[svn-r21400] Purpose:

    HDFFV-5932 - h5repack breaks files with dimension scales

Description:
    - Fixed h5repack to update values of references(object and region) of 
      attributes in h5repack for 1) references, 2) ARRAY of references, 
      3) VLEN of references, and 4) COMPOUND of references.
    - Merged from HDF5 trunk 21393, 21382, 21386, 21389. (support Peter)

Tested:
 jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE)

4 files changed, 333 insertions, 164 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 6672b68..c2cecf1 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -105,7 +105,7 @@ int h5repack_init (pack_opt_t *options,
     return (options_table_init(&(options->op_tbl)));
 }
 
-
+
 /*-------------------------------------------------------------------------
 * Function: h5repack_end
 *
@@ -119,7 +119,7 @@ int h5repack_end  (pack_opt_t *options)
     return options_table_free(options->op_tbl);
 }
 
-
+
 /*-------------------------------------------------------------------------
 * Function: h5repack_addfilter
 *
@@ -167,7 +167,7 @@ int h5repack_addfilter(const char* str,
     return 0;
 }
 
-
+
 /*-------------------------------------------------------------------------
 * Function: h5repack_addlayout
 *
@@ -233,9 +233,9 @@ int h5repack_addlayout(const char* str,
     return 0;
 }
 
-/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr() 
- * were located in h5repack_copy.c as static prior to bugfix1726. 
- * Made shared functions as copy_attr() was needed in h5repack_refs.c. 
+/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
+ * were located in h5repack_copy.c as static prior to bugfix1726.
+ * Made shared functions as copy_attr() was needed in h5repack_refs.c.
  * However copy_attr() may be obsoleted when H5Acopy is available and put back
  * others to static in h5repack_copy.c.
  */
@@ -266,21 +266,21 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
     if(H5Oget_info(type_in, &oinfo) < 0)
         goto error;
 
-    if(*named_dt_head_p) 
+    if(*named_dt_head_p)
     {
         /* Stack already exists, search for the datatype */
         while(dt && dt->addr_in != oinfo.addr)
             dt = dt->next;
 
         dt_ret = dt;
-    } 
-    else 
+    }
+    else
     {
         /* Create the stack */
         size_t  i;
 
         for(i=0; i<travt->nobjs; i++)
-            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) 
+            if(travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE)
             {
                 /* Push onto the stack */
                 if(NULL == (dt = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
@@ -293,7 +293,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
                 dt->id_out = -1;
 
                 /* Check if this type is the one requested */
-                if(oinfo.addr == dt->addr_in) 
+                if(oinfo.addr == dt->addr_in)
                 {
                     HDassert(!dt_ret);
                     dt_ret = dt;
@@ -303,7 +303,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
 
     /* Handle the case that the requested datatype was not found.  This is
      * possible if the datatype was committed anonymously in the input file. */
-    if(!dt_ret) 
+    if(!dt_ret)
     {
         /* Push the new datatype onto the stack */
         if(NULL == (dt_ret = (named_dt_t *) HDmalloc(sizeof(named_dt_t))))
@@ -318,7 +318,7 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_hea
 
     /* If the requested datatype does not yet exist in the output file, copy it
      * anonymously */
-    if(dt_ret->id_out < 0) 
+    if(dt_ret->id_out < 0)
     {
         if (options->use_native==1)
             dt_ret->id_out = h5tools_get_native_type(type_in);
@@ -360,7 +360,7 @@ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
 {
     named_dt_t *dt = *named_dt_head_p;
 
-    while(dt) 
+    while(dt)
     {
         /* Pop the datatype off the stack and free it */
         if(H5Tclose(dt->id_out) < 0 && !ignore_err)
@@ -413,6 +413,8 @@ int copy_attr(hid_t loc_in,
     H5O_info_t oinfo;             /* object info */
     int        j;
     unsigned   u;
+    hbool_t    is_ref=0;
+    H5T_class_t type_class = -1;
 
     if(H5Oget_info(loc_in, &oinfo) < 0)
         goto error;
@@ -446,7 +448,7 @@ int copy_attr(hid_t loc_in,
 
             /* Copy named dt */
             if((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p,
-                    travt, options)) < 0) 
+                    travt, options)) < 0)
             {
                 H5Fclose(fidout);
                 goto error;
@@ -462,6 +464,7 @@ int copy_attr(hid_t loc_in,
                 wtype_id = H5Tcopy(ftype_id);
         } /* end else */
 
+
         /* get the dataspace handle  */
         if((space_id = H5Aget_space(attr_id)) < 0)
             goto error;
@@ -478,15 +481,37 @@ int copy_attr(hid_t loc_in,
             goto error;
 
         /*-------------------------------------------------------------------------
-        * object references are a special case
-        * we cannot just copy the buffers, but instead we recreate the reference
-        * this is done on a second sweep of the file that just copies
-        * the referenced objects
+        * object references are a special case. We cannot just copy the buffers,
+        * but instead we recreate the reference.
+        * This is done on a second sweep of the file that just copies the referenced
+        * objects at copy_refs_attr()
         *-------------------------------------------------------------------------
         */
+        type_class = H5Tget_class(wtype_id);
+        is_ref = (type_class == H5T_REFERENCE);
+        if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
+        	H5Tclose(base_type);
+        }
 
-        if(H5T_REFERENCE == H5Tget_class(wtype_id)) {
-            ;
+        if (type_class == H5T_COMPOUND) {
+        	int nmembers = H5Tget_nmembers(wtype_id) ;
+        	for (j=0; j<nmembers; j++) {
+        		hid_t mtid = H5Tget_member_type( wtype_id, j );
+        		H5T_class_t mtclass = H5Tget_class(mtid);
+        		H5Tclose(mtid);
+
+        		if (mtclass==H5T_REFERENCE) {
+        			is_ref = 1;
+        			break;
+        		}
+        	} /* for (j=0; i<nmembers; j++) */
+        } /* if (type_class == H5T_COMPOUND) */
+
+        if(is_ref) {
+            ; /* handled by copy_refs_attr() */
         }
         else {
             /*-------------------------------------------------------------------------
@@ -602,20 +627,20 @@ static int check_options(pack_opt_t *options)
             switch (options->layout_g)
             {
             case H5D_COMPACT:
-                strcpy(slayout,"compact");
+                HDstrcpy(slayout,"compact");
                 break;
             case H5D_CONTIGUOUS:
-                strcpy(slayout,"contiguous");
+                HDstrcpy(slayout,"contiguous");
                 break;
             case H5D_CHUNKED:
-                strcpy(slayout,"chunked");
+                HDstrcpy(slayout,"chunked");
                 break;
             case H5D_LAYOUT_ERROR:
             case H5D_NLAYOUTS:
                 error_msg("invalid layout\n");
                 return -1;
             default:
-                strcpy(slayout,"invalid layout\n");
+                HDstrcpy(slayout,"invalid layout\n");
                 return -1;
             }
             printf(" Apply %s layout to all\n", slayout);
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 9b31ffe..4164133 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -83,6 +83,7 @@ test -d $TESTDIR || mkdir $TESTDIR
 # --------------------------------------------------------------------
 LIST_HDF5_TEST_FILES="
 $SRC_H5REPACK_TESTFILES/h5repack_attr.h5
+$SRC_H5REPACK_TESTFILES/h5repack_attr_refs.h5
 $SRC_H5REPACK_TESTFILES/h5repack_deflate.h5
 $SRC_H5REPACK_TESTFILES/h5repack_early.h5
 $SRC_H5REPACK_TESTFILES/h5repack_ext.h5
@@ -795,6 +796,9 @@ TOOLTEST1 tfamily%05d.h5
 # test various references (bug 1814 and 1726)
 TOOLTEST h5repack_refs.h5
 
+# test attribute with various references (bug1797 / HDFFV-5932)
+# the references in attribute of compund or vlen datatype 
+TOOLTEST h5repack_attr_refs.h5 
 
 if test $nerrors -eq 0 ; then
     echo "All $TESTNAME tests passed."
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 091133e..c6753c1 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -27,6 +27,8 @@
 static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
 static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
                           trav_table_t *travt, hid_t fidout);
+static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
+		hid_t fid_out, void *ref_out, trav_table_t *travt);
 
 /*-------------------------------------------------------------------------
  * Function: do_copy_refobjs
@@ -229,7 +231,7 @@ int do_copy_refobjs(hid_t fidin,
                     * dataset region references
                     *-------------------------------------------------------------------------
                     */
-                    else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) 
+                    else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
                     {
                         hid_t            refobj_id;
                         hdset_reg_ref_t  *refbuf = NULL; /* input buffer for region references */
@@ -390,7 +392,7 @@ int do_copy_refobjs(hid_t fidin,
         } /* end switch */
     } /* end for */
 
-    /* Finalize (link) the stack of named datatypes (if any) 
+    /* Finalize (link) the stack of named datatypes (if any)
      * This function is paired with copy_named_datatype() which is called
      * in copy_attr(), so need to free.
      */
@@ -429,6 +431,15 @@ error:
  *
  * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
+ * Modifier: xcao@hdfgroup.org, 9/12/2011
+ * 	         Update values of references(object and region) for the following types:
+ *               1) References,
+ *               2) ARRAY of reference,
+ *               3) VLEN of references.
+ *               4) COMPOUND of references.
+ *          This function does not handle references in other complicated structures,
+ *		    such as references in nested compound datatypes.
+ *
  * Date: October, 28, 2003
  *
  *-------------------------------------------------------------------------
@@ -448,34 +459,95 @@ static int copy_refs_attr(hid_t loc_in,
     hid_t      mtype_id = -1;     /* memory data type ID */
     size_t     msize;             /* memory 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];
     H5O_info_t oinfo;           /* Object info */
-    int        j;
-    unsigned   u;
+    unsigned   u, i, j;
+    int        rank;
+    H5T_class_t type_class = -1;
+    hbool_t    is_ref=0, is_ref_vlen=0, is_ref_array=0, is_ref_comp=0;
+    void  *refbuf = NULL;
+    void  *buf = NULL;
+    const char* refname;
+    int   *ref_comp_index = NULL;
+    size_t *ref_comp_size = NULL;
+    int    ref_comp_field_n = 0;
+
 
     if(H5Oget_info(loc_in, &oinfo) < 0)
         goto error;
 
     for(u = 0; u < (unsigned)oinfo.num_attrs; u++)
     {
-        /*-------------------------------------------------------------------------
-        * open
-        *-------------------------------------------------------------------------
-        */
+    	is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
+
         /* open attribute */
         if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
             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;
 
+        type_class = H5Tget_class(ftype_id);
+
+        if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
+            goto error;
+
+        if((msize = H5Tget_size(mtype_id)) == 0)
+            goto error;
+
+        is_ref = (type_class == H5T_REFERENCE);
+
+        if (type_class == H5T_VLEN ) {
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
+        	msize = H5Tget_size(base_type);
+        	H5Tclose(base_type);
+        }
+
+        if (type_class == H5T_ARRAY ) {
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
+        	msize = H5Tget_size(base_type);
+        	H5Tclose(base_type);
+        }
+
+        if (type_class == H5T_COMPOUND) {
+        	int nmembers = H5Tget_nmembers(ftype_id) ;
+        	if (nmembers < 1)
+        		goto error;
+
+            ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int));
+            ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size));
+            ref_comp_field_n = 0;
+
+        	for (i=0; i<(unsigned)nmembers; i++) {
+        		hid_t mtid = H5Tget_member_type( ftype_id, i );
+        		if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
+        			ref_comp_index[ref_comp_field_n] = i;
+        			ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
+        			ref_comp_field_n++;
+        		}
+        		H5Tclose(mtid);
+        	}
+        }
+
+        is_ref_comp = (ref_comp_field_n > 0);
+
+        if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) {
+        	H5Tclose(mtype_id);
+           	H5Tclose(ftype_id);
+        	H5Aclose(attr_id);
+        	continue;
+        }
+
+        /* get name */
+        if(H5Aget_name(attr_id, 255, name) < 0)
+            goto error;
+
         /* get the dataspace handle  */
         if((space_id = H5Aget_space(attr_id)) < 0)
             goto error;
@@ -490,35 +562,32 @@ static int copy_refs_attr(hid_t loc_in,
         *-------------------------------------------------------------------------
         */
         nelmts = 1;
-        for(j = 0; j < rank; j++)
+        for(j = 0; j < (unsigned)rank; j++)
             nelmts *= dims[j];
 
-        if((mtype_id = h5tools_get_native_type(ftype_id)) < 0)
-            goto error;
-
-        if((msize = H5Tget_size(mtype_id)) == 0)
+        if (is_ref_array) {
+        	unsigned        array_rank = 0;
+        	hsize_t    array_size = 1;
+        	hsize_t array_dims[H5S_MAX_RANK];
+        	hid_t base_type = -1;
+        	base_type = H5Tget_super(ftype_id);
+        	msize = H5Tget_size(base_type);
+           	H5Tclose(base_type);
+
+        	array_rank = H5Tget_array_ndims(mtype_id);
+        	H5Tget_array_dims2(mtype_id, array_dims);
+            for(j = 0; j <array_rank; j++)
+            	array_size *= array_dims[j];
+            nelmts *= array_size;
+         }
+
+        if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
             goto error;
 
-
-        /*-------------------------------------------------------------------------
-        * 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))
+        if (nelmts>0)
         {
-            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)
+            /* handle object references */
+            if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize))
             {
                 buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
                 if(buf == NULL)
@@ -536,65 +605,16 @@ static int copy_refs_attr(hid_t loc_in,
                     goto error;
                 } /* end if */
 
-                for(k = 0; k < nelmts; k++)
+                for(i = 0; i < (unsigned)nelmts; i++)
                 {
-                    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);
-                    }
-                    H5Oclose(refobj_id);
+                    if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
+                		continue;
+                    if(options->verbose)
+                        printf("object <%s> reference created to <%s>\n", name, refname);
                 } /* k */
-            } /*nelmts*/
-
-            /*-------------------------------------------------------------------------
-            * copy
-            *-------------------------------------------------------------------------
-            */
-            if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-                goto error;
-            if(nelmts)
-                if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
-                    goto error;
-
-            if(H5Aclose(attr_out) < 0)
-                goto error;
-
-            if(refbuf)
-                HDfree(refbuf);
-            if(buf)
-                HDfree(buf);
-        }/*H5T_STD_REF_OBJ*/
-
-        /*-------------------------------------------------------------------------
-        * dataset region references
-        *-------------------------------------------------------------------------
-        */
-        else if(H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
-        {
-            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)
+            }/*H5T_STD_REF_OBJ*/
+            /* handle region references */
+            else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize))
             {
                 buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
                 if(buf == NULL)
@@ -616,56 +636,119 @@ static int copy_refs_attr(hid_t loc_in,
                     goto error;
                 } /* end if */
 
-                for(k = 0; k < nelmts; k++)
+                for(i = 0; i < (unsigned)nelmts; i++)
                 {
-                    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 (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
+                		continue;
+                    if(options->verbose)
+                        printf("object <%s> region reference created to <%s>\n", name, refname);
+                }
+            } /* H5T_STD_REF_DSETREG */
+            else if (is_ref_vlen) {
+            	/* handle VLEN of references */
+
+                buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
+                refbuf = buf; /* reuse the read buffer for write */
 
-                        if((region_id = H5Rget_region(attr_id, H5R_DATASET_REGION, &buf[k])) < 0)
-                            goto error;
+                if(buf == NULL)
+                {
+                    printf( "cannot read into memory\n" );
+                    goto error;
+                } /* end if */
 
-                        /* 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);
-                    } /* end if */
-                    H5Oclose(refobj_id);
-                } /* k */
-            } /*nelmts */
+                if(H5Aread(attr_id, mtype_id, buf) < 0)
+                    goto error;
 
-            /*-------------------------------------------------------------------------
-            * copy
-            *-------------------------------------------------------------------------
-            */
-            if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-                goto error;
-            if(nelmts)
-            {
-                if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
+ 				if (H5R_OBJ_REF_BUF_SIZE==msize) {
+					hobj_ref_t ref_out;
+					for (i=0; i<(unsigned)nelmts; i++) {
+						hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
+						for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
+							if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
+								continue;
+							HDmemcpy(&(ptr[j]), &ref_out, msize);
+						}
+					}  /* for (i=0; i<nelems; i++) */
+				} else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
+
+					hdset_reg_ref_t ref_out;
+					for (i=0; i<(unsigned)nelmts; i++) {
+						hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
+						for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
+							if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
+								continue;
+							HDmemcpy(&(ptr[j]), &ref_out, msize);
+						}
+					}  /* for (i=0; i<nelems; i++) */
+				}
+            } /* else if (is_ref_vlen) */
+            else if (is_ref_comp) {
+            	/* handle ref fields in a compound */
+
+                buf = HDmalloc((unsigned)(nelmts * msize));
+                refbuf = buf; /* reuse the read buffer for write */
+
+                if(buf == NULL)
+                {
+                    printf( "cannot read into memory\n" );
                     goto error;
-            }
+                } /* end if */
 
-            if(H5Aclose(attr_out) < 0)
-                goto error;
+                if(H5Aread(attr_id, mtype_id, buf) < 0)
+                    goto error;
 
-            if(refbuf)
-                HDfree(refbuf);
-            if(buf)
-                HDfree(buf);
-        } /* H5T_STD_REF_DSETREG */
+                for (i=0; i<(unsigned)nelmts; i++) {
+                	for (j=0; j<(unsigned)ref_comp_field_n; j++) {
+                		if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
+                			int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
+                			hobj_ref_t ref_out;
+                			if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+                				continue;
+                			HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+                 		} /* if */
+                		else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
+                			int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
+                			hdset_reg_ref_t ref_out;
+                			if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+                				continue;
+                			HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
+                 		} /* else if */
+                	} /* j */
+                } /* i */
+            } /* else if (is_ref_comp) */
+
+            if(H5Awrite(attr_out, mtype_id, refbuf) < 0)
+                 goto error;
+
+            if (is_ref_vlen && buf)
+            	H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
+        } /* if (nelmts) */
+
+        if (refbuf == buf)
+        	refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
+
+        if(buf) {
+            HDfree(buf);
+            buf = NULL;
+        }
+
+        if(refbuf) {
+            HDfree(refbuf);
+            refbuf = NULL;
+        }
+
+        if (ref_comp_index) {
+        	HDfree(ref_comp_index);
+        	ref_comp_index = NULL;
+        }
+
+        if (ref_comp_size) {
+        	HDfree(ref_comp_size);
+        	ref_comp_size = NULL;
+        }
+
+        if(H5Aclose(attr_out) < 0)
+            goto error;
 
         /*-------------------------------------------------------------------------
         * close
@@ -679,11 +762,22 @@ static int copy_refs_attr(hid_t loc_in,
             goto error;
         if(H5Aclose(attr_id) < 0)
             goto error;
-    } /* u */
+    } /* for(u = 0; u < (unsigned)oinfo.num_attrs; u++) */
 
     return 0;
 
 error:
+	if(refbuf)
+		HDfree(refbuf);
+	if(buf)
+		HDfree(buf);
+
+    if (ref_comp_index)
+    	HDfree(ref_comp_index);
+
+    if (ref_comp_size)
+    	HDfree(ref_comp_size);
+
     H5E_BEGIN_TRY {
         H5Tclose(ftype_id);
         H5Tclose(mtype_id);
@@ -710,7 +804,7 @@ MapIdToName(hid_t refobj_id, trav_table_t *travt)
 
     /* linear search */
     for(u = 0; u < travt->nobjs; u++) {
-        if(travt->objs[u].type == H5O_TYPE_DATASET || 
+        if(travt->objs[u].type == H5O_TYPE_DATASET ||
                 travt->objs[u].type == H5O_TYPE_GROUP ||
                 travt->objs[u].type == H5O_TYPE_NAMED_DATATYPE) {
             H5O_info_t   ref_oinfo;     /* Stat for the refobj id */
@@ -730,3 +824,49 @@ out:
     return ret;
 }
 
+/*-------------------------------------------------------------------------
+ * Function:	Update_Ref_value
+ *
+ * Purpose:	Update a reference value
+ *
+ * Programmer: xcao@hdfgroup.org 9/12/2011
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
+		hid_t fid_out, void *ref_out, trav_table_t *travt)
+{
+	herr_t ret = -1;
+	const char* ref_obj_name;
+	hid_t space_id=-1, ref_obj_id=-1;
+
+    ref_obj_id = H5Rdereference(obj_id, ref_type, ref_in);
+	if (ref_obj_id<0)
+		goto done;
+
+	ref_obj_name = MapIdToName(ref_obj_id, travt);
+	if (ref_obj_name == NULL)
+		goto done;
+
+	if (ref_type == H5R_DATASET_REGION) {
+		space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
+		if (space_id < 0)
+			goto done;
+	}
+
+    ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id);
+
+    if (ret < 0)
+    	goto done;
+
+	ret = 0;
+
+done:
+    H5E_BEGIN_TRY {
+    	H5Sclose(space_id);
+    	H5Oclose(ref_obj_id);
+    } H5E_END_TRY;
+
+	return ret;
+}
+
diff --git a/tools/h5repack/testfiles/h5repack_attr_refs.h5 b/tools/h5repack/testfiles/h5repack_attr_refs.h5
new file mode 100644
index 0000000..56974a3
--- /dev/null
+++ b/tools/h5repack/testfiles/h5repack_attr_refs.h5