        {
+            /*-------------------------------------------------------------------------
+            * H5G_GROUP
+            *-------------------------------------------------------------------------
+            */
+            case H5G_GROUP:
+
+                /*-------------------------------------------------------------------------
+                * copy referenced objects in attributes
+                *-------------------------------------------------------------------------
+                */
+
+                if ((grp_out = H5Gopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                    goto error;
+
+                if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                    goto error;
+
+                if (copy_refs_attr(grp_in,grp_out,options,travt,fidout) < 0)
+                    goto error;
+
+                if (H5Gclose(grp_out) < 0)
+                    goto error;
+                if (H5Gclose(grp_in) < 0)
+                    goto error;
+
+
+                /*-------------------------------------------------------------------------
+                * check for hard links
+                *-------------------------------------------------------------------------
+                */
+
+                if(travt->objs[i].nlinks)
+                    for(j = 0; j < travt->objs[i].nlinks; j++)
+                        H5Glink(fidout, H5G_LINK_HARD, travt->objs[i].name, travt->objs[i].links[j].new_name);
+
+                break;
+
+            /*-------------------------------------------------------------------------
+            * H5G_DATASET
+            *-------------------------------------------------------------------------
+            */
+            case H5G_DATASET:
+
+                if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
+                    goto error;
+                if ((space_id=H5Dget_space(dset_in))<0)
+                    goto error;
+                if ((ftype_id=H5Dget_type (dset_in))<0)
+                    goto error;
+                if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
+                    goto error;
+                if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
+                    goto error;
+                if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
+                    goto error;
+                nelmts=1;
+                for (k=0; k<rank; k++)
+                    nelmts*=dims[k];
+
+                if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
+                    goto error;
+
+                if ((msize=H5Tget_size(mtype_id))==0)
+                    goto error;
+                /*-------------------------------------------------------------------------
+                * 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((NULL),dcpl_id)==1)
+                {
+                    /*-------------------------------------------------------------------------
+                    * test for a valid output dataset
+                    *-------------------------------------------------------------------------
+                    */
+                    dset_out = FAIL;
+
+                    /*-------------------------------------------------------------------------
+                    * object references are a special case
+                    * we cannot just copy the buffers, but instead we recreate the reference
+                    *-------------------------------------------------------------------------
+                    */
+                    if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
+                    {
+                        H5G_obj_t1       obj_type;
+                        hid_t            refobj_id;
+                        hobj_ref_t       *refbuf=NULL; /* buffer for object references */
+                        hobj_ref_t       *buf=NULL;
+                        const char*      refname;
+                        unsigned         u;
+
+                        /*-------------------------------------------------------------------------
+                        * read to memory
+                        *-------------------------------------------------------------------------
+                        */
+
+                        if (nelmts)
+                        {
+                            buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+                            if ( buf==NULL){
+                                printf( "cannot read into memory\n" );
+                                goto error;
+                            }
+                            if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+                                goto error;
+
+                            if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
+                                goto error;
+                            refbuf=HDcalloc((unsigned)nelmts,msize);
+                            if ( refbuf==NULL){
+                                printf( "cannot allocate memory\n" );
+                                goto error;
+                            }
+                            for ( u=0; u<nelmts; u++)
+                            {
+                                H5E_BEGIN_TRY {
+                                    if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
+                                        continue;
+                                } H5E_END_TRY;
+                                /* get the name. a valid name could only occur in the
+                                second traversal of the file */
+                                if ((refname=MapIdToName(refobj_id,travt))!=NULL)
+                                {
+                                    /* create the reference, -1 parameter for objects */
+                                    if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
+                                        goto error;
+                                    if (options->verbose)
+                                        printf("object <%s> object reference created to <%s>\n",
+                                            travt->objs[i].name,
+                                            refname);
+                                }/*refname*/
+                                close_obj(obj_type,refobj_id);
+                            }/*  u */
+                        }/*nelmts*/
+
+                        /*-------------------------------------------------------------------------
+                        * create/write dataset/close
+                        *-------------------------------------------------------------------------
+                        */
+                        if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
+                            goto error;
+                        if (nelmts) {
+                            if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+                                goto error;
+                        }
+
+                        if (buf)
+                            free(buf);
+                        if (refbuf)
+                            free(refbuf);
+
+                    }/*H5T_STD_REF_OBJ*/
+
+                    /*-------------------------------------------------------------------------
+                    * dataset region references
+                    *-------------------------------------------------------------------------
+                    */
+                    else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
+                    {
+                        H5G_obj_t1       obj_type;
+                        hid_t            refobj_id;
+                        hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
+                        hdset_reg_ref_t  *buf=NULL;    /* output buffer */
+                        const char*      refname;
+                        unsigned         u;
+
+                        /*-------------------------------------------------------------------------
+                        * read input to memory
+                        *-------------------------------------------------------------------------
+                        */
+                        if (nelmts)
+                        {
+                            buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+                            if ( buf==NULL){
+                                printf( "cannot read into memory\n" );
+                                goto error;
+                            }
+                            if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
+                                goto error;
+                            if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
+                                goto error;
+
+                            /*-------------------------------------------------------------------------
+                            * create output
+                            *-------------------------------------------------------------------------
+                            */
+
+                            refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
+                            if ( refbuf==NULL){
+                                printf( "cannot allocate memory\n" );
+                                goto error;
+                            }
+                            for ( u=0; u<nelmts; u++)
+                            {
+                                H5E_BEGIN_TRY {
+                                    if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
+                                        continue;
+                                } H5E_END_TRY;
+
+                                /* get the name. a valid name could only occur in the
+                                second traversal of the file */
+                                if ((refname=MapIdToName(refobj_id,travt))!=NULL)
+                                {
+                                    hid_t region_id;    /* region id of the referenced dataset */
+                                    if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
+                                        goto error;
+                                    /* create the reference, we need the space_id */
+                                    if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
+                                        goto error;
+                                    if (H5Sclose(region_id)<0)
+                                        goto error;
+                                    if (options->verbose)
+                                        printf("object <%s> region reference created to <%s>\n",
+                                            travt->objs[i].name,
+                                            refname);
+                                }/*refname*/
+                                close_obj(obj_type,refobj_id);
+                            }/*  u */
+                        }/*nelmts*/
+
+                        /*-------------------------------------------------------------------------
+                        * create/write dataset/close
+                        *-------------------------------------------------------------------------
+                        */
+                        if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
+                            goto error;
+                        if (nelmts) {
+                            if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
+                                goto error;
+                        }
+
+                        if (buf)
+                            free(buf);
+                        if (refbuf)
+                            free(refbuf);
+                    } /* H5T_STD_REF_DSETREG */
+
+
+                    /*-------------------------------------------------------------------------
+                    * not references, open previously created object in 1st traversal
+                    *-------------------------------------------------------------------------
+                    */
+                    else
+                    {
+                        if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
+                            goto error;
+                    }
+
+                    assert(dset_out!=FAIL);
+
+                    /*-------------------------------------------------------------------------
+                    * copy referenced objects in attributes
+                    *-------------------------------------------------------------------------
+                    */
+                    if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
+                        goto error;
+
+                    /*-------------------------------------------------------------------------
+                    * check for hard links
+                    *-------------------------------------------------------------------------
+                    */
+                    if(travt->objs[i].nlinks)
+                        for(j = 0; j < travt->objs[i].nlinks; j++)
+                            H5Glink(fidout, H5G_LINK_HARD, travt->objs[i].name, travt->objs[i].links[j].new_name);
+
+                    if(H5Dclose(dset_out)<0)
+                        goto error;
+
+                }/*can_read*/
+
+                /*-------------------------------------------------------------------------
+                * close
+                *-------------------------------------------------------------------------
+                */
+
+                if (H5Tclose(ftype_id)<0)
+                    goto error;
+                if (H5Tclose(mtype_id)<0)
+                    goto error;
+                if (H5Pclose(dcpl_id)<0)
+                    goto error;
+                if (H5Sclose(space_id)<0)
+                    goto error;
+                if (H5Dclose(dset_in)<0)
+                    goto error;
+
+                break;
+
+            /*-------------------------------------------------------------------------
+            * H5G_TYPE
+            *-------------------------------------------------------------------------
+            */
+            case H5G_TYPE:
+
+                if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
+                    goto error;
+
+                if (H5Tclose(type_in)<0)
+                    goto error;
+
+                break;
+
+            /*-------------------------------------------------------------------------
+            * H5G_LINK
+            *-------------------------------------------------------------------------
+            */
+
+            case H5G_LINK:
+
+                /*nothing to do */
+                break;
+
+            default:
+
+                break;
+        }
     }
-   }
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_DATASET
-   *-------------------------------------------------------------------------
-   */
-  case H5G_DATASET:
 
-   if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
-    goto error;
-   if ((space_id=H5Dget_space(dset_in))<0)
-    goto error;
-   if ((ftype_id=H5Dget_type (dset_in))<0)
-    goto error;
-   if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
-    goto error;
-   if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
-    goto error;
-   if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
-    goto error;
-   nelmts=1;
-   for (k=0; k<rank; k++)
-    nelmts*=dims[k];
-
-   if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
-    goto error;
-
-   if ((msize=H5Tget_size(mtype_id))==0)
-    goto error;
-/*-------------------------------------------------------------------------
- * 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((NULL),dcpl_id)==1)
-   {
-/*-------------------------------------------------------------------------
- * test for a valid output dataset
- *-------------------------------------------------------------------------
- */
-   dset_out = FAIL;
-
-/*-------------------------------------------------------------------------
- * object references are a special case
- * we cannot just copy the buffers, but instead we recreate the reference
- *-------------------------------------------------------------------------
- */
-   if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
-   {
-    H5G_obj_t1       obj_type;
-    hid_t            refobj_id;
-    hobj_ref_t       *refbuf=NULL; /* buffer for object references */
-    hobj_ref_t       *buf=NULL;
-    const char*      refname;
-    unsigned         u;
-
-   /*-------------------------------------------------------------------------
-    * read to memory
-    *-------------------------------------------------------------------------
-    */
-
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      printf( "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
-      goto error;
 
-     if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
-      goto error;
-     refbuf=HDcalloc((unsigned)nelmts,msize);
-     if ( refbuf==NULL){
-      printf( "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( u=0; u<nelmts; u++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
-        continue;
-      } H5E_END_TRY;
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       /* create the reference, -1 parameter for objects */
-       if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
-        goto error;
-       if (options->verbose)
-        printf("object <%s> object reference created to <%s>\n",
-        travt->objs[i].name,
-        refname);
-      }/*refname*/
-      close_obj(obj_type,refobj_id);
-     }/*  u */
-    }/*nelmts*/
 
     /*-------------------------------------------------------------------------
-     * create/write dataset/close
-     *-------------------------------------------------------------------------
-     */
-    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
-     goto error;
-    if (nelmts) {
-     if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
-      goto error;
-    }
-
-    if (buf)
-     free(buf);
-    if (refbuf)
-     free(refbuf);
-
-   }/*H5T_STD_REF_OBJ*/
-
-/*-------------------------------------------------------------------------
- * dataset region references
- *-------------------------------------------------------------------------
- */
-   else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
-   {
-    H5G_obj_t1       obj_type;
-    hid_t            refobj_id;
-    hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
-    hdset_reg_ref_t  *buf=NULL;    /* output buffer */
-    const char*      refname;
-    unsigned         u;
-
-   /*-------------------------------------------------------------------------
-    * read input to memory
+    * the root is a special case, we get an ID for the root group
+    * and copy its attributes using that ID
+    * it must be done last, because the attributes might contain references to
+    * objects in the object list
     *-------------------------------------------------------------------------
     */
-    if (nelmts)
-    {
-     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
-     if ( buf==NULL){
-      printf( "cannot read into memory\n" );
-      goto error;
-     }
-     if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
-      goto error;
-     if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
-      goto error;
 
-     /*-------------------------------------------------------------------------
-      * create output
-      *-------------------------------------------------------------------------
-      */
+    if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
+        goto error;
 
-     refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
-     if ( refbuf==NULL){
-      printf( "cannot allocate memory\n" );
-      goto error;
-     }
-     for ( u=0; u<nelmts; u++)
-     {
-      H5E_BEGIN_TRY {
-       if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
-        continue;
-      } H5E_END_TRY;
+    if ((grp_in  = H5Gopen2(fidin, "/", H5P_DEFAULT)) < 0)
+        goto error;
 
-      /* get the name. a valid name could only occur in the
-      second traversal of the file */
-      if ((refname=MapIdToName(refobj_id,travt))!=NULL)
-      {
-       hid_t region_id;    /* region id of the referenced dataset */
-       if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
+    if (copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
         goto error;
-       /* create the reference, we need the space_id */
-       if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
+
+    if (H5Gclose(grp_out) < 0)
         goto error;
-       if (H5Sclose(region_id)<0)
+    if (H5Gclose(grp_in) < 0)
         goto error;
-       if (options->verbose)
-        printf("object <%s> region reference created to <%s>\n",
-        travt->objs[i].name,
-        refname);
-      }/*refname*/
-      close_obj(obj_type,refobj_id);
-     }/*  u */
-    }/*nelmts*/
-
-    /*-------------------------------------------------------------------------
-     * create/write dataset/close
-     *-------------------------------------------------------------------------
-     */
-    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
-     goto error;
-    if (nelmts) {
-     if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
-      goto error;
-    }
-
-    if (buf)
-     free(buf);
-    if (refbuf)
-     free(refbuf);
-   } /* H5T_STD_REF_DSETREG */
-
-
-/*-------------------------------------------------------------------------
- * not references, open previously created object in 1st traversal
- *-------------------------------------------------------------------------
- */
-   else
-   {
-    if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
-     goto error;
-   }
 
-   assert(dset_out!=FAIL);
-
-/*-------------------------------------------------------------------------
- * copy referenced objects in attributes
- *-------------------------------------------------------------------------
- */
-   if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
-    goto error;
-
-/*-------------------------------------------------------------------------
- * check for hard links
- *-------------------------------------------------------------------------
- */
-   if (travt->objs[i].nlinks)
-   {
-    for ( j=0; j<travt->objs[i].nlinks; j++){
-     H5Glink(fidout,
-      H5G_LINK_HARD,
-      travt->objs[i].name,
-      travt->objs[i].links[j].new_name);
-    }
-   }
-
-   if (H5Dclose(dset_out)<0)
-    goto error;
-
-   }/*can_read*/
-
-   /*-------------------------------------------------------------------------
-    * close
-    *-------------------------------------------------------------------------
-    */
-
-   if (H5Tclose(ftype_id)<0)
-    goto error;
-   if (H5Tclose(mtype_id)<0)
-    goto error;
-   if (H5Pclose(dcpl_id)<0)
-    goto error;
-   if (H5Sclose(space_id)<0)
-    goto error;
-   if (H5Dclose(dset_in)<0)
-    goto error;
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_TYPE
-   *-------------------------------------------------------------------------
-   */
-  case H5G_TYPE:
-
-   if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
-    goto error;
-
-   if (H5Tclose(type_in)<0)
-    goto error;
-
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_LINK
-   *-------------------------------------------------------------------------
-   */
-
-  case H5G_LINK:
-
-   /*nothing to do */
-   break;
-
-  default:
-
-   break;
-  }
- }
-
-
-
-/*-------------------------------------------------------------------------
- * the root is a special case, we get an ID for the root group
- * and copy its attributes using that ID
- * it must be done last, because the attributes might contain references to
- * objects in the object list
- *-------------------------------------------------------------------------
- */
-
- if ((grp_out = H5Gopen(fidout,"/"))<0)
-  goto error;
-
- if ((grp_in  = H5Gopen(fidin,"/"))<0)
-  goto error;
-
- if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
-  goto error;
-
- if (H5Gclose(grp_out)<0)
-  goto error;
- if (H5Gclose(grp_in)<0)
-  goto error;
-
- return 0;
+    return 0;
 
 error:
- H5E_BEGIN_TRY {
-  H5Gclose(grp_in);
-  H5Gclose(grp_out);
-  H5Pclose(dcpl_id);
-  H5Sclose(space_id);
-  H5Dclose(dset_in);
-  H5Dclose(dset_out);
-  H5Tclose(ftype_id);
-  H5Tclose(mtype_id);
-  H5Tclose(type_in);
- } H5E_END_TRY;
- return -1;
-
+    H5E_BEGIN_TRY {
+        H5Gclose(grp_in);
+        H5Gclose(grp_out);
+        H5Pclose(dcpl_id);
+        H5Sclose(space_id);
+        H5Dclose(dset_in);
+        H5Dclose(dset_out);
+        H5Tclose(ftype_id);
+        H5Tclose(mtype_id);
+        H5Tclose(type_in);
+    } H5E_END_TRY;
+    return -1;
 }
 
 
@@ -461,7 +445,7 @@ error:
  *
  * Purpose: duplicate all referenced HDF5 located in attributes
  *  relative to LOC_IN, which is obtained either from
- * loc_id = H5Gopen( fid, name);
+ * loc_id = H5Gopen2( fid, name, H5P_DEFAULT);
  * loc_id = H5Dopen( fid, name);
  * loc_id = H5Topen( fid, name);
  *
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 049e059..6c02e92 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -34,8 +34,8 @@ extern char  *progname;
  *-------------------------------------------------------------------------
  */
 
-int has_filter(hid_t dcpl_id,
-               H5Z_filter_t filtnin)
+static int
+has_filter(hid_t dcpl_id, H5Z_filter_t filtnin)
 {
 
  int          nfilters;       /* number of filters */
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 3328c70..b8c7948 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -1570,7 +1570,7 @@ int make_all_objects(hid_t loc_id)
     *-------------------------------------------------------------------------
     */
     group_id  = H5Gcreate2(loc_id, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-    root_id   = H5Gopen(loc_id, "/");
+    root_id   = H5Gopen2(loc_id, "/", H5P_DEFAULT);
 
     /*-------------------------------------------------------------------------
     * H5G_TYPE
@@ -1645,7 +1645,7 @@ int make_attributes(hid_t loc_id)
     *-------------------------------------------------------------------------
     */
     group_id  = H5Gcreate2(loc_id, "g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-    root_id   = H5Gopen(loc_id, "/");
+    root_id   = H5Gopen2(loc_id, "/", H5P_DEFAULT);
 
     /*-------------------------------------------------------------------------
     * write a series of attributes on the dataset, group, and root group
diff --git a/tools/h5stat/h5stat.c b/tools/h5stat/h5stat.c
index 8f29519..280023e 100644
--- a/tools/h5stat/h5stat.c
+++ b/tools/h5stat/h5stat.c
@@ -476,7 +476,7 @@ group_stats(hid_t group, const char *name, const char *fullname,
     iter->group_ohdr_info.total_size += oi->hdr.space.total;
     iter->group_ohdr_info.free_size += oi->hdr.space.free;
 
-    gid = H5Gopen(group, name);
+    gid = H5Gopen2(group, name, H5P_DEFAULT);
     assert(gid > 0);
 
     /* Get number of links in this group */
diff --git a/tools/lib/h5diff.c b/tools/lib/h5diff.c
index 4b354b6..dc32b9e 100644
--- a/tools/lib/h5diff.c
+++ b/tools/lib/h5diff.c
@@ -1010,33 +1010,34 @@ hsize_t diff (hid_t file1_id,
     */
     case H5G_GROUP:
 
-        ret = HDstrcmp(path1,path2);
+        ret = HDstrcmp(path1, path2);
     
         /* if "path1" != "path2" then the groups are "different" */
-        nfound = (ret!=0) ? 1 : 0;
+        nfound = (ret != 0) ? 1 : 0;
         
-        if (print_objname(options,nfound))
-            do_print_objname ("group", path1, path2);
+        if(print_objname(options, nfound))
+            do_print_objname("group", path1, path2);
 
         /* always print the number of differences found in verbose mode */
-        if (options->m_verbose)
+        if(options->m_verbose)
             print_found(nfound);
         
-        if ((grp1_id = H5Gopen(file1_id, path1))<0)
+        if((grp1_id = H5Gopen2(file1_id, path1, H5P_DEFAULT)) < 0)
             goto out;
-        if ((grp2_id = H5Gopen(file2_id, path2))<0)
+        if((grp2_id = H5Gopen2(file2_id, path2, H5P_DEFAULT)) < 0)
             goto out;
+
         /*-------------------------------------------------------------------------
          * compare attributes
          * the if condition refers to cases when the dataset is a referenced object
          *-------------------------------------------------------------------------
          */
-        if (path1)
-            nfound += diff_attr(grp1_id,grp2_id,path1,path2,options);
+        if(path1)
+            nfound += diff_attr(grp1_id, grp2_id, path1, path2, options);
         
-        if ( H5Gclose(grp1_id)<0)
+        if(H5Gclose(grp1_id) < 0)
             goto out;
-        if ( H5Gclose(grp2_id)<0)
+        if(H5Gclose(grp2_id) < 0)
             goto out;
         
         break;
diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c
index 37bef3e..ab089cb 100644
--- a/tools/lib/h5diff_attr.c
+++ b/tools/lib/h5diff_attr.c
@@ -22,7 +22,7 @@
  *
  * Purpose: compare attributes located in LOC1_ID and LOC2_ID, which are
  *  obtained either from
- * loc_id = H5Gopen( fid, name);
+ * loc_id = H5Gopen2( fid, name, H5P_DEFAULT);
  * loc_id = H5Dopen( fid, name);
  * loc_id = H5Topen( fid, name);
  *
diff --git a/tools/lib/h5diff_dset.c b/tools/lib/h5diff_dset.c
index c714d45..b5a2872 100644
--- a/tools/lib/h5diff_dset.c
+++ b/tools/lib/h5diff_dset.c
@@ -25,7 +25,7 @@
  *
  *-------------------------------------------------------------------------
  */
-void
+static void
 print_size (int rank, hsize_t *dims)
 {
     int i;
diff --git a/tools/lib/h5trav.c b/tools/lib/h5trav.c
index 456b56b..c824b3d 100644
--- a/tools/lib/h5trav.c
+++ b/tools/lib/h5trav.c
@@ -340,7 +340,7 @@ static hssize_t get_nnames( hid_t loc_id, const char *group_name )
     hsize_t nobjs = 0;
 
     /* Open the group */
-    if((gid = H5Gopen(loc_id, group_name)) < 0)
+    if((gid = H5Gopen2(loc_id, group_name, H5P_DEFAULT)) < 0)
         return(-1);
 
     /* Retrieve the number of objects in it */