Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 26139)
+++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 26140)
@@ -91,16 +91,15 @@
 
 #Triangle library
-TRI_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
+CXXFLAGS_FOR_TRI = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
 
 #Matlab part
-MEX_CXXFLAGS = -D_HAVE_MATLAB_MODULES_ $(MEXOPTFLAGS) $(MEXCXXFLAGS)
-MEX_CPPFLAGS = $(MATLABINCL)
-MEX_LDFLAGS = -module -shrext $(MEXEXT) -no-undefined
-MEX_LIBADD = $(MEXLINKFLAGS) $(MEXLIB)
-
-AM_CPPFLAGS += ${MEX_CPPFLAGS}
-AM_CXXFLAGS = ${TRI_CXXFLAGS} ${MEX_CXXFLAGS}
-AM_LDFLAGS = ${MEX_LDFLAGS}
-AM_LIBADD = ${MEX_LIBADD}
+CXXFLAGS_FOR_MEX = -D_HAVE_MATLAB_MODULES_ $(MEXOPTFLAGS) $(MEXCXXFLAGS)
+CPPFLAGS_FOR_MEX = $(MATLABINCL)
+LDFLAGS_FOR_MEX = -module -shrext $(MEXEXT) -no-undefined
+LIBADD_FOR_MEX = $(MEXLINKFLAGS) $(MEXLIB)
+
+AM_CPPFLAGS += ${CXXFLAGS_FOR_MEX}
+AM_CXXFLAGS = ${CXXFLAGS_FOR_TRI} ${CPPFLAGS_FOR_MEX}
+AM_LDFLAGS = ${LDFLAGS_FOR_MEX}
 
 if !MSYS2
@@ -147,6 +146,5 @@
 endif
 
-# #MEXLIB needs to be the last (undefined references on larsen)
-# deps += ${MEXLIB}
+deps += ${LIBADD_FOR_MEX}
 
 #Optimization flags:
@@ -169,5 +167,5 @@
 libISSMMatlab_la_LDFLAGS += -static
 libISSMApi_la_LDFLAGS += -static
-deps += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(NEOPZLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS)
+deps += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(NEOPZLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS) ${LIBADD_FOR_MEX}
 endif
 
@@ -177,115 +175,87 @@
 
 BamgConvertMesh_matlab_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
-BamgConvertMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgConvertMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+BamgConvertMesh_matlab_la_LIBADD = ${deps}
 
 BamgMesher_matlab_la_SOURCES = ../BamgMesher/BamgMesher.cpp
-BamgMesher_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgMesher_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+BamgMesher_matlab_la_LIBADD = ${deps}
 
 BamgTriangulate_matlab_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
-BamgTriangulate_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgTriangulate_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+BamgTriangulate_matlab_la_LIBADD = ${deps}
 
 if CHACO
 Chaco_matlab_la_SOURCES = ../Chaco/Chaco.cpp
-Chaco_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Chaco_matlab_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+Chaco_matlab_la_LIBADD = ${deps} $(CHACOLIB)
 endif
 
 ContourToMesh_matlab_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
-ContourToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+ContourToMesh_matlab_la_LIBADD = ${deps}
 
 ContourToNodes_matlab_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
-ContourToNodes_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToNodes_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+ContourToNodes_matlab_la_LIBADD = ${deps}
 
 CoordTransform_matlab_la_SOURCES = ../CoordTransform/CoordTransform.cpp
-CoordTransform_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-CoordTransform_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+CoordTransform_matlab_la_LIBADD = ${deps}
 
 DistanceToMaskBoundary_matlab_la_SOURCES = ../DistanceToMaskBoundary/DistanceToMaskBoundary.cpp
-DistanceToMaskBoundary_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+DistanceToMaskBoundary_matlab_la_LIBADD = ${deps}
 
 ElementConnectivity_matlab_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
-ElementConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ElementConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+ElementConnectivity_matlab_la_LIBADD = ${deps}
 
 ExpToLevelSet_matlab_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp
-ExpToLevelSet_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ExpToLevelSet_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+ExpToLevelSet_matlab_la_LIBADD = ${deps}
 
 ExpSimplify_matlab_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp
-ExpSimplify_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ExpSimplify_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(NEOPZLIB)
+ExpSimplify_matlab_la_LIBADD = ${deps}
 
 InterpFromGridToMesh_matlab_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
-InterpFromGridToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+InterpFromGridToMesh_matlab_la_LIBADD = ${deps}
 
 InterpFromMesh2d_matlab_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp
-InterpFromMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+InterpFromMesh2d_matlab_la_LIBADD = ${deps}
 
 InterpFromMeshToGrid_matlab_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
-InterpFromMeshToGrid_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+InterpFromMeshToGrid_matlab_la_LIBADD = ${deps}
 
 InterpFromMeshToMesh2d_matlab_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
-InterpFromMeshToMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps}
 
 InterpFromMeshToMesh3d_matlab_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
-InterpFromMeshToMesh3d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps}
 
 IssmConfig_matlab_la_SOURCES = ../IssmConfig/IssmConfig.cpp
-IssmConfig_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-IssmConfig_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB)
+IssmConfig_matlab_la_LIBADD = ${deps}
 
 Kriging_matlab_la_SOURCES = ../Kriging/Kriging.cpp
-Kriging_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Kriging_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJLIB)
+Kriging_matlab_la_LIBADD = ${deps}
 
 M1qn3_matlab_la_SOURCES = ../M1qn3/M1qn3.cpp
-M1qn3_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-M1qn3_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(M1QN3LIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+M1qn3_matlab_la_LIBADD = ${deps}
 
 MeshPartition_matlab_la_SOURCES = ../MeshPartition/MeshPartition.cpp
-MeshPartition_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshPartition_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+MeshPartition_matlab_la_LIBADD = ${deps}
 
 MeshProfileIntersection_matlab_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
-MeshProfileIntersection_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+MeshProfileIntersection_matlab_la_LIBADD = ${deps}
 
 NodeConnectivity_matlab_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
-NodeConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-NodeConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+NodeConnectivity_matlab_la_LIBADD = ${deps}
 
 PointCloudFindNeighbors_matlab_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp
-PointCloudFindNeighbors_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+PointCloudFindNeighbors_matlab_la_LIBADD = ${deps}
 
 PropagateFlagsFromConnectivity_matlab_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp
-PropagateFlagsFromConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps}
 
 Scotch_matlab_la_SOURCES = ../Scotch/Scotch.cpp
-Scotch_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Scotch_matlab_la_LIBADD = ${deps}  $(PETSCLIB) $(HDF5LIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(BLASLAPACKLIB)
+Scotch_matlab_la_LIBADD = ${deps}
 
 ShpRead_matlab_la_SOURCES = ../ShpRead/ShpRead.cpp
-ShpRead_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB)
 
 Triangle_matlab_la_SOURCES = ../Triangle/Triangle.cpp
-Triangle_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Triangle_matlab_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+Triangle_matlab_la_LIBADD = ${deps} $(TRIANGLELIB)
 
 ProcessRifts_matlab_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp
-ProcessRifts_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ProcessRifts_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
-#}}}
+ProcessRifts_matlab_la_LIBADD = ${deps}
+#}}}