Index: /issm/trunk-jpl/patches/Makefile.am-C.patch
===================================================================
--- /issm/trunk-jpl/patches/Makefile.am-C.patch	(revision 15064)
+++ /issm/trunk-jpl/patches/Makefile.am-C.patch	(revision 15064)
@@ -0,0 +1,46 @@
+--- Makefile.am	2013-05-21 19:56:14.131300600 -0700
++++ Makefile.am.bak	2013-05-21 15:37:01.426736800 -0700
+@@ -6,11 +6,9 @@
+ lib_LIBRARIES = libISSMCore.a libISSMOverload.a
+ 
+ if SHAREDLIBS
+-lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la libISSM.la
+ endif
+ if WRAPPERS
+ if SHAREDLIBS
+-lib_LTLIBRARIES += libISSMModules.la
+ endif
+ lib_LIBRARIES += libISSMModules.a 
+ endif
+@@ -885,15 +883,15 @@
+ 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 WRAPPERS
+ libISSMModules_a_SOURCES = $(modules_sources)
+@@ -907,7 +905,7 @@
+ libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS)
+ libISSMModules_a_LIBADD = ./libISSMCore.a
+ if SHAREDLIBS
+-libISSMModules_la_SOURCES = $(libISSMModules_a_SOURCES)
++#libISSMModules_la_SOURCES = $(libISSMModules_a_SOURCES)
+ endif
+ endif
+ 
Index: /issm/trunk-jpl/patches/Makefile.am-MATLAB.patch
===================================================================
--- /issm/trunk-jpl/patches/Makefile.am-MATLAB.patch	(revision 15064)
+++ /issm/trunk-jpl/patches/Makefile.am-MATLAB.patch	(revision 15064)
@@ -0,0 +1,376 @@
+--- Makefile.am	2013-05-21 19:46:05.478487700 -0700
++++ Makefile.am.bak	2013-05-21 17:56:31.044451600 -0700
+@@ -1,13 +1,50 @@
+-AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@
++AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ /DTRILIBRARY /DANSI_DECLARATORS /DNO_TIMER /D_WRAPPERS_ /D_HAVE_MATLAB_MODULES_  /D_GNU_SOURCE
+ 
+ EXEEXT=$(MATLABWRAPPEREXT)
+ 
+ #matlab io{{{
+ lib_LIBRARIES = libISSMMatlab.a 
+-if SHAREDLIBS
+-lib_LTLIBRARIES = libISSMMatlab.la
+-else
+-lib_LTLIBRARIES =
++
++bin_PROGRAMS =  AverageFilter\
++						 BamgMesher\
++						 BamgConvertMesh\
++						 BamgTriangulate\
++						 ContourToMesh\
++						 ContourToNodes\
++						 ElementConnectivity\
++						 EnumToString\
++						 ExpSimplify\
++						 HoleFiller\
++						 InternalFront\
++						 InterpFromGridToMesh\
++						 InterpFromMeshToMesh2d\
++						 InterpFromMeshToMesh3d\
++						 InterpFromMeshToGrid\
++						 InterpFromMesh2d\
++						 Ll2xy\
++						 NodeConnectivity\
++						 MeshPartition\
++						 MeshProfileIntersection\
++						 PointCloudFindNeighbors\
++						 PropagateFlagsFromConnectivity\
++						 StringToEnum\
++						 TriaSearch\
++						 TriMesh\
++						 TriMeshProcessRifts\
++						 Scotch\
++						 Xy2ll\
++						 Chaco
++if KRIGING
++bin_PROGRAMS +=  Kriging
++endif
++if KML
++bin_PROGRAMS +=  KMLFileRead\
++				   KMLMeshWrite\
++				   KMLOverlay\
++				   Exp2Kml\
++				   Kml2Exp\
++				   Shp2Exp\
++				   Shp2Kml
+ endif
+ 
+ io_sources= ./include/matlabincludes.h\
+@@ -30,58 +67,12 @@
+ 				./io/MatlabVectorToPetscVec.cpp
+ endif
+ 
+-ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS) 
++
++ALLCXXFLAGS=  
+ libISSMMatlab_a_SOURCES = $(io_sources)
+ libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS)
+-if SHAREDLIBS
+-libISSMMatlab_la_SOURCES = $(io_sources)
+-endif
+ #}}}
+ #Wrappers {{{
+-if WRAPPERS
+-lib_LTLIBRARIES +=  AverageFilter.la\
+-						 BamgMesher.la\
+-						 BamgConvertMesh.la\
+-						 BamgTriangulate.la\
+-						 ContourToMesh.la\
+-						 ContourToNodes.la\
+-						 ElementConnectivity.la\
+-						 EnumToString.la\
+-						 ExpSimplify.la\
+-						 HoleFiller.la\
+-						 InternalFront.la\
+-						 InterpFromGridToMesh.la\
+-						 InterpFromMeshToMesh2d.la\
+-						 InterpFromMeshToMesh3d.la\
+-						 InterpFromMeshToGrid.la\
+-						 InterpFromMesh2d.la\
+-						 Ll2xy.la\
+-						 NodeConnectivity.la\
+-						 MeshPartition.la\
+-						 MeshProfileIntersection.la\
+-						 PointCloudFindNeighbors.la\
+-						 PropagateFlagsFromConnectivity.la\
+-						 StringToEnum.la\
+-						 TriaSearch.la\
+-						 TriMesh.la\
+-						 TriMeshProcessRifts.la\
+-						 Scotch.la\
+-						 Xy2ll.la\
+-						 Chaco.la
+-
+-if KRIGING
+-lib_LTLIBRARIES +=  Kriging.la
+-endif
+-if KML
+-lib_LTLIBRARIES +=  KMLFileRead.la\
+-				   KMLMeshWrite.la\
+-				   KMLOverlay.la\
+-				   Exp2Kml.la\
+-				   Kml2Exp.la\
+-				   Shp2Exp.la\
+-				   Shp2Kml.la
+-endif
+-endif 
+ #}}}
+ #Flags and libraries {{{
+ #if SHAREDLIBS
+@@ -92,25 +83,13 @@
+ #deps +=  $(MATHLIB) ${MEXLIB}
+ deps =  $(MATHLIB) ${MEXLIB}
+ 
+-#Triangle library
+-AM_CXXFLAGS =  -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER -D_WRAPPERS_
+-
+ #Matlab part
+-AM_LDFLAGS = -module $(MEXLINK) -shrext ${EXEEXT}  -L/usr/lib
+-if VERSION
+-AM_LDFLAGS +=
+-else
+-AM_LDFLAGS += -avoid-version
+-endif
++AM_LDFLAGS = $(MEXLINK)
+ if SHAREDLIBS
+-deps += ./libISSMMatlab.la 
+ else
+ deps += ./libISSMMatlab.a
+-AM_LDFLAGS += --no-warnings 
+ endif
+ 
+-AM_CXXFLAGS +=  -D_HAVE_MATLAB_MODULES_  -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread 
+-
+ if SHAREDLIBS
+ deps +=
+ else
+@@ -120,154 +99,154 @@
+ endif
+ endif
+ #Optimization flags:
+-AM_CXXFLAGS += $(CXXOPTFLAGS) 
++#AM_CXXFLAGS +=  
+ #}}}
+ #Bin sources {{{
+-AverageFilter_la_SOURCES = ../AverageFilter/AverageFilter.cpp\
++AverageFilter_SOURCES = ../AverageFilter/AverageFilter.cpp\
+ 									../AverageFilter/AverageFilter.h
+-AverageFilter_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++AverageFilter_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-BamgMesher_la_SOURCES = ../BamgMesher/BamgMesher.cpp\
++BamgMesher_SOURCES = ../BamgMesher/BamgMesher.cpp\
+ 								../BamgMesher/BamgMesher.h
+-BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++BamgMesher_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-BamgConvertMesh_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\
++BamgConvertMesh_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp\
+ 									  ../BamgConvertMesh/BamgConvertMesh.h
+-BamgConvertMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++BamgConvertMesh_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-BamgTriangulate_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\
++BamgTriangulate_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp\
+ 									  ../BamgTriangulate/BamgTriangulate.h
+-BamgTriangulate_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++BamgTriangulate_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Chaco_la_SOURCES = ../Chaco/Chaco.cpp\
++Chaco_SOURCES = ../Chaco/Chaco.cpp\
+ 						 ../Chaco/Chaco.h
+-Chaco_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(CHACOLIB)
++Chaco_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(CHACOLIB)
+ 
+-ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\
++ContourToMesh_SOURCES = ../ContourToMesh/ContourToMesh.cpp\
+ 									../ContourToMesh/ContourToMesh.h
+-ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
++ContourToMesh_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+ 
+-ContourToNodes_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp\
++ContourToNodes_SOURCES = ../ContourToNodes/ContourToNodes.cpp\
+ 									 ../ContourToNodes/ContourToNodes.h
+-ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++ContourToNodes_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-ElementConnectivity_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
++ElementConnectivity_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp\
+ 											../ElementConnectivity/ElementConnectivity.h
+-ElementConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++ElementConnectivity_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-EnumToString_la_SOURCES = ../EnumToString/EnumToString.cpp\
++EnumToString_SOURCES = ../EnumToString/EnumToString.cpp\
+ 								  ../EnumToString/EnumToString.h
+-EnumToString_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++EnumToString_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-StringToEnum_la_SOURCES = ../StringToEnum/StringToEnum.cpp\
++StringToEnum_SOURCES = ../StringToEnum/StringToEnum.cpp\
+ 								  ../StringToEnum/StringToEnum.h
+-StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++StringToEnum_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-HoleFiller_la_SOURCES = ../HoleFiller/HoleFiller.cpp\
++HoleFiller_SOURCES = ../HoleFiller/HoleFiller.cpp\
+ 								../HoleFiller/HoleFiller.h
+-HoleFiller_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) 
++HoleFiller_LDADD = ${deps} $(MPILIB) $(PETSCLIB) 
+ 
+-InternalFront_la_SOURCES = ../InternalFront/InternalFront.cpp\
++InternalFront_SOURCES = ../InternalFront/InternalFront.cpp\
+ 									../InternalFront/InternalFront.h
+-InternalFront_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++InternalFront_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-InterpFromGridToMesh_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\
++InterpFromGridToMesh_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp\
+ 											 ../InterpFromGridToMesh/InterpFromGridToMesh.h
+-InterpFromGridToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
++InterpFromGridToMesh_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+ 
+-InterpFromMeshToMesh2d_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\
++InterpFromMeshToMesh2d_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp\
+ 												../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h
+-InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
++InterpFromMeshToMesh2d_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+ 
+-InterpFromMeshToMesh3d_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\
++InterpFromMeshToMesh3d_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp\
+ 												../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h
+-InterpFromMeshToMesh3d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++InterpFromMeshToMesh3d_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-InterpFromMeshToGrid_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\
++InterpFromMeshToGrid_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp\
+ 											 ../InterpFromMeshToGrid/InterpFromMeshToGrid.h
+-InterpFromMeshToGrid_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++InterpFromMeshToGrid_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-InterpFromMesh2d_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\
++InterpFromMesh2d_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp\
+ 										../InterpFromMesh2d/InterpFromMesh2d.h
+-InterpFromMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
++InterpFromMesh2d_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+ 
+-KMLFileRead_la_SOURCES = ../KMLFileRead/KMLFileRead.cpp\
++KMLFileRead_SOURCES = ../KMLFileRead/KMLFileRead.cpp\
+ 								 ../KMLFileRead/KMLFileRead.h
+-KMLFileRead_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++KMLFileRead_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-KMLMeshWrite_la_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\
++KMLMeshWrite_SOURCES = ../KMLMeshWrite/KMLMeshWrite.cpp\
+ 								  ../KMLMeshWrite/KMLMeshWrite.h
+-KMLMeshWrite_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++KMLMeshWrite_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-KMLOverlay_la_SOURCES = ../KMLOverlay/KMLOverlay.cpp\
++KMLOverlay_SOURCES = ../KMLOverlay/KMLOverlay.cpp\
+ 								../KMLOverlay/KMLOverlay.h
+-KMLOverlay_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++KMLOverlay_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Xy2ll_la_SOURCES = ../Xy2ll/Xy2ll.cpp\
++Xy2ll_SOURCES = ../Xy2ll/Xy2ll.cpp\
+ 						 ../Xy2ll/Xy2ll.h
+-Xy2ll_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++Xy2ll_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Ll2xy_la_SOURCES = ../Ll2xy/Ll2xy.cpp\
++Ll2xy_SOURCES = ../Ll2xy/Ll2xy.cpp\
+ 						 ../Ll2xy/Ll2xy.h
+-Ll2xy_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++Ll2xy_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-ExpSimplify_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp\
++ExpSimplify_SOURCES = ../ExpSimplify/ExpSimplify.cpp\
+ 							../ExpSimplify/ExpSimplify.h
+-ExpSimplify_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++ExpSimplify_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Exp2Kml_la_SOURCES = ../Exp2Kml/Exp2Kml.cpp\
++Exp2Kml_SOURCES = ../Exp2Kml/Exp2Kml.cpp\
+ 							../Exp2Kml/Exp2Kml.h
+-Exp2Kml_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++Exp2Kml_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Kml2Exp_la_SOURCES = ../Kml2Exp/Kml2Exp.cpp\
++Kml2Exp_SOURCES = ../Kml2Exp/Kml2Exp.cpp\
+ 							../Kml2Exp/Kml2Exp.h
+-Kml2Exp_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++Kml2Exp_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Kriging_la_SOURCES = ../Kriging/Kriging.cpp\
++Kriging_SOURCES = ../Kriging/Kriging.cpp\
+ 							../Kriging/Kriging.h
+-Kriging_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(MULTITHREADINGLIB)
++Kriging_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(GSLLIB) $(MULTITHREADINGLIB)
+ 
+-MeshPartition_la_SOURCES = ../MeshPartition/MeshPartition.cpp\
++MeshPartition_SOURCES = ../MeshPartition/MeshPartition.cpp\
+ 									../MeshPartition/MeshPartition.h
+-MeshPartition_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(METISLIB)
++MeshPartition_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(METISLIB)
+ 
+-MeshProfileIntersection_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\
++MeshProfileIntersection_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\
+ 												 ../MeshProfileIntersection/MeshProfileIntersection.h
+-MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++MeshProfileIntersection_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-NodeConnectivity_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
++NodeConnectivity_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\
+ 										../NodeConnectivity/NodeConnectivity.h
+-NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++NodeConnectivity_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-PointCloudFindNeighbors_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\
++PointCloudFindNeighbors_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp\
+ 												 ../PointCloudFindNeighbors/PointCloudFindNeighbors.h
+-PointCloudFindNeighbors_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
++PointCloudFindNeighbors_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB)
+ 
+-PropagateFlagsFromConnectivity_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\
++PropagateFlagsFromConnectivity_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp\
+ 														  ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h
+-PropagateFlagsFromConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++PropagateFlagsFromConnectivity_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-Scotch_la_SOURCES = ../Scotch/Scotch.cpp\
++Scotch_SOURCES = ../Scotch/Scotch.cpp\
+ 						  ../Scotch/Scotch.h
+-Scotch_la_LIBADD = ${deps} $(SCOTCHLIB) $(MPILIB)
++Scotch_LDADD = ${deps} $(SCOTCHLIB) $(MPILIB)
+ 
+-Shp2Exp_la_SOURCES = ../Shp2Exp/Shp2Exp.cpp\
++Shp2Exp_SOURCES = ../Shp2Exp/Shp2Exp.cpp\
+ 							../Shp2Exp/Shp2Exp.h
+-Shp2Exp_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB)
++Shp2Exp_LDADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB)
+ 
+-Shp2Kml_la_SOURCES = ../Shp2Kml/Shp2Kml.cpp\
++Shp2Kml_SOURCES = ../Shp2Kml/Shp2Kml.cpp\
+ 							../Shp2Kml/Shp2Kml.h
+-Shp2Kml_la_LIBADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB)
++Shp2Kml_LDADD = ${deps} $(SHAPELIBLIB) $(MPILIB) $(PETSCLIB)
+ 
+-TriaSearch_la_SOURCES = ../TriaSearch/TriaSearch.cpp\
++TriaSearch_SOURCES = ../TriaSearch/TriaSearch.cpp\
+ 								../TriaSearch/TriaSearch.h
+-TriaSearch_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++TriaSearch_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ 
+-TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp\
++TriMesh_SOURCES = ../TriMesh/TriMesh.cpp\
+ 							../TriMesh/TriMesh.h
+-TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB)
++TriMesh_LDADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB)
+ 
+-TriMeshProcessRifts_la_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\
++TriMeshProcessRifts_SOURCES = ../TriMeshProcessRifts/TriMeshProcessRifts.cpp\
+ 											../TriMeshProcessRifts/TriMeshProcessRifts.h
+-TriMeshProcessRifts_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB)
++TriMeshProcessRifts_LDADD = ${deps} $(MPILIB) $(PETSCLIB)
+ #}}}
Index: /issm/trunk-jpl/patches/issm_options.m4.bak
===================================================================
--- /issm/trunk-jpl/patches/issm_options.m4.bak	(revision 15064)
+++ /issm/trunk-jpl/patches/issm_options.m4.bak	(revision 15064)
@@ -0,0 +1,1577 @@
+dnl ISSM Options
+
+AC_DEFUN([ISSM_OPTIONS],[
+
+	dnl ISSM's internal options
+	dnl Debugging {{{
+	AC_ARG_ENABLE([debugging],                                        dnl feature
+		AS_HELP_STRING([--enable-debugging],[turn debug support on]),  dnl help string
+		[enable_debugging=$enableval],                                 dnl action if given
+		[enable_debugging=no])                                         dnl action if not given
+	if test "x$enable_debugging" = xyes; then
+		AC_DEFINE([_ISSM_DEBUG_],[1],[Macro to enable debugging in ISSM])
+	fi
+
+	dnl }}}
+    dnl Shared build {{{
+    AC_ARG_ENABLE([sharedlibs],                                                dnl feature
+        AS_HELP_STRING([--enable-sharedlibs], [produce libISSM.so.0]),         dnl help string
+        [enable_sharedlibs=$enableval],                                        dnl action if given
+        [enable_sharedlibs=no])                                                dnl action if not given
+    AM_CONDITIONAL([SHAREDLIBS], [test x$enable_sharedlibs = xyes])
+    dnl }}}
+    dnl Version{{{
+    AC_ARG_ENABLE([version],                                                dnl feature
+        AS_HELP_STRING([--enable-version], [produce libISSM.so.0]),         dnl help string
+        [enable_version=$enableval],                                        dnl action if given
+        [enable_version=no])                                                dnl action if not given
+    AM_CONDITIONAL([VERSION], [test x$enable_VERSION = xyes])
+    dnl }}}
+	dnl Wrappers build {{{
+	AC_ARG_WITH([wrappers],
+		AS_HELP_STRING([--with-wrappers = value],[wrappers compilation. ]),
+		[WRAPPERS_VALUE=$withval],[WRAPPERS_VALUE="yes"])
+	AC_MSG_CHECKING(for wrappers compilation)
+	AM_CONDITIONAL([WRAPPERS], [test x$WRAPPERS_VALUE = xyes])
+	AC_MSG_RESULT($WRAPPERS_VALUE) 
+	dnl }}}
+	dnl Extensions{{{
+	ISSMEXT=".exe"
+	AC_SUBST([ISSMEXT])
+	dnl }}}
+
+	dnl ISSM's externalpackages
+	dnl vendor{{{
+	AC_ARG_WITH([vendor],
+	  AS_HELP_STRING([--with-vendor = VENDOR], [vendor name, ex: intel]),
+	  [VENDOR=$withval],[VENDOR=""]) 
+	AC_MSG_CHECKING(for vendor compilers)
+	if test -n "$VENDOR"; then
+
+		if  test $VENDOR = intel-win32; then
+			export CC=icl
+			export CXX=icl
+			export CFLAGS="-DWIN32 -D_INTEL_WIN_"
+			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_"
+		elif  test $VENDOR = intel-win7-32; then
+			export CC=cccl
+			export CXX=cccl
+			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export AR="ar-lib lib"
+			export RANLIB=true
+			OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib"
+		elif  test $VENDOR = intel-win7-64; then
+			export CC=cccl
+			export CXX=cccl
+			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export AR="ar-lib lib"
+			export RANLIB=true
+			OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib"
+		elif test $VENDOR = intel-linux; then
+			export CC=icc
+			export CXX=icpc
+			export CFLAGS=" -D_INTEL_LINUX_"
+			export CXXFLAGS=" -D_INTEL_LINUX_"
+		elif test $VENDOR = intel-discover; then
+			export CC=icc
+			export CXX=icpc
+			export CXXFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
+			export CFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
+		elif test $VENDOR = intel-pleiades; then
+			export CC=icc
+			export CXX=icpc
+			export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ "
+			export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ "
+        else
+		AC_MSG_ERROR([unknow compiler vendor!])
+		fi
+	fi
+	AC_SUBST([OSLIBS]) 
+	AC_MSG_RESULT(done)
+	dnl }}}
+	dnl matlab{{{
+
+	dnl 1. See if matlab has been provided
+	AC_ARG_WITH([matlab-dir],
+		AS_HELP_STRING([--with-matlab-dir=DIR], [matlab root directory. necessary for serial build.]),
+		[MATLAB_ROOT=$withval],[MATLAB_ROOT=""]) 
+
+	AC_MSG_CHECKING([whether matlab is enabled])
+	if test -d "$MATLAB_ROOT"; then
+		HAVE_MATLAB=yes
+	else
+		HAVE_MATLAB=no
+	fi
+	if test x$HAVE_MATLAB = xyes; then
+		AC_DEFINE([_HAVE_MATLAB_],[1],[with Matlab in ISSM src])
+	fi
+	AC_MSG_RESULT($HAVE_MATLAB)
+	AM_CONDITIONAL([MATLAB], [test x$HAVE_MATLAB = xyes])
+
+	dnl 2. Get Matlab libraries
+	if test x$HAVE_MATLAB = xyes; then
+
+		AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT)
+		MATLABINCL=-I `cygpath -wa /cygdrive/c/Program\ Files/MATLAB/R2011b/extern/include`;
+		
+		dnl OS-dependent variables and checks
+		case "${host_os}" in
+			*linux*)
+				if test "${host_cpu}" = "x86_64";
+				then
+					MEXLIB=-L"$MATLAB_ROOT/bin/glnxa64/ -lmex"
+					MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnxa64/mexFunction.map";
+				else
+					MEXLIB=-L"$MATLAB_ROOT/bin/glnx86/ -lmex"
+					MEXLINK="-pthread -shared -W2,--version-script,${MATLAB_ROOT}/extern/lib/glnx86/mexFunction.map";
+				fi
+				MEXEXT=`$MATLAB_ROOT/bin/mexext`
+				MEXEXT=".$MEXEXT"
+			;;
+			*darwin*)
+				dnl mex -v gives all the flags for compilation of mex files
+				dnl if matlab version is 7.9 or more, we must use mexmaci64 (64 bits)
+				MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map"
+				MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims"
+				if test $MATLAB_MAJOR -ge 7; then 
+					 if test $MATLAB_MINOR -ge 9; then 
+						  MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map"
+							 MEXLIB=" -L$MATLAB_ROOT/bin/maci64/ -lmx -lmex -lmat -lstdc++"
+					 fi
+				fi
+				MEXEXT=`$MATLAB_ROOT/bin/mexext`
+				MEXEXT=".$MEXEXT"
+			;;
+			*cygwin*) 
+				if  test $VENDOR = intel-win7-32; then
+					MEXLIB="/link /DLL /export:mexFunction libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib libf2cblas.lib libf2clapack.lib" 
+				elif  test $VENDOR = intel-win7-64; then
+					MEXLIB="/DLL /export:mexFunction -L$MATLAB_ROOT\extern\lib\win64\microsoft\ libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib  -NOLOGO -INCREMENTAL:NO -manifest" 
+				fi
+				MEXEXT=`$MATLAB_ROOT/bin/mexext.bat`
+				MEXEXT=".$MEXEXT"
+			;;
+		esac
+	   AC_MSG_RESULT(done)
+
+		AC_SUBST([MATLABINCL])
+		AC_SUBST([MEX])
+		MATLABWRAPPEREXT=$MEXEXT
+		AC_SUBST([MATLABWRAPPEREXT])
+	   AC_SUBST([MEXLIB]) 
+		AC_SUBST([MEXLINK])
+	fi
+	dnl }}}
+	dnl triangle {{{
+	AC_ARG_WITH([triangle-dir],
+			  AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory. necessary for serial build]),
+			 [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT=""]) 
+	AC_MSG_CHECKING(for triangle headers and libraries)
+
+	if test -d "$TRIANGLE_ROOT"; then
+
+		dnl defaults
+		HAVE_TRIANGLE=yes
+		TRIANGLEINCL=-I$TRIANGLE_ROOT/
+
+		case "${host_os}" in
+				*cygwin*)
+				TRIANGLELIB=$TRIANGLE_ROOT/triangle.lib
+				;;
+				*linux*)
+				TRIANGLELIB=$TRIANGLE_ROOT/triangle.a
+				;;
+				*darwin*)
+				TRIANGLELIB=$TRIANGLE_ROOT/triangle.a
+				;;
+			esac
+
+		AC_DEFINE([_HAVE_TRIANGLE_],[1],[with Triangle in ISSM src])
+		AC_SUBST([TRIANGLEINCL])
+		AC_SUBST([TRIANGLELIB])
+
+	else
+		HAVE_TRIANGLE=no
+	fi
+	AC_MSG_RESULT($HAVE_TRIANGLE)
+	dnl }}}
+	dnl dakota{{{
+	AC_ARG_WITH([dakota-dir],
+	  AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory. necessary for serial build]),
+	  [DAKOTA_ROOT=$withval],[DAKOTA_ROOT=""]) 
+	AC_MSG_CHECKING(for dakota)
+	
+	if test -d "$DAKOTA_ROOT"; then
+
+		dnl defaults
+		HAVE_DAKOTA=yes
+		AC_MSG_RESULT($HAVE_DAKOTA)
+		DAKOTAINCL=-I$DAKOTA_ROOT/include
+		AC_MSG_CHECKING(for dakota version)
+		DAKOTA_VERSION=`cat $DAKOTA_ROOT/include/dakota_config.h | grep "#define PACKAGE_VERSION" | sed 's/#define PACKAGE_VERSION//' | sed 's/ //g' | sed -e 's/\"//g' `
+		AC_MSG_RESULT($DAKOTA_VERSION)
+		AC_DEFINE_UNQUOTED([DAKOTA_VERSION],"$DAKOTA_VERSION",[Dakota version number])
+		case "${host_os}" in
+			*cygwin*)
+				if      test x$DAKOTA_VERSION = x4.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
+				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
+				else
+					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
+				fi
+				fi
+			;;
+			*linux*)
+				if      test x$DAKOTA_VERSION = x4.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
+				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
+				else
+					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
+				fi
+				fi
+			;;
+			*darwin*)
+				if      test x$DAKOTA_VERSION = x4.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" 
+					dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
+				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
+					dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
+				else
+					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
+				fi
+				fi
+			;;
+		esac
+		AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src])
+		AC_SUBST([DAKOTAINCL])
+		AC_SUBST([DAKOTALIB])
+
+	else
+		HAVE_DAKOTA=no
+		AC_MSG_RESULT($HAVE_DAKOTA)
+	fi
+	AM_CONDITIONAL([DAKOTA], [test x$HAVE_DAKOTA = xyes])
+	dnl }}}
+	dnl boost{{{
+	AC_ARG_WITH([boost-dir],
+	  AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]),
+	  [BOOST_ROOT=$withval],[BOOST_ROOT=""]) 
+	AC_MSG_CHECKING(for boost)
+	
+	if test -d "$BOOST_ROOT"; then
+		dnl defaults
+		HAVE_BOOST=yes
+		BOOSTINCL=-I$BOOST_ROOT/include
+		BOOSTLIB="-L$BOOST_ROOT/lib -lboost_python"
+
+		AC_DEFINE([_HAVE_BOOST_],[1],[with Boost in ISSM src])
+		AC_SUBST([BOOSTINCL])
+		AC_SUBST([BOOSTLIB])
+	else
+		HAVE_BOOST=no
+	fi
+	AM_CONDITIONAL([BOOST], [test x$HAVE_BOOST = xyes])
+	AC_MSG_RESULT($HAVE_BOOST)
+	dnl }}}
+	dnl python{{{
+	AC_ARG_WITH([python-dir],
+	  AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]),
+	  [PYTHON_ROOT=$withval],[PYTHON_ROOT=""]) 
+
+	AC_MSG_CHECKING(for python)
+	if test -d "$PYTHON_ROOT"; then
+		HAVE_PYTHON="yes"
+		AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src])
+	else
+		HAVE_PYTHON=no
+	fi
+	AC_MSG_RESULT($HAVE_PYTHON)
+
+	dnl get python version
+	if test x$HAVE_PYTHON = xyes; then
+		AC_MSG_CHECKING(for python version)
+		dnl Query Python for its version number.  Getting [:3] seems to be
+		dnl the best way to do this; it's what "site.py" does in the standard
+		dnl library.
+		PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]")
+		AC_MSG_RESULT($PYTHON_VERSION)
+
+		dnl recover major: 
+		PYTHON_MAJOR=${PYTHON_VERSION%.*}
+		if test x$PYTHON_MAJOR = x3; then
+			dnl are we running python 3?
+			HAVE_PYTHON3="yes"
+		else
+			HAVE_PYTHON3="no"
+		fi
+		AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major])
+
+		PYTHONINCL=-I$PYTHON_ROOT/include
+		PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHON_VERSION"
+		PYTHONEXT=.so
+
+		case "${host_os}" in
+			*cygwin*)
+			PYTHONLINK="-shared"
+			;;
+			*linux*)
+			PYTHONLINK="-shared"
+			;;
+			*darwin*)
+			PYTHONLINK="-dynamiclib"
+			;;
+		esac
+
+		AC_SUBST([PYTHONINCL])
+		AC_SUBST([PYTHONLIB])
+		PYTHONWRAPPEREXT=$PYTHONEXT
+		AC_SUBST([PYTHONWRAPPEREXT])
+		AC_SUBST([PYTHONLINK])
+	fi
+	AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes])
+	AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes])
+	dnl }}}
+	dnl python-numpy{{{
+	AC_ARG_WITH([python-numpy-dir],
+	  AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]),
+	  [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT=""]) 
+	AC_MSG_CHECKING(for python-numpy)
+	
+	if test -d "$PYTHON_NUMPY_ROOT"; then
+		dnl defaults
+		HAVE_PYTHON_NUMPY=yes
+		PYTHON_NUMPYINCL="-I$PYTHON_NUMPY_ROOT -I$PYTHON_NUMPY_ROOT/core/include/numpy"
+
+		AC_DEFINE([_HAVE_PYTHON_NUMPY_],[1],[with Python-Numpy in ISSM src])
+		AC_SUBST([PYTHON_NUMPYINCL])
+	else
+		HAVE_PYTHON_NUMPY=no
+	fi
+	AC_MSG_RESULT($HAVE_PYTHON_NUMPY)
+	dnl }}}
+	dnl chaco{{{
+	AC_ARG_WITH([chaco-dir],
+	  AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]),
+	  [CHACO_ROOT=$withval],[CHACO_ROOT=""]) 
+	AC_MSG_CHECKING(for chaco)
+	
+	if test -d "$CHACO_ROOT"; then
+
+		dnl defaults
+		HAVE_CHACO=yes
+		CHACOINCL=-I$CHACO_ROOT/include
+		CHACOLIB="-L$CHACO_ROOT/lib -lchacominusblas"
+
+		AC_DEFINE([_HAVE_CHACO_],[1],[with Chaco in ISSM src])
+		AC_SUBST([CHACOINCL])
+		AC_SUBST([CHACOLIB])
+
+	else
+		HAVE_CHACO=no
+	fi
+	AC_MSG_RESULT($HAVE_CHACO)
+	dnl }}}
+	dnl scotch{{{
+	AC_ARG_WITH([scotch-dir],
+	  AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]),
+	  [SCOTCH_ROOT=$withval],[SCOTCH_ROOT=""]) 
+	AC_MSG_CHECKING(for scotch)
+	
+	if test -d "$SCOTCH_ROOT"; then
+
+		dnl defaults
+		HAVE_SCOTCH=yes
+		SCOTCHINCL="-DNOFILEIO -I$SCOTCH_ROOT/include -DSCOTCH_VERSION=\\\"UNKNOWN\\\""
+		SCOTCHLIB="-L$SCOTCH_ROOT/lib -lnfioscotch -lnfioscotcherr -lnfioscotcherrexit -lscotchmetis"
+
+		AC_DEFINE([_HAVE_SCOTCH_],[1],[with Scotch in ISSM src])
+		AC_SUBST([SCOTCHINCL])
+		AC_SUBST([SCOTCHLIB])
+
+	else
+		HAVE_SCOTCH=no
+	fi
+	AC_MSG_RESULT($HAVE_SCOTCH)
+	dnl }}}
+	dnl adolc{{{
+	AC_ARG_WITH([adolc-dir],
+		AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]),
+		[ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) 
+	AC_MSG_CHECKING(for adolc)
+
+	if test "x$ADOLC_ROOT" = "xno"; then
+		HAVE_ADOLC=no
+	else
+		if test -d "$ADOLC_ROOT"; then
+
+			dnl defaults
+			HAVE_ADOLC=yes
+			ADOLCINCL="-I$ADOLC_ROOT/include"
+			ADOLCLIB="-L$ADOLC_ROOT/lib64 -ladolc"
+
+			AC_DEFINE([_HAVE_ADOLC_],[1],[with adolc in ISSM src])
+			AC_SUBST([ADOLCINCL])
+			AC_SUBST([ADOLCLIB])
+
+		else
+			echo  "Specified directory does not exist!"
+			exit 1
+		fi
+	fi
+	AM_CONDITIONAL([ADOLC], [test x$HAVE_ADOLC = xyes])
+	AC_MSG_RESULT($HAVE_ADOLC)
+	dnl }}}
+	dnl adolc-version{{{
+	AC_ARG_WITH([adolc-version],
+		AS_HELP_STRING([--with-adolc-version=number], [adolc version.]),
+		[ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) 
+	AC_MSG_CHECKING(for adolc-version) 
+
+	AC_DEFINE_UNQUOTED([_ADOLC_VERSION_],$ADOLC_VERSION,[ADOLC version])
+	AC_MSG_RESULT($ADOLC_VERSION)
+	dnl }}}
+	dnl adic2{{{
+	AC_ARG_WITH([adic2-dir],
+	  AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]),
+	  [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) 
+	AC_MSG_CHECKING(for adic2)
+
+	if test "x$ADIC2_ROOT" = "xno"; then
+		HAVE_ADIC2=no
+	else
+		if test -d "$ADIC2_ROOT"; then
+
+			dnl defaults
+			HAVE_ADIC2=yes
+			ADIC2INCL="-DADIC2_DENSE -I$ADIC2_ROOT/include -I$ADIC2_ROOT/share/runtime_dense/"
+			ADIC2LIB=""
+
+			AC_DEFINE([_HAVE_ADIC2_],[1],[with adic2 in ISSM src])
+			AC_SUBST([ADIC2INCL])
+			AC_SUBST([ADIC2LIB])
+
+		else
+			echo  "Specified directory does not exist!"
+			exit 1
+		fi
+	fi
+	AM_CONDITIONAL([ADIC2], [test x$HAVE_ADIC2 = xyes])
+	AC_MSG_RESULT($HAVE_ADIC2)
+	dnl }}}
+	dnl gsl{{{
+	AC_ARG_WITH([gsl-dir],
+	  AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]),
+	  [GSL_ROOT=$withval],[GSL_ROOT=""]) 
+	AC_MSG_CHECKING(for gsl)
+	
+	if test -d "$GSL_ROOT"; then
+
+		dnl defaults
+		HAVE_GSL=yes
+		GSLINCL="-I$GSL_ROOT/include"
+		GSLLIB="-dy -L$GSL_ROOT/lib -lgsl -lgslcblas -lm"
+
+		AC_DEFINE([_HAVE_GSL_],[1],[with gsl in ISSM src])
+		AC_SUBST([GSLINCL])
+		AC_SUBST([GSLLIB])
+
+	else
+		HAVE_GSL=no
+	fi
+	AM_CONDITIONAL([GSL], [test x$HAVE_GSL = xyes])
+	AC_MSG_RESULT($HAVE_GSL)
+	dnl }}}
+	dnl rose{{{
+	AC_ARG_WITH([rose-dir],
+	  AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]),
+	  [ROSE_ROOT=$withval],[ROSE_ROOT=""]) 
+	AC_MSG_CHECKING(for rose)
+	
+	if test -d "$ROSE_ROOT"; then
+
+		dnl defaults
+		HAVE_ROSE=yes
+		ROSEINCL="-I$ROSE_ROOT/include"
+		ROSELIB=""
+
+		AC_DEFINE([_HAVE_ROSE_],[1],[with rose in ISSM src])
+		AC_SUBST([ROSEINCL])
+		AC_SUBST([ROSELIB])
+
+	else
+		HAVE_ROSE=no
+	fi
+	AM_CONDITIONAL([ROSE], [test x$HAVE_ROSE = xyes])
+	AC_MSG_RESULT($HAVE_ROSE)
+	dnl }}}
+	dnl mpi{{{
+	AC_MSG_CHECKING(for mpi)
+	AC_ARG_WITH([mpi-lib],
+		AS_HELP_STRING([--with-mpi-lib = options],[mpi options, for ex: "-L$MPIROOT -lmpich]),
+		[MPILIB=$withval],[MPILIB=""])
+	
+	AC_ARG_WITH([mpi-include],
+	  AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]),
+	  [MPI_INCLUDE=$withval],[MPI_INCLUDE=""])
+	
+	if test -z "$MPILIB" ; then
+		HAVE_MPI=no
+	else
+		if test -z "$MPI_INCLUDE" ; then
+			HAVE_MPI=no
+		else
+			HAVE_MPI=yes
+			MPIINCL=-I"$MPI_INCLUDE"
+			AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
+			AC_DEFINE([HAVE_MPI],[1],[Mpi Flag for Dakota (DO NOT REMOVE)])
+			AC_SUBST([MPIINCL])
+			AC_SUBST([MPILIB])
+		fi
+	fi
+	AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes])
+	AC_MSG_RESULT($HAVE_MPI)
+	dnl }}}
+	dnl petsc{{{
+	AC_ARG_WITH([petsc-dir],
+	  AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]),
+	  [PETSC_ROOT=$withval],[PETSC_ROOT=""])
+		
+	if test -d "$PETSC_ROOT"; then
+		AC_MSG_CHECKING(for petsc version)
+		PETSC_MAJOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MAJOR" | sed 's/#define PETSC_VERSION_MAJOR//' | sed 's/ //g'`
+		PETSC_MINOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MINOR" | sed 's/#define PETSC_VERSION_MINOR//' | sed 's/ //g'`
+		AC_DEFINE_UNQUOTED([_PETSC_MAJOR_],$PETSC_MAJOR,[PETSc version major])
+		AC_DEFINE_UNQUOTED([_PETSC_MINOR_],$PETSC_MINOR,[PETSc version minor])
+		AC_MSG_RESULT($PETSC_MAJOR.$PETSC_MINOR)
+
+		PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' `
+		PETSC_RELEASE=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_RELEASE" | sed 's/#define PETSC_VERSION_RELEASE//' | sed 's/ //g'`
+
+		AC_MSG_CHECKING(whether petsc is the development version)
+		dnl if test x$PETSC_VERSION_DATE_HG = xunknown; then
+		if test "$PETSC_RELEASE" = "0"; then
+		   AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev])
+			AC_MSG_RESULT(yes)
+		else
+			AC_MSG_RESULT(no)
+		fi
+	fi
+	
+	AC_ARG_WITH([petsc-arch],
+	  AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch , necessary for parallel build]),
+	  [PETSC_ARCH=$withval],[PETSC_ARCH=""])
+
+	AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH)
+	
+	dnl To ge PETSc's libraries:
+	dnl cd externalpackages/petsc/src
+	dnl make getlinklibs
+	if test -d "$PETSC_ROOT"; then
+
+	 PETSCINCL=" -I$PETSC_ROOT/include"
+	 dnl Add other location (maybe not needed anymore)
+	 if test -d "$PETSC_ROOT/$PETSC_ARCH/include"; then
+	  PETSCINCL+=" $PETSC_ROOT/$PETSC_ARCH/include"
+	 fi
+	 if test -d "$PETSC_ROOT/include/$PETSC_ARCH"; then
+	  PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH"
+	 fi
+	
+	 case "${host_os}" in
+			*cygwin*)
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-L$PETSC_ROOT/lib libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib"
+			else
+				PETSCLIB="-L$PETSC_ROOT/lib libpetsc.lib"
+				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" libmetis.lib"; fi
+			fi
+			;;
+			*linux*)
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc  -lpetscsnes -lpetscts"
+			else
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc -ldl"
+				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi
+			fi
+			;;
+			*darwin*)
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
+			else
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc"
+				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi
+			fi
+			;;
+		esac
+		AC_DEFINE([_HAVE_PETSC_],[1],[with PETSc in ISSM src])
+		AC_SUBST([PETSCINCL])
+		AC_SUBST([PETSCLIB])
+		HAVE_PETSC=yes
+	else
+		HAVE_PETSC=no
+	fi
+	
+	AM_CONDITIONAL([PETSC], [test x$HAVE_PETSC = xyes])
+	AC_MSG_RESULT($HAVE_PETSC)
+	dnl }}}
+	dnl metis{{{
+	if test "$HAVE_PETSC" = "yes" && test "x$PETSC_MAJOR" = "x3" && test $PETSC_MINOR -ge 3; then
+
+		dnl in petsc >=3.3, metis is provided
+		HAVE_METIS="yes"
+		AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number])
+		AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src])
+	else
+		AC_ARG_WITH([metis-dir],
+		  AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]),
+		  [METIS_ROOT=$withval],[METIS_ROOT=""])
+
+		AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT)
+
+		if test -d "$METIS_ROOT"; then
+
+			dnl first figure out version of metis: does the VERSION file exist?
+			if test -e "$METIS_ROOT/VERSION"; then
+				METIS_VERSION=4
+			else
+				METIS_VERSION=5
+			fi
+
+			dnl defaults
+			HAVE_METIS=yes
+
+			if test "$METIS_VERSION" = "4" ; then
+					
+				METISINCL=-I"$METIS_ROOT/Lib" 
+				case "${host_os}" in
+					*cygwin*)
+					METISLIB="-L$METIS_ROOT libmetis.lib"
+					;;
+					*linux*)
+					METISLIB=-L"$METIS_ROOT/ -lmetis"
+					;;
+					*darwin*)
+					METISLIB=-L"$METIS_ROOT/ -lmetis"
+					;;
+				esac
+
+					AC_DEFINE([_METIS_VERSION_],[4],[ Metis version number])
+			fi
+			if test "$METIS_VERSION" = "5" ; then
+		
+				case "${host_os}" in
+					*cygwin*)
+					METISLIB="-L$METIS_ROOT libmetis.lib"
+					;;
+					*linux*)
+					METISLIB=-L"$METIS_ROOT/lib -lmetis"
+					;;
+					*darwin*)
+					METISLIB=-L"$METIS_ROOT/lib -lmetis"
+					;;
+				esac
+
+				METISINCL=-I"$METIS_ROOT/include" 
+				AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number])
+			fi
+
+			AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src])
+			AC_SUBST([METISINCL])
+			AC_SUBST([METISLIB])
+		else
+			HAVE_METIS=no
+		fi
+		AC_MSG_RESULT($HAVE_METIS)
+	fi
+	AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes])
+	dnl }}}
+	dnl tao{{{
+	AC_ARG_WITH([tao-dir],
+		AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]),
+		[TAO_ROOT=$withval],[TAO_ROOT=""]) 
+	AC_MSG_CHECKING(for tao)
+
+	if test -d "$TAO_ROOT"; then
+
+	  HAVE_TAO=yes
+	  TAOINCL="-I$TAO_ROOT/ -I$TAO_ROOT/include -I$TAO_ROOT/bmake/ "
+	  TAOLIB="-L$TAO_ROOT/lib -ltao -lpetsc"
+
+	  AC_DEFINE([_HAVE_TAO_],[1],[with Tao in ISSM src])
+	  AC_SUBST([TAOINCL])
+	  AC_SUBST([TAOLIB])
+	else
+		HAVE_TAO=no
+	fi
+	AC_MSG_RESULT($HAVE_TAO)
+	dnl }}}
+	dnl slepc{{{
+	AC_ARG_WITH([slepc-dir],
+	  AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]),
+	  [SLEPC_ROOT=$withval],[SLEPC_ROOT=""])
+			  
+	AC_MSG_CHECKING(for slepc headers and libraries in $SLEPC_ROOT)
+	if test -d "$SLEPC_ROOT"; then
+		HAVE_SLEPC=yes
+		SLEPCINCL=-I"$SLEPC_ROOT/include"
+		SLEPCLIB=-L"$SLEPC_ROOT/lib/ -lslepc"
+
+		AC_DEFINE([_HAVE_SLEPC_],[1],[with Slepc in ISSM src])
+		AC_SUBST([SLEPCINCL])
+		AC_SUBST([SLEPCLIB])
+	else
+		HAVE_SLEPC=no
+	fi
+	AC_MSG_RESULT($HAVE_SLEPC)
+	dnl }}}
+	dnl shapelib{{{
+	AC_ARG_WITH([shapelib-dir],
+	  AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]),
+	  [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT=""])
+			  
+	AC_MSG_CHECKING(for shapelib headers and libraries in $SHAPELIB_ROOT)
+	if test -d "$SHAPELIB_ROOT"; then
+
+		dnl defaults
+		HAVE_SHAPELIB=yes
+		SHAPELIBINCL=-I"$SHAPELIB_ROOT/include"
+		SHAPELIBLIB=-L"$SHAPELIB_ROOT/lib/ -lshape"
+
+		AC_DEFINE([_HAVE_SHAPELIB_],[1],[with Shapelib in ISSM src])
+		AC_SUBST([SHAPELIBINCL])
+		AC_SUBST([SHAPELIBLIB])
+	else
+		HAVE_SHAPELIB=no
+	fi
+	AC_MSG_RESULT($HAVE_SHAPELIB)
+	dnl }}}
+	dnl scalapack{{{
+	AC_ARG_WITH([scalapack-dir],
+	  AS_HELP_STRING([--with-scalapack-dir=DIR],[scalapack root directory]),
+	  [SCALAPACK_ROOT=$withval],[SCALAPACK_ROOT=""])
+			  
+	AC_MSG_CHECKING(for scalapack headers and libraries in $SCALAPACK_ROOT)
+	if test -d "$SCALAPACK_ROOT"; then
+
+		dnl defaults
+		HAVE_SCALAPACK=yes
+		if test x$VENDOR = xintel-discover; then
+		 SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lmkl_scalapack_lp64"
+		else
+		 SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack"
+		fi
+
+		AC_DEFINE([_HAVE_SCALAPACK_],[1],[with Scalapack in ISSM src])
+		AC_SUBST([SCALAPACKLIB])
+	else
+		HAVE_SCALAPACK=no
+	fi
+	AC_MSG_RESULT($HAVE_SCALAPACK)
+	dnl }}}
+	dnl blas{{{
+	AC_ARG_WITH([blas-lapack-dir],
+	  AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]),
+	  [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT=""])
+			  
+	AC_MSG_CHECKING(for blas and lapack headers and libraries in $BLASLAPACK_ROOT)
+	if test -d "$BLASLAPACK_ROOT"; then
+
+		dnl defaults
+		HAVE_BLASLAPACK=yes
+		BLASLAPACKINCL=""
+	
+		if test x$VENDOR = xintel-discover; then
+		 BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lmkl_lapack -lmkl -lguide -lpthread"
+		else
+		dnl: branch on whether we are running on windows or linux.
+		case "${host_os}" in
+			*cygwin*)
+			BLASLAPACKLIB="-L$BLASLAPACK_ROOT libf2cblas.lib  libf2clapack.lib"
+			;;
+			*linux*)
+			BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lflapack -lfblas " 
+			;;
+			*darwin*)
+			BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lflapack -lfblas " 
+			;;
+		esac
+		fi
+
+		AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src])
+		AC_SUBST([BLASLAPACKLIB])
+		AC_SUBST([BLASLAPACKINCL])
+	else
+		HAVE_BLASLAPACK=no
+	fi
+	AC_MSG_RESULT($HAVE_BLASLAPACK)
+	dnl }}}
+	dnl mkl{{{
+	AC_ARG_WITH([mkl-dir],
+	  AS_HELP_STRING([--with-mkl-dir=DIR],[mkl root directory]),
+	  [MKL_ROOT=$withval],[MKL_ROOT=""])
+			  
+	AC_MSG_CHECKING(for mkl headers and libraries in $MKL_ROOT)
+	if test -d "$MKL_ROOT"; then
+
+		dnl defaults
+		HAVE_MKL=yes
+		MKLINCL=""
+		MKLLIB=-L"$MKL_ROOT -lmkl -lmkl_lapack -lmkl_scalapack_ilp64   -lmkl_blacs_sgimpt_ilp64 -lguide  -lpthread"
+		AC_DEFINE([_HAVE_MKL_],[1],[with mkl in ISSM src])
+		AC_SUBST([MKLLIB])
+		AC_SUBST([MKLINCL])
+	else
+		HAVE_MKL=no
+	fi
+	AC_MSG_RESULT($HAVE_MKL)
+	dnl }}}
+	dnl plapack{{{
+	AC_MSG_CHECKING(for plapack)
+	
+	AC_ARG_WITH([plapack-lib],
+	  AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]),
+	  [PLAPACK_LIB=$withval],[PLAPACK_LIB=""])
+	
+	AC_ARG_WITH([plapack-include],
+			  AS_HELP_STRING([--with-plapack-include = include],
+							 [plapack include ]),
+			  [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""])
+	  
+	if test -n "$PLAPACK_LIB"; then
+		if test -n "$PLAPACK_INCLUDE"; then
+		
+			dnl defaults
+			HAVE_PLAPACK=yes
+			PLAPACKINCL="$PLAPACK_INCLUDE"
+			PLAPACKLIB="$PLAPACK_LIB"
+
+			AC_DEFINE([_HAVE_PLAPACK_],[1],[with Plapack in ISSM src])
+			AC_SUBST([PLAPACKINCL])
+			AC_SUBST([PLAPACKLIB])
+		else
+			HAVE_PLAPACK=no
+		fi
+	else
+		HAVE_PLAPACK=no
+	fi
+	AC_MSG_RESULT($HAVE_PLAPACK)
+	dnl }}}
+	dnl mumps{{{
+	AC_ARG_WITH([mumps-dir],
+	  AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]),
+	  [MUMPS_ROOT=$withval],[MUMPS_ROOT=""])
+			  
+	AC_MSG_CHECKING(for mumps headers and libraries in $MUMPS_ROOT)
+	if test -d "$MUMPS_ROOT"; then
+
+		dnl defaults
+		HAVE_MUMPS=yes
+		MUMPSINCL=-I"$MUMPS_ROOT/include"
+		if test "$PETSC_MAJOR" = "2" ; then
+		MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lpord "
+		else
+		dnl MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis -lzmumps"
+		MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis"
+		fi
+
+		AC_DEFINE([_HAVE_MUMPS_],[1],[with Mumps in ISSM src])
+		AC_SUBST([MUMPSINCL])
+		AC_SUBST([MUMPSLIB])
+	else
+		HAVE_MUMPS=no
+	fi
+	AC_MSG_RESULT($HAVE_MUMPS)
+	dnl }}}
+	dnl blacs{{{
+	AC_ARG_WITH([blacs-dir],
+		AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]),
+			  [BLACS_ROOT=$withval],[BLACS_ROOT=""])
+			  
+	AC_MSG_CHECKING(for blacs headers and libraries in $BLACS_ROOT)
+	if test -d "$BLACS_ROOT"; then
+
+		dnl defaults
+		HAVE_BLACS=yes
+		BLACSINCL=""
+		if test x$VENDOR = xintel-discover; then
+		 BLACSLIB=-L"$BLACS_ROOT/ -lmkl_blacs_intelmpi_lp64"
+		else
+		 BLACSLIB=-L"$BLACS_ROOT/ -lblacs"
+		fi
+        
+		AC_DEFINE([_HAVE_BLACS_],[1],[with Blacs in ISSM src])
+		AC_SUBST([BLACSINCL])
+		AC_SUBST([BLACSLIB])
+	else
+		HAVE_BLACS=no
+	fi
+	AC_MSG_RESULT($HAVE_BLACS)
+	dnl }}}
+	dnl hypre{{{
+	AC_ARG_WITH([hypre-dir],
+	  AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]),
+			  [HYPRE_ROOT=$withval],[HYPRE_ROOT=""])
+			  
+	AC_MSG_CHECKING(for hypre headers and libraries in $HYPRE_ROOT)
+	if test -d "$HYPRE_ROOT"; then
+
+		dnl defaults
+		HAVE_HYPRE=yes
+		HYPREINCL=""
+		HYPRELIB=-L"$HYPRE_ROOT/lib -lHYPRE"
+        
+		AC_DEFINE([_HAVE_HYPRE_],[1],[with Blacs in ISSM src])
+		AC_SUBST([HYPREINCL])
+		AC_SUBST([HYPRELIB])
+	else
+		HAVE_HYPRE=no
+	fi
+	AC_MSG_RESULT($HAVE_HYPRE)
+	dnl }}}
+	dnl prometheus{{{
+		AC_ARG_WITH([prometheus-dir],
+					AS_HELP_STRING([--with-prometheus-dir=DIR],[prometheus root directory]),
+					[PROMETHEUS_ROOT=$withval],[PROMETHEUS_ROOT=""])
+
+		  AC_MSG_CHECKING(for prometheus headers and libraries in $PROMETHEUS_ROOT)
+		  if test -d "$PROMETHEUS_ROOT"; then
+
+			dnl defaults
+			  HAVE_PROMETHEUS=yes
+			  PROMETHEUSINCL=-I"$PROMETHEUS_ROOT/include"
+			  PROMETHEUSLIB=-L"$PROMETHEUS_ROOT/lib -lpromfei -lprometheus -lparmetis"
+
+			  AC_DEFINE([_HAVE_PROMETHEUS_],[1],[with Prometheus in ISSM src])
+			  AC_SUBST([PROMETHEUSINCL])
+			  AC_SUBST([PROMETHEUSLIB])
+		  else
+				HAVE_PROMETHEUS=no
+			fi
+			AC_MSG_RESULT($HAVE_PROMETHEUS)
+		dnl }}}
+dnl spai{{{
+	AC_ARG_WITH([spai-dir],
+				AS_HELP_STRING([--with-spai-dir=DIR],[spai root directory]),
+				[SPAI_ROOT=$withval],[SPAI_ROOT=""])
+
+	  AC_MSG_CHECKING(for spai headers and libraries in $SPAI_ROOT)
+	  if test -d "$SPAI_ROOT"; then
+
+		dnl defaults
+		  HAVE_SPAI=yes
+		  SPAIINCL=-I"$SPAI_ROOT/include"
+		  SPAILIB=-L"$SPAI_ROOT/lib -lspai"
+
+		  AC_DEFINE([_HAVE_SPAI_],[1],[with Spai in ISSM src])
+		  AC_SUBST([SPAIINCL])
+		  AC_SUBST([SPAILIB])
+	  else
+		HAVE_SPAI=no
+		  fi
+		  AC_MSG_RESULT($HAVE_SPAI)
+		  dnl }}}
+dnl superlu{{{ 
+	AC_ARG_WITH([superlu-dir],
+				AS_HELP_STRING([--with-superlu-dir=DIR],[superlu root directory]),
+				[SUPERLU_ROOT=$withval],[SUPERLU_ROOT=""])
+
+	  AC_MSG_CHECKING(for superlu headers and libraries in $SUPERLU_ROOT)
+	  if test -d "$SUPERLU_ROOT"; then
+
+		dnl defaults
+		  HAVE_SUPERLU=yes
+		  SUPERLUINCL=-I"$SUPERLU_ROOT/include"
+		  SUPERLULIB=-L"$SUPERLU_ROOT/lib -lsuperlu_4.3"
+
+		  AC_DEFINE([_HAVE_SUPERLU_],[1],[with Superlu in ISSM src])
+		  AC_SUBST([SUPERLUINCL])
+		  AC_SUBST([SUPERLULIB])
+	  else
+		HAVE_SUPERLU=no
+		  fi
+		  AC_MSG_RESULT($HAVE_SUPERLU)
+		  dnl }}}
+dnl spooles{{{ 
+	AC_ARG_WITH([spooles-dir],
+				AS_HELP_STRING([--with-spooles-dir=DIR],[spooles root directory]),
+				[SPOOLES_ROOT=$withval],[SPOOLES_ROOT=""])
+
+	  AC_MSG_CHECKING(for spooles headers and libraries in $SPOOLES_ROOT)
+	  if test -d "$SPOOLES_ROOT"; then
+
+		dnl defaults
+		  HAVE_SPOOLES=yes
+		  SPOOLESINCL=-I"$SPOOLES_ROOT/include"
+		  SPOOLESLIB=-L"$SPOOLES_ROOT/lib -lspooles"
+
+		  AC_DEFINE([_HAVE_SPOOLES_],[1],[with Spooles in ISSM src])
+		  AC_SUBST([SPOOLESINCL])
+		  AC_SUBST([SPOOLESLIB])
+	  else
+		HAVE_SPOOLES=no
+		  fi
+		  AC_MSG_RESULT($HAVE_SPOOLES)
+		  dnl }}}
+dnl pastix{{{ 
+	AC_ARG_WITH([pastix-dir],
+				AS_HELP_STRING([--with-pastix-dir=DIR],[pastix root directory]),
+				[PASTIX_ROOT=$withval],[PASTIX_ROOT=""])
+
+	  AC_MSG_CHECKING(for pastix headers and libraries in $PASTIX_ROOT)
+	  if test -d "$PASTIX_ROOT"; then
+
+		dnl defaults
+		  HAVE_PASTIX=yes
+		  PASTIXINCL=-I"$PASTIX_ROOT/include"
+		  PASTIXLIB=-L"$PASTIX_ROOT/lib -lpastix_XXbit_mpi_smp_nobubble_int32_simple_real_scotch_i686_pc_linux -lptscotch -lptscotcherr -lpastix"
+
+		  AC_DEFINE([_HAVE_PASTIX_],[1],[with Pastix in ISSM src])
+		  AC_SUBST([PASTIXINCL])
+		  AC_SUBST([PASTIXLIB])
+	  else
+		HAVE_PASTIX=no
+		  fi
+		  AC_MSG_RESULT($HAVE_PASTIX)
+		  dnl }}}
+	dnl ml{{{
+	AC_ARG_WITH([ml-dir],
+	  AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]),
+			  [ML_ROOT=$withval],[ML_ROOT=""])
+			  
+	AC_MSG_CHECKING(for ml headers and libraries in $ML_ROOT)
+	if test -d "$ML_ROOT"; then
+
+		dnl defaults
+		HAVE_ML=yes
+		MLINCL=-I"$ML_ROOT/include"
+		MLLIB=-L"$ML_ROOT/lib -lml"
+        
+		AC_DEFINE([_HAVE_ML_],[1],[with Blacs in ISSM src])
+		AC_SUBST([MLINCL])
+		AC_SUBST([MLLIB])
+	else
+		HAVE_ML=no
+	fi
+	AC_MSG_RESULT($HAVE_ML)
+	dnl }}}
+	dnl umfpack{{{
+		AC_ARG_WITH([umfpack-dir],
+		  AS_HELP_STRING([--with-umfpack-dir=DIR],[UMFPACK root directory]),
+					[UMFPACK_ROOT=$withval],[UMFPACK_ROOT=""])
+
+		AC_MSG_CHECKING(for UMFPACK headers and libraries in $UMFPACK_ROOT)
+		if test -d "$UMFPACK_ROOT"; then
+
+			dnl defaults
+			HAVE_UMFPACK=yes
+			UMFPACKINCL=""
+			UMFPACKLIB=-L"$UMFPACK_ROOT/lib -lumfpack -lumfpack.5.5.1"
+
+			AC_DEFINE([_HAVE_UMFPACK_],[1],[with UMFPACK in ISSM src])
+			AC_SUBST([UMFPACKINCL])
+			AC_SUBST([UMFPACKLIB])
+		else
+			HAVE_UMFPACK=no
+		fi
+		AC_MSG_RESULT($HAVE_UMFPACK)
+	dnl }}}
+dnl math{{{
+	AC_MSG_CHECKING(for math library)
+	AC_ARG_WITH([math-lib],
+	  AS_HELP_STRING([--with-math-lib = otions],[math options, for ex: "/usr/lib/libm.a]),
+	  [MATH_LIB=$withval],[MATH_LIB=""])
+
+	dnl check that --with-math-lib may have been provided
+	if test -n "$MATH_LIB" ; then
+		HAVE_MATH=yes
+		MATHLIB="$MATH_LIB"
+
+		AC_DEFINE([_HAVE_MATH_],[1],[with MATH in ISSM src])
+		AC_SUBST([MATHLIB])
+	fi
+	AC_MSG_RESULT(done)
+	dnl }}}
+	dnl fortran{{{
+	AC_ARG_WITH([fortran],
+		AS_HELP_STRING([--with-fortran = YES], [do we compile fortran code (default is yes)]),
+		[FORTRAN=$withval],[FORTRAN=yes]) 
+	AC_MSG_CHECKING(for fortran compilation)
+	if test "x$FORTRAN" = "xyes"; then
+		dnl defaults
+		HAVE_FORTRAN=yes
+
+		AC_DEFINE([_HAVE_FORTRAN_],[1],[with fortran capability])
+	else
+		HAVE_FORTRAN=no
+	fi
+	AM_CONDITIONAL([FORTRAN], [test x$FORTRAN = xyes])
+	AC_MSG_RESULT($FORTRAN)
+
+	if test "x$FORTRAN" = "xyes"; then
+		dnl fortran library  option
+		AC_MSG_CHECKING(for fortran library)
+		AC_ARG_WITH([fortran-lib],
+		  AS_HELP_STRING([--with-fortran-lib = options],[fortran options, for ex: "/usr/lib/gfortran.a]),
+			[FORTRAN_LIB=$withval],[FORTRAN_LIB=""])
+
+		dnl check that --with-fortran-lib may have been provided
+		if test -n "$FORTRAN_LIB" ; then
+			dnl check that library provided EXISTS!
+		   FORTRAN_DIR=$(echo $FORTRAN_LIB | sed -e "s/-L//g" | awk '{print $[1]}')
+			if test -d "$FORTRAN_DIR" || test -f "$FORTRAN_DIR"; then
+				FORTRANLIB="$FORTRAN_LIB"
+				AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src])
+				AC_SUBST([FORTRANLIB])
+			else
+			 if test "x$HAVE_MPI" = "xyes"; then
+				FORTRANLIB=$(mpif77 -print-file-name="libgfortran.a")
+				if test -f "$FORTRANLIB"; then
+					 AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist, MPI suggests the following library: $FORTRANLIB]);
+				fi
+			 fi
+				AC_MSG_ERROR([frtran library provided ($FORTRAN_LIB$) does not exist!]);
+			fi
+		fi
+		AC_MSG_RESULT(done)
+	fi
+	dnl }}}
+	dnl graphics{{{
+	AC_MSG_CHECKING(for graphics library)
+	AC_ARG_WITH([graphics-lib],
+	  AS_HELP_STRING([--with-graphics-lib = options],[graphics options, for ex: "/usr/X11/lib/libX11.a]),
+	  [GRAPHICS_LIB=$withval],[GRAPHICS_LIB=""])
+
+	dnl check that --with-graphics-lib may have been provided
+	
+	if test -n "$GRAPHICS_LIB" ; then
+		dnl check that library provided EXISTS!
+		GRAPHICS_DIR=$(echo $GRAPHICS_LIB | sed -e "s/-L//g" | awk '{print $[1]}')
+		if test -d "$GRAPHICS_DIR" || test -f "$GRAPHICS_DIR"; then
+			HAVE_GRAPHICS=yes
+			GRAPHICSLIB="$GRAPHICS_LIB"
+			AC_DEFINE([_HAVE_GRAPHICS_],[1],[with GRAPHICS in ISSM src])
+			AC_SUBST([GRAPHICSLIB])
+		else
+			if test -f "$PETSC_ROOT/conf/petscvariables"; then
+				GRAPHICSLIB=$(cat $PETSC_ROOT/conf/petscvariables | grep X_LIB)
+				AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB) does not exist, PETSc suggests the following library: $GRAPHICSLIB]);
+			fi
+			AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB$) does not exist!]);
+		fi
+	fi
+	AC_MSG_RESULT(done)
+	dnl }}}
+
+	dnl Capabilities
+	dnl with-kml{{{
+	AC_ARG_WITH([kml],
+		AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is yes)]),
+		[KML=$withval],[KML=yes]) 
+	AC_MSG_CHECKING(for kml capability compilation)
+
+	if test "x$KML" = "xyes"; then
+		HAVE_KML=yes
+		AC_DEFINE([_HAVE_KML_],[1],[with kml capability])
+	else
+		HAVE_KML=no
+	fi
+	AM_CONDITIONAL([KML], [test x$HAVE_KML = xyes])
+	AC_MSG_RESULT($HAVE_KML)
+	dnl }}}
+	dnl with-kriging{{{
+	AC_ARG_WITH([kriging],
+		AS_HELP_STRING([--with-kriging = YES],[compile with kriging capabilities (default is yes)]),
+		[KRIGING=$withval],[KRIGING=yes]) 
+	AC_MSG_CHECKING(for kriging capability compilation)
+
+	if test "x$KRIGING" = "xyes"; then
+		HAVE_KRIGING=yes
+		AC_DEFINE([_HAVE_KRIGING_],[1],[with kriging capability])
+	else
+		HAVE_KRIGING=no
+	fi
+	AM_CONDITIONAL([KRIGING], [test x$HAVE_KRIGING = xyes])
+	AC_MSG_RESULT($HAVE_KRIGING)
+	dnl }}}
+	dnl with-steadystate{{{
+	AC_ARG_WITH([steadystate],
+		AS_HELP_STRING([--with-steadystate = YES],[compile with steadystate capabilities (default is yes)]),
+		[STEADYSTATE=$withval],[STEADYSTATE=yes]) 
+	AC_MSG_CHECKING(for steadystate capability compilation)
+
+	if test "x$STEADYSTATE" = "xyes"; then
+
+		dnl defaults
+		HAVE_STEADYSTATE=yes
+
+		AC_DEFINE([_HAVE_STEADYSTATE_],[1],[with steadystate capability])
+	else
+		HAVE_STEADYSTATE=no
+	fi
+	AM_CONDITIONAL([STEADYSTATE], [test x$HAVE_STEADYSTATE = xyes])
+	AC_MSG_RESULT($HAVE_STEADYSTATE)
+	dnl }}}
+	dnl with-transient{{{
+	AC_ARG_WITH([transient],
+		AS_HELP_STRING([--with-transient = YES], [compile with transient capabilities (default is yes)]),
+		[TRANSIENT=$withval],[TRANSIENT=yes]) 
+	AC_MSG_CHECKING(for transient capability compilation)
+
+	if test "x$TRANSIENT" = "xyes"; then
+
+		dnl defaults
+		HAVE_TRANSIENT=yes
+
+		AC_DEFINE([_HAVE_TRANSIENT_],[1],[with transient capability])
+	else
+		HAVE_TRANSIENT=no
+	fi
+	AM_CONDITIONAL([TRANSIENT], [test x$HAVE_TRANSIENT = xyes])
+	AC_MSG_RESULT($HAVE_TRANSIENT)
+	dnl }}}
+	dnl with-thermal{{{
+	AC_ARG_WITH([thermal],
+		AS_HELP_STRING([--with-thermal = YES], [compile with thermal capabilities (default is yes)]),
+		[THERMAL=$withval],[THERMAL=yes]) 
+	AC_MSG_CHECKING(for thermal capability compilation)
+
+	if test "x$THERMAL" = "xyes"; then
+
+		dnl defaults
+		HAVE_THERMAL=yes
+
+		AC_DEFINE([_HAVE_THERMAL_],[1],[with thermal capability])
+	else
+		HAVE_THERMAL=no
+	fi
+	AM_CONDITIONAL([THERMAL], [test x$HAVE_THERMAL = xyes])
+	AC_MSG_RESULT($HAVE_THERMAL)
+	dnl }}}
+	dnl with-prognostic{{{
+	AC_ARG_WITH([prognostic],
+		AS_HELP_STRING([--with-prognostic = YES], [compile with prognostic capabilities (default is yes)]),
+		[PROGNOSTIC=$withval],[PROGNOSTIC=yes]) 
+	AC_MSG_CHECKING(for prognostic capability compilation)
+
+	if test "x$PROGNOSTIC" = "xyes"; then
+
+		dnl defaults
+		HAVE_PROGNOSTIC=yes
+
+		AC_DEFINE([_HAVE_PROGNOSTIC_],[1],[with prognostic capability])
+	else
+		HAVE_PROGNOSTIC=no
+	fi
+	AM_CONDITIONAL([PROGNOSTIC], [test x$HAVE_PROGNOSTIC = xyes])
+	AC_MSG_RESULT($HAVE_PROGNOSTIC)
+	dnl }}}
+	dnl with-control{{{
+	AC_ARG_WITH([control],
+		AS_HELP_STRING([--with-control = YES], [compile with control capabilities (default is yes)]),
+		[CONTROL=$withval],[CONTROL=yes]) 
+	AC_MSG_CHECKING(for control capability compilation)
+
+	if test "x$CONTROL" = "xyes"; then
+
+		dnl defaults
+		HAVE_CONTROL=yes
+
+		AC_DEFINE([_HAVE_CONTROL_],[1],[with control capability])
+	else
+		HAVE_CONTROL=no
+	fi
+	AM_CONDITIONAL([CONTROL], [test x$HAVE_CONTROL = xyes])
+	AC_MSG_RESULT($HAVE_CONTROL)
+	dnl }}}
+	dnl with-hydrology{{{
+	AC_ARG_WITH([hydrology],
+		AS_HELP_STRING([--with-hydrology = YES], [compile with hydrology capabilities (default is yes)]),
+		[HYDROLOGY=$withval],[HYDROLOGY=yes]) 
+	AC_MSG_CHECKING(for hydrology capability compilation)
+
+	if test "x$HYDROLOGY" = "xyes"; then
+
+		dnl defaults
+		HAVE_HYDROLOGY=yes
+
+		AC_DEFINE([_HAVE_HYDROLOGY_],[1],[with hydrology capability])
+	else
+		HAVE_HYDROLOGY=no
+	fi
+	AM_CONDITIONAL([HYDROLOGY], [test x$HAVE_HYDROLOGY = xyes])
+	AC_MSG_RESULT($HAVE_HYDROLOGY)
+	dnl }}}
+	dnl with-diagnostic{{{
+	AC_ARG_WITH([diagnostic],
+		AS_HELP_STRING([--with-diagnostic = YES], [compile with diagnostic capabilities (default is yes)]),
+		[DIAGNOSTIC=$withval],[DIAGNOSTIC=yes]) 
+	AC_MSG_CHECKING(for diagnostic capability compilation)
+
+	if test "x$DIAGNOSTIC" = "xyes"; then
+
+		dnl defaults
+		HAVE_DIAGNOSTIC=yes
+
+		AC_DEFINE([_HAVE_DIAGNOSTIC_],[1],[with diagnostic capability])
+	else
+		HAVE_DIAGNOSTIC=no
+	fi
+	AM_CONDITIONAL([DIAGNOSTIC], [test x$HAVE_DIAGNOSTIC = xyes])
+	AC_MSG_RESULT($HAVE_DIAGNOSTIC)
+	dnl }}}
+	dnl with-balanced{{{
+	AC_ARG_WITH([balanced],
+		AS_HELP_STRING([--with-balanced = YES], [compile with balanced capabilities (default is yes)]),
+		[BALANCED=$withval],[BALANCED=yes]) 
+	AC_MSG_CHECKING(for balanced capability compilation)
+
+	if test "x$BALANCED" = "xyes"; then
+
+		dnl defaults
+		HAVE_BALANCED=yes
+
+		AC_DEFINE([_HAVE_BALANCED_],[1],[with balanced capability])
+	else
+		HAVE_BALANCED=no
+	fi
+	AM_CONDITIONAL([BALANCED], [test x$HAVE_BALANCED = xyes])
+	AC_MSG_RESULT($HAVE_BALANCED)
+	dnl }}}
+	dnl with-responses{{{
+	AC_ARG_WITH([responses],
+		AS_HELP_STRING([--with-responses = YES], [compile with responses capabilities (default is yes)]),
+		[RESPONSES=$withval],[RESPONSES=yes]) 
+	AC_MSG_CHECKING(for responses capability compilation)
+
+	if test "x$RESPONSES" = "xyes"; then
+
+		dnl defaults
+		HAVE_RESPONSES=yes
+
+		AC_DEFINE([_HAVE_RESPONSES_],[1],[with responses capability])
+	else
+		HAVE_RESPONSES=no
+	fi
+	AM_CONDITIONAL([RESPONSES], [test x$HAVE_RESPONSES = xyes])
+	AC_MSG_RESULT($HAVE_RESPONSES)
+	dnl }}}
+	dnl with-slope{{{
+	AC_ARG_WITH([slope],
+		AS_HELP_STRING([--with-slope = YES], [compile with slope capabilities (default is yes)]),
+		[SLOPE=$withval],[SLOPE=yes]) 
+	AC_MSG_CHECKING(for slope capability compilation)
+
+	if test "x$SLOPE" = "xyes"; then
+
+		dnl defaults
+		HAVE_SLOPE=yes
+
+		AC_DEFINE([_HAVE_SLOPE_],[1],[with slope capability])
+	else
+		HAVE_SLOPE=no
+	fi
+	AM_CONDITIONAL([SLOPE], [test x$HAVE_SLOPE = xyes])
+	AC_MSG_RESULT($HAVE_SLOPE)
+	dnl }}}
+	dnl with-groundingline{{{
+	AC_ARG_WITH([groundingline],
+		AS_HELP_STRING([--with-groundingline = YES], [compile with groundingline capabilities (default is yes)]),
+		[GROUNDINGLINE=$withval],[GROUNDINGLINE=yes]) 
+	AC_MSG_CHECKING(for groundingline capability compilation)
+
+	if test "x$GROUNDINGLINE" = "xyes"; then
+
+		dnl defaults
+		HAVE_GROUNDINGLINE=yes
+
+		AC_DEFINE([_HAVE_GROUNDINGLINE_],[1],[with groundingline capability])
+	else
+		HAVE_GROUNDINGLINE=no
+	fi
+	AM_CONDITIONAL([GROUNDINGLINE], [test x$HAVE_GROUNDINGLINE = xyes])
+	AC_MSG_RESULT($HAVE_GROUNDINGLINE)
+	dnl }}}
+	dnl with-rifts{{{
+	AC_ARG_WITH([rifts],
+		AS_HELP_STRING([--with-rifts = YES], [compile with rifts capabilities (default is yes)]),
+		[RIFTS=$withval],[RIFTS=yes]) 
+	AC_MSG_CHECKING(for rifts capability compilation)
+
+	if test "x$RIFTS" = "xyes"; then
+
+		dnl defaults
+		HAVE_RIFTS=yes
+
+		AC_DEFINE([_HAVE_RIFTS_],[1],[with rifts capability])
+	else
+		HAVE_RIFTS=no
+	fi
+	AM_CONDITIONAL([RIFTS], [test x$HAVE_RIFTS = xyes])
+	AC_MSG_RESULT($HAVE_RIFTS)
+	dnl }}}
+	dnl with-ios{{{
+	AC_ARG_WITH([ios],
+		AS_HELP_STRING([--with-ios = YES], [compile with iOS capabilities (default is no, alternatives are yes)]),
+		[IOS=$withval],[IOS=no]) 
+	AC_MSG_CHECKING(for iOS compilation)
+
+	if test "x$IOS" = "xyes"; then
+		dnl defaults
+		HAVE_IOS=yes
+
+		AC_DEFINE([_HAVE_IOS_],[1],[with android capability])
+	elif test "x$IOS" = "xno"; then
+		HAVE_IOS=no
+	else
+	  AC_MSG_ERROR([--with-ios should be either no or yes])
+	fi
+	AM_CONDITIONAL([IOS], [test x$HAVE_IOS != xno])
+	AC_DEFINE([_HAVE_IOS_],[1],[with ios.])
+	AC_MSG_RESULT($HAVE_IOS)
+	dnl }}}
+	dnl with-android{{{
+	AC_ARG_WITH([android],
+		AS_HELP_STRING([--with-android = EXE], [compile with android capabilities (default is no, alternatives are exe and jni)]),
+		[ANDROID=$withval],[ANDROID=no]) 
+	AC_MSG_CHECKING(for android capability compilation)
+
+	if test "x$ANDROID" = "xjni"; then
+
+		dnl defaults
+		HAVE_ANDROID=jni
+		AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability])
+		AC_DEFINE([_HAVE_ANDROID_JNI_],[1],[with android jni])
+	elif test "x$ANDROID" = "xexe"; then
+		dnl defaults
+		HAVE_ANDROID=exe
+
+		AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability])
+	elif test "x$ANDROID" = "xno"; then
+		HAVE_ANDROID=no
+	else
+	  AC_MSG_ERROR([--with-android should be either no, exe or jni])
+	fi
+	AM_CONDITIONAL([ANDROID], [test x$HAVE_ANDROID != xno])
+	AM_CONDITIONAL([ANDROIDJNI], [test x$HAVE_ANDROID = xjni])
+	AM_CONDITIONAL([ANDROIDEXE], [test x$HAVE_ANDROID = xexe])
+	AC_DEFINE([_HAVE_ANDROID_],[1],[with android.])
+	AC_MSG_RESULT($HAVE_ANDROID)
+	dnl }}}
+	dnl with-android-ndk{{{
+	AC_ARG_WITH([android-ndk],
+	  AS_HELP_STRING([--with-android-ndk=DIR], [android-ndk root directory.]),
+	  [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) 
+	AC_MSG_CHECKING(with android ndk)
+	
+	if test -d "$ANDROID_NDK_ROOT"; then
+		dnl defaults
+		HAVE_ANDROID_NDK=yes
+		ANDROID_NDKINCL="-I$ANDROID_NDK_ROOT/arm-linux-android-install/sysroot/usr/include"
+
+		AC_DEFINE([_HAVE_ANDROID_NDK_],[1],[with android ndk in ISSM src])
+		AC_SUBST([ANDROID_NDKINCL])
+	else
+		HAVE_ANDROID_NDK=no
+	fi
+	AC_MSG_RESULT($HAVE_ANDROID_NDK)
+	dnl }}}
+	dnl with-3d{{{
+	AC_ARG_WITH([3d],
+		AS_HELP_STRING([--with-3d = YES], [compile with 3d capabilities (default is yes)]),
+		[THREED=$withval],[THREED=yes]) 
+	AC_MSG_CHECKING(for 3d capability compilation)
+
+	if test "x$THREED" = "xyes"; then
+
+		dnl defaults
+		HAVE_3D=yes
+
+		AC_DEFINE([_HAVE_3D_],[1],[with 3d capability])
+	else
+		HAVE_3D=no
+	fi
+	AM_CONDITIONAL([THREED], [test x$HAVE_3D = xyes])
+	AC_MSG_RESULT($HAVE_3D)
+	dnl }}}
+	dnl checks{{{
+	AC_MSG_CHECKING(consistency between all libraries)
+	
+	dnl check that if petsc is requested , mpi should be specified
+	if test "$HAVE_PETSC" = "yes" ; then
+		if test "$HAVE_MPI" = "NO";  then
+			AC_MSG_ERROR([petsc requires mpi!]);
+		fi
+	fi
+
+	dnl check that we have either python or matlab support if we compile the modules
+	if test "$MODULES_VALUE" = "yes"  && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then
+		AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]);
+	fi
+
+	dnl check that if we have MPI, we have metis
+	if test "$HAVE_METIS" = "yes"  && test "$HAVE_MPI" = "no" ; then
+	AC_MSG_ERROR([need mpi if using the metis partitioner!]);
+	fi
+
+	AC_MSG_RESULT(done)
+	dnl }}}
+
+	dnl other options
+	dnl optimization{{{
+	dnl bypass standard optimization -g -O2 ? 
+	AC_ARG_WITH([cxxoptflags],
+	  AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]),
+	  [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2"]) 
+	AC_MSG_CHECKING(for c++ optimization flags)
+	AC_SUBST([CXXOPTFLAGS])
+	AC_MSG_RESULT(done)
+
+	dnl }}}
+	dnl multithreading{{{
+	AC_ARG_WITH([numthreads],
+	  AS_HELP_STRING([--with-numthreads = NUMTHREADS_VALUE],[numthreads, default is 1. ]),
+	  [NUMTHREADS_VALUE=$withval],[NUMTHREADS_VALUE=1])
+	AC_MSG_CHECKING(for number of threads)
+	dnl defaults
+	MULTITHREADING=no
+	MULTITHREADINLIB=""
+	if test "$NUMTHREADS_VALUE" != "1"; then
+		
+		MULTITHREADINGLIB="-lpthread -lrt"
+		case "${host_os}" in
+		*cygwin*)
+		MULTITHREADINGLIB="-lpthread -lrt"
+		;;
+		*linux*)
+		MULTITHREADINGLIB="-lpthread -lrt"
+		;;
+		*darwin*)
+		MULTITHREADINGLIB="-lpthread"
+		;;
+		esac
+
+		AC_DEFINE([_MULTITHREADING_],[1],[with numthreads enabled])
+		AC_DEFINE_UNQUOTED([_NUMTHREADS_],[$NUMTHREADS_VALUE],[number of threads])
+	fi
+	AC_SUBST([MULTITHREADINGLIB])
+	AC_MSG_RESULT($NUMTHREADS_VALUE) 
+	dnl }}}
+	dnl 64bit {{{
+	AC_ARG_WITH([64bit-indices],
+	  AS_HELP_STRING([--with-64bit-indices = bool], [use 64 bit integers, default 0, ex: --with-64bit-indices=1]),
+	  [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) 
+	AC_MSG_CHECKING(for 64 bit indices)
+
+	if test "$USE_64BIT_INDICES" == "1"; then
+	AC_DEFINE([ISSM_USE_64BIT_INDICES],[1],[with 64 bits indices])
+	else
+	AC_DEFINE([ISSM_USE_64BIT_INDICES],[0],[with 64 bits indices])
+	fi
+	AC_MSG_RESULT($USE_64BIT_INDICES)
+	dnl }}}
+])