diff --git a/configure/CONFIG_SITE b/configure/CONFIG_SITE
index a39911783..c46703f84 100644
--- a/configure/CONFIG_SITE
+++ b/configure/CONFIG_SITE
@@ -176,9 +176,10 @@ GCC_PIPE = NO
 LINKER_USE_RPATH = YES
 
 # Only used when LINKER_USE_RPATH=ORIGIN
-# The build time root of the relocatable tree.
-# Linking to libraries under this root directory will be relative.
+# The build time root(s) of the relocatable tree (separate multiple w/ ':').
+# Linking to libraries under any root directory will be relative.
 # Linking to libraries outside of this root will be absolute.
+# All root directories are considered to be the same.
 LINKER_ORIGIN_ROOT = $(INSTALL_LOCATION)
 
 # Overrides for the settings above may appear in a CONFIG_SITE.local file
diff --git a/src/tools/makeRPath.py b/src/tools/makeRPath.py
index eeda8ab55..000b8b450 100644
--- a/src/tools/makeRPath.py
+++ b/src/tools/makeRPath.py
@@ -4,6 +4,7 @@ from __future__ import print_function
 
 import sys
 import os
+from collections import OrderedDict # used as OrderedSet
 
 from argparse import ArgumentParser
 
@@ -20,26 +21,60 @@ eg. A library to be placed in /build/lib and linked against libraries in
 which prints "-Wl,-rpath,$ORIGIN/. -Wl,-rpath,$ORIGIN/../module/lib -Wl,-rpath,/other/lib"
 ''')
 P.add_argument('-F','--final',default=os.getcwd(), help='Final install location for ELF file')
-P.add_argument('-R','--root',default='/', help='Root of relocatable tree.')
+P.add_argument('-R','--root',default='', help='Root(s) of relocatable tree.  Separate with :')
 P.add_argument('-O', '--origin', default='$ORIGIN')
 P.add_argument('path', nargs='*')
 args = P.parse_args()
 
-fdir = os.path.abspath(args.final)
+# eg.
+# target to be installed as: /build/bin/blah
+#
+# post-install will copy as:  /install/bin/blah
+#
+# Need to link against:
+#   /install/lib/libA.so
+#   /build/lib/libB.so
+#   /other/lib/libC.so
+#
+# Want final result to be:
+#  -rpath $ORIGIN/../lib -rpath /other/lib \
+#  -rpath-link /build/lib -rpath-link /install/lib
 
-output = []
+fdir = os.path.abspath(args.final)
+roots = [os.path.abspath(root) for root in args.root.split(':') if len(root)]
+
+# find the root which contains the final location
+froot = None
+for root in roots:
+    frel = os.path.relpath(fdir, root)
+    if not frel.startswith('..'):
+        # final dir is under this root
+        froot = root
+        break
+
+if froot is None:
+    sys.stderr.write("makeRPath: Final location %s\nNot under any of: %s\n"%(fdir, roots))
+    sys.exit(1)
+
+output = OrderedDict()
 for path in args.path:
     path = os.path.abspath(path)
 
-    if args.root and os.path.relpath(path, args.root).startswith('../'):
-        pass # absolute rpath
-    else:
-        # some older binutils don't seem to handle $ORIGIN correctly
-        # when locating dependencies of libraries.  So also provide
-        # the absolute path for internal use by 'ld' only.
-        output.append('-Wl,-rpath-link,'+path)
-        path = os.path.relpath(path, fdir)
+    for root in roots:
+        rrel = os.path.relpath(path, root)
+        if not rrel.startswith('..'):
+            # path is under this root
 
-    output.append('-Wl,-rpath,'+os.path.join(args.origin, path))
+            # some older binutils don't seem to handle $ORIGIN correctly
+            # when locating dependencies of libraries.  So also provide
+            # the absolute path for internal use by 'ld' only.
+            output['-Wl,-rpath-link,'+path] = True
+
+            # frel is final location relative to enclosing root
+            # rrel is target location relative to enclosing root
+            path = os.path.relpath(rrel, frel)
+            break
+
+    output['-Wl,-rpath,'+os.path.join(args.origin, path)] = True
 
 print(' '.join(output))