Index: /issm/trunk/configs/linux64/linux64.sh.petsc2
===================================================================
--- /issm/trunk/configs/linux64/linux64.sh.petsc2	(revision 4647)
+++ /issm/trunk/configs/linux64/linux64.sh.petsc2	(revision 4648)
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-petsc-version=2 --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install"
+./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-petsc-version=2
Index: /issm/trunk/src/c/modules/Chacox/Chacox.cpp
===================================================================
--- /issm/trunk/src/c/modules/Chacox/Chacox.cpp	(revision 4647)
+++ /issm/trunk/src/c/modules/Chacox/Chacox.cpp	(revision 4648)
@@ -20,4 +20,7 @@
 )
 {
+	#ifdef _HAVE_CHACO_ //only works if Chaco library has been compiled in.
+	
+	
 	extern int Using_Main;	/* is main routine being called? */
 	extern char *PARAMS_FILENAME;	/* name of file with parameter updates */
@@ -61,5 +64,4 @@
 
 
-	#ifdef _HAVE_CHACO_ //only works if Chaco library has been compiled in.
 
 	if (DEBUG_TRACE > 0) {
Index: /issm/trunk/src/c/modules/Chacox/input_parse.cpp
===================================================================
--- /issm/trunk/src/c/modules/Chacox/input_parse.cpp	(revision 4647)
+++ /issm/trunk/src/c/modules/Chacox/input_parse.cpp	(revision 4648)
@@ -25,4 +25,7 @@
 )
 {
+
+	#ifdef _HAVE_CHACO_ //only works if Chaco library has been compiled in.
+
 	extern int SEQUENCE;	/* sequence instead of partition graph? */
 	extern int ARCHITECTURE;	/* 0=> hypercube, d=> d-dimensional mesh */
@@ -258,3 +261,5 @@
 
 	return(0);
+
+	#endif //#ifdef _HAVE_CHACO_ 
 }
Index: /issm/trunk/src/c/modules/Chacox/user_params.cpp
===================================================================
--- /issm/trunk/src/c/modules/Chacox/user_params.cpp	(revision 4647)
+++ /issm/trunk/src/c/modules/Chacox/user_params.cpp	(revision 4648)
@@ -7,4 +7,13 @@
 /* a more picky compiler (cc) that complains about duplicate global */
 /* declarations. */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#else
+#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
+#endif
+
+
+#ifdef _HAVE_CHACO_ //only works if dakota library has been compiled in.
 
 #include "params.h"
@@ -141,2 +150,5 @@
 int       DEBUG_TRACE = 0;	/* Trace main execution path (0..2) */
 int       DEBUG_MACH_PARAMS = 0;/* Print computed machine params? (0..1) */
+
+
+#endif //ifdef _HAVE_CHACO_