Changeset 26744 for issm/trunk/m4

Timestamp:

12/22/21 10:39:44 (3 years ago)

Author:

Mathieu Morlighem

Message:

merged trunk-jpl and trunk for revision 26742

Location:

issm/trunk

Files:

• . (modified) (1 prop)
• m4/analyses.m4 (modified) (1 diff)
• m4/issm_options.m4 (modified) (148 diffs)

issm/trunk/m4/analyses.m4

@@ -10 +10 @@
 [
 
+dnl with-HydrologyTws{{{
+
+AC_ARG_WITH([HydrologyTws],
+
+        AS_HELP_STRING([--with-HydrologyTws = YES], [compile with HydrologyTws capabilities (default is yes)]),
+
+        [HYDROLOGYTWS=$withval],[HYDROLOGYTWS=yes])
+
+AC_MSG_CHECKING(for HydrologyTws capability compilation)
+
+
+HAVE_HYDROLOGYTWS=no 
+
+if test "x$HYDROLOGYTWS" = "xyes"; then
+
+        HAVE_HYDROLOGYTWS=yes
+
+        AC_DEFINE([_HAVE_HYDROLOGYTWS_],[1],[with HydrologyTws capability])
+
+fi
+
+AM_CONDITIONAL([HYDROLOGYTWS], [test x$HAVE_HYDROLOGYTWS = xyes])
+
+AC_MSG_RESULT($HAVE_HYDROLOGYTWS)
+
+dnl }}}
 dnl with-AdjointBalancethickness2{{{
+
 AC_ARG_WITH([AdjointBalancethickness2],
+
         AS_HELP_STRING([--with-AdjointBalancethickness2 = YES], [compile with AdjointBalancethickness2 capabilities (default is yes)]),
+
         [ADJOINTBALANCETHICKNESS2=$withval],[ADJOINTBALANCETHICKNESS2=yes])
+
 AC_MSG_CHECKING(for AdjointBalancethickness2 capability compilation)
 
+
 HAVE_ADJOINTBALANCETHICKNESS2=no 
+
 if test "x$ADJOINTBALANCETHICKNESS2" = "xyes"; then
+
         HAVE_ADJOINTBALANCETHICKNESS2=yes
+
         AC_DEFINE([_HAVE_ADJOINTBALANCETHICKNESS2_],[1],[with AdjointBalancethickness2 capability])
-fi
+
+fi
+
 AM_CONDITIONAL([ADJOINTBALANCETHICKNESS2], [test x$HAVE_ADJOINTBALANCETHICKNESS2 = xyes])
+
 AC_MSG_RESULT($HAVE_ADJOINTBALANCETHICKNESS2)
+
 dnl }}}
 dnl with-AdjointBalancethickness{{{
+
 AC_ARG_WITH([AdjointBalancethickness],
+
         AS_HELP_STRING([--with-AdjointBalancethickness = YES], [compile with AdjointBalancethickness capabilities (default is yes)]),
+
         [ADJOINTBALANCETHICKNESS=$withval],[ADJOINTBALANCETHICKNESS=yes])
+
 AC_MSG_CHECKING(for AdjointBalancethickness capability compilation)
 
+
 HAVE_ADJOINTBALANCETHICKNESS=no 
+
 if test "x$ADJOINTBALANCETHICKNESS" = "xyes"; then
+
         HAVE_ADJOINTBALANCETHICKNESS=yes
+
         AC_DEFINE([_HAVE_ADJOINTBALANCETHICKNESS_],[1],[with AdjointBalancethickness capability])
-fi
+
+fi
+
 AM_CONDITIONAL([ADJOINTBALANCETHICKNESS], [test x$HAVE_ADJOINTBALANCETHICKNESS = xyes])
+
 AC_MSG_RESULT($HAVE_ADJOINTBALANCETHICKNESS)
+
 dnl }}}
 dnl with-AdjointHoriz{{{
+
 AC_ARG_WITH([AdjointHoriz],
+
         AS_HELP_STRING([--with-AdjointHoriz = YES], [compile with AdjointHoriz capabilities (default is yes)]),
+
         [ADJOINTHORIZ=$withval],[ADJOINTHORIZ=yes])
+
 AC_MSG_CHECKING(for AdjointHoriz capability compilation)
 
+
 HAVE_ADJOINTHORIZ=no 
+
 if test "x$ADJOINTHORIZ" = "xyes"; then
+
         HAVE_ADJOINTHORIZ=yes
+
         AC_DEFINE([_HAVE_ADJOINTHORIZ_],[1],[with AdjointHoriz capability])
-fi
+
+fi
+
 AM_CONDITIONAL([ADJOINTHORIZ], [test x$HAVE_ADJOINTHORIZ = xyes])
+
 AC_MSG_RESULT($HAVE_ADJOINTHORIZ)
+
 dnl }}}
 dnl with-Balancethickness2{{{
+
 AC_ARG_WITH([Balancethickness2],
+
         AS_HELP_STRING([--with-Balancethickness2 = YES], [compile with Balancethickness2 capabilities (default is yes)]),
+
         [BALANCETHICKNESS2=$withval],[BALANCETHICKNESS2=yes])
+
 AC_MSG_CHECKING(for Balancethickness2 capability compilation)
 
+
 HAVE_BALANCETHICKNESS2=no 
+
 if test "x$BALANCETHICKNESS2" = "xyes"; then
+
         HAVE_BALANCETHICKNESS2=yes
+
         AC_DEFINE([_HAVE_BALANCETHICKNESS2_],[1],[with Balancethickness2 capability])
-fi
+
+fi
+
 AM_CONDITIONAL([BALANCETHICKNESS2], [test x$HAVE_BALANCETHICKNESS2 = xyes])
+
 AC_MSG_RESULT($HAVE_BALANCETHICKNESS2)
+
 dnl }}}
 dnl with-Balancethickness{{{
+
 AC_ARG_WITH([Balancethickness],
+
         AS_HELP_STRING([--with-Balancethickness = YES], [compile with Balancethickness capabilities (default is yes)]),
+
         [BALANCETHICKNESS=$withval],[BALANCETHICKNESS=yes])
+
 AC_MSG_CHECKING(for Balancethickness capability compilation)
 
+
 HAVE_BALANCETHICKNESS=no 
+
 if test "x$BALANCETHICKNESS" = "xyes"; then
+
         HAVE_BALANCETHICKNESS=yes
+
         AC_DEFINE([_HAVE_BALANCETHICKNESS_],[1],[with Balancethickness capability])
-fi
+
+fi
+
 AM_CONDITIONAL([BALANCETHICKNESS], [test x$HAVE_BALANCETHICKNESS = xyes])
+
 AC_MSG_RESULT($HAVE_BALANCETHICKNESS)
+
 dnl }}}
 dnl with-BalancethicknessSoft{{{
+
 AC_ARG_WITH([BalancethicknessSoft],
+
         AS_HELP_STRING([--with-BalancethicknessSoft = YES], [compile with BalancethicknessSoft capabilities (default is yes)]),
+
         [BALANCETHICKNESSSOFT=$withval],[BALANCETHICKNESSSOFT=yes])
+
 AC_MSG_CHECKING(for BalancethicknessSoft capability compilation)
 
+
 HAVE_BALANCETHICKNESSSOFT=no 
+
 if test "x$BALANCETHICKNESSSOFT" = "xyes"; then
+
         HAVE_BALANCETHICKNESSSOFT=yes
+
         AC_DEFINE([_HAVE_BALANCETHICKNESSSOFT_],[1],[with BalancethicknessSoft capability])
-fi
+
+fi
+
 AM_CONDITIONAL([BALANCETHICKNESSSOFT], [test x$HAVE_BALANCETHICKNESSSOFT = xyes])
+
 AC_MSG_RESULT($HAVE_BALANCETHICKNESSSOFT)
+
 dnl }}}
 dnl with-Balancevelocity{{{
+
 AC_ARG_WITH([Balancevelocity],
+
         AS_HELP_STRING([--with-Balancevelocity = YES], [compile with Balancevelocity capabilities (default is yes)]),
+
         [BALANCEVELOCITY=$withval],[BALANCEVELOCITY=yes])
+
 AC_MSG_CHECKING(for Balancevelocity capability compilation)
 
+
 HAVE_BALANCEVELOCITY=no 
+
 if test "x$BALANCEVELOCITY" = "xyes"; then
+
         HAVE_BALANCEVELOCITY=yes
+
         AC_DEFINE([_HAVE_BALANCEVELOCITY_],[1],[with Balancevelocity capability])
-fi
+
+fi
+
 AM_CONDITIONAL([BALANCEVELOCITY], [test x$HAVE_BALANCEVELOCITY = xyes])
+
 AC_MSG_RESULT($HAVE_BALANCEVELOCITY)
+
 dnl }}}
 dnl with-DamageEvolution{{{
+
 AC_ARG_WITH([DamageEvolution],
+
         AS_HELP_STRING([--with-DamageEvolution = YES], [compile with DamageEvolution capabilities (default is yes)]),
+
         [DAMAGEEVOLUTION=$withval],[DAMAGEEVOLUTION=yes])
+
 AC_MSG_CHECKING(for DamageEvolution capability compilation)
 
+
 HAVE_DAMAGEEVOLUTION=no 
+
 if test "x$DAMAGEEVOLUTION" = "xyes"; then
+
         HAVE_DAMAGEEVOLUTION=yes
+
         AC_DEFINE([_HAVE_DAMAGEEVOLUTION_],[1],[with DamageEvolution capability])
-fi
+
+fi
+
 AM_CONDITIONAL([DAMAGEEVOLUTION], [test x$HAVE_DAMAGEEVOLUTION = xyes])
+
 AC_MSG_RESULT($HAVE_DAMAGEEVOLUTION)
+
 dnl }}}
 dnl with-DepthAverage{{{
+
 AC_ARG_WITH([DepthAverage],
+
         AS_HELP_STRING([--with-DepthAverage = YES], [compile with DepthAverage capabilities (default is yes)]),
+
         [DEPTHAVERAGE=$withval],[DEPTHAVERAGE=yes])
+
 AC_MSG_CHECKING(for DepthAverage capability compilation)
 
+
 HAVE_DEPTHAVERAGE=no 
+
 if test "x$DEPTHAVERAGE" = "xyes"; then
+
         HAVE_DEPTHAVERAGE=yes
+
         AC_DEFINE([_HAVE_DEPTHAVERAGE_],[1],[with DepthAverage capability])
-fi
+
+fi
+
 AM_CONDITIONAL([DEPTHAVERAGE], [test x$HAVE_DEPTHAVERAGE = xyes])
+
 AC_MSG_RESULT($HAVE_DEPTHAVERAGE)
+
 dnl }}}
 dnl with-Enthalpy{{{
+
 AC_ARG_WITH([Enthalpy],
+
         AS_HELP_STRING([--with-Enthalpy = YES], [compile with Enthalpy capabilities (default is yes)]),
+
         [ENTHALPY=$withval],[ENTHALPY=yes])
+
 AC_MSG_CHECKING(for Enthalpy capability compilation)
 
+
 HAVE_ENTHALPY=no 
+
 if test "x$ENTHALPY" = "xyes"; then
+
         HAVE_ENTHALPY=yes
+
         AC_DEFINE([_HAVE_ENTHALPY_],[1],[with Enthalpy capability])
-fi
+
+fi
+
 AM_CONDITIONAL([ENTHALPY], [test x$HAVE_ENTHALPY = xyes])
+
 AC_MSG_RESULT($HAVE_ENTHALPY)
+
 dnl }}}
 dnl with-Esa{{{
+
 AC_ARG_WITH([Esa],
+
         AS_HELP_STRING([--with-Esa = YES], [compile with Esa capabilities (default is yes)]),
+
         [ESA=$withval],[ESA=yes])
+
 AC_MSG_CHECKING(for Esa capability compilation)
 
+
 HAVE_ESA=no 
+
 if test "x$ESA" = "xyes"; then
+
         HAVE_ESA=yes
+
         AC_DEFINE([_HAVE_ESA_],[1],[with Esa capability])
-fi
+
+fi
+
 AM_CONDITIONAL([ESA], [test x$HAVE_ESA = xyes])
+
 AC_MSG_RESULT($HAVE_ESA)
+
 dnl }}}
 dnl with-Extrapolation{{{
+
 AC_ARG_WITH([Extrapolation],
+
         AS_HELP_STRING([--with-Extrapolation = YES], [compile with Extrapolation capabilities (default is yes)]),
+
         [EXTRAPOLATION=$withval],[EXTRAPOLATION=yes])
+
 AC_MSG_CHECKING(for Extrapolation capability compilation)
 
+
 HAVE_EXTRAPOLATION=no 
+
 if test "x$EXTRAPOLATION" = "xyes"; then
+
         HAVE_EXTRAPOLATION=yes
+
         AC_DEFINE([_HAVE_EXTRAPOLATION_],[1],[with Extrapolation capability])
-fi
+
+fi
+
 AM_CONDITIONAL([EXTRAPOLATION], [test x$HAVE_EXTRAPOLATION = xyes])
+
 AC_MSG_RESULT($HAVE_EXTRAPOLATION)
+
 dnl }}}
 dnl with-ExtrudeFromBase{{{
+
 AC_ARG_WITH([ExtrudeFromBase],
+
         AS_HELP_STRING([--with-ExtrudeFromBase = YES], [compile with ExtrudeFromBase capabilities (default is yes)]),
+
         [EXTRUDEFROMBASE=$withval],[EXTRUDEFROMBASE=yes])
+
 AC_MSG_CHECKING(for ExtrudeFromBase capability compilation)
 
+
 HAVE_EXTRUDEFROMBASE=no 
+
 if test "x$EXTRUDEFROMBASE" = "xyes"; then
+
         HAVE_EXTRUDEFROMBASE=yes
+
         AC_DEFINE([_HAVE_EXTRUDEFROMBASE_],[1],[with ExtrudeFromBase capability])
-fi
+
+fi
+
 AM_CONDITIONAL([EXTRUDEFROMBASE], [test x$HAVE_EXTRUDEFROMBASE = xyes])
+
 AC_MSG_RESULT($HAVE_EXTRUDEFROMBASE)
+
 dnl }}}
 dnl with-ExtrudeFromTop{{{
+
 AC_ARG_WITH([ExtrudeFromTop],
+
         AS_HELP_STRING([--with-ExtrudeFromTop = YES], [compile with ExtrudeFromTop capabilities (default is yes)]),
+
         [EXTRUDEFROMTOP=$withval],[EXTRUDEFROMTOP=yes])
+
 AC_MSG_CHECKING(for ExtrudeFromTop capability compilation)
 
+
 HAVE_EXTRUDEFROMTOP=no 
+
 if test "x$EXTRUDEFROMTOP" = "xyes"; then
+
         HAVE_EXTRUDEFROMTOP=yes
+
         AC_DEFINE([_HAVE_EXTRUDEFROMTOP_],[1],[with ExtrudeFromTop capability])
-fi
+
+fi
+
 AM_CONDITIONAL([EXTRUDEFROMTOP], [test x$HAVE_EXTRUDEFROMTOP = xyes])
+
 AC_MSG_RESULT($HAVE_EXTRUDEFROMTOP)
+
 dnl }}}
 dnl with-FreeSurfaceBase{{{
+
 AC_ARG_WITH([FreeSurfaceBase],
+
         AS_HELP_STRING([--with-FreeSurfaceBase = YES], [compile with FreeSurfaceBase capabilities (default is yes)]),
+
         [FREESURFACEBASE=$withval],[FREESURFACEBASE=yes])
+
 AC_MSG_CHECKING(for FreeSurfaceBase capability compilation)
 
+
 HAVE_FREESURFACEBASE=no 
+
 if test "x$FREESURFACEBASE" = "xyes"; then
+
         HAVE_FREESURFACEBASE=yes
+
         AC_DEFINE([_HAVE_FREESURFACEBASE_],[1],[with FreeSurfaceBase capability])
-fi
+
+fi
+
 AM_CONDITIONAL([FREESURFACEBASE], [test x$HAVE_FREESURFACEBASE = xyes])
+
 AC_MSG_RESULT($HAVE_FREESURFACEBASE)
+
 dnl }}}
 dnl with-FreeSurfaceTop{{{
+
 AC_ARG_WITH([FreeSurfaceTop],
+
         AS_HELP_STRING([--with-FreeSurfaceTop = YES], [compile with FreeSurfaceTop capabilities (default is yes)]),
+
         [FREESURFACETOP=$withval],[FREESURFACETOP=yes])
+
 AC_MSG_CHECKING(for FreeSurfaceTop capability compilation)
 
+
 HAVE_FREESURFACETOP=no 
+
 if test "x$FREESURFACETOP" = "xyes"; then
+
         HAVE_FREESURFACETOP=yes
+
         AC_DEFINE([_HAVE_FREESURFACETOP_],[1],[with FreeSurfaceTop capability])
-fi
+
+fi
+
 AM_CONDITIONAL([FREESURFACETOP], [test x$HAVE_FREESURFACETOP = xyes])
+
 AC_MSG_RESULT($HAVE_FREESURFACETOP)
+
 dnl }}}
 dnl with-GLheightadvection{{{
+
 AC_ARG_WITH([GLheightadvection],
+
         AS_HELP_STRING([--with-GLheightadvection = YES], [compile with GLheightadvection capabilities (default is yes)]),
+
         [GLHEIGHTADVECTION=$withval],[GLHEIGHTADVECTION=yes])
+
 AC_MSG_CHECKING(for GLheightadvection capability compilation)
 
+
 HAVE_GLHEIGHTADVECTION=no 
+
 if test "x$GLHEIGHTADVECTION" = "xyes"; then
+
         HAVE_GLHEIGHTADVECTION=yes
+
         AC_DEFINE([_HAVE_GLHEIGHTADVECTION_],[1],[with GLheightadvection capability])
-fi
+
+fi
+
 AM_CONDITIONAL([GLHEIGHTADVECTION], [test x$HAVE_GLHEIGHTADVECTION = xyes])
+
 AC_MSG_RESULT($HAVE_GLHEIGHTADVECTION)
-dnl }}}
-dnl with-Gia{{{
-AC_ARG_WITH([Gia],
-        AS_HELP_STRING([--with-Gia= YES], [compile with Gia capabilities (default is yes)]),
-        [GIA=$withval],[GIA=yes])
-AC_MSG_CHECKING(for Gia capability compilation)
-
-HAVE_GIA=no 
-if test "x$GIA" = "xyes"; then
-        HAVE_GIA=yes
-        AC_DEFINE([_HAVE_GIA_],[1],[with Giacapability])
-fi
-AM_CONDITIONAL([GIA], [test x$HAVE_GIA = xyes])
-AC_MSG_RESULT($HAVE_GIA)
+
 dnl }}}
 dnl with-HydrologyDCEfficient{{{
+
 AC_ARG_WITH([HydrologyDCEfficient],
+
         AS_HELP_STRING([--with-HydrologyDCEfficient = YES], [compile with HydrologyDCEfficient capabilities (default is yes)]),
+
         [HYDROLOGYDCEFFICIENT=$withval],[HYDROLOGYDCEFFICIENT=yes])
+
 AC_MSG_CHECKING(for HydrologyDCEfficient capability compilation)
 
+
 HAVE_HYDROLOGYDCEFFICIENT=no 
+
 if test "x$HYDROLOGYDCEFFICIENT" = "xyes"; then
+
         HAVE_HYDROLOGYDCEFFICIENT=yes
+
         AC_DEFINE([_HAVE_HYDROLOGYDCEFFICIENT_],[1],[with HydrologyDCEfficient capability])
-fi
+
+fi
+
 AM_CONDITIONAL([HYDROLOGYDCEFFICIENT], [test x$HAVE_HYDROLOGYDCEFFICIENT = xyes])
+
 AC_MSG_RESULT($HAVE_HYDROLOGYDCEFFICIENT)
+
 dnl }}}
 dnl with-HydrologyDCInefficient{{{
+
 AC_ARG_WITH([HydrologyDCInefficient],
+
         AS_HELP_STRING([--with-HydrologyDCInefficient = YES], [compile with HydrologyDCInefficient capabilities (default is yes)]),
+
         [HYDROLOGYDCINEFFICIENT=$withval],[HYDROLOGYDCINEFFICIENT=yes])
+
 AC_MSG_CHECKING(for HydrologyDCInefficient capability compilation)
 
+
 HAVE_HYDROLOGYDCINEFFICIENT=no 
+
 if test "x$HYDROLOGYDCINEFFICIENT" = "xyes"; then
+
         HAVE_HYDROLOGYDCINEFFICIENT=yes
+
         AC_DEFINE([_HAVE_HYDROLOGYDCINEFFICIENT_],[1],[with HydrologyDCInefficient capability])
-fi
+
+fi
+
 AM_CONDITIONAL([HYDROLOGYDCINEFFICIENT], [test x$HAVE_HYDROLOGYDCINEFFICIENT = xyes])
+
 AC_MSG_RESULT($HAVE_HYDROLOGYDCINEFFICIENT)
+
+dnl }}}
+dnl with-HydrologyGlaDS{{{
+
+AC_ARG_WITH([HydrologyGlaDS],
+
+        AS_HELP_STRING([--with-HydrologyGlaDS = YES], [compile with HydrologyGlaDS capabilities (default is yes)]),
+
+        [HYDROLOGYGLADS=$withval],[HYDROLOGYGLADS=yes])
+
+AC_MSG_CHECKING(for HydrologyGlaDS capability compilation)
+
+
+HAVE_HYDROLOGYGLADS=no 
+
+if test "x$HYDROLOGYGLADS" = "xyes"; then
+
+        HAVE_HYDROLOGYGLADS=yes
+
+        AC_DEFINE([_HAVE_HYDROLOGYGLADS_],[1],[with HydrologyGlaDS capability])
+
+fi
+
+AM_CONDITIONAL([HYDROLOGYGLADS], [test x$HAVE_HYDROLOGYGLADS = xyes])
+
+AC_MSG_RESULT($HAVE_HYDROLOGYGLADS)
+
+dnl }}}
+dnl with-HydrologyPism{{{
+
+AC_ARG_WITH([HydrologyPism],
+
+        AS_HELP_STRING([--with-HydrologyPism = YES], [compile with HydrologyPism capabilities (default is yes)]),
+
+        [HYDROLOGYPISM=$withval],[HYDROLOGYPISM=yes])
+
+AC_MSG_CHECKING(for HydrologyPism capability compilation)
+
+
+HAVE_HYDROLOGYPISM=no 
+
+if test "x$HYDROLOGYPISM" = "xyes"; then
+
+        HAVE_HYDROLOGYPISM=yes
+
+        AC_DEFINE([_HAVE_HYDROLOGYPISM_],[1],[with HydrologyPism capability])
+
+fi
+
+AM_CONDITIONAL([HYDROLOGYPISM], [test x$HAVE_HYDROLOGYPISM = xyes])
+
+AC_MSG_RESULT($HAVE_HYDROLOGYPISM)
+
+dnl }}}
+dnl with-HydrologyShakti{{{
+
+AC_ARG_WITH([HydrologyShakti],
+
+        AS_HELP_STRING([--with-HydrologyShakti = YES], [compile with HydrologyShakti capabilities (default is yes)]),
+
+        [HYDROLOGYSHAKTI=$withval],[HYDROLOGYSHAKTI=yes])
+
+AC_MSG_CHECKING(for HydrologyShakti capability compilation)
+
+
+HAVE_HYDROLOGYSHAKTI=no 
+
+if test "x$HYDROLOGYSHAKTI" = "xyes"; then
+
+        HAVE_HYDROLOGYSHAKTI=yes
+
+        AC_DEFINE([_HAVE_HYDROLOGYSHAKTI_],[1],[with HydrologyShakti capability])
+
+fi
+
+AM_CONDITIONAL([HYDROLOGYSHAKTI], [test x$HAVE_HYDROLOGYSHAKTI = xyes])
+
+AC_MSG_RESULT($HAVE_HYDROLOGYSHAKTI)
+
 dnl }}}
 dnl with-HydrologyShreve{{{
+
 AC_ARG_WITH([HydrologyShreve],
+
         AS_HELP_STRING([--with-HydrologyShreve = YES], [compile with HydrologyShreve capabilities (default is yes)]),
+
         [HYDROLOGYSHREVE=$withval],[HYDROLOGYSHREVE=yes])
+
 AC_MSG_CHECKING(for HydrologyShreve capability compilation)
 
+
 HAVE_HYDROLOGYSHREVE=no 
+
 if test "x$HYDROLOGYSHREVE" = "xyes"; then
+
         HAVE_HYDROLOGYSHREVE=yes
+
         AC_DEFINE([_HAVE_HYDROLOGYSHREVE_],[1],[with HydrologyShreve capability])
-fi
+
+fi
+
 AM_CONDITIONAL([HYDROLOGYSHREVE], [test x$HAVE_HYDROLOGYSHREVE = xyes])
+
 AC_MSG_RESULT($HAVE_HYDROLOGYSHREVE)
-dnl }}}
-dnl with-HydrologyGlaDS{{{
-AC_ARG_WITH([HydrologyGlaDS],
-        AS_HELP_STRING([--with-HydrologyGlaDS = YES], [compile with HydrologyGlaDS capabilities (default is yes)]),
-        [HYDROLOGYGLADS=$withval],[HYDROLOGYGLADS=yes])
-AC_MSG_CHECKING(for HydrologyGlaDS capability compilation)
-
-HAVE_HYDROLOGYGLADS=no 
-if test "x$HYDROLOGYGLADS" = "xyes"; then
-        HAVE_HYDROLOGYGLADS=yes
-        AC_DEFINE([_HAVE_HYDROLOGYGLADS_],[1],[with HydrologyGlaDS capability])
-fi
-AM_CONDITIONAL([HYDROLOGYGLADS], [test x$HAVE_HYDROLOGYGLADS = xyes])
-AC_MSG_RESULT($HAVE_HYDROLOGYGLADS)
-dnl }}}
-dnl with-HydrologyShakti{{{
-AC_ARG_WITH([HydrologyShakti],
-        AS_HELP_STRING([--with-HydrologyShakti = YES], [compile with HydrologyShakti capabilities (default is yes)]),
-        [HYDROLOGYSHAKTI=$withval],[HYDROLOGYSHAKTI=yes])
-AC_MSG_CHECKING(for HydrologyShakti capability compilation)
-
-HAVE_HYDROLOGYSHAKTI=no 
-if test "x$HYDROLOGYSHAKTI" = "xyes"; then
-        HAVE_HYDROLOGYSHAKTI=yes
-        AC_DEFINE([_HAVE_HYDROLOGYSHAKTI_],[1],[with HydrologyShakti capability])
-fi
-AM_CONDITIONAL([HYDROLOGYSHAKTI], [test x$HAVE_HYDROLOGYSHAKTI = xyes])
-AC_MSG_RESULT($HAVE_HYDROLOGYSHAKTI)
-dnl }}}
-dnl with-HydrologyPism{{{
-AC_ARG_WITH([HydrologyPism],
-        AS_HELP_STRING([--with-HydrologyPism = YES], [compile with HydrologyPism capabilities (default is yes)]),
-        [HYDROLOGYPISM=$withval],[HYDROLOGYPISM=yes])
-AC_MSG_CHECKING(for HydrologyPism capability compilation)
-
-HAVE_HYDROLOGYPISM=no 
-if test "x$HYDROLOGYPISM" = "xyes"; then
-        HAVE_HYDROLOGYPISM=yes
-        AC_DEFINE([_HAVE_HYDROLOGYPISM_],[1],[with HydrologyPism capability])
-fi
-AM_CONDITIONAL([HYDROLOGYPISM], [test x$HAVE_HYDROLOGYPISM = xyes])
-AC_MSG_RESULT($HAVE_HYDROLOGYPISM)
+
 dnl }}}
 dnl with-L2ProjectionBase{{{
+
 AC_ARG_WITH([L2ProjectionBase],
+
         AS_HELP_STRING([--with-L2ProjectionBase = YES], [compile with L2ProjectionBase capabilities (default is yes)]),
+
         [L2PROJECTIONBASE=$withval],[L2PROJECTIONBASE=yes])
+
 AC_MSG_CHECKING(for L2ProjectionBase capability compilation)
 
+
 HAVE_L2PROJECTIONBASE=no 
+
 if test "x$L2PROJECTIONBASE" = "xyes"; then
+
         HAVE_L2PROJECTIONBASE=yes
+
         AC_DEFINE([_HAVE_L2PROJECTIONBASE_],[1],[with L2ProjectionBase capability])
-fi
+
+fi
+
 AM_CONDITIONAL([L2PROJECTIONBASE], [test x$HAVE_L2PROJECTIONBASE = xyes])
+
 AC_MSG_RESULT($HAVE_L2PROJECTIONBASE)
+
 dnl }}}
 dnl with-L2ProjectionEPL{{{
+
 AC_ARG_WITH([L2ProjectionEPL],
+
         AS_HELP_STRING([--with-L2ProjectionEPL = YES], [compile with L2ProjectionEPL capabilities (default is yes)]),
+
         [L2PROJECTIONEPL=$withval],[L2PROJECTIONEPL=yes])
+
 AC_MSG_CHECKING(for L2ProjectionEPL capability compilation)
 
+
 HAVE_L2PROJECTIONEPL=no 
+
 if test "x$L2PROJECTIONEPL" = "xyes"; then
+
         HAVE_L2PROJECTIONEPL=yes
+
         AC_DEFINE([_HAVE_L2PROJECTIONEPL_],[1],[with L2ProjectionEPL capability])
-fi
+
+fi
+
 AM_CONDITIONAL([L2PROJECTIONEPL], [test x$HAVE_L2PROJECTIONEPL = xyes])
+
 AC_MSG_RESULT($HAVE_L2PROJECTIONEPL)
+
 dnl }}}
 dnl with-Levelset{{{
+
 AC_ARG_WITH([Levelset],
+
         AS_HELP_STRING([--with-Levelset = YES], [compile with Levelset capabilities (default is yes)]),
+
         [LEVELSET=$withval],[LEVELSET=yes])
+
 AC_MSG_CHECKING(for Levelset capability compilation)
 
+
 HAVE_LEVELSET=no 
+
 if test "x$LEVELSET" = "xyes"; then
+
         HAVE_LEVELSET=yes
+
         AC_DEFINE([_HAVE_LEVELSET_],[1],[with Levelset capability])
-fi
+
+fi
+
 AM_CONDITIONAL([LEVELSET], [test x$HAVE_LEVELSET = xyes])
+
 AC_MSG_RESULT($HAVE_LEVELSET)
+
 dnl }}}
 dnl with-Love{{{
+
 AC_ARG_WITH([Love],
+
         AS_HELP_STRING([--with-Love = YES], [compile with Love capabilities (default is yes)]),
+
         [LOVE=$withval],[LOVE=yes])
+
 AC_MSG_CHECKING(for Love capability compilation)
 
+
 HAVE_LOVE=no 
+
 if test "x$LOVE" = "xyes"; then
+
         HAVE_LOVE=yes
+
         AC_DEFINE([_HAVE_LOVE_],[1],[with Love capability])
-fi
+
+fi
+
 AM_CONDITIONAL([LOVE], [test x$HAVE_LOVE = xyes])
+
 AC_MSG_RESULT($HAVE_LOVE)
+
 dnl }}}
 dnl with-Masstransport{{{
+
 AC_ARG_WITH([Masstransport],
+
         AS_HELP_STRING([--with-Masstransport = YES], [compile with Masstransport capabilities (default is yes)]),
+
         [MASSTRANSPORT=$withval],[MASSTRANSPORT=yes])
+
 AC_MSG_CHECKING(for Masstransport capability compilation)
 
+
 HAVE_MASSTRANSPORT=no 
+
 if test "x$MASSTRANSPORT" = "xyes"; then
+
         HAVE_MASSTRANSPORT=yes
+
         AC_DEFINE([_HAVE_MASSTRANSPORT_],[1],[with Masstransport capability])
-fi
+
+fi
+
 AM_CONDITIONAL([MASSTRANSPORT], [test x$HAVE_MASSTRANSPORT = xyes])
+
 AC_MSG_RESULT($HAVE_MASSTRANSPORT)
+
 dnl }}}
 dnl with-Melting{{{
+
 AC_ARG_WITH([Melting],
+
         AS_HELP_STRING([--with-Melting = YES], [compile with Melting capabilities (default is yes)]),
+
         [MELTING=$withval],[MELTING=yes])
+
 AC_MSG_CHECKING(for Melting capability compilation)
 
+
 HAVE_MELTING=no 
+
 if test "x$MELTING" = "xyes"; then
+
         HAVE_MELTING=yes
+
         AC_DEFINE([_HAVE_MELTING_],[1],[with Melting capability])
-fi
+
+fi
+
 AM_CONDITIONAL([MELTING], [test x$HAVE_MELTING = xyes])
+
 AC_MSG_RESULT($HAVE_MELTING)
-dnl }}}
-dnl with-Sealevelrise{{{
-AC_ARG_WITH([Sealevelrise],
-        AS_HELP_STRING([--with-Sealevelrise = YES], [compile with Sealevelrise capabilities (default is yes)]),
-        [SEALEVELRISE=$withval],[SEALEVELRISE=yes])
-AC_MSG_CHECKING(for Sealevelrise capability compilation)
-
-HAVE_SEALEVELRISE=no 
-if test "x$SEALEVELRISE" = "xyes"; then
-        HAVE_SEALEVELRISE=yes
-        AC_DEFINE([_HAVE_SEALEVELRISE_],[1],[with Sealevelrise capability])
-fi
-AM_CONDITIONAL([SEALEVELRISE], [test x$HAVE_SEALEVELRISE = xyes])
-AC_MSG_RESULT($HAVE_SEALEVELRISE)
+
+dnl }}}
+dnl with-Oceantransport{{{
+
+AC_ARG_WITH([Oceantransport],
+
+        AS_HELP_STRING([--with-Oceantransport = YES], [compile with Oceantransport capabilities (default is yes)]),
+
+        [OCEANTRANSPORT=$withval],[OCEANTRANSPORT=yes])
+
+AC_MSG_CHECKING(for Oceantransport capability compilation)
+
+
+HAVE_OCEANTRANSPORT=no 
+
+if test "x$OCEANTRANSPORT" = "xyes"; then
+
+        HAVE_OCEANTRANSPORT=yes
+
+        AC_DEFINE([_HAVE_OCEANTRANSPORT_],[1],[with Oceantransport capability])
+
+fi
+
+AM_CONDITIONAL([OCEANTRANSPORT], [test x$HAVE_OCEANTRANSPORT = xyes])
+
+AC_MSG_RESULT($HAVE_OCEANTRANSPORT)
+
+dnl }}}
+dnl with-Recovery{{{
+
+AC_ARG_WITH([Recovery],
+
+        AS_HELP_STRING([--with-Recovery = YES], [compile with Recovery capabilities (default is yes)]),
+
+        [RECOVERY=$withval],[RECOVERY=yes])
+
+AC_MSG_CHECKING(for Recovery capability compilation)
+
+
+HAVE_RECOVERY=no 
+
+if test "x$RECOVERY" = "xyes"; then
+
+        HAVE_RECOVERY=yes
+
+        AC_DEFINE([_HAVE_RECOVERY_],[1],[with Recovery capability])
+
+fi
+
+AM_CONDITIONAL([RECOVERY], [test x$HAVE_RECOVERY = xyes])
+
+AC_MSG_RESULT($HAVE_RECOVERY)
+
+dnl }}}
+dnl with-Sampling{{{
+
+AC_ARG_WITH([Sampling],
+
+        AS_HELP_STRING([--with-Sampling = YES], [compile with Sampling capabilities (default is yes)]),
+
+        [SAMPLING=$withval],[SAMPLING=yes])
+
+AC_MSG_CHECKING(for Sampling capability compilation)
+
+
+HAVE_SAMPLING=no 
+
+if test "x$SAMPLING" = "xyes"; then
+
+        HAVE_SAMPLING=yes
+
+        AC_DEFINE([_HAVE_SAMPLING_],[1],[with Sampling capability])
+
+fi
+
+AM_CONDITIONAL([SAMPLING], [test x$HAVE_SAMPLING = xyes])
+
+AC_MSG_RESULT($HAVE_SAMPLING)
+
+dnl }}}
+dnl with-Sealevelchange{{{
+
+AC_ARG_WITH([Sealevelchange],
+
+        AS_HELP_STRING([--with-Sealevelchange = YES], [compile with Sealevelchange capabilities (default is yes)]),
+
+        [SEALEVELCHANGE=$withval],[SEALEVELCHANGE=yes])
+
+AC_MSG_CHECKING(for Sealevelchange capability compilation)
+
+
+HAVE_SEALEVELCHANGE=no 
+
+if test "x$SEALEVELCHANGE" = "xyes"; then
+
+        HAVE_SEALEVELCHANGE=yes
+
+        AC_DEFINE([_HAVE_SEALEVELCHANGE_],[1],[with Sealevelchange capability])
+
+fi
+
+AM_CONDITIONAL([SEALEVELCHANGE], [test x$HAVE_SEALEVELCHANGE = xyes])
+
+AC_MSG_RESULT($HAVE_SEALEVELCHANGE)
+
 dnl }}}
 dnl with-Smb{{{
+
 AC_ARG_WITH([Smb],
+
         AS_HELP_STRING([--with-Smb = YES], [compile with Smb capabilities (default is yes)]),
+
         [SMB=$withval],[SMB=yes])
+
 AC_MSG_CHECKING(for Smb capability compilation)
 
+
 HAVE_SMB=no 
+
 if test "x$SMB" = "xyes"; then
+
         HAVE_SMB=yes
+
         AC_DEFINE([_HAVE_SMB_],[1],[with Smb capability])
-fi
+
+fi
+
 AM_CONDITIONAL([SMB], [test x$HAVE_SMB = xyes])
+
 AC_MSG_RESULT($HAVE_SMB)
+
 dnl }}}
 dnl with-Smooth{{{
+
 AC_ARG_WITH([Smooth],
+
         AS_HELP_STRING([--with-Smooth = YES], [compile with Smooth capabilities (default is yes)]),
+
         [SMOOTH=$withval],[SMOOTH=yes])
+
 AC_MSG_CHECKING(for Smooth capability compilation)
 
+
 HAVE_SMOOTH=no 
+
 if test "x$SMOOTH" = "xyes"; then
+
         HAVE_SMOOTH=yes
+
         AC_DEFINE([_HAVE_SMOOTH_],[1],[with Smooth capability])
-fi
+
+fi
+
 AM_CONDITIONAL([SMOOTH], [test x$HAVE_SMOOTH = xyes])
+
 AC_MSG_RESULT($HAVE_SMOOTH)
+
 dnl }}}
 dnl with-Stressbalance{{{
+
 AC_ARG_WITH([Stressbalance],
+
         AS_HELP_STRING([--with-Stressbalance = YES], [compile with Stressbalance capabilities (default is yes)]),
+
         [STRESSBALANCE=$withval],[STRESSBALANCE=yes])
+
 AC_MSG_CHECKING(for Stressbalance capability compilation)
 
+
 HAVE_STRESSBALANCE=no 
+
 if test "x$STRESSBALANCE" = "xyes"; then
+
         HAVE_STRESSBALANCE=yes
+
         AC_DEFINE([_HAVE_STRESSBALANCE_],[1],[with Stressbalance capability])
-fi
+
+fi
+
 AM_CONDITIONAL([STRESSBALANCE], [test x$HAVE_STRESSBALANCE = xyes])
+
 AC_MSG_RESULT($HAVE_STRESSBALANCE)
+
 dnl }}}
 dnl with-StressbalanceSIA{{{
+
 AC_ARG_WITH([StressbalanceSIA],
+
         AS_HELP_STRING([--with-StressbalanceSIA = YES], [compile with StressbalanceSIA capabilities (default is yes)]),
+
         [STRESSBALANCESIA=$withval],[STRESSBALANCESIA=yes])
+
 AC_MSG_CHECKING(for StressbalanceSIA capability compilation)
 
+
 HAVE_STRESSBALANCESIA=no 
+
 if test "x$STRESSBALANCESIA" = "xyes"; then
+
         HAVE_STRESSBALANCESIA=yes
+
         AC_DEFINE([_HAVE_STRESSBALANCESIA_],[1],[with StressbalanceSIA capability])
-fi
+
+fi
+
 AM_CONDITIONAL([STRESSBALANCESIA], [test x$HAVE_STRESSBALANCESIA = xyes])
+
 AC_MSG_RESULT($HAVE_STRESSBALANCESIA)
+
 dnl }}}
 dnl with-StressbalanceVertical{{{
+
 AC_ARG_WITH([StressbalanceVertical],
+
         AS_HELP_STRING([--with-StressbalanceVertical = YES], [compile with StressbalanceVertical capabilities (default is yes)]),
+
         [STRESSBALANCEVERTICAL=$withval],[STRESSBALANCEVERTICAL=yes])
+
 AC_MSG_CHECKING(for StressbalanceVertical capability compilation)
 
+
 HAVE_STRESSBALANCEVERTICAL=no 
+
 if test "x$STRESSBALANCEVERTICAL" = "xyes"; then
+
         HAVE_STRESSBALANCEVERTICAL=yes
+
         AC_DEFINE([_HAVE_STRESSBALANCEVERTICAL_],[1],[with StressbalanceVertical capability])
-fi
+
+fi
+
 AM_CONDITIONAL([STRESSBALANCEVERTICAL], [test x$HAVE_STRESSBALANCEVERTICAL = xyes])
+
 AC_MSG_RESULT($HAVE_STRESSBALANCEVERTICAL)
+
 dnl }}}
 dnl with-Thermal{{{
+
 AC_ARG_WITH([Thermal],
+
         AS_HELP_STRING([--with-Thermal = YES], [compile with Thermal capabilities (default is yes)]),
+
         [THERMAL=$withval],[THERMAL=yes])
+
 AC_MSG_CHECKING(for Thermal capability compilation)
 
+
 HAVE_THERMAL=no 
+
 if test "x$THERMAL" = "xyes"; then
+
         HAVE_THERMAL=yes
+
         AC_DEFINE([_HAVE_THERMAL_],[1],[with Thermal capability])
-fi
+
+fi
+
 AM_CONDITIONAL([THERMAL], [test x$HAVE_THERMAL = xyes])
+
 AC_MSG_RESULT($HAVE_THERMAL)
+
 dnl }}}
 dnl with-UzawaPressure{{{
+
 AC_ARG_WITH([UzawaPressure],
+
         AS_HELP_STRING([--with-UzawaPressure = YES], [compile with UzawaPressure capabilities (default is yes)]),
+
         [UZAWAPRESSURE=$withval],[UZAWAPRESSURE=yes])
+
 AC_MSG_CHECKING(for UzawaPressure capability compilation)
 
+
 HAVE_UZAWAPRESSURE=no 
+
 if test "x$UZAWAPRESSURE" = "xyes"; then
+
         HAVE_UZAWAPRESSURE=yes
+
         AC_DEFINE([_HAVE_UZAWAPRESSURE_],[1],[with UzawaPressure capability])
-fi
+
+fi
+
 AM_CONDITIONAL([UZAWAPRESSURE], [test x$HAVE_UZAWAPRESSURE = xyes])
+
 AC_MSG_RESULT($HAVE_UZAWAPRESSURE)
+
 dnl }}}
 

issm/trunk/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])
@@ -290 +291 @@
                         export CFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
                 elif test "${VENDOR}" == "intel-discover"; then
-                        export CC=icc
-                        export CXX=icpc
-                        export CXXFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
+                   export CC=mpicc
+                   export CXX=mpicxx
+                        export CXXFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK -std=c++11"
                         export CFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
                 elif test "${VENDOR}" == "intel-pleiades"; then
@@ -309 +310 @@
                         export CXXFLAGS="-O3 -march=corei7-avx -std=c++11"
                         export CFLAGS="-O3 -march=corei7-avx"
+                elif test "${VENDOR}" == "intel-pleiades-mpi"; then
+                        export CC=mpicc
+                        export CXX=mpicxx
+                        export CXXFLAGS="-O3 -march=corei7-avx -std=c++11"
+                        export CFLAGS="-O3 -march=corei7-avx"
                 elif test "${VENDOR}" == "intel-pleiades-icpc"; then
                         export CXXFLAGS="-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 -std=c++11"
                         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 "${VENDOR}" == "win-msys2"; then
+                        export CXXFLAGS="-D_MSYS2_"
+                        export LDFLAGS="${LDFLAGS} -no-undefined"
+                        export OSLIBS="-Wl,-L/mingw64/lib/gcc/x86_64-w64-mingw32/10.2.0 -Wl,-L/mingw64/x86_64-w64-mingw32/lib -Wl,-lstdc++ -Wl,-lgfortran -Wl,-lmingw32 -Wl,-lgcc_s -Wl,-lmoldname -Wl,-lmingwex -Wl,-lmsvcrt -Wl,-lm -Wl,-lpthread -Wl,-lshell32 -Wl,-luser32 -Wl,-lgdi32 -Wl,-luser32 -Wl,-ladvapi32 -Wl,-lkernel32 -Wl,-lquadmath -Wl,-lstdc++ -Wl,-lgcc"
+                        IS_MSYS2=yes
                 else
                         AC_MSG_ERROR([unknown compiler vendor!])
                 fi
         fi
+        dnl Set default standard for C++
+        if test "${CXXFLAGS}" == ""; then
+                export CXXFLAGS="-std=C++11"
+        fi
         AC_SUBST([OSLIBS])
         AC_MSG_RESULT([done])
 
-        AC_MSG_CHECKING([if this is a Windows build])
+        AC_MSG_CHECKING([if this is a MSVC (Windows) build])
         AM_CONDITIONAL([WINDOWS], [test "x${IS_WINDOWS}" == "xyes"])
         AC_MSG_RESULT([${IS_WINDOWS}])
+
+        AC_MSG_CHECKING([if this is a MSYS2 (Windows) build])
+        AM_CONDITIONAL([MSYS2], [test "x${IS_MSYS2}" == "xyes"])
+        AC_MSG_RESULT([${IS_MSYS2}])
+        AC_DEFINE([_IS_MSYS2_], [1], [is a MSYS2 (Windows) build])
         dnl }}}
         dnl MATLAB{{{
 
         dnl See if MATLAB has been provided
+        AC_MSG_CHECKING([for MATLAB])
         AC_ARG_WITH(
                 [matlab-dir],                                                                                                           dnl feature
@@ -333 +354 @@
                 [MATLAB_ROOT="no"]                                                                                                      dnl action if not given
         )
-        AC_MSG_CHECKING([for MATLAB])
         if test "x${MATLAB_ROOT}" == "xno"; then
                 HAVE_MATLAB=no
         else
-                HAVE_MATLAB=yes
                 if ! test -d "${MATLAB_ROOT}"; then
                         AC_MSG_ERROR([MATLAB directory provided (${MATLAB_ROOT}) does not exist!]);
@@ -344 +363 @@
                         AC_MSG_ERROR([Couldn't find mex.h... check your installation of MATLAB])
                 fi
+                HAVE_MATLAB=yes
         fi
         AC_MSG_RESULT([${HAVE_MATLAB}])
@@ -352 +372 @@
                 AC_DEFINE([_HAVE_MATLAB_], [1], [with MATLAB in ISSM src])
 
-                dnl Set MEXLIB, MEXLINK, and MEXEXT
+                dnl Set MEX* variable
                 AC_MSG_CHECKING([MATLAB's mex compilation flags])
 
@@ -362 +382 @@
                                 if test "${VENDOR}" == "intel-win7-32"; then
                                         MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-                                        MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
+                                        MEXLINKFLAGS="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
                                         MEXEXT=`${MATLAB_ROOT}/bin/mexext.bat`
                                         MEXEXT=".${MEXEXT}"
                                 elif test "${VENDOR}" == "intel-win7-64"; then
                                         MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-                                        MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
+                                        MEXLINKFLAGS="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
                                         MEXEXT=".mexw64"
                                 elif test "${VENDOR}" == "MSVC-Win64" || test "${VENDOR}" == "MSVC-Win64-par"; then
                                         MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib"
-                                        MEXLINK="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
+                                        MEXLINKFLAGS="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL"
                                         MATLABINCL="-I`cygpath -m ${MATLAB_ROOT}/extern/include`"
                                         MEXEXT=".mexw64"
                                 fi
                         ;;
+                        *mingw*)
+                                if test "${IS_MSYS2}" == "yes"; then
+                                        dnl Value to set MEXEXT to can be found on Windows by running $MATLAB_ROOT/bin/mexext.bat
+                                        MEXEXT=".mexw64"
+                                        MATLABINCL="-I${MATLAB_ROOT}/extern/include"
+                                        MEXOPTFLAGS="-O2 -fwrapv -DNDEBUG -g"
+                                        MEXCFLAGS="-fexceptions -fno-omit-frame-pointer -m64 -DMATLAB_MEX_FILE"
+                                        MEXCXXFLAGS="-fexceptions -fno-omit-frame-pointer -std=c++11 -m64 -DMATLAB_MEX_FILE"
+                                        MEXLINKFLAGS="-m64 -Wl,--no-undefined -shared -static -Wl,${MATLAB_ROOT}/extern/lib/win64/mingw64/mexFunction.def"
+                                        MEXLIB_DIR="${MATLAB_ROOT}/extern/lib/win64/mingw64"
+                                        MEXLIB="-L${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas"
+                                fi
+                        ;;
+                        *msys*)
+                                dnl Value to set MEXEXT to can be found on Windows by running $MATLAB_ROOT/bin/mexext.bat
+                                MEXEXT=".mexw64"
+                                MATLABINCL="-I${MATLAB_ROOT}/extern/include"
+                                MEXOPTFLAGS="-O2 -fwrapv -DNDEBUG -g"
+                                MEXCFLAGS="-fexceptions -fno-omit-frame-pointer -m64 -DMATLAB_MEX_FILE"
+                                MEXCXXFLAGS="-fexceptions -fno-omit-frame-pointer -std=c++11 -m64 -DMATLAB_MEX_FILE"
+                                MEXLINKFLAGS="-m64 -Wl,--no-undefined -shared -static -Wl,${MATLAB_ROOT}/extern/lib/win64/mingw64/mexFunction.def"
+                                MEXLIB_DIR="${MATLAB_ROOT}/extern/lib/win64/mingw64"
+                                MEXLIB="-L${MEXLIB_DIR} -lmx -lmex -lmat -lm -lmwlapack -lmwblas"
+                        ;;
                         *)
+                                MEXEXT=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
                                 MATLABINCL="-I${MATLAB_ROOT}/extern/include"
-                                MEXLINK=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDFLAGS | sed -e "s/         LDFLAGS            = //g")
+                                MEXLINKFLAGS=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDFLAGS | sed -e "s/         LDFLAGS            = //g")
                                 MEXLIB=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep CXXLIBS | sed -e "s/         CXXLIBS            = //g")
-                                MEXEXT=$(${MATLAB_ROOT}/bin/mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
-                                dnl version 2014 and up
                                 if test -z "${MEXEXT}"; then
                                         echo "#include <mex.h>" > conftest.cpp
@@ -387 +430 @@
                                         ${MATLAB_ROOT}/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1
                                         rm -f conftest.cpp
-                                        MEXLINK=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g")
+                                        MEXLINKFLAGS=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g")
                                         MEXLIB=$(cat conftest.tmp | grep LINKLIBS | sed -e "s/LINKLIBS ://g")
                                         MEXEXT=$(cat conftest.tmp | grep LDEXT | sed -e "s/LDEXT ://g" | awk '{print $[1]}')
@@ -397 +440 @@
 
                                 dnl Make sure mexFunction.map is not in MEXLIB to avoid problems with global variables
-                                dnl MEXLINK=$(echo ${MEXLINK} | sed -e "s/,-expo.*mexFunction\\.map\"//g" | sed -e "s/-[[^ ]]*mexFunction\\.map//g")
-                                MEXLINK="" dnl We actually don't need MEXLINK????
+                                dnl MEXLINKFLAGS=$(echo ${MEXLINKFLAGS} | sed -e "s/,-expo.*mexFunction\\.map\"//g" | sed -e "s/-[[^ ]]*mexFunction\\.map//g")
+                                MEXLINKFLAGS="" dnl We actually don't need MEXLINK????
                         ;;
                 esac
@@ -406 +449 @@
                 fi
 
+                AC_SUBST([MEXEXT])
+                AC_SUBST([MEXOPTFLAGS])
+                AC_SUBST([MEXCFLAGS])
+                AC_SUBST([MEXCXXFLAGS])
                 AC_SUBST([MATLABINCL])
-                MATLABWRAPPEREXT=${MEXEXT}
-                AC_SUBST([MATLABWRAPPEREXT])
+                AC_SUBST([MEXLINKFLAGS])
                 AC_SUBST([MEXLIB])
-                AC_SUBST([MEXLINK])
         fi
         dnl }}}
         dnl JavaScript{{{
+        AC_MSG_CHECKING([for JavaScript])
         AC_ARG_WITH(
                 [javascript],
@@ -420 +466 @@
                 [JAVASCRIPT="no"]
         )
-        AC_MSG_CHECKING([for JavaScript])
         if test "x${JAVASCRIPT}" == "xno"; then
                 HAVE_JAVASCRIPT=no
@@ -433 +478 @@
         dnl }}}
         dnl Triangle {{{
+        AC_MSG_CHECKING([for triangle])
         AC_ARG_WITH(
                 [triangle-dir],
@@ -439 +485 @@
                 [TRIANGLE_ROOT="no"]
         )
-        AC_MSG_CHECKING([for triangle])
         if test "x${TRIANGLE_ROOT}" == "xno"; then
                 HAVE_TRIANGLE=no
@@ -478 +523 @@
                                 fi
                         ;;
+                        *mingw*)
+                                if test "x${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${TRIANGLE_ROOT}/lib -ltriangle"
+                                fi
+                        ;;
                 esac
                 AC_DEFINE([_HAVE_TRIANGLE_], [1], [with Triangle in ISSM src])
@@ -485 +546 @@
         dnl }}}
         dnl Boost{{{
+        AC_MSG_CHECKING([for Boost])
         AC_ARG_WITH(
                 [boost-dir],
@@ -491 +553 @@
                 [BOOST_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Boost])
         if test "x${BOOST_ROOT}" == "xno"; then
                 HAVE_BOOST=no
@@ -518 +579 @@
         dnl }}}
         dnl Dakota{{{
+        AC_MSG_CHECKING([for Dakota])
         AC_ARG_WITH(
                 [dakota-dir],
@@ -524 +586 @@
                 [DAKOTA_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Dakota])
         if test "x${DAKOTA_ROOT}" == "xno"; then
                 HAVE_DAKOTA=no
@@ -541 +602 @@
 
                 AC_MSG_CHECKING(for Dakota version)
-                dnl TODO:       Check if this method applies to all other versions of 
-                dnl                     Dakota (it should as long as the Dakota binaries have been
-                dnl             compiled). If so, we can remove the other methods of 
-                dnl                     getting the version.
+                dnl TODO:
+                dnl - Check if this method applies to all other versions of Dakota (it 
+                dnl   should as long as the Dakota binaries have been compiled). If so, 
+                dnl   we can remove the other methods of getting the version.
+                dnl - Modify src/wrappers/IssmConfig/IssmConfig.cpp so that strlen is 
+                dnl   not called with _DAKOTA_VERSION_ as an argument so that we can 
+                dnl   do,
                 dnl
-                DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
-                if test -n "${DAKOTA_VERSION_OUTPUT}"; then
-                        DAKOTA_VERSION=`echo ${DAKOTA_VERSION_OUTPUT} grep "Dakota version" | sed 's/Dakota version //' | sed 's/ .*//'`
-                elif test -f "${DAKOTA_ROOT}/VERSION"; then
+                dnl     AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_], ${DAKOTA_VERSION}, [Dakota version number])
+                dnl
+                if test -f "${DAKOTA_ROOT}/VERSION"; then
                         DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/VERSION | grep 'DAKOTA Version' | sed 's/.*DAKOTA Version //' | sed 's/ .*//'`
-                elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.C"; then
-                        DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
-                elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp"; then
-                        DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
                 else
-                        AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
+                        DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
+                        if test -n "${DAKOTA_VERSION_OUTPUT}"; then
+                                DAKOTA_VERSION=`echo ${DAKOTA_VERSION_OUTPUT} grep "Dakota version" | sed 's/Dakota version //' | sed 's/ .*//'`
+                        elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.C"; then
+                                DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+                        elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp"; then
+                                DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+                        else
+                                AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
+                        fi
                 fi
                 AC_MSG_RESULT([${DAKOTA_VERSION}])
@@ -674 +742 @@
                 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])
@@ -690 +758 @@
         dnl }}}
         dnl Python{{{
+        AC_MSG_CHECKING([for Python])
         AC_ARG_WITH(
                 [python-dir],
@@ -703 +772 @@
                 [PYTHON_VERSION="no"]
         )
-        AC_MSG_CHECKING([for Python])
         if test "x${PYTHON_ROOT}" == "xno"; then
                 HAVE_PYTHON=no
@@ -730 +798 @@
                 dnl Determine major version
                 PYTHON_MAJOR=${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"
@@ -746 +814 @@
                         PYTHONINCL=-I${PYTHON_ROOT}/include/python${PYTHON_VERSION}m
                 else
-                        AC_MSG_ERROR([Python.h not found, locate this file and contact ISSM developers]);
+                        AC_MSG_ERROR([Python.h not found! Please locate this file and contact ISSM developers via forum or email.]);
                 fi
                 AC_MSG_RESULT([found])
-                if test "x${PYTHON_MAJOR}" == "x3"; then
+                if ls ${PYTHON_ROOT}/lib/x86_64-linux-gnu/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then
+                        PYTHONLIB="-L${PYTHON_ROOT}/lib/x86_64-linux-gnu -lpython${PYTHON_VERSION}m"
+                elif ls ${PYTHON_ROOT}/lib/x86_64-linux-gnu/libpython${PYTHON_VERSION}.* 1> /dev/null 2>&1; then
+                        PYTHONLIB="-L${PYTHON_ROOT}/lib/x86_64-linux-gnu -lpython${PYTHON_VERSION}"
+                elif ls ${PYTHON_ROOT}/lib/libpython${PYTHON_VERSION}m.* 1> /dev/null 2>&1; then
                         PYTHONLIB="-L${PYTHON_ROOT}/lib -lpython${PYTHON_VERSION}m"
                 else
@@ -759 +831 @@
                                 PYTHONLINK="-shared"
                         ;;
+                        *darwin*)
+                                PYTHONLINK="-dynamiclib"
+                        ;;
                         *linux*)
                                 PYTHONLINK="-shared"
                         ;;
-                        *darwin*)
-                                PYTHONLINK="-dynamiclib"
+                        *mingw*)
+                                PYTHONLINK="-shared"
+                        ;;
+                        *msys*)
+                                PYTHONLINK="-shared"
                         ;;
                 esac
@@ -776 +854 @@
         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=${withval}],
-                [PYTHON_NUMPY_ROOT="no"]
-        )
-
         dnl NOTE: You can find NumPy by running,
         dnl
@@ -792 +859 @@
         dnl             >>> numpy.__file__
         dnl
-
+        dnl TODO:
+        dnl - Replace references to python-numpy with numpy (and similar terms)
+        dnl       project-wide
+        dnl
         AC_MSG_CHECKING(for python-numpy)
+        AC_ARG_WITH(
+                [python-numpy-dir],
+                AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory]),
+                [PYTHON_NUMPY_ROOT=${withval}],
+                [PYTHON_NUMPY_ROOT="no"]
+        )
         if test "x${PYTHON_NUMPY_ROOT}" == "xno"; then
                 HAVE_PYTHON_NUMPY=no
@@ -812 +888 @@
         dnl }}}
         dnl Chaco{{{
+        AC_MSG_CHECKING([for Chaco])
         AC_ARG_WITH(
                 [chaco-dir],
@@ -818 +895 @@
                 [CHACO_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Chaco])
         if test "x${CHACO_ROOT}" == "xno"; then
                 HAVE_CHACO=no
@@ -832 +908 @@
         dnl Chaco libraries and header files
         if test "x${HAVE_CHACO}" == "xyes"; then
-                CHACOINCL=-I${CHACO_ROOT}/include
-                CHACOLIB="-L${CHACO_ROOT}/lib -lchacominusblas"
+                CHACOINCL="-I${CHACO_ROOT}/include"
+                if test "${IS_MSYS2}" == "yes"; then
+                        CHACOLIB="-Wl,-L${CHACO_ROOT}/lib -Wl,-lchacominusblas"
+                else
+                        CHACOLIB="-L${CHACO_ROOT}/lib -lchacominusblas"
+                fi
                 AC_DEFINE([_HAVE_CHACO_], [1], [with Chaco in ISSM src])
                 AC_SUBST([CHACOINCL])
@@ -840 +920 @@
         dnl }}}
         dnl ESMF{{{
+        AC_MSG_CHECKING([for ESMF])
         AC_ARG_WITH(
                 [esmf-dir],
@@ -846 +927 @@
                 [ESMF_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ESMF])
         if test "x${ESMF_ROOT}" == "xno"; then
                 HAVE_ESMF=no
@@ -860 +940 @@
         if test "x${HAVE_ESMF}" == "xyes"; then
                 ESMFINCL="-I${ESMF_ROOT}/include"
-                ESMFLIB="-L${ESMF_ROOT}/lib -lesmf"
+                ESMFLIB="-L${ESMF_ROOT}/lib/libO/Linux.gfortran.64.mpich.default/ -lesmf"
                 AC_DEFINE([_HAVE_ESMF_], [1], [with ESMF in ISSM src])
                 AC_SUBST([ESMFINCL])
@@ -868 +948 @@
         dnl }}}
         dnl CoDiPack{{{
+        AC_MSG_CHECKING([for CoDiPack])
         AC_ARG_WITH(
                 [codipack-dir],
@@ -874 +955 @@
                 [CODIPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for CoDiPack])
         if test "x${CODIPACK_ROOT}" == "xno"; then
                 HAVE_CODIPACK=no
@@ -887 +967 @@
         dnl CoDiPack libraries and header files
         if test "x${HAVE_CODIPACK}" == "xyes"; then
+
+                AC_MSG_CHECKING(for CoDiPack version)
+                CODIPACK_MAJOR=`cat ${CODIPACK_ROOT}/include/codi.hpp | grep "#define CODI_MAJOR_VERSION" | sed 's/#define CODI_MAJOR_VERSION//' | sed 's/ //g'`
+                CODIPACK_MINOR=`cat ${CODIPACK_ROOT}/include/codi.hpp | grep "#define CODI_MINOR_VERSION" | sed 's/#define CODI_MINOR_VERSION//' | sed 's/ //g'`
+                if test -z "${CODIPACK_MAJOR}"; then
+                         CODIPACK_MAJOR=`cat ${CODIPACK_ROOT}/include/codi/configure.h | grep "#define CODI_MAJOR_VERSION" | sed 's/#define CODI_MAJOR_VERSION//' | sed 's/ //g'`
+                         CODIPACK_MINOR=`cat ${CODIPACK_ROOT}/include/codi/configure.h | grep "#define CODI_MINOR_VERSION" | sed 's/#define CODI_MINOR_VERSION//' | sed 's/ //g'`
+                fi
+                if test -z "${CODIPACK_MAJOR}"; then
+                        AC_MSG_ERROR([Couldn't determine CoDiPack version])
+                fi
+                AC_DEFINE_UNQUOTED([_CODIPACK_MAJOR_], ${CODIPACK_MAJOR}, [CoDiPack version major])
+                AC_DEFINE_UNQUOTED([_CODIPACK_MINOR_], ${CODIPACK_MINOR}, [CoDiPack version minor])
+                AC_MSG_RESULT([${CODIPACK_MAJOR}.${CODIPACK_MINOR}])
+
                 CODIPACKINCL="-I${CODIPACK_ROOT}/include"
                 AC_DEFINE([_HAVE_CODIPACK_], [1], [with CoDiPack in ISSM src])
@@ -896 +991 @@
         dnl }}}
         dnl Tape Allocation {{{
+        AC_MSG_CHECKING(for tape allocation)
         AC_ARG_ENABLE(
                 [tape-alloc],                                                                                                                           dnl feature
@@ -902 +998 @@
                 [enable_tape_alloc=no]
         )
-        AC_MSG_CHECKING(for tape allocation)
         if test "x${enable_tape_alloc}" == "xyes"; then
                 AC_DEFINE([_AD_TAPE_ALLOC_], [1], [enable a priori tape allocation for AD])
@@ -909 +1004 @@
         dnl }}}
         dnl ADOL-C {{{
+        AC_MSG_CHECKING([for ADOL-C])
         AC_ARG_WITH(
                 [adolc-dir],
@@ -915 +1011 @@
                 [ADOLC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ADOL-C])
         if test "x${ADOLC_ROOT}" == "xno"; then
                 HAVE_ADOLC=no
@@ -940 +1035 @@
         dnl }}}
         dnl ADOL-C version{{{
+        AC_MSG_CHECKING(for ADOL-C version)
         AC_ARG_WITH(
                 [adolc-version],
@@ -946 +1042 @@
                 [ADOLC_VERSION=2]
         )
-        AC_MSG_CHECKING(for ADOL-C version)
-
-        AC_DEFINE_UNQUOTED(_ADOLC_VERSION_, $ADOLC_VERSION, [ADOL-C version])
+        AC_DEFINE_UNQUOTED([_ADOLC_VERSION_], ${ADOLC_VERSION}, [ADOL-C version])
         AC_MSG_RESULT(${ADOLC_VERSION})
         dnl }}}
         dnl ADIC2 {{{
+        AC_MSG_CHECKING([for ADIC2])
         AC_ARG_WITH(
                 [adic2-dir],
@@ -958 +1053 @@
                 [ADIC2_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ADIC2])
         if test "x${ADIC2_ROOT}" == "xno"; then
                 HAVE_ADIC2=no
@@ -980 +1074 @@
         dnl }}}
         dnl ATLAS {{{
+        AC_MSG_CHECKING(for ATLAS and CBLAS libraries)
         AC_ARG_WITH(
                 [atlas-dir],
@@ -986 +1081 @@
                 [ATLAS_ROOT="no"]
         )
-        AC_MSG_CHECKING(for ATLAS and CBLAS libraries)
         if test "x${ATLAS_ROOT}" == "xno"; then
                 HAVE_ATLAS=no
@@ -1003 +1097 @@
                                 ATLASLIB="-L`cygpath -m ${ATLAS_ROOT}` -Wl,libatlas.lib  -Wl,libcblas.lib"
                         ;;
+                        *darwin*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                        ;;
                         *linux*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm "
-                        ;;
-                        *darwin*)
-                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm "
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                        ;;
+                        *mingw*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
+                        ;;
+                        *msys*)
+                                ATLASLIB="-L${ATLAS_ROOT}/lib -lcblas -latlas -lm"
                         ;;
                 esac
@@ -1015 +1115 @@
         dnl }}}
         dnl GSL{{{
+        AC_MSG_CHECKING([for GSL])
         AC_ARG_WITH(
                 [gsl-dir],
@@ -1021 +1122 @@
                 [GSL_ROOT="no"]
         )
-        AC_MSG_CHECKING([for GSL])
         if test "x${GSL_ROOT}" == "xno"; then
                 HAVE_GSL=no
@@ -1047 +1147 @@
         dnl }}}
         dnl AMPI (ADOL-C){{{
+        AC_MSG_CHECKING([for AMPI])
         AC_ARG_WITH(
                 [ampi-dir],
@@ -1053 +1154 @@
                 [AMPI_ROOT="no"]
         )
-        AC_MSG_CHECKING([for AMPI])
         if test "x${AMPI_ROOT}" == "xno"; then
                 HAVE_AMPI=no
@@ -1083 +1183 @@
         dnl }}}
         dnl Adjoint MPI (CoDiPack){{{
+        AC_MSG_CHECKING([for Adjoint MPI])
         AC_ARG_WITH(
                 [adjointmpi-dir],
@@ -1089 +1190 @@
                 [ADJOINTMPI_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Adjoint MPI])
         if test "x${ADJOINTMPI_ROOT}" == "xno"; then
                 HAVE_ADJOINTMPI=no
@@ -1117 +1217 @@
         dnl }}}
         dnl MeDiPack (CoDiPack, ADOL-C dev){{{
+        AC_MSG_CHECKING([for MeDiPack])
         AC_ARG_WITH(
                 [medipack-dir],
@@ -1123 +1224 @@
                 [MEDIPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MeDiPack])
         if test "x${MEDIPACK_ROOT}" == "xno"; then
                 HAVE_MEDIPACK=no
@@ -1149 +1249 @@
         dnl }}}
         dnl HDF5 {{{
+        AC_MSG_CHECKING(for HDF5 libraries)
         AC_ARG_WITH(
                 [hdf5-dir],
@@ -1155 +1256 @@
                 [HDF5_ROOT="no"]
         )
-        AC_MSG_CHECKING(for HDF5 libraries)
         if test "x${HDF5_ROOT}" == "xno"; then
                 HAVE_HDF5=no
@@ -1176 +1276 @@
                                 HDF5LIB="-L`cygpath -m ${HDF5_ROOT}` -Wl,libhdf5.lib  -Wl,libhdf5_hl.lib"
                         ;;
+                        *darwin*)
+                                HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
+                        ;;
                         *linux*)
                                 HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
                         ;;
-                        *darwin*)
+                        *mingw*)
+                                HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
+                        ;;
+                        *msys*)
                                 HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl"
                         ;;
@@ -1188 +1294 @@
         dnl }}}
         dnl PETSc{{{
+        AC_MSG_CHECKING([for PETSc])
         AC_ARG_WITH(
                 [petsc-dir],
@@ -1194 +1301 @@
                 [PETSC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for PETSc])
         if test "x${PETSC_ROOT}" == "xno"; then
                 HAVE_PETSC=no
@@ -1215 +1321 @@
                 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}])
 
@@ -1257 +1363 @@
                                         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
                         ;;
@@ -1275 +1391 @@
                                 fi
                         ;;
-                        *darwin*)
-                                if test ${PETSC_MAJOR} -lt 3; then
-                                        PETSCLIB="-L${PETSC_ROOT}/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
-                                else
-                                        PETSCLIB="-L${PETSC_ROOT}/lib -lpetsc"
-                                        if test ${PETSC_MAJOR} -gt 3 || test ${PETSC_MINOR} -ge 3; then
-                                                PETSCLIB+=" -lmetis"
-                                        fi
-                                fi
+                        *mingw*)
+                                PETSCLIB="-Wl,${PETSC_ROOT}/lib/libpetsc.a"
+                        ;;
+                        *msys*)
+                                PETSCLIB="${PETSC_ROOT}/lib -lpetsc"
                         ;;
                 esac
@@ -1294 +1406 @@
         dnl MPI{{{
         AC_MSG_CHECKING(for MPI)
-
         AC_ARG_WITH(
                 [mpi-include],
@@ -1301 +1412 @@
                 [MPI_INCLUDE=""]
         )
-
         AC_ARG_WITH(
                 [mpi-libdir],
@@ -1308 +1418 @@
                 [MPI_LIBDIR=""]
         )
-
         AC_ARG_WITH(
                 [mpi-libflags],
@@ -1315 +1424 @@
                 [MPI_LIBFLAGS=""]
         )
-
         if test -z "${MPI_INCLUDE}"; then
                 HAVE_MPI=no
@@ -1358 +1466 @@
         dnl }}}
         dnl SCOTCH{{{
+        AC_MSG_CHECKING([for SCOTCH])
         AC_ARG_WITH(
                 [scotch-dir],
@@ -1364 +1473 @@
                 [SCOTCH_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SCOTCH])
         if test "x${SCOTCH_ROOT}" == "xno"; then
                 HAVE_SCOTCH=no
@@ -1397 +1505 @@
         dnl }}}
         dnl METIS{{{
-
-        dnl NOTE: We know $VENDOR cannot be empty at this point, so no need to
-        dnl               check again in the following conditionals
-        dnl
-        if test "x${HAVE_PETSC}" == "xyes" && test "x${PETSC_MAJOR}" == "x3" && test ${PETSC_MINOR} -ge 3 && test "${VENDOR}" != "MSVC-Win64" && test "${VENDOR}" != "MSVC-Win64-par"; then
-                dnl In PETSc >=3.3, METIS is provided
-                HAVE_METIS="yes"
-                AC_DEFINE([_METIS_VERSION_], [5], [METIS version number])
+        AC_MSG_CHECKING([for METIS])
+        AC_ARG_WITH(
+                [metis-dir],
+                AS_HELP_STRING([--with-metis-dir=DIR], [METIS root directory, necessary for serial build]),
+                [METIS_ROOT=${withval}],
+                [METIS_ROOT="no"]
+        )
+        HAVE_METIS=no
+        if test "x${METIS_ROOT}" == "xno"; then
+                dnl Check if METIS was installed via PETSc
+                if test -f ${PETSC_ROOT}/install/include/metis.h; then
+                        HAVE_METIS=yes
+                        METIS_ROOT="${PETSC_ROOT}"
+                fi
+        else
+                if ! test -d "${METIS_ROOT}"; then
+                        AC_MSG_ERROR([METIS directory provided (${METIS_ROOT}) does not exist!]);
+                fi
+                HAVE_METIS=yes
+        fi
+        if test "${HAVE_METIS}" = "yes"; then
+                METIS_VERSION=$(grep "#define METIS_VER_MAJOR" ${METIS_ROOT}/include/metis.h | sed 's|.*METIS_VER_MAJOR[[:space:]]*||')
+                dnl METIS libraries and header files
+                if test "x${METIS_VERSION}" == "x4"; then
+                        METISINCL="-I${METIS_ROOT}/Lib"
+                        case "${host_os}" in
+                                *cygwin*)
+                                        METISINCL="/I`cygpath -m ${METIS_ROOT}/Lib`"
+                                        METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${METIS_ROOT}` -Wl,libmetis.lib"
+                                ;;
+                                *darwin*)
+                                        METISLIB="-L${METIS_ROOT} -lmetis"
+                                ;;
+                                *linux*)
+                                        METISLIB="-L${METIS_ROOT} -lmetis"
+                                ;;
+                                *mingw*)
+                                        METISLIB="-Wl,${METIS_ROOT}/lib/libmetis.a"
+                                ;;
+                                *msys*)
+                                        METISLIB="-L${METIS_ROOT} -lmetis"
+                                ;;
+                        esac
+                elif test "x${METIS_VERSION}" == "x5"; then
+                        METISINCL="-I${METIS_ROOT}/include"
+                        case "${host_os}" in
+                                *cygwin*)
+                                        METISLIB="-L${METIS_ROOT} libmetis.lib"
+                                ;;
+                                *darwin*)
+                                        METISLIB="-L${METIS_ROOT}/lib -lmetis"
+                                ;;
+                                *linux*)
+                                        METISLIB="-L${METIS_ROOT}/lib -lmetis"
+                                ;;
+                                *mingw*)
+                                        METISLIB="-Wl,${METIS_ROOT}/lib/libmetis.a"
+                                ;;
+                                *msys*)
+                                        METISLIB="-L${METIS_ROOT}/lib -lmetis"
+                                ;;
+                        esac
+                else
+                        AC_MSG_ERROR([METIS version ${METIS_VERSION} not yet supported! Please contact ISSM developers via forum or email.])
+                fi
                 AC_DEFINE([_HAVE_METIS_], [1], [with METIS in ISSM src])
-        else
-                AC_ARG_WITH(
-                        [metis-dir],
-                        AS_HELP_STRING([--with-metis-dir=DIR], [METIS root directory, necessary for serial build]),
-                        [METIS_ROOT=${withval}],
-                        [METIS_ROOT="no"]
-                )
-                AC_MSG_CHECKING([for METIS])
-                if test "x${METIS_ROOT}" == "xno"; then
-                        HAVE_METIS=no
-                else
-                        HAVE_METIS=yes
-                        if ! test -d "${METIS_ROOT}"; then
-                                AC_MSG_ERROR([METIS directory provided (${METIS_ROOT}) does not exist!]);
-                        fi
-                fi
-                AC_MSG_RESULT([${HAVE_METIS}])
-                AM_CONDITIONAL([METIS], [test "x${HAVE_METIS}" == "xyes"])
-
+                AC_DEFINE_UNQUOTED([_METIS_VERSION_], ${METIS_VERSION}, [METIS version number])
+                AC_SUBST([METISINCL])
+                AC_SUBST([METISLIB])
+        fi
+        AC_MSG_RESULT([${HAVE_METIS}])
+        AM_CONDITIONAL([METIS], [test "x${HAVE_METIS}" = "xyes"])
+        dnl }}}
+        dnl ParMETIS{{{
+        AC_MSG_CHECKING([for ParMETIS])
+        AC_ARG_WITH(
+                [parmetis-dir],
+                AS_HELP_STRING([--with-parmetis-dir=DIR], [ParMETIS root directory, necessary for parallel build]),
+                [PARMETIS_ROOT=${withval}],
+                [PARMETIS_ROOT="no"]
+        )
+        HAVE_PARMETIS=no
+        if test "x${PARMETIS_ROOT}" == "xno"; then
+                dnl Check if ParMETIS was installed via PETSc
+                if test -f ${PETSC_ROOT}/install/include/parmetis.h; then
+                        HAVE_PARMETIS="yes"
+                        PARMETIS_ROOT="${PETSC_ROOT}"
+                fi
+        else
+                if ! test -d "${PARMETIS_ROOT}"; then
+                        AC_MSG_ERROR([ParMETIS directory provided (${PARMETIS_ROOT}) does not exist!]);
+                fi
+                if ! test -d "${METIS_ROOT}"; then
+                        AC_MSG_ERROR([If supplying path to ParMETIS with option --with-parmetis-dir, must also supply path to METIS with option --with-metis-dir]);
+                fi
+                HAVE_PARMETIS="yes"
+        fi
+        if test "${HAVE_PARMETIS}" == "yes"; then
+                #PARMETIS_VERSION=$(grep "#define PARMETIS_MAJOR_VERSION" ${PARMETIS_ROOT}/include/parmetis.h | sed 's|.*PARMETIS_MAJOR_VERSION[[:space:]]*||')
                 dnl METIS libraries and header files
-                if test "x${HAVE_METIS}" == "xyes"; then
-                        dnl Retrieve METIS version (does the VERSION file exist?)
-                        if test -f "${METIS_ROOT}/VERSION"; then
-                                METIS_VERSION=4
-                        else
-                                METIS_VERSION=5
-                        fi
-
-                        if test "x${METIS_VERSION}" == "x4"; then
-                                METISINCL="-I${METIS_ROOT}/Lib"
-                                case "${host_os}" in
-                                        *cygwin*)
-                                                METISINCL="/I`cygpath -m ${METIS_ROOT}/Lib`"
-                                                METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${METIS_ROOT}` -Wl,libmetis.lib"
-                                        ;;
-                                        *linux*)
-                                                METISLIB="-L${METIS_ROOT} -lparmetis -lmetis"
-                                        ;;
-                                        *darwin*)
-                                                METISLIB="-L${METIS_ROOT} -lparmetis -lmetis"
-                                        ;;
-                                esac
-                                AC_DEFINE([_METIS_VERSION_], [4], [ METIS version number])
-                        fi
-
-                        if test "x${METIS_VERSION}" == "x5"; then
-                                case "${host_os}" in
-                                        *cygwin*)
-                                                METISLIB="-L${METIS_ROOT} libmetis.lib"
-                                        ;;
-                                        *linux*)
-                                                METISLIB="-L${METIS_ROOT}/lib -lparmetis -lmetis"
-                                        ;;
-                                        *darwin*)
-                                                METISLIB="-L${METIS_ROOT}/lib -lparmetis -lmetis"
-                                        ;;
-                                esac
-                                METISINCL="-I${METIS_ROOT}/include"
-                                AC_DEFINE([_METIS_VERSION_], [5], [METIS version number])
-                        fi
-
-                        AC_DEFINE([_HAVE_METIS_], [1], [with METIS in ISSM src])
-                        AC_SUBST([METISINCL])
-                        AC_SUBST([METISLIB])
-                fi
-        fi
-        AM_CONDITIONAL([METIS], [test "x${HAVE_METIS}" == "xyes"])
+                #if test "x${PARMETIS_VERSION}" == "x4"; then
+                        PARMETISINCL="-I${PARMETIS_ROOT}/include"
+                        case "${host_os}" in
+                                *cygwin*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                                *darwin*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                                *linux*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                                *mingw*)
+                                        PARMETISLIB="-Wl,${PARMETIS_ROOT}/lib/libparmetis.a"
+                                ;;
+                                *msys*)
+                                        PARMETISLIB="-L${PARMETIS_ROOT}/lib -lparmetis"
+                                ;;
+                        esac
+                #else
+                #       AC_MSG_ERROR([ParMETIS version ${PARMETIS_VERSION} not yet supported! Please contact ISSM developers via forum or email.])
+                #fi
+                AC_DEFINE([_HAVE_PARMETIS_], [1], [with ParMETIS in ISSM src])
+                #AC_DEFINE([_PARMETIS_VERSION_], [${PARMETIS_VERSION}], [ParMETIS version number])
+                AC_SUBST([PARMETISINCL])
+                AC_SUBST([PARMETISLIB])
+        fi
+        AC_MSG_RESULT([${HAVE_PARMETIS}])
+        AM_CONDITIONAL([PARMETIS], [test "x${HAVE_PARMETIS}" = "xyes"])
         dnl }}}
         dnl Toolkit for Advanced Optimization (TAO){{{
+        AC_MSG_CHECKING([for TAO])
         AC_ARG_WITH(
                 [tao-dir],
@@ -1481 +1643 @@
                 [TAO_ROOT="no"]
         )
-        AC_MSG_CHECKING([for TAO])
-
         if test "x${HAVE_PETSC}" == "xyes" && test "x${PETSC_MAJOR}" == "x3" && test ${PETSC_MINOR} -ge 5; then
                 dnl In PETSc >= 3.5, TAO is provided
@@ -1510 +1670 @@
         dnl }}}
         dnl M1QN3{{{
+        AC_MSG_CHECKING([for M1QN3])
         AC_ARG_WITH(
                 [m1qn3-dir],
@@ -1516 +1677 @@
                 [M1QN3_ROOT="no"]
         )
-        AC_MSG_CHECKING([for M1QN3])
         if test "x${M1QN3_ROOT}" == "xno"; then
                 HAVE_M1QN3=no
@@ -1529 +1689 @@
         dnl M1QN3 libraries and header files
         if test "x${HAVE_M1QN3}" == "xyes"; then
-                M1QN3LIB="${M1QN3_ROOT}/libm1qn3.a ${M1QN3_ROOT}/libddot.a"
+                if test "${IS_MSYS2}" == "yes"; then
+                        M1QN3LIB="-Wl,${M1QN3_ROOT}/libm1qn3.a -Wl,${M1QN3_ROOT}/libddot.a"
+                else
+                        M1QN3LIB="${M1QN3_ROOT}/libm1qn3.a ${M1QN3_ROOT}/libddot.a"
+                fi
                 AC_DEFINE([_HAVE_M1QN3_], [1], [with M1QN3 in ISSM src])
                 AC_SUBST([M1QN3LIB])
@@ -1535 +1699 @@
         dnl }}}
         dnl PROJ{{{
+        AC_MSG_CHECKING([for PROJ])
         AC_ARG_WITH(
                 [proj-dir],
@@ -1541 +1706 @@
                 [PROJ_ROOT="no"]
         )
-        AC_MSG_CHECKING([for PROJ])
         if test "x${PROJ_ROOT}" == "xno"; then
                 HAVE_PROJ=no
@@ -1563 +1727 @@
         dnl }}}
         dnl SLEPc{{{
+        AC_MSG_CHECKING([for SLEPc])
         AC_ARG_WITH(
                 [slepc-dir],
@@ -1569 +1734 @@
                 [SLEPC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SLEPc])
         if test "x${SLEPC_ROOT}" == "xno"; then
                 HAVE_SLEPC=no
@@ -1590 +1754 @@
         dnl }}}
         dnl shapelib{{{
+        AC_MSG_CHECKING([for shapelib])
         AC_ARG_WITH(
                 [shapelib-dir],
@@ -1596 +1761 @@
                 [SHAPELIB_ROOT="no"]
         )
-        AC_MSG_CHECKING([for shapelib])
         if test "x${SHAPELIB_ROOT}" == "xno"; then
                 HAVE_SHAPELIB=no
@@ -1615 +1779 @@
                 AC_SUBST([SHAPELIBLIB])
         fi
+        AM_CONDITIONAL([SHP], [test "x${HAVE_SHAPELIB}" == "xyes"])
         dnl }}}
         dnl ScaLAPACK{{{
-
         dnl NOTE: User should supply path to root directory or libraries, but not both
+        dnl
+        AC_MSG_CHECKING([for ScaLAPACK])
         AC_ARG_WITH(
                 [scalapack-dir],
@@ -1631 +1797 @@
                 [SCALAPACKLIB="no"]
         )
-        AC_MSG_CHECKING([for ScaLAPACK])
         if test "x${SCALAPACK_ROOT}" == "xno" && test "x${SCALAPACKLIB}" == "xno"; then
                 HAVE_SCALAPACK=no
@@ -1640 +1805 @@
                 fi
                 HAVE_SCALAPACK=yes
-                SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack"
+                if test "${VENDOR}" == "win-msys2"; then
+                        SCALAPACKLIB="-Wl,${SCALAPACK_ROOT}/lib/libscalapack.a"
+                else
+                        SCALAPACKLIB="-L${SCALAPACK_ROOT}/lib -lscalapack"
+                fi
         elif test "x${SCALAPACKLIB}" != "xno"; then
                 dnl Value of SCALAPACKLIB should be valid here, so no need to set it (as above)
@@ -1656 +1825 @@
         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],
@@ -1662 +1844 @@
                 [BLASLAPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for BLAS/LAPACK])
-        if test "x${BLASLAPACK_ROOT}" == "xno" ; then
+        if (test "x${BLAS_ROOT}" = "xno" || test "x${LAPACK_ROOT}" = "xno") && test "x${BLASLAPACK_ROOT}" = "xno"; then
                 HAVE_BLASLAPACK=no
         else
                 HAVE_BLASLAPACK=yes
-                if ! test -d "${BLASLAPACK_ROOT}"; then
-                        AC_MSG_ERROR([BLAS/LAPACK directory provided (${BLASLAPACK_ROOT}) does not exist!]);
+                if ! test -d "${BLAS_ROOT}" || ! test -d "${LAPACK_ROOT}"; then
+                        if ! test -d "${BLASLAPACK_ROOT}"; then
+                                AC_MSG_ERROR([Use either --with-blas-dir and --with-lapack-dir *or* --with-blaslapack-dir]);
+                        fi
                 fi
         fi
@@ -1675 +1858 @@
         dnl BLAS/LAPACK libraries and header files
         if test "x${HAVE_BLASLAPACK}" == "xyes"; then
-                BLASLAPACKINCL=""
                 case "${host_os}" in
                         *cygwin*)
@@ -1704 +1886 @@
                                 fi
                         ;;
+                        *mingw*)
+                                if test -d "${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${BLAS_ROOT}/lib -lblas"
+                                fi
+                        ;;
                 esac
                 AC_DEFINE([_HAVE_BLASLAPACK_], [1], [with BLAS/LAPACK in ISSM src])
                 AC_SUBST([BLASLAPACKLIB])
-                AC_SUBST([BLASLAPACKINCL])
         fi
         dnl }}}
         dnl Math Kernel Library (MKL){{{
+        AC_MSG_CHECKING([for MKL])
         AC_ARG_WITH(
                 [mkl-libflags],
@@ -1717 +1930 @@
                 [MKL_LIBFLAGS="no"]
         )
-        AC_MSG_CHECKING([for MKL])
         if test "x${MKL_LIBFLAGS}" == "xno"; then
                 HAVE_MKL=no
@@ -1730 +1942 @@
         dnl }}}
         dnl PlaLAPACK{{{
-
         dnl TODO:       Handle user supplying path to root directory *or* individual
         dnl             arguments (like ScaLAPACK)
@@ -1765 +1976 @@
         dnl }}}
         dnl MUMPS{{{
+        AC_MSG_CHECKING([for MUMPS])
         AC_ARG_WITH(
                 [mumps-dir],
@@ -1771 +1983 @@
                 [MUMPS_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MUMPS])
         if test "x${MUMPS_ROOT}" == "xno"; then
                 HAVE_MUMPS=no
@@ -1786 +1997 @@
                 MUMPSINCL="-I${MUMPS_ROOT}/include"
                 if test "x${MUMPS_ROOT}" == "x${PETSC_ROOT}"; then
-                        if test "x${PETSC_MAJOR}" == "x2"; then
-                                MUMPSLIB="-L${MUMPS_ROOT}/lib "
+                        if test "${VENDOR}" == "win-msys2"; then
+                                MUMPSLIB="-Wl,${MUMPS_ROOT}/lib/libcmumps.a -Wl,${MUMPS_ROOT}/lib/libdmumps.a -Wl,${MUMPS_ROOT}/lib/libsmumps.a -Wl,${MUMPS_ROOT}/lib/libzmumps.a -Wl,${MUMPS_ROOT}/lib/libmumps_common.a -Wl,${MUMPS_ROOT}/lib/libpord.a"
                         else
                                 MUMPSLIB="-L${MUMPS_ROOT}/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis -lzmumps -lmetis"
                         fi
                 else
-                        MUMPSLIB="-L${MUMPS_ROOT}/lib -ldmumps -lmumps_common -lpord"
+                        MUMPSLIB="-L${MUMPS_ROOT}/lib -ldmumps -lmumps_common -lpord -lparmetis"
                 fi
                 AC_DEFINE([_HAVE_MUMPS_], [1], [with MUMPS in ISSM src])
@@ -1836 +2047 @@
         dnl }}}
         dnl BLACS{{{
+        AC_MSG_CHECKING([for BLACS])
         AC_ARG_WITH(
                 [blacs-dir],
@@ -1842 +2054 @@
                 [BLACS_ROOT="no"]
         )
-        AC_MSG_CHECKING([for BLACS])
         if test "x${BLACS_ROOT}" == "xno"; then
                 HAVE_BLACS=no
@@ -1863 +2074 @@
         dnl }}}
         dnl HYPRE{{{
+        AC_MSG_CHECKING([for HYPRE])
         AC_ARG_WITH(
                 [hypre-dir],
@@ -1869 +2081 @@
                 [HYPRE_ROOT="no"]
         )
-        AC_MSG_CHECKING([for HYPRE])
         if test "x${HYPRE_ROOT}" == "xno"; then
                 HAVE_HYPRE=no
@@ -1890 +2101 @@
         dnl }}}
         dnl Prometheus{{{
+        AC_MSG_CHECKING([for Prometheus])
         AC_ARG_WITH(
                 [prometheus-dir],
@@ -1896 +2108 @@
                 [PROMETHEUS_ROOT="no"]
         )
-        AC_MSG_CHECKING([for Prometheus])
         if test "x${PROMETHEUS_ROOT}" == "xno"; then
                 HAVE_PROMETHEUS=no
@@ -1917 +2128 @@
         dnl }}}
         dnl SEMIC{{{
+        AC_MSG_CHECKING([for SEMIC])
         AC_ARG_WITH(
                 [semic-dir],
@@ -1923 +2135 @@
                 [SEMIC_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SEMIC])
         if test "x${SEMIC_ROOT}" == "xno"; then
                 HAVE_SEMIC=no
@@ -1937 +2148 @@
         if test "x${HAVE_SEMIC}" == "xyes"; then
                 SEMICINCL="-I${SEMIC_ROOT}"
+                if test "${IS_MSYS2}" == "yes"; then
+                        SEMICLIB="-Wl,-L${SEMIC_ROOT}/lib -Wl,-lsurface_physics -Wl,-lutils"
+                else
+                        SEMICLIB="-L${SEMIC_ROOT}/lib -lsurface_physics -lutils"
+                fi
                 AC_DEFINE([_HAVE_SEMIC_], [1], [with SEMIC in ISSM src])
-                SEMICLIB="-L${SEMIC_ROOT} -lsurface_physics -lutils"
                 AC_SUBST([SEMICLIB])
                 AC_SUBST([SEMICINCL])
@@ -1945 +2160 @@
         dnl }}}
         dnl SPAI{{{
+        AC_MSG_CHECKING([for SPAI])
         AC_ARG_WITH(
                 [spai-dir],
@@ -1951 +2167 @@
                 [SPAI_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SPAI])
         if test "x${SPAI_ROOT}" == "xno"; then
                 HAVE_SPAI=no
@@ -1972 +2187 @@
         dnl }}}
         dnl SuperLU{{{
+        AC_MSG_CHECKING([for SuperLU])
         AC_ARG_WITH(
                 [superlu-dir],
@@ -1978 +2194 @@
                 [SUPERLU_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SuperLU])
         if test "x${SUPERLU_ROOT}" == "xno"; then
                 HAVE_SUPERLU=no
@@ -1999 +2214 @@
         dnl }}}
         dnl SPOOLES{{{
+        AC_MSG_CHECKING([for SPOOLES])
         AC_ARG_WITH(
                 [spooles-dir],
@@ -2005 +2221 @@
                 [SPOOLES_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SPOOLES])
         if test "x${SPOOLES_ROOT}" == "xno"; then
                 HAVE_SPOOLES=no
@@ -2026 +2241 @@
         dnl }}}
         dnl PaStiX{{{
+        AC_MSG_CHECKING([for PaStiX])
         AC_ARG_WITH(
                 [pastix-dir],
@@ -2032 +2248 @@
                 [PASTIX_ROOT="no"]
         )
-        AC_MSG_CHECKING([for PaStiX])
         if test "x${PASTIX_ROOT}" == "xno"; then
                 HAVE_PASTIX=no
@@ -2054 +2269 @@
         dnl }}}
         dnl ml{{{
+        AC_MSG_CHECKING([for ml])
         AC_ARG_WITH(
                 [ml-dir],
@@ -2060 +2276 @@
                 [ML_ROOT="no"]
         )
-        AC_MSG_CHECKING([for ml])
         if test "x${ML_ROOT}" == "xno"; then
                 HAVE_ML=no
@@ -2081 +2296 @@
         dnl }}}
         dnl UMFPACK{{{
+        AC_MSG_CHECKING([for UMFPACK])
         AC_ARG_WITH(
                 [umfpack-dir],
@@ -2087 +2303 @@
                 [UMFPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for UMFPACK])
         if test "x${UMFPACK_ROOT}" == "xno"; then
                 HAVE_UMFPACK=no
@@ -2124 +2339 @@
         dnl }}}
         dnl MATH77{{{
+        AC_MSG_CHECKING([for MATH77])
         AC_ARG_WITH(
                 [math77-dir],
@@ -2130 +2346 @@
                 [MATH77_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MATH77])
         if test "x${MATH77_ROOT}" == "xno"; then
                 HAVE_MATH77=no
@@ -2149 +2364 @@
         dnl }}}
         dnl Fortran{{{
+        AC_MSG_CHECKING(for Fortran compilation)
         AC_ARG_WITH(
                 [fortran],
@@ -2155 +2371 @@
                 [FORTRAN=yes]
         )
-        AC_MSG_CHECKING(for Fortran compilation)
         if test "x${FORTRAN}" == "xyes"; then
                 HAVE_FORTRAN=yes
@@ -2219 +2434 @@
         dnl }}}
         dnl MeteoIO{{{
+        AC_MSG_CHECKING([for MeteoIO])
         AC_ARG_WITH(
                 [meteoio-dir],
@@ -2225 +2441 @@
                 [METEOIO_ROOT="no"]
         )
-        AC_MSG_CHECKING([for MeteoIO])
         if test "x${METEOIO_ROOT}" == "xno"; then
                 HAVE_METEOIO=no
@@ -2248 +2463 @@
         dnl }}}
         dnl SNOWPACK{{{
+        AC_MSG_CHECKING([for SNOWPACK])
         AC_ARG_WITH(
                 [snowpack-dir],
@@ -2254 +2470 @@
                 [SNOWPACK_ROOT="no"]
         )
-        AC_MSG_CHECKING([for SNOWPACK])
         if test "x${SNOWPACK_ROOT}" == "xno"; then
                 HAVE_SNOWPACK=no
@@ -2276 +2491 @@
         dnl }}}
         dnl NeoPZ{{{
+        AC_MSG_CHECKING([for NeoPZ])
         AC_ARG_WITH(
                 [neopz-dir],
@@ -2282 +2498 @@
                 [NEOPZ_ROOT="no"]
         )
-        AC_MSG_CHECKING([for NeoPZ])
         if test "x${NEOPZ_ROOT}" == "xno"; then
                 HAVE_NEOPZ=no
@@ -2351 +2566 @@
                 GMSH_VERSION_MAJOR=`${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_], ${GMSH_VERSION_MAJOR}, [Gmsh major version])
         fi      
         dnl }}}
         dnl Capabilities
         dnl with-bamg{{{
+        AC_MSG_CHECKING([for BAMG capability compilation])
         AC_ARG_WITH(
                 [bamg],
@@ -2362 +2578 @@
                 [BAMG=yes]
         )
-        AC_MSG_CHECKING([for BAMG capability compilation])
         HAVE_BAMG=no
         if test "x${BAMG}" == "xyes"; then
@@ -2372 +2587 @@
         dnl }}}
         dnl with-ocean{{{
+        AC_MSG_CHECKING(for ice/ocean coupling capability compilation)
         AC_ARG_WITH(
                 [ocean],
@@ -2378 +2594 @@
                 [OCEAN=no]
         )
-        AC_MSG_CHECKING(for ice/ocean coupling capability compilation)
-
         HAVE_OCEAN=no
         if test "x${OCEAN}" == "xyes"; then
@@ -2389 +2603 @@
         dnl }}}
         dnl with-kml{{{
+        AC_MSG_CHECKING(for kml capability compilation)
         AC_ARG_WITH(
                 [kml],
@@ -2395 +2610 @@
                 [KML=no]
         )
-        AC_MSG_CHECKING(for kml capability compilation)
-
         HAVE_KML=no
         if test "x${KML}" == "xyes"; then
@@ -2406 +2619 @@
         dnl }}}
         dnl with-kriging{{{
+        AC_MSG_CHECKING(for kriging capability compilation)
         AC_ARG_WITH(
                 [kriging],
@@ -2412 +2626 @@
                 [KRIGING=yes]
         )
-        AC_MSG_CHECKING(for kriging capability compilation)
-
         HAVE_KRIGING=no
         if test "x${KRIGING}" == "xyes"; then
@@ -2428 +2640 @@
         dnl Platform specifics
         dnl with-ios{{{
+        AC_MSG_CHECKING(for iOS compilation)
         AC_ARG_WITH(
                 [ios],
@@ -2434 +2647 @@
                 [IOS=no]
         )
-        AC_MSG_CHECKING(for iOS compilation)
-
         HAVE_IOS=no
         if test "x${IOS}" == "xyes"; then
@@ -2445 +2656 @@
         dnl }}}
         dnl with-android{{{
+        AC_MSG_CHECKING([for Android capability compilation])
         AC_ARG_WITH(
                 [android],
                 AS_HELP_STRING([--with-android=EXE], [compile with Android capabilities (default: "no"; alternatives: "exe", "jni")]),
                 [ANDROID=${withval}],
-                [ANDROID=no])
-        AC_MSG_CHECKING([for Android capability compilation])
-
+                [ANDROID=no]
+        )
         if test "x${ANDROID}" == "xjni"; then
                 HAVE_ANDROID=jni
@@ -2470 +2681 @@
         dnl }}}
         dnl with-android-ndk{{{
+        AC_MSG_CHECKING([with Android Native Development Kit (NDK)])
         AC_ARG_WITH(
                 [android-ndk],
@@ -2476 +2688 @@
                 [ANDROID_NDK_ROOT=""]
         )
-        AC_MSG_CHECKING([with Android Native Development Kit (NDK)])
-
         if test -d "${ANDROID_NDK_ROOT}"; then
                 HAVE_ANDROID_NDK=yes
@@ -2491 +2701 @@
         dnl other options
         dnl optimization{{{
-        dnl -- bypass standard optimization -g -O2 -fPIC -std=c++11?
+        dnl -- bypass standard optimization -g -O2 -fPIC?
+        AC_MSG_CHECKING(for C++ optimization flags)
         AC_ARG_WITH(
                 [cxxoptflags],
@@ -2498 +2709 @@
                 [CXXOPTFLAGS="-g -O2 -fPIC -std=c++11"]
         )
-        AC_MSG_CHECKING(for C++ optimization flags)
         AC_SUBST([CXXOPTFLAGS])
-        AC_MSG_RESULT([done])
+        AC_MSG_RESULT([${CXXOPTFLAGS}])
         dnl }}}
         dnl multithreading{{{
+        AC_MSG_CHECKING(for number of threads)
         AC_ARG_WITH(
                 [numthreads],
@@ -2509 +2720 @@
                 [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
@@ -2524 +2734 @@
                                 MULTITHREADINGLIB="-lpthread -lrt"
                         ;;
+                        *darwin*)
+                                MULTITHREADINGLIB="-lpthread"
+                        ;;
                         *linux*)
                                 MULTITHREADINGLIB="-lpthread -lrt"
                         ;;
-                        *darwin*)
-                                MULTITHREADINGLIB="-lpthread"
+                        *mingw*)
+                                MULTITHREADINGLIB=""
+                        ;;
+                        *msys*)
+                                MULTITHREADINGLIB=""
                         ;;
                 esac
                 AC_DEFINE([_MULTITHREADING_], [1], [with multithreading enabled])
         fi
-        AC_DEFINE_UNQUOTED(_NUMTHREADS_, $NUMTHREADS_VALUE, [number of threads])
+        AC_DEFINE_UNQUOTED([_NUMTHREADS_], ${NUMTHREADS_VALUE}, [number of threads])
         AC_SUBST([MULTITHREADINGLIB])
         AC_MSG_RESULT([${NUMTHREADS_VALUE}])
         dnl }}}
         dnl 64-bit indices{{{
+        AC_MSG_CHECKING([for 64-bit indices])
         AC_ARG_WITH(
                 [64bit-indices],
@@ -2544 +2761 @@
                 [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])
@@ -2555 +2770 @@
 
         dnl Checks {{{
-        AC_MSG_CHECKING(consistency between all libraries)
+        AC_MSG_CHECKING(consistency between all external packages)
 
         dnl Check that if PETSc is requested, MPI is specified
@@ -2585 +2800 @@
 
         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