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 13071)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/c/Makefile.am	(revision 13072)
@@ -5,22 +5,22 @@
 #Library declaration {{{
 lib_LIBRARIES = libISSMCore.a libISSMOverload.a
 
-#if SHAREDLIBS
-#lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la libISSM.la
-#endif
+if SHAREDLIBS
+lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la libISSM.la
+endif
 if PYTHON
 lib_LIBRARIES += libISSMPython.a 
 endif
 if MATLAB
-#if SHAREDLIBS
-#lib_LTLIBRARIES += libISSMMatlab.la
-#endif
+if SHAREDLIBS
+lib_LTLIBRARIES += libISSMMatlab.la
+endif
 lib_LIBRARIES += libISSMMatlab.a 
 endif
 if MODULES
-#if SHAREDLIBS
-#lib_LTLIBRARIES += libISSMModules.la
-#endif
+if SHAREDLIBS
+lib_LTLIBRARIES += libISSMModules.la
+endif
 lib_LIBRARIES += libISSMModules.a 
 endif
 #}}}
@@ -1010,23 +1010,23 @@
 libISSMCore_a_SOURCES  = $(issm_sources)
 libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS)
 
-#if SHAREDLIBS
-#libISSM_la_SOURCES = solutions/issm.cpp
-#libISSM_la_LIBADD = libISSMCore.la libISSMOverload.la
+if SHAREDLIBS
+libISSM_la_SOURCES = solutions/issm.cpp
+libISSM_la_LIBADD = libISSMCore.la libISSMOverload.la
 
-#libISSMCore_la_SOURCES  = $(issm_sources)
-#libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB)
+libISSMCore_la_SOURCES  = $(issm_sources)
+libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB)
 
-#libISSMOverload_la_SOURCES = ./shared/String/stricmp.c
-#endif
+libISSMOverload_la_SOURCES = ./shared/String/stricmp.c
+endif
 
 if MODULES
-#if SHAREDLIBS
-#libISSMModules_la_SOURCES = $(module_sources)
-#libISSMModules_la_SOURCES += $(bamg_sources)
-#libISSMModules_la_SOURCES += $(kriging_sources)
-#libISSMModules_la_SOURCES += $(kml_sources)
-#endif
+if SHAREDLIBS
+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)
@@ -1041,9 +1041,9 @@
 endif
 
 if MATLAB
-#if SHAREDLIBS
-#libISSMMatlab_la_SOURCES = $(matlab_sources)
-#endif
+if SHAREDLIBS
+libISSMMatlab_la_SOURCES = $(matlab_sources)
+endif
 libISSMMatlab_a_SOURCES = $(matlab_sources)
 libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS)
 endif
Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/matlab/Makefile.am
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/matlab/Makefile.am	(revision 13071)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/src/modules/matlab/Makefile.am	(revision 13072)
@@ -1,166 +1,232 @@
 AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @BOOSTINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@
+
 EXEEXT=$(MATLABWRAPPEREXT)
-#Bin programs {{{1
+
+#Modules {{{1
 if MODULES
-bin_PROGRAMS =  AverageFilter\
-				BamgMesher\
-				BamgConvertMesh\
-				BamgTriangulate\
-				Chaco\
-				ContourToMesh \
-				ContourToNodes \
-				ElementConnectivity\
-				EnumToString\
-				Exp2Kml \
-				HoleFiller \
-				InternalFront\
-				InterpFromGridToMesh \
-				InterpFromMeshToMesh2d \
-				InterpFromMeshToMesh3d \
-				InterpFromMeshToGrid \
-				InterpFromMesh2d \
-				KMLFileRead \
-				KMLMeshWrite \
-				KMLOverlay \
-				Kml2Exp \
-				Kriging \
-				Ll2xy \
-				NodeConnectivity \
-				MeshPartition\
-				MeshProfileIntersection\
-				PointCloudFindNeighbors\
-				PropagateFlagsFromConnectivity\
-				Scotch\
-				Shp2Kml\
-				StringToEnum\
-				TriaSearch\
-				TriMesh\
-				TriMeshProcessRifts\
-				Xy2ll
+lib_LTLIBRARIES =  AverageFilter.la\
+			       BamgMesher.la\
+				   BamgConvertMesh.la\
+				   BamgTriangulate.la\
+				   ContourToMesh.la\
+				   ContourToNodes.la\
+				   ElementConnectivity.la\
+				   EnumToString.la\
+				   Exp2Kml.la\
+				   HoleFiller.la\
+				   InternalFront.la\
+				   InterpFromGridToMesh.la\
+				   InterpFromMeshToMesh2d.la\
+				   InterpFromMeshToMesh3d.la\
+				   InterpFromMeshToGrid.la\
+				   InterpFromMesh2d.la\
+				   KMLFileRead.la\
+				   KMLMeshWrite.la\
+				   KMLOverlay.la\
+				   Kml2Exp.la\
+				   Kriging.la\
+				   Ll2xy.la\
+				   NodeConnectivity.la\
+				   MeshPartition.la\
+				   MeshProfileIntersection.la\
+				   PointCloudFindNeighbors.la\
+				   PropagateFlagsFromConnectivity.la\
+				   Shp2Kml.la\
+				   StringToEnum.la\
+				   TriaSearch.la\
+				   TriMesh.la\
+				   TriMeshProcessRifts.la\
+				   Scotch.la\
+				   Xy2ll.la\
+                   Chaco.la
 endif 
 #}}}
 #Flags and libraries {{{1
-LDADD = ../../c/libISSMCore.a ../../c/libISSMModules.a $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(SPOOLESLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB)
+if SHAREDLIBS
+deps = ../../c/libISSMCore.la ../../c/libISSMModules.la
+else
+deps = ../../c/libISSMCore.a ../../c/libISSMModules.a
+endif
 
+deps +=  $(MATHLIB) ${MEXLIB}
+
+#$(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(SPOOLESLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB) 
+
 #Triangle library
 AM_CXXFLAGS =  -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
 
 #Matlab part
-AM_LDFLAGS   = $(MEXLINK)
+AM_LDFLAGS = $(MEXLINK) -shrext ${EXEEXT} -module
+if VERSION
+AM_LDFLAGS +=
+else
+AM_LDFLAGS += -avoid-version
+endif
+if SHAREDLIBS
+deps += ../../c/libISSMMatlab.la 
+else
+deps += ../../c/libISSMMatlab.a
+AM_LDFLAGS += --no-warnings 
+endif
+
 AM_CXXFLAGS +=  -D_HAVE_MATLAB_MODULES_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread 
-LDADD       += $(MEXLIB) ../../c/libISSMMatlab.a 
-LDADD       += ../../c/libISSMCore.a 
-if CIRCULAR_DEPENDENCIES
-LDADD       += $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(SPOOLESLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB)
+
+######################################################################################
+# Circular dependencies may not be necessary here.
+#deps += ../../c/libISSMCore.a 
+#if CIRCULAR_DEPENDENCIES
+#deps += $(TRIANGLELIB) $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(SPOOLESLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(GSLLIB)
+#endif
+######################################################################################
+
+if SHAREDLIBS
+deps +=
+else
+deps += ../../c/libISSMModules.a ../../c/libISSMCore.a
 endif
-LDADD       += ../../c/libISSMModules.a
 
 #Optimization flags:
 AM_CXXFLAGS += $(CXXOPTFLAGS) 
 #}}}
+
 #Bin sources {{{1
-AverageFilter_SOURCES = ../AverageFilter/AverageFilter.cpp\
+AverageFilter_la_SOURCES = ../AverageFilter/AverageFilter.cpp\
 			  ../AverageFilter/AverageFilter.h
+AverageFilter_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-BamgMesher_SOURCES = ../BamgMesher/BamgMesher.cpp\
+BamgMesher_la_SOURCES = ../BamgMesher/BamgMesher.cpp\
 					../BamgMesher/BamgMesher.h
+BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-BamgConvertMesh_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\
+BamgConvertMesh_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\
 					../BamgConvertMesh/BamgConvertMesh.h
+BamgConvertMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-BamgTriangulate_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\
+BamgTriangulate_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\
 								  ../BamgTriangulate/BamgTriangulate.h
+BamgTriangulate_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Chaco_SOURCES = ../Chaco/Chaco.cpp\
+Chaco_la_SOURCES = ../Chaco/Chaco.cpp\
 					../Chaco/Chaco.h
+Chaco_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(CHACOLIB)
 
-ContourToMesh_SOURCES = ../ContourToMesh/ContourToMesh.cpp\
-			  ../ContourToMesh/ContourToMesh.h
+ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\
+			               ../ContourToMesh/ContourToMesh.h
+ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
 
-ContourToNodes_SOURCES = ../ContourToNodes/ContourToNodes.cpp\
+ContourToNodes_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp\
 			  ../ContourToNodes/ContourToNodes.h
+ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
+ElementConnectivity_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
 			  ../ElementConnectivity/ElementConnectivity.h
+ElementConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-EnumToString_SOURCES = ../EnumToString/EnumToString.cpp\
+EnumToString_la_SOURCES = ../EnumToString/EnumToString.cpp\
 			  ../EnumToString/EnumToString.h
+EnumToString_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-StringToEnum_SOURCES = ../StringToEnum/StringToEnum.cpp\
+StringToEnum_la_SOURCES = ../StringToEnum/StringToEnum.cpp\
 			  ../StringToEnum/StringToEnum.h
+StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-HoleFiller_SOURCES = ../HoleFiller/HoleFiller.cpp\
+HoleFiller_la_SOURCES = ../HoleFiller/HoleFiller.cpp\
 			  ../HoleFiller/HoleFiller.h
+HoleFiller_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) 
 
-InternalFront_SOURCES = ../InternalFront/InternalFront.cpp\
+InternalFront_la_SOURCES = ../InternalFront/InternalFront.cpp\
 										 ../InternalFront/InternalFront.h
+InternalFront_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-InterpFromGridToMesh_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\
+InterpFromGridToMesh_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\
 			  ../InterpFromGridToMesh/InterpFromGridToMesh.h
+InterpFromGridToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
 
-InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\
+InterpFromMeshToMesh2d_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\
 							../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h
+InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
 
-InterpFromMeshToMesh3d_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\
+InterpFromMeshToMesh3d_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\
 									../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h
+InterpFromMeshToMesh3d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-InterpFromMeshToGrid_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\
+InterpFromMeshToGrid_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\
 									../InterpFromMeshToGrid/InterpFromMeshToGrid.h
+InterpFromMeshToGrid_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-InterpFromMesh2d_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\
+InterpFromMesh2d_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\
 									../InterpFromMesh2d/InterpFromMesh2d.h
+InterpFromMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
 
-KMLFileRead_SOURCES = ../KMLFileRead/KMLFileRead.cpp\
+KMLFileRead_la_SOURCES = ../KMLFileRead/KMLFileRead.cpp\
 			  ../KMLFileRead/KMLFileRead.h
+KMLFileRead_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-KMLMeshWrite_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\
+KMLMeshWrite_la_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\
 			  ../KMLMeshWrite/KMLMeshWrite.h
+KMLMeshWrite_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-KMLOverlay_SOURCES = ../KMLOverlay/KMLOverlay.cpp\
+KMLOverlay_la_SOURCES = ../KMLOverlay/KMLOverlay.cpp\
 			  ../KMLOverlay/KMLOverlay.h
+KMLOverlay_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Xy2ll_SOURCES = ../Xy2ll/Xy2ll.cpp\
+Xy2ll_la_SOURCES = ../Xy2ll/Xy2ll.cpp\
 			  ../Xy2ll/Xy2ll.h
+Xy2ll_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Ll2xy_SOURCES = ../Ll2xy/Ll2xy.cpp\
+Ll2xy_la_SOURCES = ../Ll2xy/Ll2xy.cpp\
 			  ../Ll2xy/Ll2xy.h
+Ll2xy_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Exp2Kml_SOURCES = ../Exp2Kml/Exp2Kml.cpp\
+Exp2Kml_la_SOURCES = ../Exp2Kml/Exp2Kml.cpp\
 			  ../Exp2Kml/Exp2Kml.h
+Exp2Kml_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Kml2Exp_SOURCES = ../Kml2Exp/Kml2Exp.cpp\
+Kml2Exp_la_SOURCES = ../Kml2Exp/Kml2Exp.cpp\
 			  ../Kml2Exp/Kml2Exp.h
+Kml2Exp_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Kriging_SOURCES = ../Kriging/Kriging.cpp\
+Kriging_la_SOURCES = ../Kriging/Kriging.cpp\
 						../Kriging/Kriging.h
+Kriging_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
 
-MeshPartition_SOURCES = ../MeshPartition/MeshPartition.cpp\
+MeshPartition_la_SOURCES = ../MeshPartition/MeshPartition.cpp\
 			  ../MeshPartition/MeshPartition.h
+MeshPartition_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-MeshProfileIntersection_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\
+MeshProfileIntersection_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\
 			  ../MeshProfileIntersection/MeshProfileIntersection.h
+MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
+NodeConnectivity_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
 										../NodeConnectivity/NodeConnectivity.h
+NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-PointCloudFindNeighbors_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\
+PointCloudFindNeighbors_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\
 			  ../PointCloudFindNeighbors/PointCloudFindNeighbors.h
+PointCloudFindNeighbors_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
 
-PropagateFlagsFromConnectivity_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\
+PropagateFlagsFromConnectivity_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\
 			  ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h
+PropagateFlagsFromConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-Scotch_SOURCES = ../Scotch/Scotch.cpp\
-			  ../Scotch/Scotch.h
+Scotch_la_SOURCES = ../Scotch/Scotch.cpp\
+                    ../Scotch/Scotch.h
+Scotch_la_LIBADD = ${deps} $(SCOTCHLIB)
 
-Shp2Kml_SOURCES = ../Shp2Kml/Shp2Kml.cpp\
-			  ../Shp2Kml/Shp2Kml.h
+Shp2Kml_la_SOURCES = ../Shp2Kml/Shp2Kml.cpp\
+                     ../Shp2Kml/Shp2Kml.h
+Shp2Kml_la_LIBADD = ${deps}
 
-TriaSearch_SOURCES = ../TriaSearch/TriaSearch.cpp\
+TriaSearch_la_SOURCES = ../TriaSearch/TriaSearch.cpp\
 			  ../TriaSearch/TriaSearch.h
+TriaSearch_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
-TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\
-			  ../TriMesh/TriMesh.h
+TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp\
+                     ../TriMesh/TriMesh.h
+TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB)
 
-TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\
+TriMeshProcessRifts_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\
 			  ../TriMeshProcessRifts/TriMeshProcessRifts.h
+TriMeshProcessRifts_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 #}}}
Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/configure.ac
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/configure.ac	(revision 13071)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/configure.ac	(revision 13072)
@@ -5,11 +5,13 @@
 AC_CONFIG_AUX_DIR([./aux-config])         #Put config files in aux-config
 AC_CONFIG_MACRO_DIR([m4])                 #m4 macros are located in m4
 AC_CANONICAL_TARGET                       #Determine the system type
+
 #Compilers
 AC_PROG_CC([cccl cl icl gcc])
 AC_PROG_CPP
 AC_PROG_CXX([cccl cl icl g++])
 AC_PROG_F77([ifort g77 gfortran])
+
 #Libraries and linking
 AC_F77_LIBRARY_LDFLAGS
 AC_PATH_XTRA      #figure out X library and include paths
@@ -21,10 +23,9 @@
 AM_SILENT_RULES([yes])           #Do not show compilation command by default
 AM_PROG_CC_C_O
 AM_PROG_AR
-AC_PROG_RANLIB
 
 #Libtool
-#LT_INIT
+LT_INIT
 
 #Run issm_options.m4
 ISSM_OPTIONS
@@ -36,8 +37,7 @@
 			src/modules/Makefile
 			src/modules/python/Makefile
 			src/modules/matlab/Makefile
-			src/m/Makefile
-			bin/Makefile])
+			src/m/Makefile])
 
 #End of configure.ac
 AC_OUTPUT
Index: /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/Makefile.am
===================================================================
--- /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/Makefile.am	(revision 13071)
+++ /u/astrid-r1b/morlighe/issmuci/trunk-jpl/../trunk-jpl/Makefile.am	(revision 13072)
@@ -1,3 +1,3 @@
 EXTRA_DIST = reconf scripts test m4 examples cron etc doc packages contributors.txt 
-SUBDIRS = src bin
+SUBDIRS = src
 bin_SCRIPTS=config.h startup.m README.rtf