Index: ../trunk-jpl/m4/issm_options.m4
===================================================================
--- ../trunk-jpl/m4/issm_options.m4	(revision 13747)
+++ ../trunk-jpl/m4/issm_options.m4	(revision 13748)
@@ -91,7 +91,7 @@
 	AC_SUBST([OSLIBS]) 
 	AC_MSG_RESULT(done)
 	dnl }}}
-	dnl Matlab{{{
+	dnl matlab{{{
 
 	dnl 1. See if matlab has been provided
 	AC_ARG_WITH([matlab-dir],
@@ -232,9 +232,11 @@
 	AC_MSG_CHECKING(for python)
 	
 	if test -d "$PYTHON_ROOT"; then
+	 AC_MSG_RESULT($HAVE_PYTHON)
 		dnl defaults
 		HAVE_PYTHON3="no"
-		HAVE_PYTHON=yes
+		HAVE_PYTHON="yes"
+		AC_MSG_RESULT($HAVE_PYTHON)
 		
 		AC_ARG_WITH([python-version],
 		  AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]),
@@ -275,11 +277,10 @@
 		AC_SUBST([PYTHONLINK])
 	else
 		HAVE_PYTHON=no
+		AC_MSG_RESULT($HAVE_PYTHON)
 	fi
 	AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes])
 	AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes])
-	AC_MSG_RESULT($HAVE_PYTHON)
-
 	dnl }}}
 	dnl python-numpy{{{
 	AC_ARG_WITH([python-numpy-dir],
@@ -578,36 +579,41 @@
 	dnl make getlinklibs
 	if test -d "$PETSC_ROOT"; then
 
-		PETSCINCL="-I$PETSC_ROOT/$PETSC_ARCH/include -I$PETSC_ROOT/include/$PETSC_ARCH/ -I$PETSC_ROOT/include -I$PETSC_ROOT/ -I$PETSC_ROOT/bmake/$PETSC_ARCH -I$PETSC_ROOT/src/mat/impls/dense/mpi/plapack/"
+	 PETSCINCL=" -I$PETSC_ROOT/include"
+	 dnl Add other location (maybe not needed anymore)
+	 if test -d "$PETSC_ROOT/$PETSC_ARCH/include"; then
+	  PETSCINCL+=" $PETSC_ROOT/$PETSC_ARCH/include"
+	 fi
+	 if test -d "$PETSC_ROOT/include/$PETSC_ARCH"; then
+	  PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH"
+	 fi
 	
-		case "${host_os}" in
+	 case "${host_os}" in
 			*cygwin*)
-			if test "$PETSC_MAJOR" = "2" ; then
-				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib  libpetscdm.lib  libpetscmat.lib  libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib"
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib libpetsc.lib"
 			else
-				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetsc.lib"
+				PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib\" libpetsc.lib"
 			fi
 			;;
 			*linux*)
-			if test "$PETSC_MAJOR" = "2" ; then
-			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc  -lpetscsnes -lpetscts"
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc  -lpetscsnes -lpetscts"
 			else
-			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc -ldl"
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc -ldl"
 			fi
 			;;
 			*darwin*)
-			if test "$PETSC_MAJOR" = "2" ; then
-			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
 			else
-			PETSCLIB="-L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH/ -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lpetsc"
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc"
 			fi
 			;;
 		esac
-
 		AC_DEFINE([_HAVE_PETSC_],[1],[with PETSc in ISSM src])
 		AC_SUBST([PETSCINCL])
 		AC_SUBST([PETSCLIB])
-
 		HAVE_PETSC=yes
 	else
 		HAVE_PETSC=no