Changeset 26036

Timestamp:

02/26/21 19:41:25 (4 years ago)

Author:

jdquinn

Message:

CHG: Reverting temporarily

Location:

issm/trunk-jpl

Files:

• jenkins/jenkins.sh (modified) (27 diffs)
• m4/issm_options.m4 (modified) (141 diffs)
• src/c/Makefile.am (modified) (7 diffs)
• src/wrappers/Triangle/Triangle.h (modified) (1 diff)
• src/wrappers/javascript/Makefile.am (modified) (2 diffs)
• src/wrappers/matlab/Makefile.am (modified) (5 diffs)
• src/wrappers/matlab/include/wrapper_macros.h (modified) (1 diff)
• src/wrappers/python/Makefile.am (modified) (4 diffs)

issm/trunk-jpl/jenkins/jenkins.sh

@@ -7 +7 @@
 # members of the ISSM development team.
 #
-# NOTE:
-# - Variable OS is set in environment by running 
-#       `source $ISSM_DIR/etc/environment.sh`.
-#
 # TODO:
 # - Rename TEMP to something more descriptive (ensure first that other parts of
@@ -18 +14 @@
 
 echo "Cleaning up execution directory"
-rm -rf ${ISSM_DIR}/execution/*
-rm -rf ${ISSM_DIR}/nightlylog
-mkdir ${ISSM_DIR}/nightlylog
+rm -rf $ISSM_DIR/execution/*
+rm -rf $ISSM_DIR/nightlylog
+mkdir $ISSM_DIR/nightlylog
 
 #Server URI
@@ -57 +53 @@
 fi
 
+#Get Operating system (OS) name{{{
+OS=$(uname -s)
+if [[ $OS == CYGWIN* ]]; then
+        OS="win";
+fi
+#}}}
+
 #Install ISSM
 #Determining installation type depending on svn changes{{{
@@ -62 +65 @@
 echo "             Determining Installation type            "
 echo "======================================================";
-if [ -a ${ISSM_DIR}/svn_revision_old ]; then
-        SVN_PREVIOUS=$(cat ${ISSM_DIR}/svn_revision_old)
+if [ -a $ISSM_DIR/svn_revision_old ]; then
+        SVN_PREVIOUS=$(cat $ISSM_DIR/svn_revision_old)
         SVN_CURRENT=$SVN_REVISION_1
         echo "Previous revision number: $SVN_PREVIOUS"
@@ -71 +74 @@
         #
 
-        #svn --non-interactive --no-auth-cache --trust-server-cert diff -r $SVN_PREVIOUS:$SVN_CURRENT --summarize ${ISSM_DIR} | awk '{print $NF}' > ${ISSM_DIR}/TEMP
+        #svn --non-interactive --no-auth-cache --trust-server-cert diff -r $SVN_PREVIOUS:$SVN_CURRENT --summarize $ISSM_DIR | awk '{print $NF}' > $ISSM_DIR/TEMP
 
         # Get list of changes from Jenkins itself as svn requires credentials
@@ -78 +81 @@
 
         # Process html page and get the list of files that has changed (tricky...)
-        #cat changes | grep '="The file was modified"' | sed -e 's/.*<\/td><td><a>\(.*\)<\/a><\/td><td>.*/\1/' > ${ISSM_DIR}/TEMP
+        #cat changes | grep '="The file was modified"' | sed -e 's/.*<\/td><td><a>\(.*\)<\/a><\/td><td>.*/\1/' > $ISSM_DIR/TEMP
         #cat changes | grep 'document_edit' |sed -e 's/document_edit.png/document_edit.png\
-                #/g' | sed -e 's/.*<\/a><\/td><td>\(.*\)<\/td><\/tr>.*/\1/' | grep -v 'document_edit.png' > ${ISSM_DIR}/TEMP
-        cat changes | tr " " "\n" | grep trunk | sed -e 's/.*<a>\(.*\)<\/a>.*/\1/' > ${ISSM_DIR}/TEMP
+                #/g' | sed -e 's/.*<\/a><\/td><td>\(.*\)<\/td><\/tr>.*/\1/' | grep -v 'document_edit.png' > $ISSM_DIR/TEMP
+        cat changes | tr " " "\n" | grep trunk | sed -e 's/.*<a>\(.*\)<\/a>.*/\1/' > $ISSM_DIR/TEMP
 
         # Print list of changed files
         echo "   "
         echo "List of updated files"
-        cat ${ISSM_DIR}/TEMP
+        cat $ISSM_DIR/TEMP
         echo "   "
 
@@ -96 +99 @@
         # If the contents of the externalpackages directory were modified in any
         # way, check for changed external packages
-        if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep externalpackages)" ]; then
+        if [ ! -z "$(cat $ISSM_DIR/TEMP | grep externalpackages)" ]; then
                 echo "  -- checking for changed externalpackages... yes"
                 ISSM_EXTERNALPACKAGES="yes"
@@ -106 +109 @@
         # If the Makefile or m4 diirectory were changed in any way or if certain
         # binary files from a previous compilation do not exist, reconfigure
-        if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep -e "Makefile.am" -e "m4" )" ] ||
-                [ ! -f "${ISSM_DIR}/bin/issm.exe" ] && [ ! -f "${ISSM_DIR}/bin/issm-bin.js" ] ||
+        if [ ! -z "$(cat $ISSM_DIR/TEMP | grep -e "Makefile.am" -e "m4" )" ] ||
+                [ ! -f "$ISSM_DIR/bin/issm.exe" ] && [ ! -f "$ISSM_DIR/bin/issm-bin.js" ] ||
                 [ "$ISSM_EXTERNALPACKAGES" == "yes" ]; then
                 echo "  -- checking for reconfiguration... yes"
@@ -117 +120 @@
 
         # If source files were changed in any way, recompile
-        if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep -e "\.cpp" -e "\.h" )" ] ||
+        if [ ! -z "$(cat $ISSM_DIR/TEMP | grep -e "\.cpp" -e "\.h" )" ] ||
                 [ "$ISSM_RECONFIGURE" == "yes" ]; then
                 echo "  -- checking for recompilation... yes"
@@ -128 +131 @@
         # Cleanup
         rm changes
-        rm ${ISSM_DIR}/TEMP
+        rm $ISSM_DIR/TEMP
 else
         echo "Previous revision not found, this must be a fresh install"
@@ -141 +144 @@
 echo " "
 echo "Recording current svn version: $SVN_REVISION_1"
-echo $SVN_REVISION_1 > ${ISSM_DIR}/svn_revision_old
+echo $SVN_REVISION_1 > $ISSM_DIR/svn_revision_old
 #}}}
 
@@ -151 +154 @@
 
 #Jenkins XML files for individual packages
-EXTERNAL_TEST_FILE="${ISSM_DIR}/nightlylog/results/external.xml"
-mkdir -p ${ISSM_DIR}/nightlylog/results
+EXTERNAL_TEST_FILE="$ISSM_DIR/nightlylog/results/external.xml"
+mkdir -p $ISSM_DIR/nightlylog/results
 echo "<testsuite tests=\"$NUMPACKAGES\">" > $EXTERNAL_TEST_FILE
 
 # Need a source here for when builds start midway through installation of externalpackages.
-source ${ISSM_DIR}/etc/environment.sh
-
-if [ "${OS}" == CYGWIN* ]; then
+source $ISSM_DIR/etc/environment.sh
+
+if [ "$OS" == "win" ]; then
         echo " == WINDOWS ENVIRONMENT DETECTED =="
-        source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh
+        source $ISSM_DIR/externalpackages/windows/windows_environment.sh
 fi
 
@@ -172 +175 @@
 
         #install if requested or if previous install has not been successful
-        if [ "${ISSM_EXTERNALPACKAGES}" == "yes" ]; then # NOTE: Removed check on if 'install' directory exist
-                cd ${ISSM_DIR}/externalpackages/$PACKAGENAME
+        if [ "$ISSM_EXTERNALPACKAGES" == "yes" ]; then # NOTE: Removed check on if 'install' directory exist
+                cd $ISSM_DIR/externalpackages/$PACKAGENAME
 
                 echo "======================================================";
@@ -180 +183 @@
 
                 ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log
-                if [ $? -ne 0 ] && [ "${PACKAGENAME}" != "boost" ]; then
+                if [ $? -ne 0 ] && [ "$PACKAGENAME" != "boost" ]; then
                         cat compil.log
                         echo "======================================================";
@@ -194 +197 @@
                         echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\"/>" >> $EXTERNAL_TEST_FILE
                 fi
-                source ${ISSM_DIR}/etc/environment.sh
+                source $ISSM_DIR/etc/environment.sh
 
                 #If external package is rebuilt, we also need to recompile
@@ -217 +220 @@
 
 # Source here to include any newly installed externalpackages on the path.
-source ${ISSM_DIR}/etc/environment.sh
-
-if [ "${OS}" == CYGWIN* ]; then
+source $ISSM_DIR/etc/environment.sh
+
+if [ "$OS" == "win" ]; then
         echo " == WINDOWS ENVIRONMENT DETECTED =="
-        source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh
+        source $ISSM_DIR/externalpackages/windows/windows_environment.sh
 fi
 
@@ -241 +244 @@
         #export EMCC_DEBUG=1 # Uncomment to enable debugging
         export EMCC_CFLAGS="-s ERROR_ON_UNDEFINED_SYMBOLS=0" # Required after v1.38.14 to avoid undefined symbol warnings from our Fortran object files being treated as errors
-        source ${ISSM_DIR}/externalpackages/emscripten/install/emsdk_env.sh
+        source $ISSM_DIR/externalpackages/emscripten/install/emsdk_env.sh
 fi
 
 #}}}
 #ISSM compilation yes/no                (ISSM_COMPILATION) {{{
-if [ "${ISSM_COMPILATION}" == "yes" ]; then
+if [ "$ISSM_COMPILATION" == "yes" ]; then
         cd $ISSM_DIR
-        if [ "${ISSM_RECONFIGURE}" == "yes" ]; then
+        if [ "$ISSM_RECONFIGURE" == "yes" ]; then
                 echo "======================================================";
                 echo "             Cleaning up and reconfiguring            "
@@ -259 +262 @@
                         exit 1
                 fi
-                eval "./configure ${ISSM_CONFIG}"
+                eval "./configure $ISSM_CONFIG"
                 if [ $? -ne 0 ]; then
                         echo "ISSM configuration failed (see options below)"
@@ -273 +276 @@
         echo "======================================================"
         if [ $NUMCPUS_INSTALL -gt 1 ]; then
-                echo "Making with ${NUMCPUS_INSTALL} cpus"
-
-                # To debug compilation/linking, add 'V=1' option to the call to make
-                #make -j $NUMCPUS_INSTALL V=1
+                echo "Making with " $NUMCPUS_INSTALL " cpus"
                 make -j $NUMCPUS_INSTALL
         else
-                #make V=1
                 make
         fi
@@ -293 +292 @@
         fi
         make install
-elif [ "${ISSM_COMPILATION}" == "no" ]; then
+elif [ "$ISSM_COMPILATION" == "no" ]
+then
         echo "Skipping ISSM compilation"
 else
@@ -311 +311 @@
         for (( i=1;i<=$NUMCPUS_RUN;i++ )); do
                 #Launch matlab and the nightly run script
-                cat > ${ISSM_DIR}/nightlylog/matlab_run$i.m << EOF
+                cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF
                 warning off %necessary to avoid a log of several Go for parallel runs
                 try,
-                        $(if [ "${MATLAB_NROPTIONS}" = "" ]; then
-                                echo "runme('output','nightly','rank',${i},'numprocs',${NUMCPUS_RUN});"
+                        $(if [ "$MATLAB_NROPTIONS" = "" ]; then
+                                echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
                         else
-                                echo "runme(${MATLAB_NROPTIONS},'output','nightly','rank',${i},'numprocs',${NUMCPUS_RUN});"
+                                echo "runme($MATLAB_NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
                         fi)
                 catch me,
@@ -332 +332 @@
 EOF
                 cd $ISSM_DIR/test/NightlyRun
-                if [[ "${OS}" == CYGWIN* || "${OS}" == MINGW* ]]; then
-                        $MATLAB_PATH/bin/matlab -nodesktop -nosplash -nojvm -r "addpath ${ISSM_DIR_WIN}/src/m/dev; devpath; addpath ${ISSM_DIR_WIN}/nightlylog; matlab_run$i" -logfile ${ISSM_DIR_WIN}/nightlylog/matlab_log$i.log &
+                if [ "$OS" = "win" ]; then
+                        $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR_WIN/src/m/dev; devpath; addpath $ISSM_DIR_WIN/nightlylog/; matlab_run$i" -logfile $ISSM_DIR_WIN/nightlylog/matlab_log$i.log &
                 else
-                        $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath ${ISSM_DIR}/src/m/dev; devpath; addpath ${ISSM_DIR}/nightlylog; matlab_run$i" -logfile ${ISSM_DIR}/nightlylog/matlab_log$i.log &
+                        $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; matlab_run$i" -logfile $ISSM_DIR/nightlylog/matlab_log$i.log &
                 fi
         done
 
-        # Wait for MATLAB to exit
-        if [[ "${OS}" == CYGWIN* ]]; then
+        #wait until matlab closes
+        if [ "$OS" = "win" ]; then
                 sleep 5;
-                echo "Waiting for MATLAB to exit"
+                echo "Waiting for matlab on windows"
                 pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}')
                 echo '-----------------------------'
-                echo "pid: ${pid}"
+                echo "pid: $pid"
                 echo '-----------------------------'
-                while [ -n "${pid}" ]; do
+                while [ -n "$pid" ]; do
                         pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}')
                         sleep 1;
                 done
                 echo "DONE!"
-        elif [[ "${OS}" == MINGW* ]]; then
-                # NOTE: The PID query used here may work as well on Cygwin. If so, combine the two conditional blocks.
-                sleep 5;
-                echo "Waiting for MATLAB to exit"
-                pid=$(ps -W | grep MATLAB | awk '{print $1}')
-                echo '-----------------------------'
-                echo "pid: ${pid}"
-                echo '-----------------------------'
-                while [ -n "${pid}" ]; do
-                        pid=$(ps -W | grep MATLAB | awk '{print $1}')
-                        sleep 1;
-                done
         else
                 wait
         fi
 
-        # Concatenate logs
-        cd $ISSM_DIR/nightlylog
+        #concatenate reports
+        cd $ISSM_DIR/nightlylog/
+        #echo 'CHECKING NIGHTLYLOG DIRECTORY'
+        #echo '-----------------------------'
+        #ls -la
+        #echo '-----------------------------'
 
         if [ -f matlab_log.log ]; then
@@ -376 +368 @@
 
         for job in `jobs -p`; do
-                #echo "Waiting on: ${job}" # Commented out because it really has nothing to do with MATLAB processes
+                echo "Waiting on: $job"
                 wait $job
         done
@@ -395 +387 @@
 if [ $PYTHON_TEST -eq 1 ]; then
         #Launch all tests on different cpus
-        export PYTHONPATH="${ISSM_DIR}/src/m/dev"
+        export PYTHONPATH="$ISSM_DIR/src/m/dev"
         export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
         export PYTHONUNBUFFERED=1 #we don't want python to buffer otherwise issm.exe output is not captured
@@ -406 +398 @@
         done
 
-        # Concatenate logs
-        cd $ISSM_DIR/nightlylog
+        # concatenate reports
+        cd $ISSM_DIR/nightlylog/
         if [ -f python_log.log ]; then
                 rm python_log.log
@@ -414 +406 @@
         for job in `jobs -p`
         do
-                echo "Waiting on: ${job}"
+                echo "Waiting on: $job"
                 wait $job
         done
@@ -437 +429 @@
 # }}}
 
-# Process logs to be JUnit compatible
+#process logs to be junit compatible
 #{{{
 cd $ISSM_DIR/nightlylog

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])
@@ -319 +318 @@
                         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 MSVC (Windows) build])
+        AC_MSG_CHECKING([if this is a 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
@@ -353 +338 @@
                 [MATLAB_ROOT="no"]                                                                                                      dnl action if not given
         )
+        AC_MSG_CHECKING([for MATLAB])
         if test "x${MATLAB_ROOT}" == "xno"; then
                 HAVE_MATLAB=no
@@ -371 +357 @@
                 AC_DEFINE([_HAVE_MATLAB_], [1], [with MATLAB in ISSM src])
 
-                dnl Set MEX* variable
+                dnl Set MEXLIB, MEXLINK, and MEXEXT
                 AC_MSG_CHECKING([MATLAB's mex compilation flags])
 
@@ -381 +367 @@
                                 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"
+                                        MEXLINK="-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"
+                                        MEXLINK="-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"
+                                        MEXLINK="-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${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas"
-                        ;;
-                        *)
+                                MEXLINK=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDFLAGS | sed -e "s/         LDFLAGS            = //g")
+                                MEXLIB=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep CXXLIBS | sed -e "s/         CXXLIBS            = //g")
                                 MEXEXT=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
-                                MATLABINCL="-I${MATLAB_ROOT}/extern/include"
-                                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")
+                                dnl version 2014 and up
                                 if test -z "${MEXEXT}"; then
                                         echo "#include <mex.h>" > conftest.cpp
@@ -429 +392 @@
                                         ${MATLAB_ROOT}/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1
                                         rm -f conftest.cpp
-                                        MEXLINKFLAGS=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g")
+                                        MEXLINK=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g")
                                         MEXLIB=$(cat conftest.tmp | grep LINKLIBS | sed -e "s/LINKLIBS ://g")
                                         MEXEXT=$(cat conftest.tmp | grep LDEXT | sed -e "s/LDEXT ://g" | awk '{print $[1]}')
@@ -439 +402 @@
 
                                 dnl Make sure mexFunction.map is not in MEXLIB to avoid problems with global variables
-                                dnl MEXLINKFLAGS=$(echo ${MEXLINKFLAGS} | sed -e "s/,-expo.*mexFunction\\.map\"//g" | sed -e "s/-[[^ ]]*mexFunction\\.map//g")
-                                MEXLINKFLAGS="" dnl We actually don't need MEXLINK????
+                                dnl MEXLINK=$(echo ${MEXLINK} | sed -e "s/,-expo.*mexFunction\\.map\"//g" | sed -e "s/-[[^ ]]*mexFunction\\.map//g")
+                                MEXLINK="" dnl We actually don't need MEXLINK????
                         ;;
                 esac
@@ -448 +411 @@
                 fi
 
-                AC_SUBST([MEXEXT])
-                AC_SUBST([MEXOPTFLAGS])
-                AC_SUBST([MEXCFLAGS])
-                AC_SUBST([MEXCXXFLAGS])
                 AC_SUBST([MATLABINCL])
-                AC_SUBST([MEXLINKFLAGS])
+                MATLABWRAPPEREXT=${MEXEXT}
+                AC_SUBST([MATLABWRAPPEREXT])
                 AC_SUBST([MEXLIB])
+                AC_SUBST([MEXLINK])
         fi
         dnl }}}
         dnl JavaScript{{{
-        AC_MSG_CHECKING([for JavaScript])
         AC_ARG_WITH(
                 [javascript],
@@ -465 +425 @@
                 [JAVASCRIPT="no"]
         )
+        AC_MSG_CHECKING([for JavaScript])
         if test "x${JAVASCRIPT}" == "xno"; then
                 HAVE_JAVASCRIPT=no
@@ -477 +438 @@
         dnl }}}
         dnl Triangle {{{
-        AC_MSG_CHECKING([for triangle])
         AC_ARG_WITH(
                 [triangle-dir],
@@ -484 +444 @@
                 [TRIANGLE_ROOT="no"]
         )
+        AC_MSG_CHECKING([for triangle])
         if test "x${TRIANGLE_ROOT}" == "xno"; then
                 HAVE_TRIANGLE=no
@@ -522 +483 @@
                                 fi
                         ;;
-                        *mingw*)
-                                if test "x${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${TRIANGLE_ROOT}/lib -ltriangle"
-                                fi
-                        ;;
                 esac
                 AC_DEFINE([_HAVE_TRIANGLE_], [1], [with Triangle in ISSM src])
@@ -545 +490 @@
         dnl }}}
         dnl Boost{{{
-        AC_MSG_CHECKING([for Boost])
         AC_ARG_WITH(
                 [boost-dir],
@@ -552 +496 @@
                 [BOOST_ROOT="no"]
         )
+        AC_MSG_CHECKING([for Boost])
         if test "x${BOOST_ROOT}" == "xno"; then
                 HAVE_BOOST=no
@@ -578 +523 @@
         dnl }}}
         dnl Dakota{{{
-        AC_MSG_CHECKING([for Dakota])
         AC_ARG_WITH(
                 [dakota-dir],
@@ -585 +529 @@
                 [DAKOTA_ROOT="no"]
         )
+        AC_MSG_CHECKING([for Dakota])
         if test "x${DAKOTA_ROOT}" == "xno"; then
                 HAVE_DAKOTA=no
@@ -602 +547 @@
                 AC_MSG_CHECKING(for Dakota version)
                 dnl TODO:       Check if this method applies to all other versions of 
-                dnl                     Dakota (it should as long as the Dakota binaries have been 
+                dnl                     Dakota (it should as long as the Dakota binaries have been
                 dnl             compiled). If so, we can remove the other methods of 
                 dnl                     getting the version.
@@ -619 +564 @@
                 fi
                 AC_MSG_RESULT([${DAKOTA_VERSION}])
-                AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_], ${DAKOTA_VERSION}, [Dakota version number])
+                AC_DEFINE_UNQUOTED(_DAKOTA_VERSION_, "${DAKOTA_VERSION}", [Dakota version number])
 
                 DAKOTAFLAGS=""
@@ -734 +679 @@
                 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])
@@ -750 +695 @@
         dnl }}}
         dnl Python{{{
-        AC_MSG_CHECKING([for Python])
         AC_ARG_WITH(
                 [python-dir],
@@ -764 +708 @@
                 [PYTHON_VERSION="no"]
         )
+        AC_MSG_CHECKING([for Python])
         if test "x${PYTHON_ROOT}" == "xno"; then
                 HAVE_PYTHON=no
@@ -790 +735 @@
                 dnl Determine major version
                 PYTHON_MAJOR=${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"
@@ -806 +751 @@
                         PYTHONINCL=-I${PYTHON_ROOT}/include/python${PYTHON_VERSION}m
                 else
-                        AC_MSG_ERROR([Python.h not found! Please locate this file and contact ISSM developers via forum or email.]);
+                        AC_MSG_ERROR([Python.h not found, locate this file and contact ISSM developers]);
                 fi
                 AC_MSG_RESULT([found])
@@ -819 +764 @@
                                 PYTHONLINK="-shared"
                         ;;
+                        *linux*)
+                                PYTHONLINK="-shared"
+                        ;;
                         *darwin*)
                                 PYTHONLINK="-dynamiclib"
-                        ;;
-                        *linux*)
-                                PYTHONLINK="-shared"
-                        ;;
-                        *mingw*)
-                                PYTHONLINK="-shared"
-                        ;;
-                        *msys*)
-                                PYTHONLINK="-shared"
                         ;;
                 esac
@@ -842 +781 @@
         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=${withval}],
+                [PYTHON_NUMPY_ROOT="no"]
+        )
+
         dnl NOTE: You can find NumPy by running,
         dnl
@@ -847 +797 @@
         dnl             >>> numpy.__file__
         dnl
-        dnl TODO:
-        dnl - Replace references to python-numpy with numpy (and similar terms)
-        dnl       project-wide
-        dnl
+
         AC_MSG_CHECKING(for python-numpy)
-        AC_ARG_WITH(
-                [python-numpy-dir],
-                AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory]),
-                [PYTHON_NUMPY_ROOT=${withval}],
-                [PYTHON_NUMPY_ROOT="no"]
-        )
         if test "x${PYTHON_NUMPY_ROOT}" == "xno"; then
                 HAVE_PYTHON_NUMPY=no
@@ -876 +817 @@
         dnl }}}
         dnl Chaco{{{
-        AC_MSG_CHECKING([for Chaco])
         AC_ARG_WITH(
                 [chaco-dir],
@@ -883 +823 @@
                 [CHACO_ROOT="no"]
         )
+        AC_MSG_CHECKING([for Chaco])
         if test "x${CHACO_ROOT}" == "xno"; then
                 HAVE_CHACO=no
@@ -904 +845 @@
         dnl }}}
         dnl ESMF{{{
-        AC_MSG_CHECKING([for ESMF])
         AC_ARG_WITH(
                 [esmf-dir],
@@ -911 +851 @@
                 [ESMF_ROOT="no"]
         )
+        AC_MSG_CHECKING([for ESMF])
         if test "x${ESMF_ROOT}" == "xno"; then
                 HAVE_ESMF=no
@@ -932 +873 @@
         dnl }}}
         dnl CoDiPack{{{
-        AC_MSG_CHECKING([for CoDiPack])
         AC_ARG_WITH(
                 [codipack-dir],
@@ -939 +879 @@
                 [CODIPACK_ROOT="no"]
         )
+        AC_MSG_CHECKING([for CoDiPack])
         if test "x${CODIPACK_ROOT}" == "xno"; then
                 HAVE_CODIPACK=no
@@ -960 +901 @@
         dnl }}}
         dnl Tape Allocation {{{
-        AC_MSG_CHECKING(for tape allocation)
         AC_ARG_ENABLE(
                 [tape-alloc],                                                                                                                           dnl feature
@@ -967 +907 @@
                 [enable_tape_alloc=no]
         )
+        AC_MSG_CHECKING(for tape allocation)
         if test "x${enable_tape_alloc}" == "xyes"; then
                 AC_DEFINE([_AD_TAPE_ALLOC_], [1], [enable a priori tape allocation for AD])
@@ -973 +914 @@
         dnl }}}
         dnl ADOL-C {{{
-        AC_MSG_CHECKING([for ADOL-C])
         AC_ARG_WITH(
                 [adolc-dir],
@@ -980 +920 @@
                 [ADOLC_ROOT="no"]
         )
+        AC_MSG_CHECKING([for ADOL-C])
         if test "x${ADOLC_ROOT}" == "xno"; then
                 HAVE_ADOLC=no
@@ -1004 +945 @@
         dnl }}}
         dnl ADOL-C version{{{
-        AC_MSG_CHECKING(for ADOL-C version)
         AC_ARG_WITH(
                 [adolc-version],
@@ -1011 +951 @@
                 [ADOLC_VERSION=2]
         )
-        AC_DEFINE_UNQUOTED([_ADOLC_VERSION_], ${ADOLC_VERSION}, [ADOL-C version])
+        AC_MSG_CHECKING(for 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],
@@ -1022 +963 @@
                 [ADIC2_ROOT="no"]
         )
+        AC_MSG_CHECKING([for ADIC2])
         if test "x${ADIC2_ROOT}" == "xno"; then
                 HAVE_ADIC2=no
@@ -1043 +985 @@
         dnl }}}
         dnl ATLAS {{{
-        AC_MSG_CHECKING(for ATLAS and CBLAS libraries)
         AC_ARG_WITH(
                 [atlas-dir],
@@ -1050 +991 @@
                 [ATLAS_ROOT="no"]
         )
+        AC_MSG_CHECKING(for ATLAS and CBLAS libraries)
         if test "x${ATLAS_ROOT}" == "xno"; then
                 HAVE_ATLAS=no
@@ -1066 +1008 @@
                                 ATLASLIB="-L`cygpath -m ${ATLAS_ROOT}` -Wl,libatlas.lib  -Wl,libcblas.lib"
                         ;;
+                        *linux*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm "
+                        ;;
                         *darwin*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
-                        ;;
-                        *linux*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
-                        ;;
-                        *mingw*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
-                        ;;
-                        *msys*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm "
                         ;;
                 esac
@@ -1084 +1020 @@
         dnl }}}
         dnl GSL{{{
-        AC_MSG_CHECKING([for GSL])
         AC_ARG_WITH(
                 [gsl-dir],
@@ -1091 +1026 @@
                 [GSL_ROOT="no"]
         )
+        AC_MSG_CHECKING([for GSL])
         if test "x${GSL_ROOT}" == "xno"; then
                 HAVE_GSL=no
@@ -1116 +1052 @@
         dnl }}}
         dnl AMPI (ADOL-C){{{
-        AC_MSG_CHECKING([for AMPI])
         AC_ARG_WITH(
                 [ampi-dir],
@@ -1123 +1058 @@
                 [AMPI_ROOT="no"]
         )
+        AC_MSG_CHECKING([for AMPI])
         if test "x${AMPI_ROOT}" == "xno"; then
                 HAVE_AMPI=no
@@ -1152 +1088 @@
         dnl }}}
         dnl Adjoint MPI (CoDiPack){{{
-        AC_MSG_CHECKING([for Adjoint MPI])
         AC_ARG_WITH(
                 [adjointmpi-dir],
@@ -1159 +1094 @@
                 [ADJOINTMPI_ROOT="no"]
         )
+        AC_MSG_CHECKING([for Adjoint MPI])
         if test "x${ADJOINTMPI_ROOT}" == "xno"; then
                 HAVE_ADJOINTMPI=no
@@ -1186 +1122 @@
         dnl }}}
         dnl MeDiPack (CoDiPack, ADOL-C dev){{{
-        AC_MSG_CHECKING([for MeDiPack])
         AC_ARG_WITH(
                 [medipack-dir],
@@ -1193 +1128 @@
                 [MEDIPACK_ROOT="no"]
         )
+        AC_MSG_CHECKING([for MeDiPack])
         if test "x${MEDIPACK_ROOT}" == "xno"; then
                 HAVE_MEDIPACK=no
@@ -1218 +1154 @@
         dnl }}}
         dnl HDF5 {{{
-        AC_MSG_CHECKING(for HDF5 libraries)
         AC_ARG_WITH(
                 [hdf5-dir],
@@ -1225 +1160 @@
                 [HDF5_ROOT="no"]
         )
+        AC_MSG_CHECKING(for HDF5 libraries)
         if test "x${HDF5_ROOT}" == "xno"; then
                 HAVE_HDF5=no
@@ -1245 +1181 @@
                                 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${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
                         ;;
-                        *mingw*)
-                                HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
-                        ;;
-                        *msys*)
+                        *darwin*)
                                 HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
                         ;;
@@ -1263 +1193 @@
         dnl }}}
         dnl PETSc{{{
-        AC_MSG_CHECKING([for PETSc])
         AC_ARG_WITH(
                 [petsc-dir],
@@ -1270 +1199 @@
                 [PETSC_ROOT="no"]
         )
+        AC_MSG_CHECKING([for PETSc])
         if test "x${PETSC_ROOT}" == "xno"; then
                 HAVE_PETSC=no
@@ -1290 +1220 @@
                 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}])
 
@@ -1332 +1262 @@
                                         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 ${PETSC_MINOR} -ge 3; then
-                                                PETSCLIB+=" -lmetis"
-                                        fi
                                 fi
                         ;;
@@ -1360 +1280 @@
                                 fi
                         ;;
-                        *mingw*)
-                                PETSCLIB="-Wl,${PETSC_ROOT}/lib/libpetsc.a"
-                        ;;
-                        *msys*)
-                                PETSCLIB="${PETSC_ROOT}/lib -lpetsc"
+                        *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 ${PETSC_MINOR} -ge 3; then
+                                                PETSCLIB+=" -lmetis"
+                                        fi
+                                fi
                         ;;
                 esac
@@ -1375 +1299 @@
         dnl MPI{{{
         AC_MSG_CHECKING(for MPI)
+
         AC_ARG_WITH(
                 [mpi-include],
@@ -1381 +1306 @@
                 [MPI_INCLUDE=""]
         )
+
         AC_ARG_WITH(
                 [mpi-libdir],
@@ -1387 +1313 @@
                 [MPI_LIBDIR=""]
         )
+
         AC_ARG_WITH(
                 [mpi-libflags],
@@ -1393 +1320 @@
                 [MPI_LIBFLAGS=""]
         )
+
         if test -z "${MPI_INCLUDE}"; then
                 HAVE_MPI=no
@@ -1435 +1363 @@
         dnl }}}
         dnl SCOTCH{{{
-        AC_MSG_CHECKING([for SCOTCH])
         AC_ARG_WITH(
                 [scotch-dir],
@@ -1442 +1369 @@
                 [SCOTCH_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SCOTCH])
         if test "x${SCOTCH_ROOT}" == "xno"; then
                 HAVE_SCOTCH=no
@@ -1474 +1402 @@
         dnl }}}
         dnl METIS{{{
-        AC_MSG_CHECKING([for METIS])
-        AC_ARG_WITH(
-                [metis-dir],
-                AS_HELP_STRING([--with-metis-dir=DIR], [METIS root directory, necessary for serial build]),
-                [METIS_ROOT=${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
+
+        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 "${VENDOR}" != "MSVC-Win64-par"; then
+                dnl In PETSc >=3.3, METIS is provided
+                HAVE_METIS="yes"
+                AC_DEFINE([_METIS_VERSION_], [5], [METIS version number])
+                AC_DEFINE([_HAVE_METIS_], [1], [with METIS in ISSM src])
+        else
+                AC_ARG_WITH(
+                        [metis-dir],
+                        AS_HELP_STRING([--with-metis-dir=DIR], [METIS root directory, necessary for serial build]),
+                        [METIS_ROOT=${withval}],
+                        [METIS_ROOT="no"]
+                )
+                AC_MSG_CHECKING([for METIS])
+                if test "x${METIS_ROOT}" == "xno"; then
+                        HAVE_METIS=no
+                else
                         HAVE_METIS=yes
-                        METIS_ROOT="${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" ${METIS_ROOT}/include/metis.h | sed 's|.*METIS_VER_MAJOR[[:space:]]*||')
+                        if ! test -d "${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${HAVE_METIS}" == "xyes"])
+
                 dnl METIS libraries and header files
-                if test "x${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])
-                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" ${PARMETIS_ROOT}/include/parmetis.h | sed 's|.*PARMETIS_MAJOR_VERSION[[:space:]]*||')
-                dnl METIS libraries and header files
-                #if test "x${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"])
+                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"])
         dnl }}}
         dnl Toolkit for Advanced Optimization (TAO){{{
-        AC_MSG_CHECKING([for TAO])
         AC_ARG_WITH(
                 [tao-dir],
@@ -1612 +1486 @@
                 [TAO_ROOT="no"]
         )
+        AC_MSG_CHECKING([for TAO])
+
         if test "x${HAVE_PETSC}" == "xyes" && test "x${PETSC_MAJOR}" == "x3" && test ${PETSC_MINOR} -ge 5; then
                 dnl In PETSc >= 3.5, TAO is provided
@@ -1639 +1515 @@
         dnl }}}
         dnl M1QN3{{{
-        AC_MSG_CHECKING([for M1QN3])
         AC_ARG_WITH(
                 [m1qn3-dir],
@@ -1646 +1521 @@
                 [M1QN3_ROOT="no"]
         )
+        AC_MSG_CHECKING([for M1QN3])
         if test "x${M1QN3_ROOT}" == "xno"; then
                 HAVE_M1QN3=no
@@ -1664 +1540 @@
         dnl }}}
         dnl PROJ{{{
-        AC_MSG_CHECKING([for PROJ])
         AC_ARG_WITH(
                 [proj-dir],
@@ -1671 +1546 @@
                 [PROJ_ROOT="no"]
         )
+        AC_MSG_CHECKING([for PROJ])
         if test "x${PROJ_ROOT}" == "xno"; then
                 HAVE_PROJ=no
@@ -1692 +1568 @@
         dnl }}}
         dnl SLEPc{{{
-        AC_MSG_CHECKING([for SLEPc])
         AC_ARG_WITH(
                 [slepc-dir],
@@ -1699 +1574 @@
                 [SLEPC_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SLEPc])
         if test "x${SLEPC_ROOT}" == "xno"; then
                 HAVE_SLEPC=no
@@ -1719 +1595 @@
         dnl }}}
         dnl shapelib{{{
-        AC_MSG_CHECKING([for shapelib])
         AC_ARG_WITH(
                 [shapelib-dir],
@@ -1726 +1601 @@
                 [SHAPELIB_ROOT="no"]
         )
+        AC_MSG_CHECKING([for shapelib])
         if test "x${SHAPELIB_ROOT}" == "xno"; then
                 HAVE_SHAPELIB=no
@@ -1746 +1622 @@
         dnl }}}
         dnl ScaLAPACK{{{
+
         dnl NOTE: User should supply path to root directory or libraries, but not both
-        dnl
-        AC_MSG_CHECKING([for ScaLAPACK])
         AC_ARG_WITH(
                 [scalapack-dir],
@@ -1761 +1636 @@
                 [SCALAPACKLIB="no"]
         )
+        AC_MSG_CHECKING([for ScaLAPACK])
         if test "x${SCALAPACK_ROOT}" == "xno" && test "x${SCALAPACKLIB}" == "xno"; then
                 HAVE_SCALAPACK=no
@@ -1769 +1645 @@
                 fi
                 HAVE_SCALAPACK=yes
-                if test "${VENDOR}" == "win-msys2"; then
-                        SCALAPACKLIB="-Wl,${SCALAPACK_ROOT}/lib/libscalapack.a"
-                else
-                        SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack"
-                fi
+                SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack"
         elif test "x${SCALAPACKLIB}" != "xno"; then
                 dnl Value of SCALAPACKLIB should be valid here, so no need to set it (as above)
@@ -1789 +1661 @@
         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],
@@ -1808 +1667 @@
                 [BLASLAPACK_ROOT="no"]
         )
-        if (test "x${BLAS_ROOT}" = "xno" || test "x${LAPACK_ROOT}" = "xno") && test "x${BLASLAPACK_ROOT}" = "xno"; then
+        AC_MSG_CHECKING([for BLAS/LAPACK])
+        if test "x${BLASLAPACK_ROOT}" == "xno" ; then
                 HAVE_BLASLAPACK=no
         else
                 HAVE_BLASLAPACK=yes
-                if ! test -d "${BLAS_ROOT}" || ! test -d "${LAPACK_ROOT}"; then
-                        if ! test -d "${BLASLAPACK_ROOT}"; then
-                                AC_MSG_ERROR([Use either --with-blas-dir and --with-lapack-dir *or* --with-blaslapack-dir]);
-                        fi
+                if ! test -d "${BLASLAPACK_ROOT}"; then
+                        AC_MSG_ERROR([BLAS/LAPACK directory provided (${BLASLAPACK_ROOT}) does not exist!]);
                 fi
         fi
@@ -1822 +1680 @@
         dnl BLAS/LAPACK libraries and header files
         if test "x${HAVE_BLASLAPACK}" == "xyes"; then
+                BLASLAPACKINCL=""
                 case "${host_os}" in
                         *cygwin*)
@@ -1850 +1709 @@
                                 fi
                         ;;
-                        *mingw*)
-                                if test -d "${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${BLAS_ROOT}/lib -lblas"
-                                fi
-                        ;;
                 esac
                 AC_DEFINE([_HAVE_BLASLAPACK_], [1], [with BLAS/LAPACK in ISSM src])
                 AC_SUBST([BLASLAPACKLIB])
+                AC_SUBST([BLASLAPACKINCL])
         fi
         dnl }}}
         dnl Math Kernel Library (MKL){{{
-        AC_MSG_CHECKING([for MKL])
         AC_ARG_WITH(
                 [mkl-libflags],
@@ -1894 +1722 @@
                 [MKL_LIBFLAGS="no"]
         )
+        AC_MSG_CHECKING([for MKL])
         if test "x${MKL_LIBFLAGS}" == "xno"; then
                 HAVE_MKL=no
@@ -1906 +1735 @@
         dnl }}}
         dnl PlaLAPACK{{{
+
         dnl TODO:       Handle user supplying path to root directory *or* individual
         dnl             arguments (like ScaLAPACK)
@@ -1940 +1770 @@
         dnl }}}
         dnl MUMPS{{{
-        AC_MSG_CHECKING([for MUMPS])
         AC_ARG_WITH(
                 [mumps-dir],
@@ -1947 +1776 @@
                 [MUMPS_ROOT="no"]
         )
+        AC_MSG_CHECKING([for MUMPS])
         if test "x${MUMPS_ROOT}" == "xno"; then
                 HAVE_MUMPS=no
@@ -1961 +1791 @@
                 MUMPSINCL="-I${MUMPS_ROOT}/include"
                 if test "x${MUMPS_ROOT}" == "x${PETSC_ROOT}"; then
-                        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,${MUMPS_ROOT}/lib/libpord.a"
+                        if test "x${PETSC_MAJOR}" == "x2"; then
+                                MUMPSLIB="-L${MUMPS_ROOT}/lib "
                         else
                                 MUMPSLIB="-L${MUMPS_ROOT}/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis -lzmumps -lmetis"
@@ -2011 +1841 @@
         dnl }}}
         dnl BLACS{{{
-        AC_MSG_CHECKING([for BLACS])
         AC_ARG_WITH(
                 [blacs-dir],
@@ -2018 +1847 @@
                 [BLACS_ROOT="no"]
         )
+        AC_MSG_CHECKING([for BLACS])
         if test "x${BLACS_ROOT}" == "xno"; then
                 HAVE_BLACS=no
@@ -2038 +1868 @@
         dnl }}}
         dnl HYPRE{{{
-        AC_MSG_CHECKING([for HYPRE])
         AC_ARG_WITH(
                 [hypre-dir],
@@ -2045 +1874 @@
                 [HYPRE_ROOT="no"]
         )
+        AC_MSG_CHECKING([for HYPRE])
         if test "x${HYPRE_ROOT}" == "xno"; then
                 HAVE_HYPRE=no
@@ -2065 +1895 @@
         dnl }}}
         dnl Prometheus{{{
-        AC_MSG_CHECKING([for Prometheus])
         AC_ARG_WITH(
                 [prometheus-dir],
@@ -2072 +1901 @@
                 [PROMETHEUS_ROOT="no"]
         )
+        AC_MSG_CHECKING([for Prometheus])
         if test "x${PROMETHEUS_ROOT}" == "xno"; then
                 HAVE_PROMETHEUS=no
@@ -2092 +1922 @@
         dnl }}}
         dnl SEMIC{{{
-        AC_MSG_CHECKING([for SEMIC])
         AC_ARG_WITH(
                 [semic-dir],
@@ -2099 +1928 @@
                 [SEMIC_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SEMIC])
         if test "x${SEMIC_ROOT}" == "xno"; then
                 HAVE_SEMIC=no
@@ -2120 +1950 @@
         dnl }}}
         dnl SPAI{{{
-        AC_MSG_CHECKING([for SPAI])
         AC_ARG_WITH(
                 [spai-dir],
@@ -2127 +1956 @@
                 [SPAI_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SPAI])
         if test "x${SPAI_ROOT}" == "xno"; then
                 HAVE_SPAI=no
@@ -2147 +1977 @@
         dnl }}}
         dnl SuperLU{{{
-        AC_MSG_CHECKING([for SuperLU])
         AC_ARG_WITH(
                 [superlu-dir],
@@ -2154 +1983 @@
                 [SUPERLU_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SuperLU])
         if test "x${SUPERLU_ROOT}" == "xno"; then
                 HAVE_SUPERLU=no
@@ -2174 +2004 @@
         dnl }}}
         dnl SPOOLES{{{
-        AC_MSG_CHECKING([for SPOOLES])
         AC_ARG_WITH(
                 [spooles-dir],
@@ -2181 +2010 @@
                 [SPOOLES_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SPOOLES])
         if test "x${SPOOLES_ROOT}" == "xno"; then
                 HAVE_SPOOLES=no
@@ -2201 +2031 @@
         dnl }}}
         dnl PaStiX{{{
-        AC_MSG_CHECKING([for PaStiX])
         AC_ARG_WITH(
                 [pastix-dir],
@@ -2208 +2037 @@
                 [PASTIX_ROOT="no"]
         )
+        AC_MSG_CHECKING([for PaStiX])
         if test "x${PASTIX_ROOT}" == "xno"; then
                 HAVE_PASTIX=no
@@ -2229 +2059 @@
         dnl }}}
         dnl ml{{{
-        AC_MSG_CHECKING([for ml])
         AC_ARG_WITH(
                 [ml-dir],
@@ -2236 +2065 @@
                 [ML_ROOT="no"]
         )
+        AC_MSG_CHECKING([for ml])
         if test "x${ML_ROOT}" == "xno"; then
                 HAVE_ML=no
@@ -2256 +2086 @@
         dnl }}}
         dnl UMFPACK{{{
-        AC_MSG_CHECKING([for UMFPACK])
         AC_ARG_WITH(
                 [umfpack-dir],
@@ -2263 +2092 @@
                 [UMFPACK_ROOT="no"]
         )
+        AC_MSG_CHECKING([for UMFPACK])
         if test "x${UMFPACK_ROOT}" == "xno"; then
                 HAVE_UMFPACK=no
@@ -2299 +2129 @@
         dnl }}}
         dnl MATH77{{{
-        AC_MSG_CHECKING([for MATH77])
         AC_ARG_WITH(
                 [math77-dir],
@@ -2306 +2135 @@
                 [MATH77_ROOT="no"]
         )
+        AC_MSG_CHECKING([for MATH77])
         if test "x${MATH77_ROOT}" == "xno"; then
                 HAVE_MATH77=no
@@ -2324 +2154 @@
         dnl }}}
         dnl Fortran{{{
-        AC_MSG_CHECKING(for Fortran compilation)
         AC_ARG_WITH(
                 [fortran],
@@ -2331 +2160 @@
                 [FORTRAN=yes]
         )
+        AC_MSG_CHECKING(for Fortran compilation)
         if test "x${FORTRAN}" == "xyes"; then
                 HAVE_FORTRAN=yes
@@ -2394 +2224 @@
         dnl }}}
         dnl MeteoIO{{{
-        AC_MSG_CHECKING([for MeteoIO])
         AC_ARG_WITH(
                 [meteoio-dir],
@@ -2401 +2230 @@
                 [METEOIO_ROOT="no"]
         )
+        AC_MSG_CHECKING([for MeteoIO])
         if test "x${METEOIO_ROOT}" == "xno"; then
                 HAVE_METEOIO=no
@@ -2423 +2253 @@
         dnl }}}
         dnl SNOWPACK{{{
-        AC_MSG_CHECKING([for SNOWPACK])
         AC_ARG_WITH(
                 [snowpack-dir],
@@ -2430 +2259 @@
                 [SNOWPACK_ROOT="no"]
         )
+        AC_MSG_CHECKING([for SNOWPACK])
         if test "x${SNOWPACK_ROOT}" == "xno"; then
                 HAVE_SNOWPACK=no
@@ -2451 +2281 @@
         dnl }}}
         dnl NeoPZ{{{
-        AC_MSG_CHECKING([for NeoPZ])
         AC_ARG_WITH(
                 [neopz-dir],
@@ -2458 +2287 @@
                 [NEOPZ_ROOT="no"]
         )
+        AC_MSG_CHECKING([for NeoPZ])
         if test "x${NEOPZ_ROOT}" == "xno"; then
                 HAVE_NEOPZ=no
@@ -2526 +2356 @@
                 GMSH_VERSION_MAJOR=`${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_, $GMSH_VERSION_MAJOR, [Gmsh major version])
         fi      
         dnl }}}
         dnl Capabilities
         dnl with-bamg{{{
-        AC_MSG_CHECKING([for BAMG capability compilation])
         AC_ARG_WITH(
                 [bamg],
@@ -2538 +2367 @@
                 [BAMG=yes]
         )
+        AC_MSG_CHECKING([for BAMG capability compilation])
         HAVE_BAMG=no
         if test "x${BAMG}" == "xyes"; then
@@ -2547 +2377 @@
         dnl }}}
         dnl with-ocean{{{
-        AC_MSG_CHECKING(for ice/ocean coupling capability compilation)
         AC_ARG_WITH(
                 [ocean],
@@ -2554 +2383 @@
                 [OCEAN=no]
         )
+        AC_MSG_CHECKING(for ice/ocean coupling capability compilation)
+
         HAVE_OCEAN=no
         if test "x${OCEAN}" == "xyes"; then
@@ -2563 +2394 @@
         dnl }}}
         dnl with-kml{{{
-        AC_MSG_CHECKING(for kml capability compilation)
         AC_ARG_WITH(
                 [kml],
@@ -2570 +2400 @@
                 [KML=no]
         )
+        AC_MSG_CHECKING(for kml capability compilation)
+
         HAVE_KML=no
         if test "x${KML}" == "xyes"; then
@@ -2579 +2411 @@
         dnl }}}
         dnl with-kriging{{{
-        AC_MSG_CHECKING(for kriging capability compilation)
         AC_ARG_WITH(
                 [kriging],
@@ -2586 +2417 @@
                 [KRIGING=yes]
         )
+        AC_MSG_CHECKING(for kriging capability compilation)
+
         HAVE_KRIGING=no
         if test "x${KRIGING}" == "xyes"; then
@@ -2600 +2433 @@
         dnl Platform specifics
         dnl with-ios{{{
-        AC_MSG_CHECKING(for iOS compilation)
         AC_ARG_WITH(
                 [ios],
@@ -2607 +2439 @@
                 [IOS=no]
         )
+        AC_MSG_CHECKING(for iOS compilation)
+
         HAVE_IOS=no
         if test "x${IOS}" == "xyes"; then
@@ -2616 +2450 @@
         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=${withval}],
-                [ANDROID=no]
-        )
+                [ANDROID=no])
+        AC_MSG_CHECKING([for Android capability compilation])
+
         if test "x${ANDROID}" == "xjni"; then
                 HAVE_ANDROID=jni
@@ -2641 +2475 @@
         dnl }}}
         dnl with-android-ndk{{{
-        AC_MSG_CHECKING([with Android Native Development Kit (NDK)])
         AC_ARG_WITH(
                 [android-ndk],
@@ -2648 +2481 @@
                 [ANDROID_NDK_ROOT=""]
         )
+        AC_MSG_CHECKING([with Android Native Development Kit (NDK)])
+
         if test -d "${ANDROID_NDK_ROOT}"; then
                 HAVE_ANDROID_NDK=yes
@@ -2661 +2496 @@
         dnl other options
         dnl optimization{{{
-        dnl -- bypass standard optimization -g -O2 -fPIC?
-        AC_MSG_CHECKING(for C++ optimization flags)
+        dnl -- bypass standard optimization -g -O2 -fPIC -std=c++11?
         AC_ARG_WITH(
                 [cxxoptflags],
                 AS_HELP_STRING([--with-cxxoptflags=CXXOPTFLAGS], [C++ optimization flags (i.e. --with-cxxoptflags="-march=opteron -O3 -std=c++11"]),
                 [CXXOPTFLAGS=${withval}],
-                [CXXOPTFLAGS="-g -O2 -fPIC"]
-        )
+                [CXXOPTFLAGS="-g -O2 -fPIC -std=c++11"]
+        )
+        AC_MSG_CHECKING(for C++ optimization flags)
         AC_SUBST([CXXOPTFLAGS])
-        AC_MSG_RESULT([${CXXOPTFLAGS}])
+        AC_MSG_RESULT([done])
         dnl }}}
         dnl multithreading{{{
-        AC_MSG_CHECKING(for number of threads)
         AC_ARG_WITH(
                 [numthreads],
@@ -2680 +2514 @@
                 [NUMTHREADS_VALUE=1]
         )
+        AC_MSG_CHECKING(for number of threads)
         dnl Check that supplied value is an integer
         if [[ "${NUMTHREADS_VALUE}" != "${NUMTHREADS_VALUE}" 2> /dev/null ]]; then
@@ -2694 +2529 @@
                                 MULTITHREADINGLIB="-lpthread -lrt"
                         ;;
+                        *linux*)
+                                MULTITHREADINGLIB="-lpthread -lrt"
+                        ;;
                         *darwin*)
                                 MULTITHREADINGLIB="-lpthread"
                         ;;
-                        *linux*)
-                                MULTITHREADINGLIB="-lpthread -lrt"
-                        ;;
-                        *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],
@@ -2721 +2549 @@
                 [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])
@@ -2730 +2560 @@
 
         dnl Checks {{{
-        AC_MSG_CHECKING(consistency between all external packages)
+        AC_MSG_CHECKING(consistency between all libraries)
 
         dnl Check that if PETSc is requested, MPI is specified
@@ -2760 +2590 @@
 
         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@ @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@ @BLASLAPACKINCL@ @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
-if !MSYS2
-lib_LTLIBRARIES += libISSMOverload.la
-endif
+lib_LTLIBRARIES = libISSMCore.la libISSMOverload.la
 if WRAPPERS
 lib_LTLIBRARIES += libISSMModules.la
@@ -685 +682 @@
 #}}}
 #Library flags and sources {{{
-ALL_CXXFLAGS = $(CXXFLAGS) $(CXXOPTFLAGS)
-
-# Cannot have undefined symbols under msys2
-if MSYS2
-ALL_CXXFLAGS += -D_DO_NOT_LOAD_GLOBALS_
-endif
+ALLCXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS)
 
 libISSMCore_la_SOURCES  = $(issm_sources)
-libISSMCore_la_CXXFLAGS = $(ALL_CXXFLAGS) $(DAKOTAFLAGS)
+libISSMCore_la_CXXFLAGS = $(ALLCXXFLAGS) $(DAKOTAFLAGS)
 libISSMCore_la_FFLAGS = $(AM_FFLAGS)
 
 if !WINDOWS
 if !STANDALONE_LIBRARIES
-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)
+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)
 if FORTRAN
 libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB)
@@ -719 +711 @@
 endif
 
-libISSMModules_la_CXXFLAGS = $(ALL_CXXFLAGS)
+libISSMModules_la_CXXFLAGS = $(ALLCXXFLAGS)
 if !WINDOWS
 if STANDALONE_LIBRARIES
@@ -751 +743 @@
 endif
 
-if VERSION
+if STANDALONE_LIBRARIES
+libISSMCore_la_LDFLAGS = -static
+libISSMOverload_la_LDFLAGS = -static
+if WRAPPERS
+libISSMModules_la_LDFLAGS = -static
+else
+libISSMModules_la_LDFLAGS =
+endif
+else
 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
-if WRAPPERS
-libISSMModules_la_LDFLAGS += -static
-endif
-endif
-#}}}
-
-if !MSYS2
+libISSMOverload_la_LDFLAGS =
+endif
+
+#}}}
 #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 {{{
@@ -803 +778 @@
 
 #Standard libraries
-LDADD = ./libISSMCore.la 
-
-if !MSYS2
-LDADD += ./libISSMOverload.la
-endif
-
+LDADD = ./libISSMCore.la ./libISSMOverload.la
 if WRAPPERS
 LDADD += ./libISSMModules.la $(TRIANGLELIB)
@@ -814 +784 @@
 
 #External packages
-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)
+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)
 
 if FORTRAN

issm/trunk-jpl/src/wrappers/Triangle/Triangle.h

@@ -19 +19 @@
 #ifdef _HAVE_JAVASCRIPT_MODULES_
 #undef _DO_NOT_LOAD_GLOBALS_ /*only module where this needs to be undefined, so as to 
-                                                           not include IssmComm several times in the JavaScript module construct.*/
+                                                           not include IssmComm several times in the javascript Modle construct.*/
 #endif
 

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

@@ -1 @@
-AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
@@ -60 +60 @@
 AM_CXXFLAGS +=  -D_HAVE_JAVASCRIPT_MODULES_ -fPIC
 
-deps = ./libISSMJavascript.la ./libISSMApi.la ../../c/libISSMCore.la ../../c/libISSMModules.la
+deps = ./libISSMJavascript.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
 
 #Optimization flags:

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

@@ -20 +20 @@
         ./io/WriteMatlabData.cpp
 
-ALL_CXXFLAGS = -fPIC -D_WRAPPERS_
-
-# Cannot have undefined symbols under msys2
-if MSYS2
-ALL_CXXFLAGS += -D_DO_NOT_LOAD_GLOBALS_
-endif
-
-ALL_CXXFLAGS += $(CXXOPTFLAGS) $(CXXFLAGS)
+ALLCXXFLAGS= -fPIC -D_WRAPPERS_ $(CXXFLAGS) $(CXXOPTFLAGS)
 
 libISSMMatlab_la_SOURCES = $(io_sources)
-libISSMMatlab_la_CXXFLAGS = ${ALL_CXXFLAGS}
+libISSMMatlab_la_CXXFLAGS= $(ALLCXXFLAGS)
 #}}}
 #api io{{{
@@ -39 +32 @@
 endif
 
-if !MSYS2
 api_sources= ./io/ApiPrintf.cpp
 
 libISSMApi_la_SOURCES = $(api_sources)
-libISSMApi_la_CXXFLAGS = ${ALL_CXXFLAGS}
-endif
+libISSMApi_la_CXXFLAGS= $(ALLCXXFLAGS)
 #}}}
 #Wrappers {{{
@@ -91 +82 @@
 
 #Triangle library
-TRI_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER
+AM_CXXFLAGS =  -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER -D_WRAPPERS_
 
 #Matlab part
-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
+AM_LDFLAGS = -module $(MEXLINK) -shrext ${EXEEXT} --export-dynamic -rdynamic -no-undefined
 
 if !VERSION
@@ -129 +108 @@
 AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -fPIC
 
-deps += ./libISSMMatlab.la ../../c/libISSMCore.la ../../c/libISSMModules.la
-
-if !MSYS2
-deps += ./libISSMApi.la
-endif
-
-# if WINDOWS
-# deps += $(METISLIB)
-# endif
+deps += ./libISSMMatlab.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
+
+if WINDOWS
+deps += $(METISLIB)
+endif
 
 if ADOLC
@@ -147 +122 @@
 endif
 
-# #MEXLIB needs to be the last (undefined references on larsen)
-# deps += ${MEXLIB}
-
-# #Optimization flags:
-# AM_CXXFLAGS += $(CXXOPTFLAGS)
+#MEXLIB needs to be the last (undefined references on larsen)
+deps += ${MEXLIB}
+
+#Optimization flags:
+AM_CXXFLAGS += $(CXXOPTFLAGS)
 #}}}
 # Module sources and dependencies {{{
 if !WINDOWS
-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
+libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB)
 endif
 
 if STANDALONE_LIBRARIES
-libISSMMatlab_la_LDFLAGS += -static
-libISSMApi_la_LDFLAGS += -static
-deps +=  $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(CHACOLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(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)
+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)
 endif
 
 BamgConvertMesh_matlab_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp
 BamgConvertMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgConvertMesh_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+BamgConvertMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 BamgMesher_matlab_la_SOURCES = ../BamgMesher/BamgMesher.cpp
 BamgMesher_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgMesher_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+BamgMesher_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 BamgTriangulate_matlab_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp
 BamgTriangulate_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-BamgTriangulate_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+BamgTriangulate_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 if CHACO
 Chaco_matlab_la_SOURCES = ../Chaco/Chaco.cpp
 Chaco_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Chaco_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+Chaco_matlab_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 endif
 
 ContourToMesh_matlab_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp
 ContourToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToMesh_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+ContourToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 ContourToNodes_matlab_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp
 ContourToNodes_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ContourToNodes_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+ContourToNodes_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 CoordTransform_matlab_la_SOURCES = ../CoordTransform/CoordTransform.cpp
 CoordTransform_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-CoordTransform_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+CoordTransform_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 DistanceToMaskBoundary_matlab_la_SOURCES = ../DistanceToMaskBoundary/DistanceToMaskBoundary.cpp
 DistanceToMaskBoundary_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 ElementConnectivity_matlab_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp
 ElementConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ElementConnectivity_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+ElementConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 ExpToLevelSet_matlab_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp
 ExpToLevelSet_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ExpToLevelSet_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+ExpToLevelSet_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 ExpSimplify_matlab_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp
 ExpSimplify_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ExpSimplify_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+ExpSimplify_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(NEOPZLIB)
 
 InterpFromGridToMesh_matlab_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp
 InterpFromGridToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromGridToMesh_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 InterpFromMesh2d_matlab_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp
 InterpFromMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMesh2d_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 InterpFromMeshToGrid_matlab_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp
 InterpFromMeshToGrid_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 InterpFromMeshToMesh2d_matlab_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp
 InterpFromMeshToMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 InterpFromMeshToMesh3d_matlab_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp
 InterpFromMeshToMesh3d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 IssmConfig_matlab_la_SOURCES = ../IssmConfig/IssmConfig.cpp
 IssmConfig_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-IssmConfig_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+IssmConfig_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB)
 
 Kriging_matlab_la_SOURCES = ../Kriging/Kriging.cpp
 Kriging_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Kriging_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+Kriging_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJLIB)
 
 M1qn3_matlab_la_SOURCES = ../M1qn3/M1qn3.cpp
 M1qn3_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-M1qn3_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+M1qn3_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(M1QN3LIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 MeshPartition_matlab_la_SOURCES = ../MeshPartition/MeshPartition.cpp
 MeshPartition_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshPartition_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+MeshPartition_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 MeshProfileIntersection_matlab_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp
 MeshProfileIntersection_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-MeshProfileIntersection_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 NodeConnectivity_matlab_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp
 NodeConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-NodeConnectivity_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+NodeConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 PointCloudFindNeighbors_matlab_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp
 PointCloudFindNeighbors_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 PropagateFlagsFromConnectivity_matlab_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp
 PropagateFlagsFromConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 Scotch_matlab_la_SOURCES = ../Scotch/Scotch.cpp
 Scotch_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Scotch_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+Scotch_matlab_la_LIBADD = ${deps}  $(PETSCLIB) $(HDF5LIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(BLASLAPACKLIB)
 
 ShpRead_matlab_la_SOURCES = ../ShpRead/ShpRead.cpp
 ShpRead_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ShpRead_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
+ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 Triangle_matlab_la_SOURCES = ../Triangle/Triangle.cpp
 Triangle_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-Triangle_matlab_la_LIBADD = ${deps} $(TRIANGLELIB) ${AM_LIBADD}
+Triangle_matlab_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
 
 ProcessRifts_matlab_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp
 ProcessRifts_matlab_la_CXXFLAGS = ${AM_CXXFLAGS}
-ProcessRifts_matlab_la_LIBADD = ${deps} ${AM_LIBADD}
-#}}}
+ProcessRifts_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB)
+#}}}

issm/trunk-jpl/src/wrappers/matlab/include/wrapper_macros.h

@@ -34 +34 @@
 /*}}}*/
 /* WRAPPER {{{*/
-#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) /* NOTE: In this case, modulename is thrown away in the macro expansion whereas it is used in for the Python wrappers (see also: src/wrappers/python/include/wrapper_macros.h, any result of `grep -r 'WRAPPER(' $ISSM_DIR/src)` */
+#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) 
 /*}}}*/
 /* CHECKARGUMENTS {{{*/

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

@@ -1 @@
-AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @PYTHONINCL@ @PYTHON_NUMPYINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
@@ -70 +70 @@
 #       will be linked to, whether we like it or not, if no static version is
 #       available.
-# - On macOC, static linking of binaries is not supported.
+# - On macOS, static linking of binaries is not supported.
 #
 if STANDALONE_MODULES
@@ -87 +87 @@
 endif
 
-deps += ./libISSMPython.la ./libISSMApi.la ../../c/libISSMCore.la ../../c/libISSMModules.la
+deps += ./libISSMPython.la ../../c/libISSMModules.la ../../c/libISSMCore.la ./libISSMApi.la
 
 if ADOLC
@@ -106 +106 @@
 libISSMPython_la_LDFLAGS = -static
 libISSMApi_la_LDFLAGS = -static
-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)
+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)
 endif