[svn-r12888]

Introduced the second sweep of the file for a case a reference is present and H5Ocopy was not used.
Moved the code from file h5repack_refs.c to h5repack_copy.c and removed the first file

10 files changed, 822 insertions, 159 deletions

diff --git a/MANIFEST b/MANIFEST
index 5978e3f..ffb8f20 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -890,7 +890,6 @@
 ./tools/h5repack/h5repack_main.c
 ./tools/h5repack/h5repack_opttable.c
 ./tools/h5repack/h5repack_parse.c
-./tools/h5repack/h5repack_refs.c
 ./tools/h5repack/h5repack_verify.c
 ./tools/h5repack/testh5repack.h
 ./tools/h5repack/testh5repack_attr.c
diff --git a/configure b/configure
index a778f9d..1836ed4 100755
--- a/configure
+++ b/configure
@@ -1,5 +1,5 @@
 #! /bin/sh
-# From configure.in Id: configure.in 12886 2006-11-09 18:39:33Z jlaird .
+# From configure.in Id: configure.in 12887 2006-11-10 20:56:04Z jlaird .
 # Guess values for system-dependent variables and create Makefiles.
 # Generated by GNU Autoconf 2.60 for HDF5 1.8.0-alpha6.
 #
diff --git a/src/H5Edefin.h b/src/H5Edefin.h
index 4a4a98c..72441c7 100644
--- a/src/H5Edefin.h
+++ b/src/H5Edefin.h
@@ -181,6 +181,13 @@ hid_t H5E_CANTNEXT_g       = FAIL;      /* Can't move to next iterator location
 hid_t H5E_BADSELECT_g      = FAIL;      /* Invalid selection */
 hid_t H5E_CANTCOMPARE_g    = FAIL;      /* Can't compare objects */
 
+/* Argument errors */
+hid_t H5E_UNINITIALIZED_g  = FAIL;      /* Information is uinitialized */
+hid_t H5E_UNSUPPORTED_g    = FAIL;      /* Feature is unsupported */
+hid_t H5E_BADTYPE_g        = FAIL;      /* Inappropriate type */
+hid_t H5E_BADRANGE_g       = FAIL;      /* Out of range */
+hid_t H5E_BADVALUE_g       = FAIL;      /* Bad value */
+
 /* B-tree related errors */
 hid_t H5E_NOTFOUND_g       = FAIL;      /* Object not found */
 hid_t H5E_EXISTS_g         = FAIL;      /* Object already exists */
@@ -194,13 +201,6 @@ hid_t H5E_CANTLIST_g       = FAIL;      /* Unable to list node */
 hid_t H5E_CANTMODIFY_g     = FAIL;      /* Unable to modify record */
 hid_t H5E_CANTREMOVE_g     = FAIL;      /* Unable to remove object */
 
-/* Argument errors */
-hid_t H5E_UNINITIALIZED_g  = FAIL;      /* Information is uinitialized */
-hid_t H5E_UNSUPPORTED_g    = FAIL;      /* Feature is unsupported */
-hid_t H5E_BADTYPE_g        = FAIL;      /* Inappropriate type */
-hid_t H5E_BADRANGE_g       = FAIL;      /* Out of range */
-hid_t H5E_BADVALUE_g       = FAIL;      /* Bad value */
-
 /* Datatype conversion errors */
 hid_t H5E_CANTCONVERT_g    = FAIL;      /* Can't convert datatypes */
 hid_t H5E_BADSIZE_g        = FAIL;      /* Bad size for object */
diff --git a/src/H5Einit.h b/src/H5Einit.h
index 1ac6a99..3cd9ea1 100644
--- a/src/H5Einit.h
+++ b/src/H5Einit.h
@@ -683,6 +683,33 @@ if((msg = H5E_create_msg(cls, H5E_MINOR, "Can't compare objects"))==NULL)
 if((H5E_CANTCOMPARE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
     HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
 
+/* Argument errors */
+assert(H5E_UNINITIALIZED_g==(-1));
+if((msg = H5E_create_msg(cls, H5E_MINOR, "Information is uinitialized"))==NULL)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
+if((H5E_UNINITIALIZED_g = H5I_register(H5I_ERROR_MSG, msg))<0)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
+assert(H5E_UNSUPPORTED_g==(-1));
+if((msg = H5E_create_msg(cls, H5E_MINOR, "Feature is unsupported"))==NULL)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
+if((H5E_UNSUPPORTED_g = H5I_register(H5I_ERROR_MSG, msg))<0)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
+assert(H5E_BADTYPE_g==(-1));
+if((msg = H5E_create_msg(cls, H5E_MINOR, "Inappropriate type"))==NULL)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
+if((H5E_BADTYPE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
+assert(H5E_BADRANGE_g==(-1));
+if((msg = H5E_create_msg(cls, H5E_MINOR, "Out of range"))==NULL)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
+if((H5E_BADRANGE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
+assert(H5E_BADVALUE_g==(-1));
+if((msg = H5E_create_msg(cls, H5E_MINOR, "Bad value"))==NULL)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
+if((H5E_BADVALUE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
+    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
+
 /* B-tree related errors */
 assert(H5E_NOTFOUND_g==(-1));
 if((msg = H5E_create_msg(cls, H5E_MINOR, "Object not found"))==NULL)
@@ -740,33 +767,6 @@ if((msg = H5E_create_msg(cls, H5E_MINOR, "Unable to remove object"))==NULL)
 if((H5E_CANTREMOVE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
     HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
 
-/* Argument errors */
-assert(H5E_UNINITIALIZED_g==(-1));
-if((msg = H5E_create_msg(cls, H5E_MINOR, "Information is uinitialized"))==NULL)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
-if((H5E_UNINITIALIZED_g = H5I_register(H5I_ERROR_MSG, msg))<0)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
-assert(H5E_UNSUPPORTED_g==(-1));
-if((msg = H5E_create_msg(cls, H5E_MINOR, "Feature is unsupported"))==NULL)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
-if((H5E_UNSUPPORTED_g = H5I_register(H5I_ERROR_MSG, msg))<0)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
-assert(H5E_BADTYPE_g==(-1));
-if((msg = H5E_create_msg(cls, H5E_MINOR, "Inappropriate type"))==NULL)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
-if((H5E_BADTYPE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
-assert(H5E_BADRANGE_g==(-1));
-if((msg = H5E_create_msg(cls, H5E_MINOR, "Out of range"))==NULL)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
-if((H5E_BADRANGE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
-assert(H5E_BADVALUE_g==(-1));
-if((msg = H5E_create_msg(cls, H5E_MINOR, "Bad value"))==NULL)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, "error message initialization failed")
-if((H5E_BADVALUE_g = H5I_register(H5I_ERROR_MSG, msg))<0)
-    HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, "can't register error message")
-
 /* Datatype conversion errors */
 assert(H5E_CANTCONVERT_g==(-1));
 if((msg = H5E_create_msg(cls, H5E_MINOR, "Can't convert datatypes"))==NULL)
diff --git a/src/H5Epubgen.h b/src/H5Epubgen.h
index c705ddc..34e9340 100644
--- a/src/H5Epubgen.h
+++ b/src/H5Epubgen.h
@@ -310,6 +310,18 @@ H5_DLLVAR hid_t H5E_CANTNEXT_g;      /* Can't move to next iterator location */
 H5_DLLVAR hid_t H5E_BADSELECT_g;     /* Invalid selection */
 H5_DLLVAR hid_t H5E_CANTCOMPARE_g;   /* Can't compare objects */
 
+/* Argument errors */
+#define H5E_UNINITIALIZED    (H5OPEN H5E_UNINITIALIZED_g)
+#define H5E_UNSUPPORTED      (H5OPEN H5E_UNSUPPORTED_g)
+#define H5E_BADTYPE          (H5OPEN H5E_BADTYPE_g)
+#define H5E_BADRANGE         (H5OPEN H5E_BADRANGE_g)
+#define H5E_BADVALUE         (H5OPEN H5E_BADVALUE_g)
+H5_DLLVAR hid_t H5E_UNINITIALIZED_g; /* Information is uinitialized */
+H5_DLLVAR hid_t H5E_UNSUPPORTED_g;   /* Feature is unsupported */
+H5_DLLVAR hid_t H5E_BADTYPE_g;       /* Inappropriate type */
+H5_DLLVAR hid_t H5E_BADRANGE_g;      /* Out of range */
+H5_DLLVAR hid_t H5E_BADVALUE_g;      /* Bad value */
+
 /* B-tree related errors */
 #define H5E_NOTFOUND         (H5OPEN H5E_NOTFOUND_g)
 #define H5E_EXISTS           (H5OPEN H5E_EXISTS_g)
@@ -334,18 +346,6 @@ H5_DLLVAR hid_t H5E_CANTLIST_g;      /* Unable to list node */
 H5_DLLVAR hid_t H5E_CANTMODIFY_g;    /* Unable to modify record */
 H5_DLLVAR hid_t H5E_CANTREMOVE_g;    /* Unable to remove object */
 
-/* Argument errors */
-#define H5E_UNINITIALIZED    (H5OPEN H5E_UNINITIALIZED_g)
-#define H5E_UNSUPPORTED      (H5OPEN H5E_UNSUPPORTED_g)
-#define H5E_BADTYPE          (H5OPEN H5E_BADTYPE_g)
-#define H5E_BADRANGE         (H5OPEN H5E_BADRANGE_g)
-#define H5E_BADVALUE         (H5OPEN H5E_BADVALUE_g)
-H5_DLLVAR hid_t H5E_UNINITIALIZED_g; /* Information is uinitialized */
-H5_DLLVAR hid_t H5E_UNSUPPORTED_g;   /* Feature is unsupported */
-H5_DLLVAR hid_t H5E_BADTYPE_g;       /* Inappropriate type */
-H5_DLLVAR hid_t H5E_BADRANGE_g;      /* Out of range */
-H5_DLLVAR hid_t H5E_BADVALUE_g;      /* Bad value */
-
 /* Datatype conversion errors */
 #define H5E_CANTCONVERT      (H5OPEN H5E_CANTCONVERT_g)
 #define H5E_BADSIZE          (H5OPEN H5E_BADSIZE_g)
diff --git a/src/H5Eterm.h b/src/H5Eterm.h
index 2f0028a..3743c08 100644
--- a/src/H5Eterm.h
+++ b/src/H5Eterm.h
@@ -183,6 +183,13 @@ H5E_CANTNEXT_g=
 H5E_BADSELECT_g=    
 H5E_CANTCOMPARE_g=
 
+/* Argument errors */    
+H5E_UNINITIALIZED_g=    
+H5E_UNSUPPORTED_g=    
+H5E_BADTYPE_g=    
+H5E_BADRANGE_g=    
+H5E_BADVALUE_g=
+
 /* B-tree related errors */    
 H5E_NOTFOUND_g=    
 H5E_EXISTS_g=    
@@ -196,13 +203,6 @@ H5E_CANTLIST_g=
 H5E_CANTMODIFY_g=    
 H5E_CANTREMOVE_g=
 
-/* Argument errors */    
-H5E_UNINITIALIZED_g=    
-H5E_UNSUPPORTED_g=    
-H5E_BADTYPE_g=    
-H5E_BADRANGE_g=    
-H5E_BADVALUE_g=
-
 /* Datatype conversion errors */    
 H5E_CANTCONVERT_g=    
 H5E_BADSIZE_g= (-1);
diff --git a/tools/h5repack/Makefile.am b/tools/h5repack/Makefile.am
index 29fd26b..8a664ef 100644
--- a/tools/h5repack/Makefile.am
+++ b/tools/h5repack/Makefile.am
@@ -40,7 +40,7 @@ LDADD=$(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
 
 # Source files
 COMMON_SOURCES=h5repack.c h5repack_copy.c h5repack_filters.c \
-        h5repack_list.c h5repack_opttable.c h5repack_parse.c h5repack_refs.c   \
+        h5repack_list.c h5repack_opttable.c h5repack_parse.c \
         h5repack_verify.c
 
 h5repack_SOURCES=$(COMMON_SOURCES) h5repack_main.c
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index 6e2ac79..ab1e7a4 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -73,7 +73,7 @@ PROGRAMS = $(bin_PROGRAMS) $(noinst_PROGRAMS)
 am__objects_1 = h5repack.$(OBJEXT) h5repack_copy.$(OBJEXT) \
 	h5repack_filters.$(OBJEXT) h5repack_list.$(OBJEXT) \
 	h5repack_opttable.$(OBJEXT) h5repack_parse.$(OBJEXT) \
-	h5repack_refs.$(OBJEXT) h5repack_verify.$(OBJEXT)
+	h5repack_verify.$(OBJEXT)
 am_h5repack_OBJECTS = $(am__objects_1) h5repack_main.$(OBJEXT)
 h5repack_OBJECTS = $(am_h5repack_OBJECTS)
 h5repack_LDADD = $(LDADD)
@@ -368,7 +368,7 @@ LDADD = $(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
 
 # Source files
 COMMON_SOURCES = h5repack.c h5repack_copy.c h5repack_filters.c \
-        h5repack_list.c h5repack_opttable.c h5repack_parse.c h5repack_refs.c   \
+        h5repack_list.c h5repack_opttable.c h5repack_parse.c \
         h5repack_verify.c
 
 h5repack_SOURCES = $(COMMON_SOURCES) h5repack_main.c
@@ -494,7 +494,6 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_main.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_opttable.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_parse.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_refs.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/h5repack_verify.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testh5repack_attr.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testh5repack_detect_szip.Po@am__quote@
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 6b3e4d0..5dbb5ce 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -23,18 +23,23 @@
 
 extern char  *progname;
 
+static int do_create_refs;
+
 
 #define PER(A,B) { per = 0;                                       \
                    if (A!=0)                                      \
-                    per = (float)fabs(1-( (float)B / (float)A )); \
+                    per = (float)fabs( ((float)B - (float)A) / (float) A  ); \
                  }
 
 #define FORMAT_OBJ      " %-21s %s\n"  /* obj type, name */
 #define FORMAT_OBJ_ATTR "  %-21s %s\n"  /* obj type, name */
 
-
-static
-int do_hardlinks(hid_t fidout,trav_table_t *travt);
+/* local functions */
+static int   do_hardlinks(hid_t fidout,trav_table_t *travt);
+static void  close_obj(H5G_obj_t obj_type, hid_t obj_id);
+static int   do_copy_refobjs(hid_t fidin, hid_t fidout,trav_table_t *travt,pack_opt_t *options); 
+static int   copy_refs_attr(hid_t loc_in,hid_t loc_out,pack_opt_t *options,trav_table_t *travt,hid_t fidout);
+static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
 
 /*-------------------------------------------------------------------------
  * Function: print_dataset_info
@@ -88,7 +93,6 @@ static void print_dataset_info(hid_t dcpl_id,
    NULL);
 #endif /* H5_WANT_H5_V1_6_COMPAT */
 
-
   switch (filtn)
   {
   default:
@@ -207,6 +211,18 @@ int copy_objects(const char* fnamein,
  }
 
 /*-------------------------------------------------------------------------
+ * do the copy of referenced objects in a second sweep if needed (references 
+ *  detected in the first traversal)
+ *-------------------------------------------------------------------------
+ */
+ if (do_create_refs){
+  if(do_copy_refobjs(fidin,fidout,travt,options)<0) {
+   error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
+   goto out;
+  }
+ }
+
+/*-------------------------------------------------------------------------
  * create hard links
  *-------------------------------------------------------------------------
  */
@@ -265,6 +281,12 @@ out:
  *  October 2006:  Read/write using the file type by default.
  *                 Read/write by hyperslabs for big datasets.
  *
+ *  November 2006:  Use H5Ocopy in the copy of objects. The logic for using 
+ *   H5Ocopy or not is if the input DCPL has filters or non default layout or these are 
+ *   requested by the user then use read/write else use H5Ocopy. 
+ *   A detection is made for the cases where the recreation of references is needed
+ *   in a second sweep of the file
+ *
  *-------------------------------------------------------------------------
  */
 
@@ -444,7 +466,11 @@ int do_copy_objects(hid_t fidin,
      * in a second traversal of the output file
      *-------------------------------------------------------------------------
      */
-     if ( (H5T_REFERENCE!=H5Tget_class(wtype_id)))
+     if (H5T_REFERENCE==H5Tget_class(wtype_id))
+     {
+         do_create_refs = 1;
+     }
+     else /* H5T_REFERENCE */
      {
       /* get the storage size of the input dataset */
       dsize_in=H5Dget_storage_size(dset_in);
@@ -629,8 +655,8 @@ int do_copy_objects(hid_t fidin,
      if (H5Dclose(dset_out)<0)
       goto error;
      
-    }/*H5T_STD_REF_OBJ*/
-   }/*can_read*/
+    }/*H5T_REFERENCE*/
+   }/*h5tools_canreadf*/
    
    
    /*-------------------------------------------------------------------------
@@ -1029,3 +1055,734 @@ int do_hardlinks(hid_t fidout,trav_table_t *travt)
  return 0;
 
 }
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: do_copy_refobjs
+ *
+ * Purpose: duplicate all referenced HDF5 objects in the file in a second traversal
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: December, 10, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static
+int do_copy_refobjs(hid_t fidin,
+                    hid_t fidout,
+                    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 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 */
+ int       next;              /* external files */
+ int       i, j;
+
+/*-------------------------------------------------------------------------
+ * browse
+ *-------------------------------------------------------------------------
+ */
+
+ for ( i = 0; i < travt->nobjs; i++)
+ {
+  switch ( travt->objs[i].type )
+  {
+
+  case H5G_GROUP:
+
+   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 (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 for external files
+ *-------------------------------------------------------------------------
+ */
+   if ((next=H5Pget_external_count (dcpl_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 (next==0 && 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(wtype_id, H5T_STD_REF_OBJ))
+   {
+    H5G_obj_t        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){
+      error_msg(progname, "cannot read into memory\n" );
+      goto error;
+     }
+     if (H5Dread(dset_in,wtype_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=HDmalloc((unsigned)nelmts*msize);
+     if ( refbuf==NULL){
+      error_msg(progname, "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,wtype_id,space_id,dcpl_id))<0)
+     goto error;
+    if (nelmts) {
+     if (H5Dwrite(dset_out,wtype_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(wtype_id, H5T_STD_REF_DSETREG))
+   {
+    H5G_obj_t        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){
+      error_msg(progname, "cannot read into memory\n" );
+      goto error;
+     }
+     if (H5Dread(dset_in,wtype_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){
+      error_msg(progname, "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,wtype_id,space_id,dcpl_id))<0)
+     goto error;
+    if (nelmts) {
+     if (H5Dwrite(dset_out,wtype_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;
+
+
+
+   if (H5Dclose(dset_out)<0)
+    goto error;
+
+   }/*can_read*/
+
+   /*-------------------------------------------------------------------------
+    * close
+    *-------------------------------------------------------------------------
+    */
+
+   if (H5Tclose(ftype_id)<0)
+    goto error;
+   if (H5Tclose(wtype_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;
+
+
+  case H5G_TYPE:
+  case H5G_LINK:
+  case H5G_UDLINK:
+
+   /*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;
+
+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(wtype_id);
+  H5Tclose(type_in);
+ } H5E_END_TRY;
+ return -1;
+
+}
+
+
+
+/*-------------------------------------------------------------------------
+ * Function: copy_refs_attr
+ *
+ * Purpose: duplicate all referenced HDF5 objects located in attributes
+ *  relative to LOC_IN, which is obtained either from
+ * loc_id = H5Gopen( fid, name);
+ * loc_id = H5Dopen( fid, name);
+ * loc_id = H5Topen( fid, name);
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: October, 28, 2003
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static int copy_refs_attr(hid_t loc_in,
+                          hid_t loc_out,
+                          pack_opt_t *options,
+                          trav_table_t *travt,
+                          hid_t fidout         /* for saving references */
+                          )
+{
+ hid_t      attr_id;      /* attr ID */
+ hid_t      attr_out;     /* attr ID */
+ hid_t      space_id;     /* space ID */
+ hid_t      ftype_id;     /* file type ID */
+ hid_t      wtype_id;     /* 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 */
+ char       name[255];
+ int        n, j;
+ unsigned   u;
+
+ if ((n = H5Aget_num_attrs(loc_in))<0)
+  goto error;
+
+ for ( u = 0; u < (unsigned)n; u++)
+ {
+
+/*-------------------------------------------------------------------------
+ * open
+ *-------------------------------------------------------------------------
+ */
+  /* open attribute */
+  if ((attr_id = H5Aopen_idx(loc_in, u))<0)
+   goto error;
+
+  /* get name */
+  if (H5Aget_name( attr_id, 255, name )<0)
+   goto error;
+
+  /* get the file datatype  */
+  if ((ftype_id = H5Aget_type( attr_id )) < 0 )
+   goto error;
+
+  /* get the dataspace handle  */
+  if ((space_id = H5Aget_space( attr_id )) < 0 )
+   goto error;
+
+  /* get dimensions  */
+  if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
+   goto error;
+
+
+  /*-------------------------------------------------------------------------
+   * elements
+   *-------------------------------------------------------------------------
+   */
+  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;
+
+/*-------------------------------------------------------------------------
+ * object references are a special case
+ * we cannot just copy the buffers, but instead we recreate the reference
+ *-------------------------------------------------------------------------
+ */
+   if (H5Tequal(wtype_id, H5T_STD_REF_OBJ))
+   {
+    H5G_obj_t   obj_type;
+    hid_t       refobj_id;
+    hobj_ref_t  *refbuf=NULL;
+    unsigned    k;
+    const char* refname;
+    hobj_ref_t  *buf=NULL;
+
+   /*-------------------------------------------------------------------------
+    * read input to memory
+    *-------------------------------------------------------------------------
+    */
+
+    if (nelmts)
+    {
+     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+     if ( buf==NULL){
+      error_msg(progname, "cannot read into memory\n" );
+      goto error;
+     }
+     if (H5Aread(attr_id,wtype_id,buf)<0)
+      goto error;
+
+     if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
+      goto error;
+     refbuf=HDmalloc((unsigned)nelmts*msize);
+     if ( refbuf==NULL){
+      error_msg(progname, "cannot allocate memory\n" );
+      goto error;
+     }
+     for ( k=0; k<nelmts; k++)
+     {
+      H5E_BEGIN_TRY {
+       if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
+        goto error;
+      } 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 */
+       if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
+        goto error;
+       if (options->verbose)
+        printf("object <%s> reference created to <%s>\n",name,refname);
+      }
+      close_obj(obj_type,refobj_id);
+     }/*  k */
+    }/*nelmts*/
+
+    /*-------------------------------------------------------------------------
+     * copy
+     *-------------------------------------------------------------------------
+     */
+
+    if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
+     goto error;
+    if (nelmts) {
+     if(H5Awrite(attr_out,wtype_id,refbuf)<0)
+      goto error;
+    }
+
+    if (H5Aclose(attr_out)<0)
+     goto error;
+
+    if (refbuf)
+     free(refbuf);
+    if (buf)
+     free(buf);
+
+   }/*H5T_STD_REF_OBJ*/
+
+/*-------------------------------------------------------------------------
+ * dataset region references
+ *-------------------------------------------------------------------------
+ */
+   else if (H5Tequal(wtype_id, H5T_STD_REF_DSETREG))
+   {
+    H5G_obj_t        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         k;
+
+   /*-------------------------------------------------------------------------
+    * read input to memory
+    *-------------------------------------------------------------------------
+    */
+
+    if (nelmts)
+    {
+     buf=(void *) HDmalloc((unsigned)(nelmts*msize));
+     if ( buf==NULL){
+      error_msg(progname, "cannot read into memory\n" );
+      goto error;
+     }
+     if (H5Aread(attr_id,wtype_id,buf)<0)
+      goto error;
+     if ((obj_type = H5Rget_obj_type(attr_id,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){
+      error_msg(progname, "cannot allocate memory\n" );
+      goto error;
+     }
+     for ( k=0; k<nelmts; k++)
+     {
+      H5E_BEGIN_TRY {
+       if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<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(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
+        goto error;
+       /* create the reference, we need the space_id */
+       if (H5Rcreate(&refbuf[k],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",name,refname);
+      }
+      close_obj(obj_type,refobj_id);
+     }/*  k */
+    }/*nelmts */
+
+    /*-------------------------------------------------------------------------
+     * copy
+     *-------------------------------------------------------------------------
+     */
+
+    if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
+     goto error;
+    if (nelmts) {
+     if(H5Awrite(attr_out,wtype_id,refbuf)<0)
+      goto error;
+    }
+    if (H5Aclose(attr_out)<0)
+     goto error;
+    if (refbuf)
+     free(refbuf);
+    if (buf)
+     free(buf);
+   } /* H5T_STD_REF_DSETREG */
+
+/*-------------------------------------------------------------------------
+ * close
+ *-------------------------------------------------------------------------
+ */
+
+  if (H5Tclose(ftype_id)<0) goto error;
+  if (H5Tclose(wtype_id)<0) goto error;
+  if (H5Sclose(space_id)<0) goto error;
+  if (H5Aclose(attr_id)<0) goto error;
+ } /* u */
+
+  return 0;
+
+error:
+ H5E_BEGIN_TRY {
+  H5Tclose(ftype_id);
+  H5Tclose(wtype_id);
+  H5Sclose(space_id);
+  H5Aclose(attr_id);
+  H5Aclose(attr_out);
+ } H5E_END_TRY;
+ return -1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: close_obj
+ *
+ * Purpose: Auxiliary function to close an object
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
+{
+ H5E_BEGIN_TRY
+ {
+  switch (obj_type)
+  {
+  case H5G_GROUP:
+   H5Gclose(obj_id);
+   break;
+  case H5G_DATASET:
+   H5Dclose(obj_id);
+   break;
+  case H5G_TYPE:
+   H5Tclose(obj_id);
+   break;
+  default:
+   break;
+  }
+ } H5E_END_TRY;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: MapIdToName
+ *
+ * Purpose: map an object ID to a name
+ *
+ *-------------------------------------------------------------------------
+ */
+
+static const char* MapIdToName(hid_t refobj_id,
+                               trav_table_t *travt)
+{
+ hid_t id;
+ hid_t fid;
+ H5G_stat_t refstat;    /* Stat for the refobj id */
+ H5G_stat_t objstat;    /* Stat for objects in the file */
+ int   i;
+
+ /* obtain information to identify the referenced object uniquely */
+ if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0)
+  return NULL;
+
+ /* obtains the file ID given an object ID.  This ID must be closed */
+ if ((fid = H5Iget_file_id(refobj_id))<0)
+ {
+  return NULL;
+ }
+
+ /* linear search */
+ for ( i=0; i<travt->nobjs; i++)
+ {
+  switch ( travt->objs[i].type )
+  {
+  default:
+   break;
+
+  /*-------------------------------------------------------------------------
+   * H5G_DATASET
+   *-------------------------------------------------------------------------
+   */
+
+  case H5G_DATASET:
+
+   if ((id = H5Dopen(fid,travt->objs[i].name))<0)
+    return NULL;
+   if(H5Gget_objinfo(id, ".", 0, &objstat) <0)
+    return NULL;
+   if (H5Dclose(id)<0)
+    return NULL;
+   if (!HDmemcmp(&refstat.fileno, &objstat.fileno, sizeof(refstat.fileno)) && !HDmemcmp(&refstat.objno, &objstat.objno, sizeof(refstat.objno)))
+   {
+    H5Fclose(fid);
+    return travt->objs[i].name;
+   }
+   break;
+  }  /* switch */
+ } /* i */
+
+ if (H5Fclose(fid)<0)
+  return NULL;
+
+ return NULL;
+}
+
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
deleted file mode 100644
index e01af2d..0000000
--- a/tools/h5repack/h5repack_refs.c
+++ /dev/null
@@ -1,92 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by the Board of Trustees of the University of Illinois.         *
- * All rights reserved.                                                      *
- *                                                                           *
- * This file is part of HDF5.  The full HDF5 copyright notice, including     *
- * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
- * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include "H5private.h"
-#include "h5tools_utils.h"
-#include "h5repack.h"
-
-extern char  *progname;
-
-static const char* MapIdToName(hid_t refobj_id,
-                               trav_table_t *travt);
-
-
-
-
-/*-------------------------------------------------------------------------
- * Function: MapIdToName
- *
- * Purpose: map an object ID to a name
- *
- *-------------------------------------------------------------------------
- */
-
-static const char* MapIdToName(hid_t refobj_id,
-                               trav_table_t *travt)
-{
- hid_t id;
- hid_t fid;
- H5G_stat_t refstat;    /* Stat for the refobj id */
- H5G_stat_t objstat;    /* Stat for objects in the file */
- int   i;
-
- /* obtain information to identify the referenced object uniquely */
- if(H5Gget_objinfo(refobj_id, ".", 0, &refstat) <0)
-  return NULL;
-
- /* obtains the file ID given an object ID.  This ID must be closed */
- if ((fid = H5Iget_file_id(refobj_id))<0)
- {
-  return NULL;
- }
-
- /* linear search */
- for ( i=0; i<travt->nobjs; i++)
- {
-  switch ( travt->objs[i].type )
-  {
-  default:
-   break;
-
-  /*-------------------------------------------------------------------------
-   * H5G_DATASET
-   *-------------------------------------------------------------------------
-   */
-
-  case H5G_DATASET:
-
-   if ((id = H5Dopen(fid,travt->objs[i].name))<0)
-    return NULL;
-   if(H5Gget_objinfo(id, ".", 0, &objstat) <0)
-    return NULL;
-   if (H5Dclose(id)<0)
-    return NULL;
-   if (!HDmemcmp(&refstat.fileno, &objstat.fileno, sizeof(refstat.fileno)) && !HDmemcmp(&refstat.objno, &objstat.objno, sizeof(refstat.objno)))
-   {
-    H5Fclose(fid);
-    return travt->objs[i].name;
-   }
-   break;
-  }  /* switch */
- } /* i */
-
- if (H5Fclose(fid)<0)
-  return NULL;
-
- return NULL;
-}
-