Index: sm/trunk/externalpackages/metis/Makefile.patch
===================================================================
--- /issm/trunk/externalpackages/metis/Makefile.patch	(revision 8569)
+++ 	(revision )
@@ -1,6 +1,0 @@
-5,6c5,6
-< #	(cd Programs ; make ) 
-< #	(cd Test ; make ) 
----
-> 	(cd Programs ; make ) 
-> 	(cd Test ; make ) 
Index: /issm/trunk/externalpackages/metis/install.sh
===================================================================
--- /issm/trunk/externalpackages/metis/install.sh	(revision 8569)
+++ /issm/trunk/externalpackages/metis/install.sh	(revision 8570)
@@ -23,8 +23,5 @@
 #Apply patches
 cd install 
-patch -R Makefile ../Makefile.patch
-patch -R Makefile.in ../Makefile.in.patch
-patch -R Lib/metis.h ../metis.h.patch
-patch Lib/Makefile ../lib_Makefile.patch
+patch -p1 < ../metis-4.0.patch
 
 #Compile metis
@@ -35,5 +32,2 @@
 	make -j $NUMCPUS
 fi
-
-#Patch proto.h
-patch Lib/proto.h ../proto.h.patch
Index: sm/trunk/externalpackages/metis/lib_Makefile.patch
===================================================================
--- /issm/trunk/externalpackages/metis/lib_Makefile.patch	(revision 8569)
+++ 	(revision )
@@ -1,40 +1,0 @@
-9,18c9,18
-< OBJS = coarsen.o fm.o initpart.o match.o ccgraph.o memory.o \
-<        pmetis.o pqueue.o refine.o util.o timing.o debug.o \
-<        bucketsort.o graph.o stat.o kmetis.o kwayrefine.o \
-<        kwayfm.o balance.o ometis.o srefine.o sfm.o separator.o \
-<        mincover.o mmd.o mesh.o meshpart.o frename.o fortran.o \
-<        myqsort.o compress.o parmetis.o estmem.o \
-<        mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o \
-<        mrefine.o mutil.o mfm.o mkmetis.o mkwayrefine.o mkwayfmh.o \
-<        mrefine2.o minitpart2.o mbalance2.o mfm2.o \
-<        kvmetis.o kwayvolrefine.o kwayvolfm.o subdomains.o
----
-> OBJS = coarsen.$(OBJ_EXT) fm.$(OBJ_EXT) initpart.$(OBJ_EXT) match.$(OBJ_EXT) ccgraph.$(OBJ_EXT) memory.$(OBJ_EXT) \
->        pmetis.$(OBJ_EXT) pqueue.$(OBJ_EXT) refine.$(OBJ_EXT) util.$(OBJ_EXT) timing.$(OBJ_EXT) debug.$(OBJ_EXT) \
->        bucketsort.$(OBJ_EXT) graph.$(OBJ_EXT) stat.$(OBJ_EXT) kmetis.$(OBJ_EXT) kwayrefine.$(OBJ_EXT) \
->        kwayfm.$(OBJ_EXT) balance.$(OBJ_EXT) ometis.$(OBJ_EXT) srefine.$(OBJ_EXT) sfm.$(OBJ_EXT) separator.$(OBJ_EXT) \
->        mincover.$(OBJ_EXT) mmd.$(OBJ_EXT) mesh.$(OBJ_EXT) meshpart.$(OBJ_EXT) frename.$(OBJ_EXT) fortran.$(OBJ_EXT) \
->        myqsort.$(OBJ_EXT) compress.$(OBJ_EXT) parmetis.$(OBJ_EXT) estmem.$(OBJ_EXT) \
->        mpmetis.$(OBJ_EXT) mcoarsen.$(OBJ_EXT) mmatch.$(OBJ_EXT) minitpart.$(OBJ_EXT) mbalance.$(OBJ_EXT) \
->        mrefine.$(OBJ_EXT) mutil.$(OBJ_EXT) mfm.$(OBJ_EXT) mkmetis.$(OBJ_EXT) mkwayrefine.$(OBJ_EXT) mkwayfmh.$(OBJ_EXT) \
->        mrefine2.$(OBJ_EXT) minitpart2.$(OBJ_EXT) mbalance2.$(OBJ_EXT) mfm2.$(OBJ_EXT) \
->        kvmetis.$(OBJ_EXT) kwayvolrefine.$(OBJ_EXT) kwayvolfm.$(OBJ_EXT) subdomains.$(OBJ_EXT)
-20,21c20,21
-< .c.o:
-< 	$(CC) $(CFLAGS) -c $*.c
----
-> %.$(OBJ_EXT) : %.c
-> 	$(CC) -c $(CFLAGS) -o $@ $<
-23c23
-< ../libmetis.a: $(OBJS)
----
-> ../libmetis.$(LIB_EXT): $(OBJS)
-28c28
-< 	rm -f *.o
----
-> 	rm -f *.$(OBJ_EXT)
-31c31
-< 	rm -f *.o ; rm -f ../libmetis.a
----
-> 	rm -f *.$(OBJ_EXT) ; rm -f ../libmetis.$(LIB_EXT)
Index: /issm/trunk/externalpackages/metis/metis-4.0.patch
===================================================================
--- /issm/trunk/externalpackages/metis/metis-4.0.patch	(revision 8570)
+++ /issm/trunk/externalpackages/metis/metis-4.0.patch	(revision 8570)
@@ -0,0 +1,263 @@
+diff -crB install/Lib/kmetis.c install2/Lib/kmetis.c
+*** install/Lib/kmetis.c	1998-11-30 08:26:47.000000000 -0800
+--- install2/Lib/kmetis.c	2011-06-08 15:47:33.911358942 -0700
+***************
+*** 66,72 ****
+      ctrl.dbglvl = options[OPTION_DBGLVL];
+    }
+    ctrl.optype = OP_KMETIS;
+!   ctrl.CoarsenTo = amax((*nvtxs)/(40*log2(*nparts)), 20*(*nparts));
+    ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo);
+  
+    InitRandom(-1);
+--- 66,72 ----
+      ctrl.dbglvl = options[OPTION_DBGLVL];
+    }
+    ctrl.optype = OP_KMETIS;
+!   ctrl.CoarsenTo = amax((*nvtxs)/(40*log2_function(*nparts)), 20*(*nparts));
+    ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo);
+  
+    InitRandom(-1);
+diff -crB install/Lib/kvmetis.c install2/Lib/kvmetis.c
+*** install/Lib/kvmetis.c	1998-11-30 08:26:47.000000000 -0800
+--- install2/Lib/kvmetis.c	2011-06-08 15:47:33.916358976 -0700
+***************
+*** 66,72 ****
+      ctrl.dbglvl = options[OPTION_DBGLVL];
+    }
+    ctrl.optype = OP_KVMETIS;
+!   ctrl.CoarsenTo = amax((*nvtxs)/(40*log2(*nparts)), 20*(*nparts));
+    ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo);
+  
+    InitRandom(-1);
+--- 66,72 ----
+      ctrl.dbglvl = options[OPTION_DBGLVL];
+    }
+    ctrl.optype = OP_KVMETIS;
+!   ctrl.CoarsenTo = amax((*nvtxs)/(40*log2_function(*nparts)), 20*(*nparts));
+    ctrl.maxvwgt = 1.5*((graph.vwgt ? idxsum(*nvtxs, graph.vwgt) : (*nvtxs))/ctrl.CoarsenTo);
+  
+    InitRandom(-1);
+diff -crB install/Lib/Makefile install2/Lib/Makefile
+*** install/Lib/Makefile	1998-09-22 05:08:29.000000000 -0700
+--- install2/Lib/Makefile	2011-06-08 15:19:00.551540482 -0700
+***************
+*** 6,31 ****
+  LD = $(CC) -L. 
+  
+  
+! OBJS = coarsen.o fm.o initpart.o match.o ccgraph.o memory.o \
+!        pmetis.o pqueue.o refine.o util.o timing.o debug.o \
+!        bucketsort.o graph.o stat.o kmetis.o kwayrefine.o \
+!        kwayfm.o balance.o ometis.o srefine.o sfm.o separator.o \
+!        mincover.o mmd.o mesh.o meshpart.o frename.o fortran.o \
+!        myqsort.o compress.o parmetis.o estmem.o \
+!        mpmetis.o mcoarsen.o mmatch.o minitpart.o mbalance.o \
+!        mrefine.o mutil.o mfm.o mkmetis.o mkwayrefine.o mkwayfmh.o \
+!        mrefine2.o minitpart2.o mbalance2.o mfm2.o \
+!        kvmetis.o kwayvolrefine.o kwayvolfm.o subdomains.o
+  
+! .c.o:
+! 	$(CC) $(CFLAGS) -c $*.c
+  
+! ../libmetis.a: $(OBJS)
+  	$(AR) $@ $(OBJS)
+  	$(RANLIB) $@
+  
+  clean:
+! 	rm -f *.o
+  
+  realclean:
+! 	rm -f *.o ; rm -f ../libmetis.a
+--- 6,31 ----
+  LD = $(CC) -L. 
+  
+  
+! OBJS = coarsen.$(OBJ_EXT) fm.$(OBJ_EXT) initpart.$(OBJ_EXT) match.$(OBJ_EXT) ccgraph.$(OBJ_EXT) memory.$(OBJ_EXT) \
+!        pmetis.$(OBJ_EXT) pqueue.$(OBJ_EXT) refine.$(OBJ_EXT) util.$(OBJ_EXT) timing.$(OBJ_EXT) debug.$(OBJ_EXT) \
+!        bucketsort.$(OBJ_EXT) graph.$(OBJ_EXT) stat.$(OBJ_EXT) kmetis.$(OBJ_EXT) kwayrefine.$(OBJ_EXT) \
+!        kwayfm.$(OBJ_EXT) balance.$(OBJ_EXT) ometis.$(OBJ_EXT) srefine.$(OBJ_EXT) sfm.$(OBJ_EXT) separator.$(OBJ_EXT) \
+!        mincover.$(OBJ_EXT) mmd.$(OBJ_EXT) mesh.$(OBJ_EXT) meshpart.$(OBJ_EXT) frename.$(OBJ_EXT) fortran.$(OBJ_EXT) \
+!        myqsort.$(OBJ_EXT) compress.$(OBJ_EXT) parmetis.$(OBJ_EXT) estmem.$(OBJ_EXT) \
+!        mpmetis.$(OBJ_EXT) mcoarsen.$(OBJ_EXT) mmatch.$(OBJ_EXT) minitpart.$(OBJ_EXT) mbalance.$(OBJ_EXT) \
+!        mrefine.$(OBJ_EXT) mutil.$(OBJ_EXT) mfm.$(OBJ_EXT) mkmetis.$(OBJ_EXT) mkwayrefine.$(OBJ_EXT) mkwayfmh.$(OBJ_EXT) \
+!        mrefine2.$(OBJ_EXT) minitpart2.$(OBJ_EXT) mbalance2.$(OBJ_EXT) mfm2.$(OBJ_EXT) \
+!        kvmetis.$(OBJ_EXT) kwayvolrefine.$(OBJ_EXT) kwayvolfm.$(OBJ_EXT) subdomains.$(OBJ_EXT)
+  
+! %.$(OBJ_EXT) : %.c
+! 	$(CC) -c $(CFLAGS) -o $@ $<
+  
+! ../libmetis.$(LIB_EXT): $(OBJS)
+  	$(AR) $@ $(OBJS)
+  	$(RANLIB) $@
+  
+  clean:
+! 	rm -f *.$(OBJ_EXT)
+  
+  realclean:
+! 	rm -f *.$(OBJ_EXT) ; rm -f ../libmetis.$(LIB_EXT)
+diff -crB install/Lib/metis.h install2/Lib/metis.h
+*** install/Lib/metis.h	1998-11-30 08:26:50.000000000 -0800
+--- install2/Lib/metis.h	2011-06-08 15:19:00.544540433 -0700
+***************
+*** 18,24 ****
+--- 18,26 ----
+  #else
+  #include <malloc.h>
+  #endif
++ #ifndef WIN32
+  #include <strings.h>
++ #endif
+  #include <string.h>
+  #include <ctype.h>
+  #include <math.h>
+diff -crB install/Lib/mkmetis.c install2/Lib/mkmetis.c
+*** install/Lib/mkmetis.c	1998-11-30 08:26:48.000000000 -0800
+--- install2/Lib/mkmetis.c	2011-06-08 15:47:33.921359010 -0700
+***************
+*** 47,53 ****
+      ctrl.dbglvl = options[OPTION_DBGLVL];
+    }
+    ctrl.optype = OP_KMETIS;
+!   ctrl.CoarsenTo = amax((*nvtxs)/(20*log2(*nparts)), 30*(*nparts));
+  
+    ctrl.nmaxvwgt = 1.5/(1.0*ctrl.CoarsenTo);
+  
+--- 47,53 ----
+      ctrl.dbglvl = options[OPTION_DBGLVL];
+    }
+    ctrl.optype = OP_KMETIS;
+!   ctrl.CoarsenTo = amax((*nvtxs)/(20*log2_function(*nparts)), 30*(*nparts));
+  
+    ctrl.nmaxvwgt = 1.5/(1.0*ctrl.CoarsenTo);
+  
+diff -crB install/Lib/proto.h install2/Lib/proto.h
+*** install/Lib/proto.h	1998-11-30 08:26:50.000000000 -0800
+--- install2/Lib/proto.h	2011-06-08 15:47:34.009359613 -0700
+***************
+*** 230,237 ****
+--- 230,243 ----
+  void QUADNODALMETIS(int, int, idxtype *, idxtype *, idxtype *adjncy);
+  
+  /* meshpart.c */
++ #ifdef __cplusplus
++ extern "C" {
++ #endif
+  void METIS_PartMeshNodal(int *, int *, idxtype *, int *, int *, int *, int *, idxtype *, idxtype *);
+  void METIS_PartMeshDual(int *, int *, idxtype *, int *, int *, int *, int *, idxtype *, idxtype *);
++ #ifdef __cplusplus
++ }
++ #endif
+  
+  /* mfm.c */
+  void MocFM_2WayEdgeRefine(CtrlType *, GraphType *, float *, int);
+***************
+*** 459,465 ****
+  void srand48(long);
+  int ispow2(int);
+  void InitRandom(int);
+! int log2(int);
+  
+  
+  
+--- 465,471 ----
+  void srand48(long);
+  int ispow2(int);
+  void InitRandom(int);
+! int log2_function(int);
+  
+  
+  
+diff -crB install/Lib/rename.h install2/Lib/rename.h
+*** install/Lib/rename.h	1998-11-30 08:26:50.000000000 -0800
+--- install2/Lib/rename.h	2011-06-08 15:47:34.014359647 -0700
+***************
+*** 410,416 ****
+  #define RandomPermute			__RandomPermute
+  #define ispow2				__ispow2
+  #define InitRandom			__InitRandom
+! #define log2				__log2
+  
+  
+  
+--- 410,417 ----
+  #define RandomPermute			__RandomPermute
+  #define ispow2				__ispow2
+  #define InitRandom			__InitRandom
+! /* Correction bug Nadir SOUALEM*/
+! #define log2_function				__log2_function
+  
+  
+  
+diff -crB install/Lib/util.c install2/Lib/util.c
+*** install/Lib/util.c	1998-11-30 08:26:50.000000000 -0800
+--- install2/Lib/util.c	2011-06-08 15:47:34.018359675 -0700
+***************
+*** 507,515 ****
+  }
+  
+  /*************************************************************************
+! * This function returns the log2(x)
+  **************************************************************************/
+! int log2(int a)
+  {
+    int i;
+  
+--- 507,515 ----
+  }
+  
+  /*************************************************************************
+! * This function returns the log2_function(x)
+  **************************************************************************/
+! int log2_function(int a)
+  {
+    int i;
+  
+diff -crB install/Makefile install2/Makefile
+*** install/Makefile	1998-09-20 11:15:31.000000000 -0700
+--- install2/Makefile	2011-06-08 15:19:00.511540204 -0700
+***************
+*** 2,9 ****
+  
+  default:
+  	(cd Lib ; make ) 
+! 	(cd Programs ; make ) 
+! 	(cd Test ; make ) 
+  
+  clean:
+  	(cd Lib ; make clean )
+--- 2,9 ----
+  
+  default:
+  	(cd Lib ; make ) 
+! #	(cd Programs ; make ) 
+! #	(cd Test ; make ) 
+  
+  clean:
+  	(cd Lib ; make clean )
+diff -crB install/Makefile.in install2/Makefile.in
+*** install/Makefile.in	1998-10-02 14:28:35.000000000 -0700
+--- install2/Makefile.in	2011-06-08 15:19:00.536540378 -0700
+***************
+*** 1,9 ****
+  
+  # Which compiler to use
+! CC = cc
+  
+  # What optimization level to use
+! OPTFLAGS = -O2 
+  
+  # What options to be used by the compiler
+  COPTIONS = 
+--- 1,11 ----
+  
+  # Which compiler to use
+! CC = gcc
+! OBJ_EXT=o
+! LIB_EXT=a
+  
+  # What optimization level to use
+! OPTFLAGS = -DLINUX -fPIC
+  
+  # What options to be used by the compiler
+  COPTIONS = 
Index: sm/trunk/externalpackages/metis/metis.h.patch
===================================================================
--- /issm/trunk/externalpackages/metis/metis.h.patch	(revision 8569)
+++ 	(revision )
@@ -1,6 +1,0 @@
-21d20
-< #ifndef WIN32
-23d21
-< #endif
-40d37
-< 
Index: sm/trunk/externalpackages/metis/proto.h.patch
===================================================================
--- /issm/trunk/externalpackages/metis/proto.h.patch	(revision 8569)
+++ 	(revision )
@@ -1,8 +1,0 @@
-232a233,235
-> #ifdef __cplusplus
-> extern "C" {
-> #endif
-234a238,240
-> #ifdef __cplusplus
-> }
-> #endif