Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 27630)
+++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 27631)
@@ -90,5 +90,5 @@
 deps = $(MATHLIB)
 
-#Triangle library
+# Triangle
 CXXFLAGS_FOR_TRI = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
 
Index: /issm/trunk-jpl/src/wrappers/python/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 27630)
+++ /issm/trunk-jpl/src/wrappers/python/Makefile.am	(revision 27631)
@@ -2,11 +2,14 @@
 AUTOMAKE_OPTIONS = subdir-objects
 
-EXEEXT=$(PYTHONWRAPPEREXT)
-
 #define prefix (from http://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Defining-Directories.html)
 AM_CPPFLAGS += -DISSM_PREFIX='"$(prefix)"'
 
 #python io{{{
+if !WINDOWS
 lib_LTLIBRARIES = libISSMPython.la
+else
+noinst_LTLIBRARIES = libISSMPython.la
+lib_LTLIBRARIES =
+endif
 
 io_sources = \
@@ -15,15 +18,29 @@
 	./io/WritePythonData.cpp
 
-ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
+ALL_CXXFLAGS = -fPIC -D_WRAPPERS_
+
+if MSYS2
+ALL_CXXFLAGS += -D_DO_NOT_LOAD_GLOBALS_ # Cannot have undefined symbols under MSYS2
+ALL_CXXFLAGS += -D_USE_MATH_DEFINES # Need to open fence to math.h definitions when --std=c++ is used (which is the default)
+endif
+
+ALL_CXXFLAGS += $(CXXOPTFLAGS) $(CXXFLAGS)
 
 libISSMPython_la_SOURCES = $(io_sources)
-libISSMPython_la_CXXFLAGS= $(ALLCXXFLAGS)
+libISSMPython_la_CXXFLAGS= ${ALL_CXXFLAGS}
 #}}}
 #api io{{{
+if !WINDOWS
 lib_LTLIBRARIES += libISSMApi.la
-api_sources		 = ./io/ApiPrintf.cpp
+else
+noinst_LTLIBRARIES += libISSMApi.la
+endif
+
+if !MSYS2
+api_sources= ./io/ApiPrintf.cpp
 
 libISSMApi_la_SOURCES = $(api_sources)
-libISSMApi_la_CXXFLAGS= $(ALLCXXFLAGS)
+libISSMApi_la_CXXFLAGS = ${ALL_CXXFLAGS}
+endif
 #}}}
 #Wrappers {{{
@@ -52,12 +69,26 @@
 endif
 #}}}
-#Flags and libraries {{{
+# Dependencies {{{
 deps = $(MATHLIB) $(PYTHONLIB)
 
-#Triangle library
-AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER -D_WRAPPERS_
-
-#Python part
-AM_LDFLAGS = -module $(PYTHONLINK) -shrext ${EXEEXT} --export-dynamic -rdynamic -no-undefined
+# Triangle
+CXXFLAGS_FOR_TRI = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
+
+# Python
+LDFLAGS_FOR_PY = -module $(PYTHONLINK) -shrext $(PYTHONWRAPPEREXT) -no-undefined
+
+LDFLAGS_FOR_PY += --no-warnings
+CXXFLAGS_FOR_PY = -D_HAVE_PYTHON_MODULES_
+
+if PYTHON3
+CXXFLAGS_FOR_PY += -DNPY_NO_DEPRECATED_API
+endif
+
+AM_CXXFLAGS = ${CXXFLAGS_FOR_TRI} ${CXXFLAGS_FOR_PY}
+AM_LDFLAGS = ${LDFLAGS_FOR_PY}
+
+if !MSYS2
+AM_LDFLAGS += --export-dynamic -rdynamic
+endif
 
 if !VERSION
@@ -80,12 +111,11 @@
 endif
 
-AM_LDFLAGS 	+= --no-warnings
-AM_CXXFLAGS += -D_HAVE_PYTHON_MODULES_ -fPIC
-
-if PYTHON3
-AM_CXXFLAGS += -DNPY_NO_DEPRECATED_API
-endif
-
-deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
+AM_CXXFLAGS += -fPIC -D_WRAPPERS_
+
+deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la
+
+if !MSYS2
+deps += ./libISSMApi.la
+endif
 
 if ADOLC
@@ -109,82 +139,82 @@
 endif
 
-libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(MATHLIB)
+libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(MATHLIB)
 
 BamgConvertMesh_python_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
 BamgConvertMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgConvertMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+BamgConvertMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 BamgMesher_python_la_SOURCES = ../BamgMesher/BamgMesher.cpp
 BamgMesher_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgMesher_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+BamgMesher_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 BamgTriangulate_python_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
 BamgTriangulate_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgTriangulate_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+BamgTriangulate_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 if CHACO
 Chaco_python_la_SOURCES = ../Chaco/Chaco.cpp
 Chaco_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-Chaco_python_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+Chaco_python_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 endif
 
 ContourToMesh_python_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
 ContourToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+ContourToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 ContourToNodes_python_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
 ContourToNodes_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToNodes_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+ContourToNodes_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 ElementConnectivity_python_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
 ElementConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ElementConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+ElementConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 ExpToLevelSet_python_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp
 ExpToLevelSet_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ExpToLevelSet_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(NEOPZLIB)
+ExpToLevelSet_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(NEOPZLIB)
 
 InterpFromMesh2d_python_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp
 InterpFromMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+InterpFromMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 InterpFromGridToMesh_python_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
 InterpFromGridToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromGridToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+InterpFromGridToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 InterpFromMeshToGrid_python_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
 InterpFromMeshToGrid_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
+InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB)
 
 InterpFromMeshToMesh2d_python_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
 InterpFromMeshToMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
+InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
 
 InterpFromMeshToMesh3d_python_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
 InterpFromMeshToMesh3d_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
+InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB)
 
 IssmConfig_python_la_SOURCES = ../IssmConfig/IssmConfig.cpp
 IssmConfig_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-IssmConfig_python_la_LIBADD = ${deps} $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB)
+IssmConfig_python_la_LIBADD = ${deps} $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB)
 
 MeshPartition_python_la_SOURCES = ../MeshPartition/MeshPartition.cpp
 MeshPartition_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshPartition_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(METISLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+MeshPartition_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(METISLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 MeshProfileIntersection_python_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
 MeshProfileIntersection_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshProfileIntersection_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+MeshProfileIntersection_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 NodeConnectivity_python_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
 NodeConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-NodeConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+NodeConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 Triangle_python_la_SOURCES = ../Triangle/Triangle.cpp
 Triangle_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
 
 ProcessRifts_python_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp
 ProcessRifts_python_la_CXXFLAGS = ${AM_CXXFLAGS}
-ProcessRifts_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
-#}}}
+ProcessRifts_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB)
+#}}}