Index: sm/trunk-jpl/patches/Makefile.am-C.patch
===================================================================
--- /issm/trunk-jpl/patches/Makefile.am-C.patch	(revision 15084)
+++ 	(revision )
@@ -1,46 +1,0 @@
---- 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 = $(libISSMModules_a_SOURCES)
- endif
- endif
- 
Index: sm/trunk-jpl/patches/Makefile.am-MATLAB.patch
===================================================================
--- /issm/trunk-jpl/patches/Makefile.am-MATLAB.patch	(revision 15084)
+++ 	(revision )
@@ -1,376 +1,0 @@
---- Makefile.am	2013-05-21 19:46:05.478487700 -0700
-+++ Makefile.am.bak	2013-05-21 17:56:31.044451600 -0700
-@@ -1,13 +1,50 @@
--AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@
-+AM_CPPFLAGS = @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ /DTRILIBRARY /DANSI_DECLARATORS /DNO_TIMER /D_WRAPPERS_ /D_HAVE_MATLAB_MODULES_  /D_GNU_SOURCE
- 
- EXEEXT=$(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) $(PETSCLIB)
- #}}}
Index: sm/trunk-jpl/patches/issm_options.m4.bak
===================================================================
--- /issm/trunk-jpl/patches/issm_options.m4.bak	(revision 15084)
+++ 	(revision )
@@ -1,1577 +1,0 @@
-dnl ISSM Options
-
-AC_DEFUN([ISSM_OPTIONS],[
-
-	dnl ISSM's internal options
-	dnl Debugging {{{
-	AC_ARG_ENABLE([debugging],                                        dnl feature
-		AS_HELP_STRING([--enable-debugging],[turn debug support on]),  dnl help string
-		[enable_debugging=$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 }}}
-])