diff -upr mpich-3.0.4/src/pm/hydra/configure.ac mpich-3.0.4.new/src/pm/hydra/configure.ac
--- mpich-3.0.4/src/pm/hydra/configure.ac	2013-04-24 10:05:00.000000000 -0400
+++ mpich-3.0.4.new/src/pm/hydra/configure.ac	2013-09-05 11:49:01.000000000 -0400
@@ -10,28 +10,6 @@ AC_INIT([Hydra], MPICH_VERSION_m4)
 AC_CONFIG_AUX_DIR(confdb)
 AC_CONFIG_MACRO_DIR(confdb)
 
-# needed by hwloc in embedded mode.  Must come very early to avoid
-# bizarre expansion ordering warnings
-AC_CANONICAL_TARGET
-AC_ARG_PROGRAM
-
-dnl must come before LT_INIT, which AC_REQUIREs AC_PROG_CC
-dnl must also come before AC_USE_SYSTEM_EXTENSIONS
-PAC_PROG_CC
-
-# also needed by hwloc in embedded mode, must also come early for expansion
-# ordering reasons
-AC_USE_SYSTEM_EXTENSIONS
-
-# Define -D_DARWIN_C_SOURCE on OS/X to ensure that hwloc will build even if we
-# are building under MPICH with --enable-strict that defined _POSIX_C_SOURCE.
-# Some standard Darwin headers don't build correctly under a strict posix
-# environment.
-AS_CASE([$host],
-    [*-*-darwin*], [PAC_APPEND_FLAG([-D_DARWIN_C_SOURCE],[CPPFLAGS])]
-)
-
-
 AM_INIT_AUTOMAKE([-Wall -Werror foreign 1.12.3])
 
 AM_PROG_AR
@@ -353,54 +331,16 @@ AC_MSG_RESULT([$hydra_topolib_list])
 
 hydra_topolibs="`echo $hydra_topolib_list | sed -e 's/:/ /g' -e 's/,/ /g'`"
 
-# Unconditionally include the hwloc macros, even if we are using an
-# external hwloc (or hwloc is disabled). This is needed for the
-# AM_CONDITIONALS that we will set later.
-m4_include([tools/topo/hwloc/hwloc/config/hwloc.m4])
-m4_include([tools/topo/hwloc/hwloc/config/hwloc_check_attributes.m4])
-m4_include([tools/topo/hwloc/hwloc/config/hwloc_check_visibility.m4])
-m4_include([tools/topo/hwloc/hwloc/config/hwloc_check_vendor.m4])
-m4_include([tools/topo/hwloc/hwloc/config/hwloc_components.m4])
-m4_include([tools/topo/hwloc/hwloc/config/hwloc_pkg.m4])
-
 have_hwloc=no
-for hydra_topolib in ${hydra_topolibs}; do
-    case "$hydra_topolib" in
-	hwloc)
-		if test "$with_hwloc_prefix" = "embedded" ; then
-		   HWLOC_SETUP_CORE([tools/topo/hwloc/hwloc],[have_hwloc=yes],[have_hwloc=no],[1])
-		   # Only build hwloc in embedded mode
-		   if test "$have_hwloc" = "yes" ; then
-		      hydra_use_embedded_hwloc=yes
-		      CFLAGS="$HWLOC_EMBEDDED_CFLAGS $CFLAGS"
-		      CPPFLAGS="$HWLOC_EMBEDDED_CPPFLAGS $CPPFLAGS"
-		      LIBS="$HWLOC_EMBEDDED_LIBS $LIBS"
-		   fi
-                else
-                    AC_CHECK_HEADERS([hwloc.h])
-                    # hwloc_topology_set_pid was added in hwloc-1.0.0, which is our minimum
-                    # required version
-                    AC_CHECK_LIB([hwloc],[hwloc_topology_set_pid])
-                    AC_MSG_CHECKING([if non-embedded hwloc works])
-                    if test "$ac_cv_header_hwloc_h" = "yes" -a "$ac_cv_lib_hwloc_hwloc_topology_set_pid" = "yes" ; then
-                        have_hwloc=yes
-                    fi
-                    AC_MSG_RESULT([$have_hwloc])
-                fi
-
-                # FIXME: Disable hwloc on Cygwin for now. The hwloc package, atleast as of 1.0.2,
-                # does not install correctly on Cygwin
-                AS_CASE([$host], [*-*-cygwin], [have_hwloc=no])
-
-		if test "$have_hwloc" = "yes" ; then
-		   AC_DEFINE(HAVE_HWLOC,1,[Define if hwloc is available])
-		   available_topolibs="$available_topolibs hwloc"
-		fi
-		;;
-	*)
-		;;
-    esac
-done
+AC_CHECK_HEADERS([hwloc.h])
+# hwloc_topology_set_pid was added in hwloc-1.0.0, which is our minimum
+# required version
+AC_CHECK_LIB([hwloc],[hwloc_topology_set_pid])
+AC_MSG_CHECKING([if non-embedded hwloc works])
+if test "$ac_cv_header_hwloc_h" = "yes" -a "$ac_cv_lib_hwloc_hwloc_topology_set_pid" = "yes" ; then
+    have_hwloc=yes
+fi
+AC_MSG_RESULT([$have_hwloc])
 
 tmp_list=
 for hydra_topolib in ${available_topolibs}; do
@@ -424,7 +364,6 @@ fi
 
 HWLOC_DO_AM_CONDITIONALS
 AM_CONDITIONAL([hydra_have_hwloc], [test "${have_hwloc}" = "yes"])
-AM_CONDITIONAL([hydra_use_embedded_hwloc], [test "${hydra_use_embedded_hwloc}" = "yes"])
 
 AC_MSG_CHECKING([available processor topology libraries])
 AC_MSG_RESULT([$available_topolibs])
diff -upr mpich-3.0.4/src/pm/hydra/autogen.sh mpich-3.0.4.new/src/pm/hydra/autogen.sh
--- mpich-3.0.4/src/pm/hydra/autogen.sh	2013-04-24 10:05:00.000000000 -0400
+++ mpich-3.0.4.new/src/pm/hydra/autogen.sh	2013-09-05 11:50:18.000000000 -0400
@@ -8,8 +8,6 @@ fi
 
 echo "=== running autoreconf in 'mpl' ==="
 (cd mpl && $autoreconf ${autoreconf_args:-"-vif"})
-echo "=== running autoreconf in 'tools/topo/hwloc/hwloc' ==="
-(cd tools/topo/hwloc/hwloc && $autoreconf ${autoreconf_args:-"-vif"})
 $autoreconf ${autoreconf_args:-"-vif"}
 
 # Remove the autom4te.cache folders for a release-like structure.