Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 20962)
+++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 20963)
@@ -142,114 +142,151 @@
 
 BamgMesher_matlab_la_SOURCES = ../BamgMesher/BamgMesher.cpp
+BamgMesher_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 BamgMesher_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 BamgConvertMesh_matlab_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
+BamgConvertMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 BamgConvertMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 BamgTriangulate_matlab_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
+BamgTriangulate_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 BamgTriangulate_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 if CHACO
 Chaco_matlab_la_SOURCES = ../Chaco/Chaco.cpp
+Chaco_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Chaco_matlab_la_LIBADD = ${deps} $(MPILIB) $(CHACOLIB) $(GSLLIB) $(PROJ4LIB) $(PETSCLIB)
 endif
 
 ContourToMesh_matlab_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
+ContourToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 ContourToMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 ExpToLevelSet_matlab_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp
+ExpToLevelSet_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 ExpToLevelSet_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 ContourToNodes_matlab_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
+ContourToNodes_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 ContourToNodes_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 DistanceToMaskBoundary_matlab_la_SOURCES = ../DistanceToMaskBoundary/DistanceToMaskBoundary.cpp
+DistanceToMaskBoundary_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 ElementConnectivity_matlab_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
+ElementConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 ElementConnectivity_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 EnumToString_matlab_la_SOURCES = ../EnumToString/EnumToString.cpp
+EnumToString_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 EnumToString_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 StringToEnum_matlab_la_SOURCES = ../StringToEnum/StringToEnum.cpp
+StringToEnum_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 StringToEnum_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromGridToMesh_matlab_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
+InterpFromGridToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMeshToMesh2d_matlab_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
+InterpFromMeshToMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMeshToMesh3d_matlab_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
+InterpFromMeshToMesh3d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMeshToGrid_matlab_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
+InterpFromMeshToGrid_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMesh2d_matlab_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp
+InterpFromMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 IssmConfig_matlab_la_SOURCES = ../IssmConfig/IssmConfig.cpp
+IssmConfig_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 IssmConfig_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
 KMLFileRead_matlab_la_SOURCES = ../KMLFileRead/KMLFileRead.cpp
+KMLFileRead_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 KMLFileRead_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 KMLMeshWrite_matlab_la_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp
+KMLMeshWrite_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 KMLMeshWrite_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 KMLOverlay_matlab_la_SOURCES = ../KMLOverlay/KMLOverlay.cpp
+KMLOverlay_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 KMLOverlay_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Xy2ll_matlab_la_SOURCES = ../Xy2ll/Xy2ll.cpp
+Xy2ll_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Xy2ll_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Ll2xy_matlab_la_SOURCES = ../Ll2xy/Ll2xy.cpp
+Ll2xy_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Ll2xy_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 ExpSimplify_matlab_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp
+ExpSimplify_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 ExpSimplify_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Exp2Kml_matlab_la_SOURCES = ../Exp2Kml/Exp2Kml.cpp
+Exp2Kml_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Exp2Kml_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Kml2Exp_matlab_la_SOURCES = ../Kml2Exp/Kml2Exp.cpp
+Kml2Exp_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Kml2Exp_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Kriging_matlab_la_SOURCES = ../Kriging/Kriging.cpp
+Kriging_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Kriging_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 MeshPartition_matlab_la_SOURCES = ../MeshPartition/MeshPartition.cpp
+MeshPartition_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 MeshPartition_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(METISLIB) $(GSLLIB) $(PROJ4LIB)
 
 M1qn3_matlab_la_SOURCES = ../M1qn3/M1qn3.cpp
+M1qn3_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 M1qn3_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(METISLIB) $(M1QN3LIB) $(GSLLIB) $(PROJ4LIB)
 
 MeshProfileIntersection_matlab_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
+MeshProfileIntersection_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 NodeConnectivity_matlab_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
+NodeConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 NodeConnectivity_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 PointCloudFindNeighbors_matlab_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp
+PointCloudFindNeighbors_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 PropagateFlagsFromConnectivity_matlab_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp
+PropagateFlagsFromConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Scotch_matlab_la_SOURCES = ../Scotch/Scotch.cpp
+Scotch_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Scotch_matlab_la_LIBADD = ${deps} $(SCOTCHLIB) $(MPILIB) $(PETSCLIB) $(BLASLAPACKLIB)
 
 ShpRead_matlab_la_SOURCES = ../ShpRead/ShpRead.cpp
+ShpRead_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 Shp2Kml_matlab_la_SOURCES = ../Shp2Kml/Shp2Kml.cpp
+Shp2Kml_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 Shp2Kml_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 TriMesh_matlab_la_SOURCES = ../TriMesh/TriMesh.cpp
+TriMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 TriMesh_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) $(GSLLIB) $(PROJ4LIB)
 
 TriMeshProcessRifts_matlab_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp
+TriMeshProcessRifts_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
 TriMeshProcessRifts_matlab_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 #}}}
Index: /issm/trunk-jpl/src/wrappers/python/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 20962)
+++ /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 20963)
@@ -1,4 +1,4 @@
 AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@
-#AUTOMAKE_OPTIONS = subdir-objects
+AUTOMAKE_OPTIONS = subdir-objects
 
 EXEEXT=$(PYTHONWRAPPEREXT)
@@ -92,52 +92,69 @@
 #Bin sources {{{
 BamgConvertMesh_python_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
+BamgConvertMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 BamgConvertMesh_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 BamgMesher_python_la_SOURCES = ../BamgMesher/BamgMesher.cpp
+BamgMesher_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 BamgMesher_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 BamgTriangulate_python_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
+BamgTriangulate_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 BamgTriangulate_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 ContourToMesh_python_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
+ContourToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 ContourToMesh_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 ContourToNodes_python_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
+ContourToNodes_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 ContourToNodes_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 ElementConnectivity_python_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
+ElementConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 ElementConnectivity_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 EnumToString_python_la_SOURCES = ../EnumToString/EnumToString.cpp
+EnumToString_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 EnumToString_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMeshToMesh2d_python_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
+InterpFromMeshToMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMeshToMesh3d_python_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
+InterpFromMeshToMesh3d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromGridToMesh_python_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
+InterpFromGridToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromGridToMesh_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 InterpFromMeshToGrid_python_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
+InterpFromMeshToGrid_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB)
 
 IssmConfig_python_la_SOURCES = ../IssmConfig/IssmConfig.cpp
+IssmConfig_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 IssmConfig_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
 
 MeshProfileIntersection_python_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
+MeshProfileIntersection_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 MeshProfileIntersection_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 NodeConnectivity_python_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
+NodeConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 NodeConnectivity_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 StringToEnum_python_la_SOURCES = ../StringToEnum/StringToEnum.cpp
+StringToEnum_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 StringToEnum_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 
 TriMesh_python_la_SOURCES = ../TriMesh/TriMesh.cpp
+TriMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 TriMesh_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) $(GSLLIB) $(PROJ4LIB)
 
 TriMeshProcessRifts_python_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp
+TriMeshProcessRifts_python_la_CXXFLAGS = ${AM_CXXFLAGS}
 TriMeshProcessRifts_python_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(PROJ4LIB)
 #}}}