Index: /issm/trunk-jpl/m4/issm_options.m4
===================================================================
--- /issm/trunk-jpl/m4/issm_options.m4	(revision 28004)
+++ /issm/trunk-jpl/m4/issm_options.m4	(revision 28005)
@@ -394,21 +394,4 @@
 		dnl
 		case "${host_os}" in
-			*cygwin*)
-				if test "${VENDOR}" == "intel-win7-32"; then
-					MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-					MEXLINKFLAGS="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
-					MEXEXT=`${MATLAB_ROOT}/bin/mexext.bat`
-					MEXEXT=".${MEXEXT}"
-				elif test "${VENDOR}" == "intel-win7-64"; then
-					MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-					MEXLINKFLAGS="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
-					MEXEXT=".mexw64"
-				elif test "${VENDOR}" == "MSVC-Win64" || test "${VENDOR}" == "MSVC-Win64-par"; then
-					MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-					MEXLINKFLAGS="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
-					MATLABINCL="-I`cygpath -m ${MATLAB_ROOT}/extern/include`"
-					MEXEXT=".mexw64"
-				fi
-			;;
 			*mingw*)
 				if test "${IS_MSYS2}" == "yes"; then
@@ -423,15 +406,4 @@
 					MEXLIB="-L${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas"
 				fi
-			;;
-			*msys*)
-				dnl Value to set MEXEXT to can be found on Windows by running $MATLAB_ROOT/bin/mexext.bat
-				MEXEXT=".mexw64"
-				MATLABINCL="-I${MATLAB_ROOT}/extern/include"
-				MEXOPTFLAGS="-O2 -fwrapv -DNDEBUG -g"
-				MEXCFLAGS="-fexceptions -fno-omit-frame-pointer -m64 -DMATLAB_MEX_FILE"
-				MEXCXXFLAGS="-fexceptions -fno-omit-frame-pointer -std=c++11 -m64 -DMATLAB_MEX_FILE"
-				MEXLINKFLAGS="-m64 -Wl,--no-undefined -shared -static -Wl,${MATLAB_ROOT}/extern/lib/win64/mingw64/mexFunction.def"
-				MEXLIB_DIR="${MATLAB_ROOT}/extern/lib/win64/mingw64"
-				MEXLIB="-L${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas"
 			;;
 			*)
@@ -518,8 +490,4 @@
 		TRIANGLEINCL=-I${TRIANGLE_ROOT}/include
 		case "${host_os}" in
-			*cygwin*)
-				TRIANGLEINCL="/I`cygpath -m ${TRIANGLE_ROOT}/include`"
-				TRIANGLELIB="-Wl,`cygpath -m ${TRIANGLE_ROOT}/lib/libtriangle.lib`"
-			;;
 			*darwin*)
 				if test "x${HAVE_JAVASCRIPT}" == "xyes"; then
@@ -546,12 +514,4 @@
 				fi
 			;;
-			*msys*)
-				if test "x${HAVE_JAVASCRIPT}" == "xyes"; then
-					dnl Link to the object file, not the library
-					TRIANGLELIB=${TRIANGLE_ROOT}/share/triangle.o
-				else
-					TRIANGLELIB="-L${TRIANGLE_ROOT}/lib -ltriangle"
-				fi
-			;;
 		esac
 		AC_DEFINE([_HAVE_TRIANGLE_], [1], [with Triangle in ISSM src])
@@ -661,16 +621,4 @@
 		dnl
 		case "${host_os}" in
-			*cygwin*)
-				if test "${DAKOTA_VERSION}" == "5.1" || test "${DAKOTA_VERSION}" == "5.2"; then
-					DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_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"
-				elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
-					DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
-					DAKOTALIB="-L${DAKOTA_ROOT}/lib -L${BOOST_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -lscolib -ljega_fe -llhs -lpebbl -lcolin -linterfaces -llhs_mods -lmoga -loptpp -lsoga -lsurfpack -lutilib -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -l3po -lamplsolver -lcport -ldfftpack -leutils -lfsudace -lhopspack -ljega -lnidr -lpecos -lpsuade -ltinyxml -lutilities -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
-					AC_DEFINE([DISABLE_DAKOTA_CONFIG_H], [1], [enabling DAKOTA_CONFIG_H])
-					AC_DEFINE([DAKOTA_HAVE_MPI], [1], [enabling parallel MPI])
-				else
-					AC_MSG_ERROR([Dakota version not found or version (${DAKOTA_VERSION}) not supported!]);
-				fi
-			;;
 			*darwin*)
 				if test "${DAKOTA_VERSION}" == "5.1" || test "${DAKOTA_VERSION}" == "5.2"; then
@@ -854,7 +802,4 @@
 		PYWRAPPEREXT=.so
 		case "${host_os}" in
-			*cygwin*)
-				PYTHONLINK="-shared"
-			;;
 			*darwin*)
 				PYTHONLINK="-dynamiclib"
@@ -864,7 +809,4 @@
 			;;
 			*mingw*)
-				PYTHONLINK="-shared"
-			;;
-			*msys*)
 				PYTHONLINK="-shared"
 			;;
@@ -1120,7 +1062,4 @@
 	if test "x${HAVE_ATLAS}" == "xyes"; then
 		case "${host_os}" in
-			*cygwin*)
-				ATLASLIB="-L`cygpath -m ${ATLAS_ROOT}` -Wl,libatlas.lib  -Wl,libcblas.lib"
-			;;
 			*darwin*)
 				ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
@@ -1132,7 +1071,4 @@
 				ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
 			;;
-			*msys*)
-				ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
-			;;
 		esac
 		AC_DEFINE([_HAVE_ATLAS_], [1], [with ATLAS in ISSM src])
@@ -1299,7 +1235,4 @@
 	if test "x${HAVE_HDF5}" == "xyes"; then
 		case "${host_os}" in
-			*cygwin*)
-				HDF5LIB="-L`cygpath -m ${HDF5_ROOT}` -Wl,libhdf5.lib  -Wl,libhdf5_hl.lib"
-			;;
 			*darwin*)
 				HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
@@ -1309,7 +1242,4 @@
 			;;
 			*mingw*)
-				HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
-			;;
-			*msys*)
 				HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
 			;;
@@ -1383,12 +1313,4 @@
 
 		case "${host_os}" in
-			*cygwin*)
-				if test ${PETSC_MAJOR} -lt 3; then
-					PETSCLIB=-Wl,/LIBPATH:`cygpath -w ${PETSC_ROOT}/lib` -Wl,libpetscksp.lib  -Wl,libpetscdm.lib -Wl,libpetscmat.lib -Wl,libpetscvec.lib -Wl,libpetscsnes.lib  -Wl,libpetscts.lib -Wl,libmpiuni.lib -Wl,libpetsc.lib
-				else
-					PETSCLIB="/link -Wl,/LIBPATH:`cygpath -m ${PETSC_ROOT}/lib` -Wl,libpetsc.lib"
-					PETSCINCL="/I`cygpath -m ${PETSC_ROOT}/include`"
-				fi
-			;;
 			*darwin*)
 				if test ${PETSC_MAJOR} -lt 3; then
@@ -1420,7 +1342,4 @@
 				PETSCLIB="-Wl,-L${PETSC_ROOT}/lib -Wl,-lpetsc"
 			;;
-			*msys*)
-				PETSCLIB="${PETSC_ROOT}/lib -lpetsc"
-			;;
 		esac
 		AC_MSG_RESULT([done])
@@ -1557,8 +1476,4 @@
 			METISINCL="-I${METIS_ROOT}/Lib"
 			case "${host_os}" in
-				*cygwin*)
-					METISINCL="/I`cygpath -m ${METIS_ROOT}/Lib`"
-					METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${METIS_ROOT}` -Wl,libmetis.lib"
-				;;
 				*darwin*)
 					METISLIB="-L${METIS_ROOT} -lmetis"
@@ -1570,14 +1485,8 @@
 					METISLIB="-Wl,-L${METIS_ROOT}/lib -Wl,-lmetis"
 				;;
-				*msys*)
-					METISLIB="-L${METIS_ROOT} -lmetis"
-				;;
 			esac
 		elif test "x${METIS_VERSION}" == "x5"; then
 			METISINCL="-I${METIS_ROOT}/include"
 			case "${host_os}" in
-				*cygwin*)
-					METISLIB="-L${METIS_ROOT} libmetis.lib"
-				;;
 				*darwin*)
 					METISLIB="-L${METIS_ROOT}/lib -lmetis"
@@ -1589,7 +1498,4 @@
 					METISLIB="-Wl,-L${METIS_ROOT}/lib -Wl,-lmetis"
 				;;
-				*msys*)
-					METISLIB="-L${METIS_ROOT}/lib -lmetis"
-				;;
 			esac
 		else
@@ -1634,7 +1540,4 @@
 			PARMETISINCL="-I${PARMETIS_ROOT}/include"
 			case "${host_os}" in
-				*cygwin*)
-					PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
-				;;
 				*darwin*)
 					PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
@@ -1886,7 +1789,4 @@
 	if test "x${HAVE_BLASLAPACK}" == "xyes"; then
 		case "${host_os}" in
-			*cygwin*)
-				BLASLAPACKLIB="-L`cygpath -m ${BLASLAPACK_ROOT}` -Wl,libf2cblas.lib  -Wl,libf2clapack.lib"
-			;;
 			*darwin*)
 				BLASLAPACKLIB="-L${BLASLAPACK_ROOT}/lib"
@@ -1929,19 +1829,4 @@
 				fi
 			;;
-			*msys*)
-				if test -d "${BLASLAPACK_ROOT}"; then
-					if ls ${BLASLAPACK_ROOT}/lib/libopenblas.* 1> /dev/null 2>&1; then
-						BLASLAPACKLIB=" -lopenblas"
-					elif ls ${BLASLAPACK_ROOT}/lib/libf2clapack.* 1> /dev/null 2>&1; then
-						BLASLAPACKLIB=" -lf2clapack -lf2cblas"
-					elif ls ${BLASLAPACK_ROOT}/lib/libflapack.* 1> /dev/null 2>&1; then
-						BLASLAPACKLIB+=" -lflapack -lfblas"
-					else
-						BLASLAPACKLIB=" -llapack -lblas"
-					fi
-				else
-					BLASLAPACKLIB="-L${LAPACK_ROOT}/lib -llapack -L${BLAS_ROOT}/lib -lblas"
-				fi
-			;;
 		esac
 		AC_DEFINE([_HAVE_BLASLAPACK_], [1], [with BLAS/LAPACK in ISSM src])
@@ -2793,7 +2678,4 @@
 		MULTITHREADINGLIB="-lpthread -lrt"
 		case "${host_os}" in
-			*cygwin*)
-				MULTITHREADINGLIB="-lpthread -lrt"
-			;;
 			*darwin*)
 				MULTITHREADINGLIB="-lpthread"
@@ -2805,7 +2687,4 @@
 				MULTITHREADINGLIB=""
 			;;
-			*msys*)
-				MULTITHREADINGLIB=""
-			;;
 		esac
 		AC_DEFINE([_MULTITHREADING_], [1], [with multithreading enabled])