Changeset 26044

Timestamp:

03/08/21 16:32:33 (4 years ago)

Author:

jdquinn

Message:

CHG: Recommitting changes for Windows build (tested on macOS now)

Location:

issm/trunk-jpl

Files:

• jenkins/jenkins.sh (modified) (1 diff)
• m4/issm_options.m4 (modified) (141 diffs)
• src/c/Makefile.am (modified) (7 diffs)
• src/wrappers/matlab/Makefile.am (modified) (6 diffs)
• src/wrappers/python/Makefile.am (modified) (2 diffs)

issm/trunk-jpl/jenkins/jenkins.sh

@@ -12 +12 @@
 # - Investigate refactoring parsing of list of changed files
 ################################################################################
+
+# Override certain aliases
+alias grep=$(which grep)
 
 echo "Cleaning up execution directory"

issm/trunk-jpl/m4/issm_options.m4

@@ -31 +31 @@
                 PACKAGE_DATE="unknown"
         fi
-        AC_DEFINE_UNQUOTED(PACKAGE_BUILD_DATE, "$PACKAGE_DATE", [build date])
+        AC_DEFINE_UNQUOTED([PACKAGE_BUILD_DATE], "${PACKAGE_DATE}", [build date])
         AC_MSG_RESULT([${PACKAGE_DATE}])
 
@@ -46 +46 @@
                 fi
         fi
-        AC_DEFINE_UNQUOTED(USER_NAME, "$user_name", [user name])
+        AC_DEFINE_UNQUOTED([USER_NAME], "${user_name}", [user name])
         AC_MSG_RESULT([${user_name}])
 
@@ -55 +55 @@
                 linux-gnu* | lignux* )  host_os=linux ;;
         esac
-        AC_DEFINE_UNQUOTED(HOST_OS, "$host_os", [host full OS name and version])
+        AC_DEFINE_UNQUOTED([HOST_OS], "${host_os}", [host full OS name and version])
         AC_MSG_RESULT([${host_os}])
 
         AC_MSG_CHECKING([host cpu])
-        AC_DEFINE_UNQUOTED(HOST_CPU, "$host_cpu", [host CPU])
+        AC_DEFINE_UNQUOTED([HOST_CPU], "${host_cpu}", [host CPU])
         AC_MSG_RESULT([${host_cpu}])
 
         AC_MSG_CHECKING([vendor])
-        AC_DEFINE_UNQUOTED(HOST_VENDOR, "$host_vendor", [host vendor])
+        AC_DEFINE_UNQUOTED([HOST_VENDOR], "${host_vendor}", [host vendor])
         AC_MSG_RESULT([${host_vendor}])
 
@@ -73 +73 @@
                 linux-gnu* | lignux* )  host_os_name=linux ;;
         esac
-        AC_DEFINE_UNQUOTED(HOST_OS_NAME, "$host_os_name", [host OS name])
+        AC_DEFINE_UNQUOTED([HOST_OS_NAME], "${host_os_name}", [host OS name])
         AC_MSG_RESULT([${host_os_name}])
 
@@ -82 +82 @@
                 host_os_version=`(uname -r) 2>/dev/null` || host_os_version=unknown
         fi
-        AC_DEFINE_UNQUOTED(HOST_OS_VERSION, "$host_os_version", [host OS version])
+        AC_DEFINE_UNQUOTED([HOST_OS_VERSION], "${host_os_version}", [host OS version])
         AC_MSG_RESULT([${host_os_version}])
 
@@ -95 +95 @@
                 i?86 )  host_arch=i386 ;; # all x86 should show up as i386
         esac
-        AC_DEFINE_UNQUOTED(HOST_ARCH, "$host_arch", [host archictecture])
+        AC_DEFINE_UNQUOTED([HOST_ARCH], "${host_arch}", [host archictecture])
         AC_MSG_RESULT([${host_arch}])
 
@@ -219 +219 @@
                 AC_MSG_RESULT([no])
         fi
-        AC_DEFINE_UNQUOTED([_SYSTEM_HAS_FMEMOPEN_], $SYSTEM_FMEMOPEN, [does system copy of libc have fmemopen])
+        AC_DEFINE_UNQUOTED([_SYSTEM_HAS_FMEMOPEN_], ${SYSTEM_FMEMOPEN}, [does system copy of libc have fmemopen])
         AM_CONDITIONAL([SYSTEM_HAS_FMEMOPEN], [test "${SYSTEM_FMEMOPEN}" == "1"])
 
+        IS_MSYS2=no
         IS_WINDOWS=no
         AC_MSG_CHECKING([for vendor compilers])
@@ -318 +319 @@
                         export CFLAGS="-g -O3 -ipo -axAVX -ipo -no-inline-min-size -inline-max-size=345 -no-inline-max-total-size -no-inline-max-per-routine -no-inline-max-per-compile -restrict"
                         AC_DEFINE([_HAVE_RESTRICT_], [1], [with restrict buffers])
+                elif test "${VENDOR}" == "win-msys2"; then
+                        export LDFLAGS="${LDFLAGS} -no-undefined"
+                        export OSLIBS="-Wl,-L/mingw64/lib/gcc/x86_64-w64-mingw32/10.2.0 -Wl,-L/mingw64/x86_64-w64-mingw32/lib -Wl,-lstdc++ -Wl,-lgfortran -Wl,-lmingw32 -Wl,-lgcc_s -Wl,-lmoldname -Wl,-lmingwex -Wl,-lmsvcrt -Wl,-lm -Wl,-lpthread -Wl,-lshell32 -Wl,-luser32 -Wl,-lgdi32 -Wl,-luser32 -Wl,-ladvapi32 -Wl,-lkernel32 -Wl,-lquadmath -Wl,-lstdc++ -Wl,-lgcc"
+                        IS_MSYS2=yes
                 else
                         AC_MSG_ERROR([unknown compiler vendor!])
                 fi
         fi
+        dnl Set default standard for C++
+        if test "${CXXFLAGS}" == ""; then
+                export CXXFLAGS="-std=C++11"
+        fi
         AC_SUBST([OSLIBS])
         AC_MSG_RESULT([done])
 
-        AC_MSG_CHECKING([if this is a Windows build])
+        AC_MSG_CHECKING([if this is a MSVC (Windows) build])
         AM_CONDITIONAL([WINDOWS], [test "x${IS_WINDOWS}" == "xyes"])
         AC_MSG_RESULT([${IS_WINDOWS}])
+
+        AC_MSG_CHECKING([if this is a MSYS2 (Windows) build])
+        AM_CONDITIONAL([MSYS2], [test "x${IS_MSYS2}" == "xyes"])
+        AC_MSG_RESULT([${IS_MSYS2}])
+        AC_DEFINE([_IS_MSYS2_], [1], [is a MSYS2 (Windows) build])
         dnl }}}
         dnl MATLAB{{{
 
         dnl See if MATLAB has been provided
+        AC_MSG_CHECKING([for MATLAB])
         AC_ARG_WITH(
                 [matlab-dir],                                                                                                           dnl feature
@@ -338 +353 @@
                 [MATLAB_ROOT="no"]                                                                                                      dnl action if not given
         )
-        AC_MSG_CHECKING([for MATLAB])
         if test "x${MATLAB_ROOT}" == "xno"; then
                 HAVE_MATLAB=no
@@ -357 +371 @@
                 AC_DEFINE([_HAVE_MATLAB_], [1], [with MATLAB in ISSM src])
 
-                dnl Set MEXLIB, MEXLINK, and MEXEXT
+                dnl Set MEX* variable
                 AC_MSG_CHECKING([MATLAB's mex compilation flags])
 
@@ -367 +381 @@
                                 if test "${VENDOR}" == "intel-win7-32"; then
                                         MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-                                        MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
+                                        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"
-                                        MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
+                                        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"
-                                        MEXLINK="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
+                                        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
+                                        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"
+                                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${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas"
+                        ;;
                         *)
+                                MEXEXT=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
                                 MATLABINCL="-I${MATLAB_ROOT}/extern/include"
-                                MEXLINK=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDFLAGS | sed -e "s/         LDFLAGS            = //g")
+                                MEXLINKFLAGS=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDFLAGS | sed -e "s/         LDFLAGS            = //g")
                                 MEXLIB=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep CXXLIBS | sed -e "s/         CXXLIBS            = //g")
-                                MEXEXT=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
-                                dnl version 2014 and up
                                 if test -z "${MEXEXT}"; then
                                         echo "#include <mex.h>" > conftest.cpp
@@ -392 +429 @@
                                         ${MATLAB_ROOT}/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1
                                         rm -f conftest.cpp
-                                        MEXLINK=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g")
+                                        MEXLINKFLAGS=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g")
                                         MEXLIB=$(cat conftest.tmp | grep LINKLIBS | sed -e "s/LINKLIBS ://g")
                                         MEXEXT=$(cat conftest.tmp | grep LDEXT | sed -e "s/LDEXT ://g" | awk '{print $[1]}')
@@ -402 +439 @@
 
                                 dnl Make sure mexFunction.map is not in MEXLIB to avoid problems with global variables
-                                dnl MEXLINK=$(echo ${MEXLINK} | sed -e "s/,-expo.*mexFunction\\.map\"//g" | sed -e "s/-[[^ ]]*mexFunction\\.map//g")
-                                MEXLINK="" dnl We actually don't need MEXLINK????
+                                dnl MEXLINKFLAGS=$(echo ${MEXLINKFLAGS} | sed -e "s/,-expo.*mexFunction\\.map\"//g" | sed -e "s/-[[^ ]]*mexFunction\\.map//g")
+                                MEXLINKFLAGS="" dnl We actually don't need MEXLINK????
                         ;;
                 esac
@@ -411 +448 @@
                 fi
 
+                AC_SUBST([MEXEXT])
+                AC_SUBST([MEXOPTFLAGS])
+                AC_SUBST([MEXCFLAGS])
+                AC_SUBST([MEXCXXFLAGS])
                 AC_SUBST([MATLABINCL])
-                MATLABWRAPPEREXT=${MEXEXT}
-                AC_SUBST([MATLABWRAPPEREXT])
+                AC_SUBST([MEXLINKFLAGS])
                 AC_SUBST([MEXLIB])
-                AC_SUBST([MEXLINK])
         fi
         dnl }}}
         dnl JavaScript{{{
+        AC_MSG_CHECKING([for JavaScript])
         AC_ARG_WITH(
                 [javascript],
@@ -425 +465 @@
                 [JAVASCRIPT="no"]
         )
-        AC_MSG_CHECKING([for JavaScript])
         if test "x${JAVASCRIPT}" == "xno"; then
                 HAVE_JAVASCRIPT=no
@@ -438 +477 @@
         dnl }}}
         dnl Triangle {{{
+        AC_MSG_CHECKING([for triangle])
         AC_ARG_WITH(
                 [triangle-dir],
@@ -444 +484 @@
                 [TRIANGLE_ROOT="no"]
         )
-        AC_MSG_CHECKING([for triangle])
         if test "x${TRIANGLE_ROOT}" == "xno"; then
                 HAVE_TRIANGLE=no
@@ -483 +522 @@
                                 fi
                         ;;
+                        *mingw*)
+                                if test "x${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
+                        ;;
+                        *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${TRIANGLE_ROOT}/lib -ltriangle"
+                                fi
+                        ;;
                 esac
                 AC_DEFINE([_HAVE_TRIANGLE_], [1], [with Triangle in ISSM src])
@@ -490 +545 @@
         dnl }}}
         dnl Boost{{{
+        AC_MSG_CHECKING([for Boost])
         AC_ARG_WITH(
                 [boost-dir],
@@ -496 +552 @@
                 [BOOST_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Boost])
         if test "x${BOOST_ROOT}" == "xno"; then
                 HAVE_BOOST=no
@@ -523 +578 @@
         dnl }}}
         dnl Dakota{{{
+        AC_MSG_CHECKING([for Dakota])
         AC_ARG_WITH(
                 [dakota-dir],
@@ -529 +585 @@
                 [DAKOTA_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Dakota])
         if test "x${DAKOTA_ROOT}" == "xno"; then
                 HAVE_DAKOTA=no
@@ -546 +601 @@
 
                 AC_MSG_CHECKING(for Dakota version)
-                dnl TODO:       Check if this method applies to all other versions of 
-                dnl                     Dakota (it should as long as the Dakota binaries have been
-                dnl             compiled). If so, we can remove the other methods of 
-                dnl                     getting the version.
+                dnl TODO:
+                dnl - Check if this method applies to all other versions of Dakota (it 
+                dnl   should as long as the Dakota binaries have been compiled). If so, 
+                dnl   we can remove the other methods of getting the version.
+                dnl - Modify src/wrappers/IssmConfig/IssmConfig.cpp so that strlen is 
+                dnl   not called with _DAKOTA_VERSION_ as an argument so that we can 
+                dnl   do,
+                dnl
+                dnl     AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_], ${DAKOTA_VERSION}, [Dakota version number])
                 dnl
                 DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
@@ -679 +739 @@
                 AC_MSG_CHECKING(for Dakota major version)
                 AC_MSG_RESULT(${DAKOTA_MAJOR})
-                AC_DEFINE_UNQUOTED(_DAKOTA_MAJOR_, $DAKOTA_MAJOR, [Dakota major version number])
+                AC_DEFINE_UNQUOTED([_DAKOTA_MAJOR_], ${DAKOTA_MAJOR}, [Dakota major version number])
                 AC_MSG_CHECKING(for Dakota minor version)
                 AC_MSG_RESULT(${DAKOTA_MINOR})
-                AC_DEFINE_UNQUOTED(_DAKOTA_MINOR_, $DAKOTA_MINOR, [Dakota minor version number])
+                AC_DEFINE_UNQUOTED([_DAKOTA_MINOR_], ${DAKOTA_MINOR}, [Dakota minor version number])
                 AC_MSG_CHECKING(for Dakota build version)
                 AC_MSG_RESULT(${DAKOTA_BUILD})
-                AC_DEFINE_UNQUOTED(_DAKOTA_BUILD_, $DAKOTA_BUILD, [Dakota build version number])
+                AC_DEFINE_UNQUOTED([_DAKOTA_BUILD_], ${DAKOTA_BUILD}, [Dakota build version number])
 
                 AC_DEFINE([_HAVE_DAKOTA_], [1], [with Dakota in ISSM src])
@@ -695 +755 @@
         dnl }}}
         dnl Python{{{
+        AC_MSG_CHECKING([for Python])
         AC_ARG_WITH(
                 [python-dir],
@@ -708 +769 @@
                 [PYTHON_VERSION="no"]
         )
-        AC_MSG_CHECKING([for Python])
         if test "x${PYTHON_ROOT}" == "xno"; then
                 HAVE_PYTHON=no
@@ -735 +795 @@
                 dnl Determine major version
                 PYTHON_MAJOR=${PYTHON_VERSION%.*}
-                AC_DEFINE_UNQUOTED(_PYTHON_MAJOR_, $PYTHON_MAJOR, [Python version major])
+                AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_], ${PYTHON_MAJOR}, [Python version major])
                 if test "x${PYTHON_MAJOR}" == "x3"; then
                         HAVE_PYTHON3="yes"
@@ -751 +811 @@
                         PYTHONINCL=-I${PYTHON_ROOT}/include/python${PYTHON_VERSION}m
                 else
-                        AC_MSG_ERROR([Python.h not found, locate this file and contact ISSM developers]);
+                        AC_MSG_ERROR([Python.h not found! Please locate this file and contact ISSM developers via forum or email.]);
                 fi
                 AC_MSG_RESULT([found])
@@ -764 +824 @@
                                 PYTHONLINK="-shared"
                         ;;
+                        *darwin*)
+                                PYTHONLINK="-dynamiclib"
+                        ;;
                         *linux*)
                                 PYTHONLINK="-shared"
                         ;;
-                        *darwin*)
-                                PYTHONLINK="-dynamiclib"
+                        *mingw*)
+                                PYTHONLINK="-shared"
+                        ;;
+                        *msys*)
+                                PYTHONLINK="-shared"
                         ;;
                 esac
@@ -781 +847 @@
         dnl }}}
         dnl NumPy{{{
-        dnl TODO:
-        dnl - Replace references to python-numpy with numpy (and similar terms)
-        dnl       project-wide
-        dnl
-        AC_ARG_WITH(
-                [python-numpy-dir],
-                AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory]),
-                [PYTHON_NUMPY_ROOT=${withval}],
-                [PYTHON_NUMPY_ROOT="no"]
-        )
-
         dnl NOTE: You can find NumPy by running,
         dnl
@@ -797 +852 @@
         dnl             >>> numpy.__file__
         dnl
-
+        dnl TODO:
+        dnl - Replace references to python-numpy with numpy (and similar terms)
+        dnl       project-wide
+        dnl
         AC_MSG_CHECKING(for python-numpy)
+        AC_ARG_WITH(
+                [python-numpy-dir],
+                AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory]),
+                [PYTHON_NUMPY_ROOT=${withval}],
+                [PYTHON_NUMPY_ROOT="no"]
+        )
         if test "x${PYTHON_NUMPY_ROOT}" == "xno"; then
                 HAVE_PYTHON_NUMPY=no
@@ -817 +881 @@
         dnl }}}
         dnl Chaco{{{
+        AC_MSG_CHECKING([for Chaco])
         AC_ARG_WITH(
                 [chaco-dir],
@@ -823 +888 @@
                 [CHACO_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Chaco])
         if test "x${CHACO_ROOT}" == "xno"; then
                 HAVE_CHACO=no
@@ -845 +909 @@
         dnl }}}
         dnl ESMF{{{
+        AC_MSG_CHECKING([for ESMF])
         AC_ARG_WITH(
                 [esmf-dir],
@@ -851 +916 @@
                 [ESMF_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ESMF])
         if test "x${ESMF_ROOT}" == "xno"; then
                 HAVE_ESMF=no
@@ -873 +937 @@
         dnl }}}
         dnl CoDiPack{{{
+        AC_MSG_CHECKING([for CoDiPack])
         AC_ARG_WITH(
                 [codipack-dir],
@@ -879 +944 @@
                 [CODIPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for CoDiPack])
         if test "x${CODIPACK_ROOT}" == "xno"; then
                 HAVE_CODIPACK=no
@@ -901 +965 @@
         dnl }}}
         dnl Tape Allocation {{{
+        AC_MSG_CHECKING(for tape allocation)
         AC_ARG_ENABLE(
                 [tape-alloc],                                                                                                                           dnl feature
@@ -907 +972 @@
                 [enable_tape_alloc=no]
         )
-        AC_MSG_CHECKING(for tape allocation)
         if test "x${enable_tape_alloc}" == "xyes"; then
                 AC_DEFINE([_AD_TAPE_ALLOC_], [1], [enable a priori tape allocation for AD])
@@ -914 +978 @@
         dnl }}}
         dnl ADOL-C {{{
+        AC_MSG_CHECKING([for ADOL-C])
         AC_ARG_WITH(
                 [adolc-dir],
@@ -920 +985 @@
                 [ADOLC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ADOL-C])
         if test "x${ADOLC_ROOT}" == "xno"; then
                 HAVE_ADOLC=no
@@ -945 +1009 @@
         dnl }}}
         dnl ADOL-C version{{{
+        AC_MSG_CHECKING(for ADOL-C version)
         AC_ARG_WITH(
                 [adolc-version],
@@ -951 +1016 @@
                 [ADOLC_VERSION=2]
         )
-        AC_MSG_CHECKING(for ADOL-C version)
-
-        AC_DEFINE_UNQUOTED(_ADOLC_VERSION_, $ADOLC_VERSION, [ADOL-C version])
+        AC_DEFINE_UNQUOTED([_ADOLC_VERSION_], ${ADOLC_VERSION}, [ADOL-C version])
         AC_MSG_RESULT(${ADOLC_VERSION})
         dnl }}}
         dnl ADIC2 {{{
+        AC_MSG_CHECKING([for ADIC2])
         AC_ARG_WITH(
                 [adic2-dir],
@@ -963 +1027 @@
                 [ADIC2_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ADIC2])
         if test "x${ADIC2_ROOT}" == "xno"; then
                 HAVE_ADIC2=no
@@ -985 +1048 @@
         dnl }}}
         dnl ATLAS {{{
+        AC_MSG_CHECKING(for ATLAS and CBLAS libraries)
         AC_ARG_WITH(
                 [atlas-dir],
@@ -991 +1055 @@
                 [ATLAS_ROOT="no"]
         )
-        AC_MSG_CHECKING(for ATLAS and CBLAS libraries)
         if test "x${ATLAS_ROOT}" == "xno"; then
                 HAVE_ATLAS=no
@@ -1008 +1071 @@
                                 ATLASLIB="-L`cygpath -m ${ATLAS_ROOT}` -Wl,libatlas.lib  -Wl,libcblas.lib"
                         ;;
+                        *darwin*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                        ;;
                         *linux*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm "
-                        ;;
-                        *darwin*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm "
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                        ;;
+                        *mingw*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                        ;;
+                        *msys*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
                         ;;
                 esac
@@ -1020 +1089 @@
         dnl }}}
         dnl GSL{{{
+        AC_MSG_CHECKING([for GSL])
         AC_ARG_WITH(
                 [gsl-dir],
@@ -1026 +1096 @@
                 [GSL_ROOT="no"]
         )
-        AC_MSG_CHECKING([for GSL])
         if test "x${GSL_ROOT}" == "xno"; then
                 HAVE_GSL=no
@@ -1052 +1121 @@
         dnl }}}
         dnl AMPI (ADOL-C){{{
+        AC_MSG_CHECKING([for AMPI])
         AC_ARG_WITH(
                 [ampi-dir],
@@ -1058 +1128 @@
                 [AMPI_ROOT="no"]
         )
-        AC_MSG_CHECKING([for AMPI])
         if test "x${AMPI_ROOT}" == "xno"; then
                 HAVE_AMPI=no
@@ -1088 +1157 @@
         dnl }}}
         dnl Adjoint MPI (CoDiPack){{{
+        AC_MSG_CHECKING([for Adjoint MPI])
         AC_ARG_WITH(
                 [adjointmpi-dir],
@@ -1094 +1164 @@
                 [ADJOINTMPI_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Adjoint MPI])
         if test "x${ADJOINTMPI_ROOT}" == "xno"; then
                 HAVE_ADJOINTMPI=no
@@ -1122 +1191 @@
         dnl }}}
         dnl MeDiPack (CoDiPack, ADOL-C dev){{{
+        AC_MSG_CHECKING([for MeDiPack])
         AC_ARG_WITH(
                 [medipack-dir],
@@ -1128 +1198 @@
                 [MEDIPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MeDiPack])
         if test "x${MEDIPACK_ROOT}" == "xno"; then
                 HAVE_MEDIPACK=no
@@ -1154 +1223 @@
         dnl }}}
         dnl HDF5 {{{
+        AC_MSG_CHECKING(for HDF5 libraries)
         AC_ARG_WITH(
                 [hdf5-dir],
@@ -1160 +1230 @@
                 [HDF5_ROOT="no"]
         )
-        AC_MSG_CHECKING(for HDF5 libraries)
         if test "x${HDF5_ROOT}" == "xno"; then
                 HAVE_HDF5=no
@@ -1181 +1250 @@
                                 HDF5LIB="-L`cygpath -m ${HDF5_ROOT}` -Wl,libhdf5.lib  -Wl,libhdf5_hl.lib"
                         ;;
+                        *darwin*)
+                                HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
+                        ;;
                         *linux*)
                                 HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
                         ;;
-                        *darwin*)
+                        *mingw*)
+                                HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
+                        ;;
+                        *msys*)
                                 HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
                         ;;
@@ -1193 +1268 @@
         dnl }}}
         dnl PETSc{{{
+        AC_MSG_CHECKING([for PETSc])
         AC_ARG_WITH(
                 [petsc-dir],
@@ -1199 +1275 @@
                 [PETSC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for PETSc])
         if test "x${PETSC_ROOT}" == "xno"; then
                 HAVE_PETSC=no
@@ -1220 +1295 @@
                 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_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}])
 
@@ -1262 +1337 @@
                                         PETSCLIB="/link -Wl,/LIBPATH:`cygpath -m ${PETSC_ROOT}/lib` -Wl,libpetsc.lib"
                                         PETSCINCL="/I`cygpath -m ${PETSC_ROOT}/include`"
+                                fi
+                        ;;
+                        *darwin*)
+                                if test ${PETSC_MAJOR} -lt 3; then
+                                        PETSCLIB="-L${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
                         ;;
@@ -1280 +1365 @@
                                 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 ${PETSC_MINOR} -ge 3; then
-                                                PETSCLIB+=" -lmetis"
-                                        fi
-                                fi
+                        *mingw*)
+                                PETSCLIB="-Wl,${PETSC_ROOT}/lib/libpetsc.a"
+                        ;;
+                        *msys*)
+                                PETSCLIB="${PETSC_ROOT}/lib -lpetsc"
                         ;;
                 esac
@@ -1299 +1380 @@
         dnl MPI{{{
         AC_MSG_CHECKING(for MPI)
-
         AC_ARG_WITH(
                 [mpi-include],
@@ -1306 +1386 @@
                 [MPI_INCLUDE=""]
         )
-
         AC_ARG_WITH(
                 [mpi-libdir],
@@ -1313 +1392 @@
                 [MPI_LIBDIR=""]
         )
-
         AC_ARG_WITH(
                 [mpi-libflags],
@@ -1320 +1398 @@
                 [MPI_LIBFLAGS=""]
         )
-
         if test -z "${MPI_INCLUDE}"; then
                 HAVE_MPI=no
@@ -1363 +1440 @@
         dnl }}}
         dnl SCOTCH{{{
+        AC_MSG_CHECKING([for SCOTCH])
         AC_ARG_WITH(
                 [scotch-dir],
@@ -1369 +1447 @@
                 [SCOTCH_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SCOTCH])
         if test "x${SCOTCH_ROOT}" == "xno"; then
                 HAVE_SCOTCH=no
@@ -1402 +1479 @@
         dnl }}}
         dnl METIS{{{
-
-        dnl NOTE: We know $VENDOR cannot be empty at this point, so no need to
-        dnl               check again in the following conditionals
-        dnl
-        if test "x${HAVE_PETSC}" == "xyes" && test "x${PETSC_MAJOR}" == "x3" && test ${PETSC_MINOR} -ge 3 && test "${VENDOR}" != "MSVC-Win64" && test "${VENDOR}" != "MSVC-Win64-par"; then
-                dnl In PETSc >=3.3, METIS is provided
-                HAVE_METIS="yes"
-                AC_DEFINE([_METIS_VERSION_], [5], [METIS version number])
+        AC_MSG_CHECKING([for METIS])
+        AC_ARG_WITH(
+                [metis-dir],
+                AS_HELP_STRING([--with-metis-dir=DIR], [METIS root directory, necessary for serial build]),
+                [METIS_ROOT=${withval}],
+                [METIS_ROOT="no"]
+        )
+        HAVE_METIS=no
+        if test "x${METIS_ROOT}" == "xno"; then
+                dnl Check if METIS was installed via PETSc
+                if test -f ${PETSC_ROOT}/install/include/metis.h; then
+                        HAVE_METIS=yes
+                        METIS_ROOT="${PETSC_ROOT}"
+                fi
+        else
+                if ! test -d "${METIS_ROOT}"; then
+                        AC_MSG_ERROR([METIS directory provided (${METIS_ROOT}) does not exist!]);
+                fi
+                HAVE_METIS=yes
+        fi
+        if test "${HAVE_METIS}" = "yes"; then
+                METIS_VERSION=$(grep "#define METIS_VER_MAJOR" ${METIS_ROOT}/include/metis.h | sed 's|.*METIS_VER_MAJOR[[:space:]]*||')
+                dnl METIS libraries and header files
+                if test "x${METIS_VERSION}" == "x4"; then
+                        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"
+                                ;;
+                                *linux*)
+                                        METISLIB="-L${METIS_ROOT} -lmetis"
+                                ;;
+                                *mingw*)
+                                        METISLIB="-Wl,${METIS_ROOT}/lib/libmetis.a"
+                                ;;
+                                *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"
+                                ;;
+                                *linux*)
+                                        METISLIB="-L${METIS_ROOT}/lib -lmetis"
+                                ;;
+                                *mingw*)
+                                        METISLIB="-Wl,${METIS_ROOT}/lib/libmetis.a"
+                                ;;
+                                *msys*)
+                                        METISLIB="-L${METIS_ROOT}/lib -lmetis"
+                                ;;
+                        esac
+                else
+                        AC_MSG_ERROR([METIS version ${METIS_VERSION} not yet supported! Please contact ISSM developers via forum or email.])
+                fi
                 AC_DEFINE([_HAVE_METIS_], [1], [with METIS in ISSM src])
-        else
-                AC_ARG_WITH(
-                        [metis-dir],
-                        AS_HELP_STRING([--with-metis-dir=DIR], [METIS root directory, necessary for serial build]),
-                        [METIS_ROOT=${withval}],
-                        [METIS_ROOT="no"]
-                )
-                AC_MSG_CHECKING([for METIS])
-                if test "x${METIS_ROOT}" == "xno"; then
-                        HAVE_METIS=no
-                else
-                        HAVE_METIS=yes
-                        if ! test -d "${METIS_ROOT}"; then
-                                AC_MSG_ERROR([METIS directory provided (${METIS_ROOT}) does not exist!]);
-                        fi
-                fi
-                AC_MSG_RESULT([${HAVE_METIS}])
-                AM_CONDITIONAL([METIS], [test "x${HAVE_METIS}" == "xyes"])
-
+                AC_DEFINE_UNQUOTED([_METIS_VERSION_], ${METIS_VERSION}, [METIS version number])
+                AC_SUBST([METISINCL])
+                AC_SUBST([METISLIB])
+        fi
+        AC_MSG_RESULT([${HAVE_METIS}])
+        AM_CONDITIONAL([METIS], [test "x${HAVE_METIS}" = "xyes"])
+        dnl }}}
+        dnl ParMETIS{{{
+        AC_MSG_CHECKING([for ParMETIS])
+        AC_ARG_WITH(
+                [parmetis-dir],
+                AS_HELP_STRING([--with-parmetis-dir=DIR], [ParMETIS root directory, necessary for parallel build]),
+                [PARMETIS_ROOT=${withval}],
+                [PARMETIS_ROOT="no"]
+        )
+        HAVE_PARMETIS=no
+        if test "x${PARMETIS_ROOT}" == "xno"; then
+                dnl Check if ParMETIS was installed via PETSc
+                if test -f ${PETSC_ROOT}/install/include/parmetis.h; then
+                        HAVE_PARMETIS="yes"
+                        PARMETIS_ROOT="${PETSC_ROOT}"
+                fi
+        else
+                if ! test -d "${PARMETIS_ROOT}"; then
+                        AC_MSG_ERROR([ParMETIS directory provided (${PARMETIS_ROOT}) does not exist!]);
+                fi
+                if ! test -d "${METIS_ROOT}"; then
+                        AC_MSG_ERROR([If supplying path to ParMETIS with option --with-parmetis-dir, must also supply path to METIS with option --with-metis-dir]);
+                fi
+                HAVE_PARMETIS="yes"
+        fi
+        if test "${HAVE_PARMETIS}" == "yes"; then
+                #PARMETIS_VERSION=$(grep "#define PARMETIS_MAJOR_VERSION" ${PARMETIS_ROOT}/include/parmetis.h | sed 's|.*PARMETIS_MAJOR_VERSION[[:space:]]*||')
                 dnl METIS libraries and header files
-                if test "x${HAVE_METIS}" == "xyes"; then
-                        dnl Retrieve METIS version (does the VERSION file exist?)
-                        if test -f "${METIS_ROOT}/VERSION"; then
-                                METIS_VERSION=4
-                        else
-                                METIS_VERSION=5
-                        fi
-
-                        if test "x${METIS_VERSION}" == "x4"; then
-                                METISINCL="-I${METIS_ROOT}/Lib"
-                                case "${host_os}" in
-                                        *cygwin*)
-                                                METISINCL="/I`cygpath -m ${METIS_ROOT}/Lib`"
-                                                METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${METIS_ROOT}` -Wl,libmetis.lib"
-                                        ;;
-                                        *linux*)
-                                                METISLIB="-L${METIS_ROOT} -lparmetis -lmetis"
-                                        ;;
-                                        *darwin*)
-                                                METISLIB="-L${METIS_ROOT} -lparmetis -lmetis"
-                                        ;;
-                                esac
-                                AC_DEFINE([_METIS_VERSION_], [4], [ METIS version number])
-                        fi
-
-                        if test "x${METIS_VERSION}" == "x5"; then
-                                case "${host_os}" in
-                                        *cygwin*)
-                                                METISLIB="-L${METIS_ROOT} libmetis.lib"
-                                        ;;
-                                        *linux*)
-                                                METISLIB="-L${METIS_ROOT}/lib -lparmetis -lmetis"
-                                        ;;
-                                        *darwin*)
-                                                METISLIB="-L${METIS_ROOT}/lib -lparmetis -lmetis"
-                                        ;;
-                                esac
-                                METISINCL="-I${METIS_ROOT}/include"
-                                AC_DEFINE([_METIS_VERSION_], [5], [METIS version number])
-                        fi
-
-                        AC_DEFINE([_HAVE_METIS_], [1], [with METIS in ISSM src])
-                        AC_SUBST([METISINCL])
-                        AC_SUBST([METISLIB])
-                fi
-        fi
-        AM_CONDITIONAL([METIS], [test "x${HAVE_METIS}" == "xyes"])
+                #if test "x${PARMETIS_VERSION}" == "x4"; then
+                        PARMETISINCL="-I${PARMETIS_ROOT}/include"
+                        case "${host_os}" in
+                                *cygwin*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                                *darwin*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                                *linux*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                                *mingw*)
+                                        PARMETISLIB="-Wl,${PARMETIS_ROOT}/lib/libparmetis.a"
+                                ;;
+                                *msys*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                        esac
+                #else
+                #       AC_MSG_ERROR([ParMETIS version ${PARMETIS_VERSION} not yet supported! Please contact ISSM developers via forum or email.])
+                #fi
+                AC_DEFINE([_HAVE_PARMETIS_], [1], [with ParMETIS in ISSM src])
+                #AC_DEFINE([_PARMETIS_VERSION_], [${PARMETIS_VERSION}], [ParMETIS version number])
+                AC_SUBST([PARMETISINCL])
+                AC_SUBST([PARMETISLIB])
+        fi
+        AC_MSG_RESULT([${HAVE_PARMETIS}])
+        AM_CONDITIONAL([PARMETIS], [test "x${HAVE_PARMETIS}" = "xyes"])
         dnl }}}
         dnl Toolkit for Advanced Optimization (TAO){{{
+        AC_MSG_CHECKING([for TAO])
         AC_ARG_WITH(
                 [tao-dir],
@@ -1486 +1617 @@
                 [TAO_ROOT="no"]
         )
-        AC_MSG_CHECKING([for TAO])
-
         if test "x${HAVE_PETSC}" == "xyes" && test "x${PETSC_MAJOR}" == "x3" && test ${PETSC_MINOR} -ge 5; then
                 dnl In PETSc >= 3.5, TAO is provided
@@ -1515 +1644 @@
         dnl }}}
         dnl M1QN3{{{
+        AC_MSG_CHECKING([for M1QN3])
         AC_ARG_WITH(
                 [m1qn3-dir],
@@ -1521 +1651 @@
                 [M1QN3_ROOT="no"]
         )
-        AC_MSG_CHECKING([for M1QN3])
         if test "x${M1QN3_ROOT}" == "xno"; then
                 HAVE_M1QN3=no
@@ -1540 +1669 @@
         dnl }}}
         dnl PROJ{{{
+        AC_MSG_CHECKING([for PROJ])
         AC_ARG_WITH(
                 [proj-dir],
@@ -1546 +1676 @@
                 [PROJ_ROOT="no"]
         )
-        AC_MSG_CHECKING([for PROJ])
         if test "x${PROJ_ROOT}" == "xno"; then
                 HAVE_PROJ=no
@@ -1568 +1697 @@
         dnl }}}
         dnl SLEPc{{{
+        AC_MSG_CHECKING([for SLEPc])
         AC_ARG_WITH(
                 [slepc-dir],
@@ -1574 +1704 @@
                 [SLEPC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SLEPc])
         if test "x${SLEPC_ROOT}" == "xno"; then
                 HAVE_SLEPC=no
@@ -1595 +1724 @@
         dnl }}}
         dnl shapelib{{{
+        AC_MSG_CHECKING([for shapelib])
         AC_ARG_WITH(
                 [shapelib-dir],
@@ -1601 +1731 @@
                 [SHAPELIB_ROOT="no"]
         )
-        AC_MSG_CHECKING([for shapelib])
         if test "x${SHAPELIB_ROOT}" == "xno"; then
                 HAVE_SHAPELIB=no
@@ -1622 +1751 @@
         dnl }}}
         dnl ScaLAPACK{{{
-
         dnl NOTE: User should supply path to root directory or libraries, but not both
+        dnl
+        AC_MSG_CHECKING([for ScaLAPACK])
         AC_ARG_WITH(
                 [scalapack-dir],
@@ -1636 +1766 @@
                 [SCALAPACKLIB="no"]
         )
-        AC_MSG_CHECKING([for ScaLAPACK])
         if test "x${SCALAPACK_ROOT}" == "xno" && test "x${SCALAPACKLIB}" == "xno"; then
                 HAVE_SCALAPACK=no
@@ -1645 +1774 @@
                 fi
                 HAVE_SCALAPACK=yes
-                SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack"
+                if test "${VENDOR}" == "win-msys2"; then
+                        SCALAPACKLIB="-Wl,${SCALAPACK_ROOT}/lib/libscalapack.a"
+                else
+                        SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack"
+                fi
         elif test "x${SCALAPACKLIB}" != "xno"; then
                 dnl Value of SCALAPACKLIB should be valid here, so no need to set it (as above)
@@ -1661 +1794 @@
         dnl }}}
         dnl BLAS/LAPACK{{{
+        AC_MSG_CHECKING([for BLAS/LAPACK])
+        AC_ARG_WITH(
+                [blas-dir],
+                [AS_HELP_STRING([--with-blas-dir=DIR], [BLAS root directory])],
+                [BLAS_ROOT=$withval],
+                [BLAS_ROOT="no"]
+        )
+        AC_ARG_WITH(
+                [lapack-dir],
+                [AS_HELP_STRING([--with-lapack-dir=DIR], [LAPACK root directory])],
+                [LAPACK_ROOT=$withval],
+                [LAPACK_ROOT="no"]
+        )
         AC_ARG_WITH(
                 [blas-lapack-dir],
@@ -1667 +1813 @@
                 [BLASLAPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for BLAS/LAPACK])
-        if test "x${BLASLAPACK_ROOT}" == "xno" ; then
+        if (test "x${BLAS_ROOT}" = "xno" || test "x${LAPACK_ROOT}" = "xno") && test "x${BLASLAPACK_ROOT}" = "xno"; then
                 HAVE_BLASLAPACK=no
         else
                 HAVE_BLASLAPACK=yes
-                if ! test -d "${BLASLAPACK_ROOT}"; then
-                        AC_MSG_ERROR([BLAS/LAPACK directory provided (${BLASLAPACK_ROOT}) does not exist!]);
+                if ! test -d "${BLAS_ROOT}" || ! test -d "${LAPACK_ROOT}"; then
+                        if ! test -d "${BLASLAPACK_ROOT}"; then
+                                AC_MSG_ERROR([Use either --with-blas-dir and --with-lapack-dir *or* --with-blaslapack-dir]);
+                        fi
                 fi
         fi
@@ -1680 +1827 @@
         dnl BLAS/LAPACK libraries and header files
         if test "x${HAVE_BLASLAPACK}" == "xyes"; then
-                BLASLAPACKINCL=""
                 case "${host_os}" in
                         *cygwin*)
@@ -1709 +1855 @@
                                 fi
                         ;;
+                        *mingw*)
+                                if test -d "${BLASLAPACK_ROOT}"; then
+                                        BLASLAPACKLIB="-L${BLASLAPACK_ROOT}/lib"
+                                        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 ${BLASLAPACK_ROOT}/lib/libflapack.* 1> /dev/null 2>&1; then
+                                                BLASLAPACKLIB="-Wl,${BLASLAPACK_ROOT}/lib/libflapack.a -Wl,${BLASLAPACK_ROOT}/lib/libfblas.a"
+                                        else
+                                                BLASLAPACKLIB+=" -llapack -lblas"
+                                        fi
+                                else
+                                        BLASLAPACKLIB="-Wl,${LAPACK_ROOT}/lib/liblapack.a -Wl,${BLAS_ROOT}/lib/libblas.a"
+                                fi
+                        ;;
+                        *msys*)
+                                if test -d "${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${BLAS_ROOT}/lib -lblas"
+                                fi
+                        ;;
                 esac
                 AC_DEFINE([_HAVE_BLASLAPACK_], [1], [with BLAS/LAPACK in ISSM src])
                 AC_SUBST([BLASLAPACKLIB])
-                AC_SUBST([BLASLAPACKINCL])
         fi
         dnl }}}
         dnl Math Kernel Library (MKL){{{
+        AC_MSG_CHECKING([for MKL])
         AC_ARG_WITH(
                 [mkl-libflags],
@@ -1722 +1899 @@
                 [MKL_LIBFLAGS="no"]
         )
-        AC_MSG_CHECKING([for MKL])
         if test "x${MKL_LIBFLAGS}" == "xno"; then
                 HAVE_MKL=no
@@ -1735 +1911 @@
         dnl }}}
         dnl PlaLAPACK{{{
-
         dnl TODO:       Handle user supplying path to root directory *or* individual
         dnl             arguments (like ScaLAPACK)
@@ -1770 +1945 @@
         dnl }}}
         dnl MUMPS{{{
+        AC_MSG_CHECKING([for MUMPS])
         AC_ARG_WITH(
                 [mumps-dir],
@@ -1776 +1952 @@
                 [MUMPS_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MUMPS])
         if test "x${MUMPS_ROOT}" == "xno"; then
                 HAVE_MUMPS=no
@@ -1791 +1966 @@
                 MUMPSINCL="-I${MUMPS_ROOT}/include"
                 if test "x${MUMPS_ROOT}" == "x${PETSC_ROOT}"; then
-                        if test "x${PETSC_MAJOR}" == "x2"; then
-                                MUMPSLIB="-L${MUMPS_ROOT}/lib "
+                        if test "${VENDOR}" == "win-msys2"; then
+                                MUMPSLIB="-Wl,${MUMPS_ROOT}/lib/libcmumps.a -Wl,${MUMPS_ROOT}/lib/libdmumps.a -Wl,${MUMPS_ROOT}/lib/libsmumps.a -Wl,${MUMPS_ROOT}/lib/libzmumps.a -Wl,${MUMPS_ROOT}/lib/libmumps_common.a -Wl,${MUMPS_ROOT}/lib/libpord.a"
                         else
                                 MUMPSLIB="-L${MUMPS_ROOT}/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis -lzmumps -lmetis"
@@ -1841 +2016 @@
         dnl }}}
         dnl BLACS{{{
+        AC_MSG_CHECKING([for BLACS])
         AC_ARG_WITH(
                 [blacs-dir],
@@ -1847 +2023 @@
                 [BLACS_ROOT="no"]
         )
-        AC_MSG_CHECKING([for BLACS])
         if test "x${BLACS_ROOT}" == "xno"; then
                 HAVE_BLACS=no
@@ -1868 +2043 @@
         dnl }}}
         dnl HYPRE{{{
+        AC_MSG_CHECKING([for HYPRE])
         AC_ARG_WITH(
                 [hypre-dir],
@@ -1874 +2050 @@
                 [HYPRE_ROOT="no"]
         )
-        AC_MSG_CHECKING([for HYPRE])
         if test "x${HYPRE_ROOT}" == "xno"; then
                 HAVE_HYPRE=no
@@ -1895 +2070 @@
         dnl }}}
         dnl Prometheus{{{
+        AC_MSG_CHECKING([for Prometheus])
         AC_ARG_WITH(
                 [prometheus-dir],
@@ -1901 +2077 @@
                 [PROMETHEUS_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Prometheus])
         if test "x${PROMETHEUS_ROOT}" == "xno"; then
                 HAVE_PROMETHEUS=no
@@ -1922 +2097 @@
         dnl }}}
         dnl SEMIC{{{
+        AC_MSG_CHECKING([for SEMIC])
         AC_ARG_WITH(
                 [semic-dir],
@@ -1928 +2104 @@
                 [SEMIC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SEMIC])
         if test "x${SEMIC_ROOT}" == "xno"; then
                 HAVE_SEMIC=no
@@ -1950 +2125 @@
         dnl }}}
         dnl SPAI{{{
+        AC_MSG_CHECKING([for SPAI])
         AC_ARG_WITH(
                 [spai-dir],
@@ -1956 +2132 @@
                 [SPAI_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SPAI])
         if test "x${SPAI_ROOT}" == "xno"; then
                 HAVE_SPAI=no
@@ -1977 +2152 @@
         dnl }}}
         dnl SuperLU{{{
+        AC_MSG_CHECKING([for SuperLU])
         AC_ARG_WITH(
                 [superlu-dir],
@@ -1983 +2159 @@
                 [SUPERLU_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SuperLU])
         if test "x${SUPERLU_ROOT}" == "xno"; then
                 HAVE_SUPERLU=no
@@ -2004 +2179 @@
         dnl }}}
         dnl SPOOLES{{{
+        AC_MSG_CHECKING([for SPOOLES])
         AC_ARG_WITH(
                 [spooles-dir],
@@ -2010 +2186 @@
                 [SPOOLES_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SPOOLES])
         if test "x${SPOOLES_ROOT}" == "xno"; then
                 HAVE_SPOOLES=no
@@ -2031 +2206 @@
         dnl }}}
         dnl PaStiX{{{
+        AC_MSG_CHECKING([for PaStiX])
         AC_ARG_WITH(
                 [pastix-dir],
@@ -2037 +2213 @@
                 [PASTIX_ROOT="no"]
         )
-        AC_MSG_CHECKING([for PaStiX])
         if test "x${PASTIX_ROOT}" == "xno"; then
                 HAVE_PASTIX=no
@@ -2059 +2234 @@
         dnl }}}
         dnl ml{{{
+        AC_MSG_CHECKING([for ml])
         AC_ARG_WITH(
                 [ml-dir],
@@ -2065 +2241 @@
                 [ML_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ml])
         if test "x${ML_ROOT}" == "xno"; then
                 HAVE_ML=no
@@ -2086 +2261 @@
         dnl }}}
         dnl UMFPACK{{{
+        AC_MSG_CHECKING([for UMFPACK])
         AC_ARG_WITH(
                 [umfpack-dir],
@@ -2092 +2268 @@
                 [UMFPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for UMFPACK])
         if test "x${UMFPACK_ROOT}" == "xno"; then
                 HAVE_UMFPACK=no
@@ -2129 +2304 @@
         dnl }}}
         dnl MATH77{{{
+        AC_MSG_CHECKING([for MATH77])
         AC_ARG_WITH(
                 [math77-dir],
@@ -2135 +2311 @@
                 [MATH77_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MATH77])
         if test "x${MATH77_ROOT}" == "xno"; then
                 HAVE_MATH77=no
@@ -2154 +2329 @@
         dnl }}}
         dnl Fortran{{{
+        AC_MSG_CHECKING(for Fortran compilation)
         AC_ARG_WITH(
                 [fortran],
@@ -2160 +2336 @@
                 [FORTRAN=yes]
         )
-        AC_MSG_CHECKING(for Fortran compilation)
         if test "x${FORTRAN}" == "xyes"; then
                 HAVE_FORTRAN=yes
@@ -2224 +2399 @@
         dnl }}}
         dnl MeteoIO{{{
+        AC_MSG_CHECKING([for MeteoIO])
         AC_ARG_WITH(
                 [meteoio-dir],
@@ -2230 +2406 @@
                 [METEOIO_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MeteoIO])
         if test "x${METEOIO_ROOT}" == "xno"; then
                 HAVE_METEOIO=no
@@ -2253 +2428 @@
         dnl }}}
         dnl SNOWPACK{{{
+        AC_MSG_CHECKING([for SNOWPACK])
         AC_ARG_WITH(
                 [snowpack-dir],
@@ -2259 +2435 @@
                 [SNOWPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SNOWPACK])
         if test "x${SNOWPACK_ROOT}" == "xno"; then
                 HAVE_SNOWPACK=no
@@ -2281 +2456 @@
         dnl }}}
         dnl NeoPZ{{{
+        AC_MSG_CHECKING([for NeoPZ])
         AC_ARG_WITH(
                 [neopz-dir],
@@ -2287 +2463 @@
                 [NEOPZ_ROOT="no"]
         )
-        AC_MSG_CHECKING([for NeoPZ])
         if test "x${NEOPZ_ROOT}" == "xno"; then
                 HAVE_NEOPZ=no
@@ -2356 +2531 @@
                 GMSH_VERSION_MAJOR=`${GMSH_ROOT}/bin/gmsh -info | grep "Version" | sed -e "s/Version@<:@@<:@:blank:@:>@@:>@*:@<:@@<:@:blank:@:>@@:>@//" | cut -d "." -f 1`
                 AC_MSG_RESULT([${GMSH_VERSION_MAJOR}])
-                AC_DEFINE_UNQUOTED(_GMSH_VERSION_MAJOR_, $GMSH_VERSION_MAJOR, [Gmsh major version])
+                AC_DEFINE_UNQUOTED([_GMSH_VERSION_MAJOR_], ${GMSH_VERSION_MAJOR}, [Gmsh major version])
         fi      
         dnl }}}
         dnl Capabilities
         dnl with-bamg{{{
+        AC_MSG_CHECKING([for BAMG capability compilation])
         AC_ARG_WITH(
                 [bamg],
@@ -2367 +2543 @@
                 [BAMG=yes]
         )
-        AC_MSG_CHECKING([for BAMG capability compilation])
         HAVE_BAMG=no
         if test "x${BAMG}" == "xyes"; then
@@ -2377 +2552 @@
         dnl }}}
         dnl with-ocean{{{
+        AC_MSG_CHECKING(for ice/ocean coupling capability compilation)
         AC_ARG_WITH(
                 [ocean],
@@ -2383 +2559 @@
                 [OCEAN=no]
         )
-        AC_MSG_CHECKING(for ice/ocean coupling capability compilation)
-
         HAVE_OCEAN=no
         if test "x${OCEAN}" == "xyes"; then
@@ -2394 +2568 @@
         dnl }}}
         dnl with-kml{{{
+        AC_MSG_CHECKING(for kml capability compilation)
         AC_ARG_WITH(
                 [kml],
@@ -2400 +2575 @@
                 [KML=no]
         )
-        AC_MSG_CHECKING(for kml capability compilation)
-
         HAVE_KML=no
         if test "x${KML}" == "xyes"; then
@@ -2411 +2584 @@
         dnl }}}
         dnl with-kriging{{{
+        AC_MSG_CHECKING(for kriging capability compilation)
         AC_ARG_WITH(
                 [kriging],
@@ -2417 +2591 @@
                 [KRIGING=yes]
         )
-        AC_MSG_CHECKING(for kriging capability compilation)
-
         HAVE_KRIGING=no
         if test "x${KRIGING}" == "xyes"; then
@@ -2433 +2605 @@
         dnl Platform specifics
         dnl with-ios{{{
+        AC_MSG_CHECKING(for iOS compilation)
         AC_ARG_WITH(
                 [ios],
@@ -2439 +2612 @@
                 [IOS=no]
         )
-        AC_MSG_CHECKING(for iOS compilation)
-
         HAVE_IOS=no
         if test "x${IOS}" == "xyes"; then
@@ -2450 +2621 @@
         dnl }}}
         dnl with-android{{{
+        AC_MSG_CHECKING([for Android capability compilation])
         AC_ARG_WITH(
                 [android],
                 AS_HELP_STRING([--with-android=EXE], [compile with Android capabilities (default: "no"; alternatives: "exe", "jni")]),
                 [ANDROID=${withval}],
-                [ANDROID=no])
-        AC_MSG_CHECKING([for Android capability compilation])
-
+                [ANDROID=no]
+        )
         if test "x${ANDROID}" == "xjni"; then
                 HAVE_ANDROID=jni
@@ -2475 +2646 @@
         dnl }}}
         dnl with-android-ndk{{{
+        AC_MSG_CHECKING([with Android Native Development Kit (NDK)])
         AC_ARG_WITH(
                 [android-ndk],
@@ -2481 +2653 @@
                 [ANDROID_NDK_ROOT=""]
         )
-        AC_MSG_CHECKING([with Android Native Development Kit (NDK)])
-
         if test -d "${ANDROID_NDK_ROOT}"; then
                 HAVE_ANDROID_NDK=yes
@@ -2496 +2666 @@
         dnl other options
         dnl optimization{{{
-        dnl -- bypass standard optimization -g -O2 -fPIC -std=c++11?
+        dnl -- bypass standard optimization -g -O2 -fPIC?
+        AC_MSG_CHECKING(for C++ optimization flags)
         AC_ARG_WITH(
                 [cxxoptflags],
@@ -2503 +2674 @@
                 [CXXOPTFLAGS="-g -O2 -fPIC -std=c++11"]
         )
-        AC_MSG_CHECKING(for C++ optimization flags)
         AC_SUBST([CXXOPTFLAGS])
-        AC_MSG_RESULT([done])
+        AC_MSG_RESULT([${CXXOPTFLAGS}])
         dnl }}}
         dnl multithreading{{{
+        AC_MSG_CHECKING(for number of threads)
         AC_ARG_WITH(
                 [numthreads],
@@ -2514 +2685 @@
                 [NUMTHREADS_VALUE=1]
         )
-        AC_MSG_CHECKING(for number of threads)
         dnl Check that supplied value is an integer
         if [[ "${NUMTHREADS_VALUE}" != "${NUMTHREADS_VALUE}" 2> /dev/null ]]; then
@@ -2529 +2699 @@
                                 MULTITHREADINGLIB="-lpthread -lrt"
                         ;;
+                        *darwin*)
+                                MULTITHREADINGLIB="-lpthread"
+                        ;;
                         *linux*)
                                 MULTITHREADINGLIB="-lpthread -lrt"
                         ;;
-                        *darwin*)
-                                MULTITHREADINGLIB="-lpthread"
+                        *mingw*)
+                                MULTITHREADINGLIB=""
+                        ;;
+                        *msys*)
+                                MULTITHREADINGLIB=""
                         ;;
                 esac
                 AC_DEFINE([_MULTITHREADING_], [1], [with multithreading enabled])
         fi
-        AC_DEFINE_UNQUOTED(_NUMTHREADS_, $NUMTHREADS_VALUE, [number of threads])
+        AC_DEFINE_UNQUOTED([_NUMTHREADS_], ${NUMTHREADS_VALUE}, [number of threads])
         AC_SUBST([MULTITHREADINGLIB])
         AC_MSG_RESULT([${NUMTHREADS_VALUE}])
         dnl }}}
         dnl 64-bit indices{{{
+        AC_MSG_CHECKING([for 64-bit indices])
         AC_ARG_WITH(
                 [64bit-indices],
@@ -2549 +2726 @@
                 [USE_64BIT_INDICES=0]
         )
-        AC_MSG_CHECKING([for 64-bit indices])
-
         if test "x${USE_64BIT_INDICES}" == "x1"; then
                 AC_DEFINE([ISSM_USE_64BIT_INDICES], [1], [with 64-bit indices])
@@ -2560 +2735 @@
 
         dnl Checks {{{
-        AC_MSG_CHECKING(consistency between all libraries)
+        AC_MSG_CHECKING(consistency between all external packages)
 
         dnl Check that if PETSc is requested, MPI is specified
@@ -2590 +2765 @@
 
         dnl Check that if we run ADOL-C, we don't compile kriging.exe
-        if test "x$HAVE_ADOLC" == "xyes" && test "${HAVE_KRIGING}" == "xyes"; then
+        if test "x${HAVE_ADOLC}" == "xyes" && test "${HAVE_KRIGING}" == "xyes"; then
                 AC_MSG_ERROR([cannot compile kriging.exe under ADOL-C conditions!]);
         fi

issm/trunk-jpl/src/c/Makefile.am

@@ -1 @@
-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@
+AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@
 AM_FCFLAGS = @SEMICINCL@
 
@@ -8 +8 @@
 #Library declaration {{{
 if !WINDOWS
-lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la
+lib_LTLIBRARIES = libISSMCore.la
+if !MSYS2
+lib_LTLIBRARIES += libISSMOverload.la
+endif
 if WRAPPERS
 lib_LTLIBRARIES += libISSMModules.la
@@ -682 +685 @@
 #}}}
 #Library flags and sources {{{
-ALLCXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS)
+ALL_CXXFLAGS = $(CXXFLAGS) $(CXXOPTFLAGS)
+
+if MSYS2
+ALL_CXXFLAGS += -D_DO_NOT_LOAD_GLOBALS_ # Cannot have undefined symbols under MSYS2
+ALL_CXXFLAGS += -D_USE_MATH_DEFINES # Need to open fence to math.h definitions when --std=c++ is used (which is the default)
+endif
 
 libISSMCore_la_SOURCES  = $(issm_sources)
-libISSMCore_la_CXXFLAGS = $(ALLCXXFLAGS) $(DAKOTAFLAGS)
+libISSMCore_la_CXXFLAGS = $(ALL_CXXFLAGS) $(DAKOTAFLAGS)
 libISSMCore_la_FFLAGS = $(AM_FFLAGS)
 
 if !WINDOWS
 if !STANDALONE_LIBRARIES
-libISSMCore_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB)
+libISSMCore_la_LIBADD = $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
 if FORTRAN
 libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB)
@@ -711 +719 @@
 endif
 
-libISSMModules_la_CXXFLAGS = $(ALLCXXFLAGS)
+libISSMModules_la_CXXFLAGS = $(ALL_CXXFLAGS)
 if !WINDOWS
 if STANDALONE_LIBRARIES
@@ -743 +751 @@
 endif
 
+if VERSION
+libISSMCore_la_LDFLAGS =
+if WRAPPERS
+libISSMModules_la_LDFLAGS =
+endif
+else
+libISSMCore_la_LDFLAGS = -avoid-version
+if WRAPPERS
+libISSMModules_la_LDFLAGS = -avoid-version
+endif
+endif
+
 if STANDALONE_LIBRARIES
-libISSMCore_la_LDFLAGS = -static
-libISSMOverload_la_LDFLAGS = -static
+libISSMCore_la_LDFLAGS += -static
 if WRAPPERS
-libISSMModules_la_LDFLAGS = -static
-else
-libISSMModules_la_LDFLAGS =
-endif
-else
-libISSMCore_la_LDFLAGS =
-libISSMOverload_la_LDFLAGS =
-endif
-
-#}}}
+libISSMModules_la_LDFLAGS += -static
+endif
+endif
+#}}}
+
+if !MSYS2
 #Overload library, to overload any non-standard symbols. {{{
 libISSMOverload_la_SOURCES = ./shared/String/ApiPrintf.cpp
-
 libISSMOverload_la_CFLAGS  = -D_C_ -fPIC $(COPTFLAGS) $(CFLAGS)
+
+if VERSION
+libISSMOverload_la_LDFLAGS =
+else
+libISSMOverload_la_LDFLAGS = -avoid-version
+endif
+
+if STANDALONE_LIBRARIES
+libISSMOverload_la_LDFLAGS += -static
+endif
+endif
 #}}}
 #Executable {{{
@@ -778 +803 @@
 
 #Standard libraries
-LDADD = ./libISSMCore.la ./libISSMOverload.la
+LDADD = ./libISSMCore.la 
+
+if !MSYS2
+LDADD += ./libISSMOverload.la
+endif
+
 if WRAPPERS
 LDADD += ./libISSMModules.la $(TRIANGLELIB)
@@ -784 +814 @@
 
 #External packages
-LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB)
+LDADD +=  $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
 
 if FORTRAN

issm/trunk-jpl/src/wrappers/matlab/Makefile.am

@@ -20 +20 @@
         ./io/WriteMatlabData.cpp
 
-ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
+ALL_CXXFLAGS = -fPIC -D_WRAPPERS_
+
+if MSYS2
+ALL_CXXFLAGS += -D_DO_NOT_LOAD_GLOBALS_ # Cannot have undefined symbols under MSYS2
+ALL_CXXFLAGS += -D_USE_MATH_DEFINES # Need to open fence to math.h definitions when --std=c++ is used (which is the default)
+endif
+
+ALL_CXXFLAGS += $(CXXOPTFLAGS) $(CXXFLAGS)
 
 libISSMMatlab_la_SOURCES = $(io_sources)
-libISSMMatlab_la_CXXFLAGS= $(ALLCXXFLAGS)
+libISSMMatlab_la_CXXFLAGS = ${ALL_CXXFLAGS}
 #}}}
 #api io{{{
@@ -32 +39 @@
 endif
 
+if !MSYS2
 api_sources= ./io/ApiPrintf.cpp
 
 libISSMApi_la_SOURCES = $(api_sources)
-libISSMApi_la_CXXFLAGS= $(ALLCXXFLAGS)
+libISSMApi_la_CXXFLAGS = ${ALL_CXXFLAGS}
+endif
 #}}}
 #Wrappers {{{
@@ -82 +91 @@
 
 #Triangle library
-AM_CXXFLAGS =  -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER -D_WRAPPERS_
+TRI_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
 
 #Matlab part
-AM_LDFLAGS = -module $(MEXLINK) -shrext ${EXEEXT} --export-dynamic -rdynamic -no-undefined
+MEX_CXXFLAGS = -D_HAVE_MATLAB_MODULES_ $(MEXOPTFLAGS) $(MEXCXXFLAGS)
+MEX_CPPFLAGS = $(MATLABINCL)
+MEX_LDFLAGS = -module -shrext $(MEXEXT) -no-undefined
+MEX_LIBADD = $(MEXLINKFLAGS) $(MEXLIB)
+
+AM_CPPFLAGS += ${MEX_CPPFLAGS}
+AM_CXXFLAGS = ${TRI_CXXFLAGS} ${MEX_CXXFLAGS}
+AM_LDFLAGS = ${MEX_LDFLAGS}
+AM_LIBADD = ${MEX_LIBADD}
+
+if !MSYS2
+AM_LDFLAGS += --export-dynamic -rdynamic
+endif
 
 if !VERSION
@@ -106 +127 @@
 endif
 
-AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -fPIC
-
-deps += ./libISSMMatlab.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
-
-if WINDOWS
-deps += $(METISLIB)
-endif
+AM_CXXFLAGS += -fPIC -D_WRAPPERS_
+
+deps += ./libISSMMatlab.la ../../c/libISSMCore.la ../../c/libISSMModules.la
+
+if !MSYS2
+deps += ./libISSMApi.la
+endif
+
+# if WINDOWS
+# deps += $(METISLIB)
+# endif
 
 if ADOLC
@@ -122 +147 @@
 endif
 
-#MEXLIB needs to be the last (undefined references on larsen)
-deps += ${MEXLIB}
+# #MEXLIB needs to be the last (undefined references on larsen)
+# deps += ${MEXLIB}
 
 #Optimization flags:
@@ -130 +155 @@
 # Module sources and dependencies {{{
 if !WINDOWS
-libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB)
+libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB)
+endif
+
+if VERSION
+libISSMMatlab_la_LDFLAGS =
+libISSMApi_la_LDFLAGS =
+else
+libISSMMatlab_la_LDFLAGS = -avoid-version
+libISSMApi_la_LDFLAGS = -avoid-version
 endif
 
 if STANDALONE_LIBRARIES
-libISSMMatlab_la_LDFLAGS = -static
-libISSMApi_la_LDFLAGS = -static
-deps += $(PETSCLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB)
-endif
-
-if !WINDOWS
-libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB)
+libISSMMatlab_la_LDFLAGS += -static
+libISSMApi_la_LDFLAGS += -static
+deps +=  $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(NEOPZLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(OSLIBS)
+endif
+
+if !WINDOWS
+libISSMApi_la_LIBADD = $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB)
 endif
 

issm/trunk-jpl/src/wrappers/python/Makefile.am

@@ -1 @@
-AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
@@ -106 +106 @@
 libISSMPython_la_LDFLAGS = -static
 libISSMApi_la_LDFLAGS = -static
-deps += $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB)
+deps += $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
 endif