Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/m4/issm_options.m4
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/m4/issm_options.m4	(revision 12988)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/m4/issm_options.m4	(revision 12989)
@@ -220,7 +220,7 @@
 		AC_SUBST([MEX])
 		MATLABWRAPPEREXT=$MEXEXT
 		AC_SUBST([MATLABWRAPPEREXT])
-		AC_SUBST([MEXLIB]) 
+	    AC_SUBST([MEXLIB]) 
 		AC_SUBST([MEXLINK])
 	fi
 	dnl }}}
@@ -665,23 +665,23 @@
 		case "${host_os}" in
 			*cygwin*)
 			if test "$PETSC_MAJOR" = "2" ; then
-				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib  libpetscdm.lib  libpetscmat.lib  libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib"
+				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib  libpetscdm.lib  libpetscmat.lib  libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib"
 			else
-				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetsc.lib"
+				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetsc.lib"
 			fi
 			;;
 			*linux*)
 			if test "$PETSC_MAJOR" = "2" ; then
-			PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc  -lpetscsnes -lpetscts"
+			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc  -lpetscsnes -lpetscts"
 			else
-			PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc -ldl"
+			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc -ldl"
 			fi
 			;;
 			*darwin*)
 			if test "$PETSC_MAJOR" = "2" ; then
-			PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
+			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
 			else
-			PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc"
+			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc"
 			fi
 			;;
 		esac
Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/c/Makefile.am
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/c/Makefile.am	(revision 12988)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/c/Makefile.am	(revision 12989)
@@ -1,4 +1,4 @@
-INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
 
 EXEEXT=$(ISSMEXT)
 
@@ -12,9 +12,15 @@
 lib_LIBRARIES += libISSMPython.a 
 endif
 if MATLAB
+#if SHARED
+#lib_LTLIBRARIES += libISSMMatlab.la
+#endif
 lib_LIBRARIES += libISSMMatlab.a 
 endif
 if MODULES
+#if SHARED
+#lib_LTLIBRARIES += libISSMModules.la
+#endif
 lib_LIBRARIES += libISSMModules.a 
 endif
 #}}}
@@ -383,9 +389,7 @@
 					  ./modules/Dakotax/DakotaFree.cpp\
 					  ./modules/Dakotax/SpawnCore.cpp\
 					  ./modules/Dakotax/DescriptorIndex.cpp\
-					  ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\
 					  ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\
-					  ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\
 					  ./modules/Dakotax/SpawnCoreParallel.cpp
 #}}}
 #Transient sources  {{{
@@ -1016,6 +1020,12 @@
 #endif
 
 if MODULES
+#if SHARED
+#libISSMModules_la_SOURCES = $(module_sources)
+#libISSMModules_la_SOURCES += $(bamg_sources)
+#libISSMModules_la_SOURCES += $(kriging_sources)
+#libISSMModules_la_SOURCES += $(kml_sources)
+#endif
 libISSMModules_a_SOURCES = $(module_sources)
 libISSMModules_a_SOURCES += $(bamg_sources)
 libISSMModules_a_SOURCES += $(kriging_sources)
@@ -1029,6 +1039,9 @@
 endif
 
 if MATLAB
+if SHARED
+libISSMMatlab_la_SOURCES = $(matlab_sources)
+endif
 libISSMMatlab_a_SOURCES = $(matlab_sources)
 libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS)
 endif
Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/python/Makefile.am
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/python/Makefile.am	(revision 12988)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/python/Makefile.am	(revision 12989)
@@ -1,4 +1,4 @@
-INCLUDES = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
 EXEEXT=$(PYTHONWRAPPEREXT)
 #Bin programs {{{1
 if MODULES
Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/matlab/Makefile.am
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/matlab/Makefile.am	(revision 12988)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/matlab/Makefile.am	(revision 12989)
@@ -1,4 +1,4 @@
-INCLUDES = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
 EXEEXT=$(MATLABWRAPPEREXT)
 #Bin programs {{{1
 if MODULES