Index: /issm/trunk-jpl/packagers/ubuntu/issmpkg/README
===================================================================
--- /issm/trunk-jpl/packagers/ubuntu/issmpkg/README	(revision 16002)
+++ /issm/trunk-jpl/packagers/ubuntu/issmpkg/README	(revision 16002)
@@ -0,0 +1,138 @@
+UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION 
+
+PREFACE:
+	There are configuration files included in the dir where this document
+	 resides. Use them, that's why they're there. But I know, since some of
+	 you like to go against the grain, at least one of you is going to try
+	 building a package from an install that differs from mine.
+
+	If you choose to go down that dark road, then bear in mind that there
+	 are ways to do this right, and there are ways to do this wrong....
+	 Make sure that you mind where you decide to install the bin and lib.
+	 If you specify a target outside of the trunk, and don't, let's say,
+	 write the same dir somewhere else, then the package won't work. 
+
+	Make sure when putting together a dir hierarchy for a package, that you
+	 create something sime to what you specifed during compile. If you
+	 change "--bindir" then create a dir in the package that corresponds to
+	 that. The trunk doesn't necessarily have to be in the same place as it
+	 is on the build system.
+
+-------------------------------------------------------------------------------
+		    Installing ISSM to create a deb package:
+-------------------------------------------------------------------------------
+
+1.	Install mpich from the ubuntu repositories:
+
+		> sudo apt-get install mpich2 (or something similar)
+
+		Check to make sure that it installs the "-dev" libs
+			if not:
+			 > sudo apt-get install libmpich-dev (or something similar)
+			Otherwise you won't get "/usr/lib/mpich2"
+
+		You can use "apt-cache search" to find a package's full name
+
+2a.	Compile petsc and metis (preferred versions: 3.2 and 4.0, respectively):
+
+		Make sure that petsc's installer file is pointing to the
+		 correct mpich dir
+
+			You should use "/usr/lib/mpich2" (or something similar)
+
+		As of now, it is preferable to use the separate mpich package
+		 because the infrastructure of the mpich package under petsc
+		 is having issues with being packaged
+
+		Also make sure that you mind the target of the installation.
+			Right now /usr/share/petsc and /usr/share/metis are the
+			 best options suffixed by version numbers
+
+2b.	Install dependencies from the ubuntu repositories
+
+		Use apt-get install to install:
+			triangle-bin, libtriangle-dev, python2.7-dev, 
+			 python-scipy, python-netcdf4, netcdf-bin, python-nose, 
+			 libnetcdfc++4, hdf5-tools
+
+		REMEMBER: that this tutorial assumes you are creating the
+		 python interface
+			
+3.	Be sure to patch the system triangle.h file
+
+		> sudo patch /usr/include/triangle.h $ISSM_DIR/externalpackages/triangle/triangle.h.patch
+			the header may also be called "libtriangle.h"
+
+		Just like always, this will move the original to 
+		 "triangle.h.old" incase you need to revert
+
+4.	Compile ISSM
+
+		> autoreconf -iv && configs/config-*-packaging.sh && make && sudo -E make install
+
+-------------------------------------------------------------------------------
+		          Creating an issm.deb package
+-------------------------------------------------------------------------------
+	THIS ASSUMES YOU ARE USING THE CONFIG FILE SUPPLIED HERE.
+	IF YOU ARE DOING AN ALTERNATE CONFIG, MAKE SURE THE DIR
+	HIERARCHY IS PROPERLY REFLECTED BY THE BINDIR AND LIBDIR!
+
+1.	Make a directory to work from (the dir dpkg-deb will build)
+		Anywhere will do, but using a ~/tmp dir works best
+
+		> mkdir issmpkgdir
+		> cd issmpkgdir
+
+2.	Create the dir hierarchy:
+
+		> mkdir -p usr/{bin,lib,share/issm-trunk} etc/issm DEBIAN
+
+		This is will create:
+		issmpkgdir/
+		|_ usr/
+		|  |_ bin/
+		|  |_ lib/
+		|  |_ share/
+		|     |_issm-trunk/ - this is the trunk
+		|_ etc/
+		|  |_ issm/ - this is where issmrc and other conf files go
+		|_DEBIAN/ - where control files and install scripts go
+
+		As stated, if you change "--bindir" or "--libdir" in the config
+		 file, then make sure that you create matching dirs in this
+		 step, or vice-versa.
+
+3.	Copy the contents of the package over:
+
+		> sudo cp -r /usr/bin/issm usr/bin
+		> sudo cp -r /usr/lib/issm usr/lib
+		> cp -r $ISSM_DIR/* usr/share/issm-trunk
+
+		When you copy the trunk over, this your opportunity to weed out
+		 anything you don't want included in the build.
+		Again, the config file installs the bin and lib files to a dir
+		 that's separate from the rest of the bin and lib files. If you
+		 change "--bindir" or "--libdir", make sure you install them to
+		 a subdirectory of your target to keep things neat or else 
+		 you'll have to pick them out, one-by-one to complete this step.
+
+4.	Write your control file. A template is provided, that is the bare minimum to
+		 create the package 
+
+		You will NEED the following dependencies:
+		mpich2, petsc3.2-issm, metis4.0-issm, triangle-bin, libtriangle-dev, 
+		 python2.7-dev, python-scipy, python-netcdf4, netcdf-bin, python-nose, 
+		 libnetcdfc++4, hdf5-tools
+
+5.	Create any install/uninstall scripts needed (preinst, postinst, prerm, postrm)
+		There are already some templates provided for you.
+
+		Make sure you address the issue of any user created content. By
+		 default, apt-get won't remove anything that wasn't created by
+		 the installer, even if you use purge. Put this in a rm script.
+
+6.	Build the package:
+
+		> dpkg-deb --build <workingDir> <nameOfPackage>
+
+UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION 
Index: /issm/trunk-jpl/packagers/ubuntu/issmpkg/environment.sh
===================================================================
--- /issm/trunk-jpl/packagers/ubuntu/issmpkg/environment.sh	(revision 16002)
+++ /issm/trunk-jpl/packagers/ubuntu/issmpkg/environment.sh	(revision 16002)
@@ -0,0 +1,287 @@
+#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
+
+pathprepend(){ #{{{
+	if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
+		export PATH="$1:$PATH"
+	fi
+} #}}}
+pathappend(){ #{{{
+	if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
+		export PATH="$PATH:$1"
+	fi
+} #}}}
+libpathprepend(){ #{{{
+	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$1:$LD_RUN_PATH"
+	fi
+} #}}}
+libpathappend(){ #{{{
+	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$LD_RUN_PATH:$1"
+	fi
+} #}}}
+dylibpathprepend(){ #{{{
+	if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export DYLD_LIBRARY_PATH="$1:$DYLD_LIBRARY_PATH"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$1:$LD_RUN_PATH"
+	fi
+} #}}}
+dylibpathappend(){ #{{{
+	if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$1"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$LD_RUN_PATH:$1"
+	fi
+} #}}}
+
+#FIXME: during installation packages are installed one by one but environment.sh was sourced
+#before so new packages are NOT in the path.
+#may resource environment.sh with:
+#if [ -z $(echo "$PATH" | grep "$MATLAB_DIR") ]; then export $PATH...; fi
+
+#Windows compilers: 
+if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
+	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
+fi
+
+#Some basic path, in case it is not included by default
+libpathappend "/usr/local/lib"
+
+#Load ISSM scripts
+pathappend "$ISSM_DIR/scripts"
+
+MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
+export MATLAB_DIR
+pathprepend   "$MATLAB_DIR/bin" #take precedence over /usr/local/bin/matlab
+libpathappend "$MATLAB_DIR/lib"
+
+#legacy mpich2 (To be removed)
+MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
+if [ -d "$MPI_DIR" ]; then
+	export MPI_DIR
+	pathprepend   "$MPI_DIR/bin"
+	libpathappend "$MPI_DIR/lib"
+fi
+
+MPI_DIR="$ISSM_DIR/externalpackages/mpich/install"
+if [ -d "$MPI_DIR" ]; then
+	export MPI_DIR
+	pathprepend   "$MPI_DIR/bin"
+	libpathappend "$MPI_DIR/lib"
+fi
+
+PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
+export PETSC_DIR
+libpathappend "$PETSC_DIR/lib"
+
+SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
+libpathappend "$SLEPC_DIR/lib"
+
+TAO_DIR="$ISSM_DIR/externalpackages/tao/install"
+libpathappend "$TAO_DIR/lib"
+
+DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
+pathappend "$DAKOTA_DIR/bin"
+libpathappend "$DAKOTA_DIR/lib"
+
+DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
+pathprepend "$DOXYGEN_DIR/bin"
+
+AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install"
+pathprepend "$AUTOTOOLS_DIR/bin"
+
+SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
+pathappend "$SDK_DIR"
+
+SSH_DIR="$ISSM_DIR/externalpackages/ssh"
+pathappend "$SSH_DIR"
+
+VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install"
+pathprepend "$VALGRIND_DIR/bin"
+
+CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
+pathappend "$CPPCHECK_DIR/bin"
+
+GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
+pathprepend "$GDAL_DIR/bin"
+libpathappend "$GDAL_DIR/lib"
+
+PROJ4_DIR="$ISSM_DIR/externalpackages/proj.4/install"
+libpathappend "$PROJ4_DIR/lib"
+
+MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
+if [ -d "$MERCURIAL_DIR" ]; then
+	export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
+	pathappend "$MERCURIAL_DIR"
+fi
+
+BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
+BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
+if [ -d "$BOOST_DIR" ]; then
+	export BOOSTROOT
+	export BOOST_DIR
+	libpathappend   "$BOOST_DIR/lib"
+	dylibpathappend "$BOOST_DIR/lib"
+	pathappend      "$BOOST_DIR/bin"
+fi
+
+XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
+XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
+if [ -d "$XERCESROOT" ]; then
+	export XERCESROOT 
+	export XERCESCROOT
+fi
+
+XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
+XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/"
+XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
+PLATFORM="x86-Linux"
+if [ -d "$XAIF_DIR" ]; then
+	export XAIFBOOSTERROOT
+	export XAIFBOOSTER_HOME
+	export XAIF_DIR
+	export PLATFORM
+fi
+
+ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
+if [ -d "$ANGELROOT" ]; then
+	export ANGELROOT
+fi
+
+OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
+if [ -d "$OPENANALYSISROOT" ]; then
+	export OPENANALYSISROOT
+	libpathappend "$OPENANALYSISROOT/lib"
+fi
+
+JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
+libpathappend "$JVM_DIR"
+
+BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
+pathappend "$BBFTP_DIR/bin"
+
+ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
+pathappend "$ADIC_DIR/bin"
+libpathappend "$ADIC_DIR/lib"
+
+COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
+libpathappend "$COLPACK_DIR/lib"
+
+ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
+pathappend "$ECLIPSE_DIR"
+
+APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan/install"
+pathappend "$APPSCAN_DIR/bin"
+
+RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
+pathappend "$RATS_DIR/bin"
+
+DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
+pathappend "$DYSON_DIR"
+
+CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
+pathprepend "$CMAKE_DIR/bin"
+
+SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
+pathappend "$SHAPELIB_DIR/exec"
+
+CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
+pathappend "$CCCL_DIR/bin"
+
+PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
+pathappend "$PACKAGEMAKER_DIR"
+
+#android-dev-dir
+export ANDROID_DIR="$ISSM_DIR/externalpackages/android"
+
+export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
+pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin"
+
+export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install"
+pathappend "$ANDROID_SDK_DIR/"
+
+GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
+libpathappend "$GSL_DIR/lib"
+
+GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
+pathprepend "$GMAKE_DIR/bin"
+
+PYTHON_DIR="/usr"
+if [ -d "$PYTHON_DIR" ]; then
+	export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/lib"
+	export PYTHONSTARTUP="$ISSM_DIR/startup.py"
+	pathprepend    "/usr"
+	libpathprepend "$ISSM_DIR/lib"
+	libpathprepend "/usr/lib/python2.7"
+fi
+
+MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install"
+pathappend "$MODELE_DIR/src/exec"
+
+GIT_DIR="$ISSM_DIR/externalpackages/git/install"
+pathprepend "$GIT_DIR/bin"
+
+NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install"
+pathappend "$NCVIEW_DIR"
+
+TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4"
+libpathappend "$TCLX_DIR"
+
+ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/install"
+pathappend "$ASPELL_DIR/bin"
+
+HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install"
+dylibpathappend "$HDF5_DIR/lib"
+libpathappend "$HDF5_DIR/lib"
+if [ -d "$HDF5_DIR" ]; then
+	export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
+	export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
+fi
+
+NETCDF_DIR="$ISSM_DIR/externalpackages/netcdf/install"
+pathappend "$NETCDF_DIR/bin"
+dylibpathappend "$NETCDF_DIR/lib"
+libpathappend "$NETCDF_DIR/lib"
+if [ -d "$NETCDF_DIR" ]; then
+	export LIBRARY_PATH="$LIBRARY_PATH:$NETCDF_DIR/lib"
+	dylibpathappend "$NETCDF_DIR/lib"
+	libpathappend "$NETCDF_DIR/lib"
+	export C_INCLUDE_PATH="$C_INCLUDE_PATH:$NETCDF_DIR/include"
+fi
+
+NETCDF_CXX_DIR="$ISSM_DIR/externalpackages/netcdf-cxx/install"
+libpathappend "$NETCDF_CXX_DIR/lib"
+
+SVN_DIR="$ISSM_DIR/externalpackages/svn/install"
+pathprepend   "$SVN_DIR/bin"
+libpathappend "$SVN_DIR/lib"
+
+APR_DIR="$ISSM_DIR/externalpackages/apr/install"
+pathappend    "$APR_DIR/bin"
+libpathappend "$APR_DIR/lib"
+
+APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install"
+pathappend   "$APR_UTIL_DIR/bin:$PATH"
+libpathappend "$APR_UTIL_DIR/lib"
+
+SQLITE_DIR="$ISSM_DIR/externalpackages/sqlite/install"
+pathappend   "$SQLITE_DIR/bin"
+libpathappend "$SQLITE_DIR/lib"
+
+YAMS_DIR="$ISSM_DIR/externalpackages/yams/install"
+pathappend   "$YAMS_DIR"
+
+SWIG_DIR="$ISSM_DIR/externalpackages/swig/install"
+pathappend   "$SWIG_DIR"
+
+#AUX-CONFIG
+pathappend   "$ISSM_DIR/aux-config"
Index: /issm/trunk-jpl/packagers/ubuntu/issmpkg/install-3.2-linux64.sh
===================================================================
--- /issm/trunk-jpl/packagers/ubuntu/issmpkg/install-3.2-linux64.sh	(revision 16002)
+++ /issm/trunk-jpl/packagers/ubuntu/issmpkg/install-3.2-linux64.sh	(revision 16002)
@@ -0,0 +1,37 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf install petsc-3.2-p3 src
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz'
+
+#Untar and move petsc to install directory
+tar -zxvf  petsc-3.2-p3.tar.gz
+mv petsc-3.2-p3/* src/
+rm -rf petsc-3.2-p3
+
+#configure
+cd src
+./config/configure.py \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--with-mpi-dir="/usr/lib/mpich2/" \
+	--with-clanguage=C++ \
+	--PETSC_ARCH=linux-gnu-amd64 \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+	--with-debugging=0 \
+	--with-shared-libraries=1 \
+	--download-mumps=yes \
+	--download-scalapack=yes \
+	--download-blacs=yes \
+	--download-blas=yes \
+	--download-f-blas-lapack=yes \
+	--download-plapack=yes \
+	--download-parmetis=yes \
+	--with-pic=1
+
+#Compile petsc and install it
+make
+make install
Index: /issm/trunk-jpl/packagers/ubuntu/issmpkg/issm_options.m4
===================================================================
--- /issm/trunk-jpl/packagers/ubuntu/issmpkg/issm_options.m4	(revision 16002)
+++ /issm/trunk-jpl/packagers/ubuntu/issmpkg/issm_options.m4	(revision 16002)
@@ -0,0 +1,1690 @@
+dnl ISSM Options
+
+AC_DEFUN([ISSM_OPTIONS],[
+
+	dnl ISSM's internal options
+	dnl Debugging {{{
+	AC_ARG_ENABLE([debugging],                                        dnl feature
+		AS_HELP_STRING([--enable-debugging],[turn debug support on]),  dnl help string
+		[enable_debugging=$enableval],                                 dnl action if given
+		[enable_debugging=no])                                         dnl action if not given
+	if test "x$enable_debugging" = xyes; then
+		AC_DEFINE([_ISSM_DEBUG_],[1],[Macro to enable debugging in ISSM])
+	fi
+
+	dnl }}}
+    dnl Shared build {{{
+    AC_ARG_ENABLE([sharedlibs],                                                dnl feature
+        AS_HELP_STRING([--enable-sharedlibs], [produce libISSM.so.0]),         dnl help string
+        [enable_sharedlibs=$enableval],                                        dnl action if given
+        [enable_sharedlibs=no])                                                dnl action if not given
+    AM_CONDITIONAL([SHAREDLIBS], [test x$enable_sharedlibs = xyes])
+    dnl }}}
+    dnl Version{{{
+    AC_ARG_ENABLE([version],                                                dnl feature
+        AS_HELP_STRING([--enable-version], [produce libISSM.so.0]),         dnl help string
+        [enable_version=$enableval],                                        dnl action if given
+        [enable_version=no])                                                dnl action if not given
+    AM_CONDITIONAL([VERSION], [test x$enable_VERSION = xyes])
+    dnl }}}
+	dnl Wrappers build {{{
+	AC_ARG_WITH([wrappers],
+		AS_HELP_STRING([--with-wrappers = value],[wrappers compilation. ]),
+		[WRAPPERS_VALUE=$withval],[WRAPPERS_VALUE="yes"])
+	AC_MSG_CHECKING(for wrappers compilation)
+	AM_CONDITIONAL([WRAPPERS], [test x$WRAPPERS_VALUE = xyes])
+	AC_MSG_RESULT($WRAPPERS_VALUE) 
+	dnl }}}
+	dnl Extensions{{{
+	ISSMEXT=".exe"
+	AC_SUBST([ISSMEXT])
+	dnl }}}
+
+	dnl ISSM's externalpackages
+	dnl vendor{{{
+	AC_ARG_WITH([vendor],
+	  AS_HELP_STRING([--with-vendor = VENDOR], [vendor name, ex: intel]),
+	  [VENDOR=$withval],[VENDOR=""]) 
+	AC_MSG_CHECKING(for vendor compilers)
+	if test -n "$VENDOR"; then
+
+		if  test $VENDOR = intel-win32; then
+			export CC=icl
+			export CXX=icl
+			export CFLAGS="-DWIN32 -D_INTEL_WIN_"
+			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_"
+		elif  test $VENDOR = intel-win7-32; then
+			export CC=cl
+			export CXX=cccl
+			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export AR="ar-lib lib"
+			export OS_LDFLAG="-Wl,"
+			export RANLIB=true
+			OSLIBS="-Wl,kernel32.lib -Wl,user32.lib -Wl,gdi32.lib -Wl,winspool.lib -Wl,comdlg32.lib -Wl,advapi32.lib -Wl,shell32.lib -Wl,ole32.lib -Wl,oleaut32.lib -Wl,uuid.lib -Wl,odbc32.lib -Wl,odbccp32.lib"
+		elif  test $VENDOR = intel-win7-64; then
+			export CC=cl
+			export CXX=cccl
+			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
+			export AR="ar-lib lib"
+			export OS_LDFLAG="-Wl,"
+			export RANLIB=true
+			OSLIBS="-Wl,kernel32.lib -Wl,user32.lib -Wl,gdi32.lib -Wl,winspool.lib -Wl,comdlg32.lib -Wl,advapi32.lib -Wl,shell32.lib -Wl,ole32.lib -Wl,oleaut32.lib -Wl,uuid.lib -Wl,odbc32.lib -Wl,odbccp32.lib"
+		elif test $VENDOR = intel-linux; then
+			export CC=icc
+			export CXX=icpc
+			export CFLAGS=" -D_INTEL_LINUX_"
+			export CXXFLAGS=" -D_INTEL_LINUX_"
+		elif test $VENDOR = intel-discover; then
+			export CC=icc
+			export CXX=icpc
+			export CXXFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
+			export CFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
+		elif test $VENDOR = intel-pleiades; then
+			export CC=icc
+			export CXX=icpc
+			export CXXFLAGS=" -O3 -D_INTEL_LINUX_ "
+			export CFLAGS=" -O3 -D_INTEL_LINUX_ "
+        else
+		AC_MSG_ERROR([unknown compiler vendor!])
+		fi
+	fi
+	AC_SUBST([OSLIBS]) 
+	AC_MSG_RESULT(done)
+	dnl }}}
+	dnl matlab{{{
+
+	dnl 1. See if matlab has been provided
+	AC_ARG_WITH([matlab-dir],
+		AS_HELP_STRING([--with-matlab-dir=DIR], [matlab root directory. necessary for serial build.]),
+		[MATLAB_ROOT=$withval],[MATLAB_ROOT=""]) 
+
+	AC_MSG_CHECKING([whether matlab is enabled])
+	if test -d "$MATLAB_ROOT"; then
+		HAVE_MATLAB=yes
+	else
+		HAVE_MATLAB=no
+	fi
+	if test x$HAVE_MATLAB = xyes; then
+		AC_DEFINE([_HAVE_MATLAB_],[1],[with Matlab in ISSM src])
+	fi
+	AC_MSG_RESULT($HAVE_MATLAB)
+	AM_CONDITIONAL([MATLAB], [test x$HAVE_MATLAB = xyes])
+
+	dnl 2. Get Matlab libraries
+	if test x$HAVE_MATLAB = xyes; then
+
+		AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT)
+  		MATLABINCL="-I$MATLAB_ROOT/extern/include/"
+		
+		dnl 4. get MEXLIB MEXLINK and MEXEXT (experimental)
+      dnl OS-dependent variables and checks
+  		case "${host_os}" in
+  			*cygwin*) 
+  				if  test $VENDOR = intel-win7-32; then
+  					MEXLIB="-Wl,./../../c/libISSMCore.a -Wl,libISSMApi.a -Wl,libISSMMatlab.a -Wl,./../../c/libISSMModules.a -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` -no-undefined -Wl,/export:mexFunction" 
+  				elif  test l-win7-64; then
+  					MEXLIB="-Wl,./../../c/libISSMCore.a -Wl,libISSMApi.a -Wl,libISSMMatlab.a -Wl,./../../c/libISSMModules.a -Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" 
+               MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -no-undefined -Wl,/export:mexFunction" 
+  				fi
+  				MEXEXT=`$MATLAB_ROOT/bin/mexext.bat`
+  				MEXEXT=".$MEXEXT"
+  			;;
+		   *)
+		      MEXLINK=$(mex -v 2>&1 < /dev/null | grep LDFLAGS     | sed -e "s/         LDFLAGS            = //g")
+	         MEXLIB=$( mex -v 2>&1 < /dev/null | grep CXXLIBS     | sed -e "s/         CXXLIBS            = //g")
+		      MEXEXT=$( mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
+  			;;
+      esac
+	   AC_MSG_RESULT(done)
+
+		AC_SUBST([MATLABINCL])
+		AC_SUBST([MEX])
+		MATLABWRAPPEREXT=$MEXEXT
+		AC_SUBST([MATLABWRAPPEREXT])
+	   AC_SUBST([MEXLIB]) 
+		AC_SUBST([MEXLINK])
+	fi
+	dnl }}}
+	dnl triangle {{{
+	AC_ARG_WITH([triangle-dir],
+		AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory. necessary for serial build]),
+		[TRIANGLE_ROOT=$withval],
+		[TRIANGLE_ROOT=""]) 
+	AC_ARG_WITH([triangle-include-dir],
+		AS_HELP_STRING([--with-triangle-include-dir], [triangle include dir]),
+		[TRIANGLE_INCL=$withval],
+		[TRIANGLE_INCL="$TRIANGLE_ROOT"])
+	AC_ARG_WITH([triangle-lib-dir],
+		AS_HELP_STRING([--with-triangle-lib-dir], [triangle lib dir]),
+		[TRIANGLE_LIB=$withval],
+		[TRIANGLE_LIB="$TRIANGLE_ROOT"])
+	AC_MSG_CHECKING(for triangle headers and libraries)
+
+	if test -d "$TRIANGLE_ROOT"; then
+
+		dnl defaults
+		HAVE_TRIANGLE=yes
+		TRIANGLEINCL=-I$TRIANGLE_INCL
+
+		case "${host_os}" in
+				*cygwin*)
+				TRIANGLELIB="-Wl,`cygpath -m $TRIANGLE_LIB/`triangle.lib"
+				;;
+				*linux*)
+				TRIANGLELIB="-ltriangle"
+				;;
+				*darwin*)
+				TRIANGLELIB=$TRIANGLE_LIB/triangle.a
+				;;
+			esac
+
+		AC_DEFINE([_HAVE_TRIANGLE_],[1],[with Triangle in ISSM src])
+		AC_SUBST([TRIANGLEINCL])
+		AC_SUBST([TRIANGLELIB])
+
+	else
+		HAVE_TRIANGLE=no
+	fi
+	AC_MSG_RESULT($HAVE_TRIANGLE)
+	dnl }}}
+	dnl boost{{{
+	AC_ARG_WITH([boost-dir],
+	  AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]),
+	  [BOOST_ROOT=$withval],[BOOST_ROOT=""]) 
+	AC_MSG_CHECKING(for boost)
+	
+	if test -d "$BOOST_ROOT"; then
+		dnl defaults
+		HAVE_BOOST=yes
+		BOOSTINCL=-I$BOOST_ROOT/include
+		BOOSTLIB="-L$BOOST_ROOT/lib -lboost_python"
+
+		AC_DEFINE([_HAVE_BOOST_],[1],[with Boost in ISSM src])
+		AC_SUBST([BOOSTINCL])
+		AC_SUBST([BOOSTLIB])
+	else
+		HAVE_BOOST=no
+	fi
+	AM_CONDITIONAL([BOOST], [test x$HAVE_BOOST = xyes])
+	AC_MSG_RESULT($HAVE_BOOST)
+	dnl }}}
+	dnl dakota{{{
+	AC_ARG_WITH([dakota-dir],
+	  AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory. necessary for serial build]),
+	  [DAKOTA_ROOT=$withval],[DAKOTA_ROOT=""]) 
+	AC_MSG_CHECKING(for dakota)
+	
+	if test -d "$DAKOTA_ROOT"; then
+
+		dnl defaults
+		HAVE_DAKOTA=yes
+		AC_MSG_RESULT($HAVE_DAKOTA)
+		DAKOTAINCL=-I$DAKOTA_ROOT/include
+		AC_MSG_CHECKING(for dakota version)
+		if test -f "$DAKOTA_ROOT/../src/src/CommandLineHandler.C"; then
+			DAKOTA_VERSION=`cat $DAKOTA_ROOT/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+		else if test -f "$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)
+		AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_],"$DAKOTA_VERSION",[Dakota version number])
+		DAKOTAFLAGS=""
+		case "${host_os}" in
+			*cygwin*)
+				if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
+				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem"
+				else
+					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
+				fi
+				fi
+			;;
+			*linux*)
+				if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
+				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system -ldl"
+				else if test x$DAKOTA_VERSION = x5.3 || test x$DAKOTA_VERSION = x5.3.1; then
+					DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -lmods -lmod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack_fortran -lutilib -lcolin -linterfaces -lscolib -l3po -lpebbl -ltinyxml -lconmin -ldace -lanalyzer -lrandom -lsampling -lbose -lfsudace -lhopspack -ljega -ljega_fe -lmoga -lsoga -leutils -lutilities -lncsuopt -lcport -loptpp -lpsuade -lamplsolver -L$BOOST_ROOT/lib -lboost_signals -lboost_regex -lboost_filesystem -lboost_system "
+				else
+					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
+				fi
+				fi
+				fi
+			;;
+			*darwin*)
+				if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" 
+					dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
+				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
+					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
+					dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
+				else
+					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
+				fi
+				fi
+			;;
+		esac
+		AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src])
+
+		case $DAKOTA_VERSION in
+			@<:@1-9@:>@.@<:@0-9@:>@.@<:@0-9@:>@)
+				DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
+				DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\)\..*/\1/'`
+				DAKOTA_BUILD=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
+			;;
+			@<:@1-9@:>@.@<:@0-9@:>@)
+				DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
+				DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
+				DAKOTA_BUILD=0
+			;;
+			@<:@1-9@:>@.@<:@0-9@:>@+)
+				DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
+				DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
+				DAKOTA_BUILD=0
+			;;
+			*)
+				AC_MSG_ERROR([Dakota version ($DAKOTA_VERSION) not supported!]);
+		   ;;
+		esac
+		AC_MSG_CHECKING(for dakota major version)
+		AC_MSG_RESULT($DAKOTA_MAJOR)
+		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_],$DAKOTA_MINOR,[Dakota minor version number])
+		AC_MSG_CHECKING(for dakota build version)
+		AC_MSG_RESULT($DAKOTA_BUILD)
+		AC_DEFINE_UNQUOTED([_DAKOTA_BUILD_],$DAKOTA_BUILD,[Dakota build version number])
+
+		AC_SUBST([DAKOTAINCL])
+		AC_SUBST([DAKOTAFLAGS])
+		AC_SUBST([DAKOTALIB])
+
+	else
+		HAVE_DAKOTA=no
+		AC_MSG_RESULT($HAVE_DAKOTA)
+	fi
+
+	AM_CONDITIONAL([DAKOTA], [test x$HAVE_DAKOTA = xyes])
+	dnl }}}
+	dnl python{{{
+	AC_ARG_WITH([python-dir],
+		AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]),
+		[PYTHON_ROOT=$withval],
+		[PYTHON_ROOT=""]) 
+
+	AC_ARG_WITH([python-include-dir],
+		AS_HELP_STRING([--with-python-include-dir=DIR], [python include directory.]),
+		[PYTHON_INCL=$withval],
+		[PYTHON_INCL="$PYTHON_ROOT/include"]) 
+
+	AC_ARG_WITH([python-lib-dir],
+		AS_HELP_STRING([--with-python-lib-dir=DIR], [python lib directory.]),
+		[PYTHON_LIB=$withval],
+		[PYTHON_LIB="$PYTHON_ROOT/lib"]) 
+
+	AC_MSG_CHECKING(for python)
+	if test -d "$PYTHON_ROOT"; then
+		HAVE_PYTHON="yes"
+		AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src])
+	else
+		HAVE_PYTHON=no
+	fi
+	AC_MSG_RESULT($HAVE_PYTHON)
+
+	dnl get python version
+	if test x$HAVE_PYTHON = xyes; then
+		AC_MSG_CHECKING(for python version)
+		dnl Query Python for its version number.  Getting [:3] seems to be
+		dnl the best way to do this; it's what "site.py" does in the standard
+		dnl library.
+		PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]")
+		AC_MSG_RESULT($PYTHON_VERSION)
+
+		dnl recover major: 
+		PYTHON_MAJOR=${PYTHON_VERSION%.*}
+		if test x$PYTHON_MAJOR = x3; then
+			dnl are we running python 3?
+			HAVE_PYTHON3="yes"
+		else
+			HAVE_PYTHON3="no"
+		fi
+		AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major])
+
+		PYTHONINCL="-I$PYTHON_INCL"
+		PYTHONLIB="-L$PYTHON_LIB -lpython$PYTHON_VERSION"
+		PYTHONEXT=.so
+
+		case "${host_os}" in
+			*cygwin*)
+			PYTHONLINK="-shared"
+			;;
+			*linux*)
+			PYTHONLINK="-shared"
+			;;
+			*darwin*)
+			PYTHONLINK="-dynamiclib"
+			;;
+		esac
+
+		AC_SUBST([PYTHONINCL])
+		AC_SUBST([PYTHONLIB])
+		PYTHONWRAPPEREXT=$PYTHONEXT
+		AC_SUBST([PYTHONWRAPPEREXT])
+		AC_SUBST([PYTHONLINK])
+	fi
+	AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes])
+	AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes])
+	dnl }}}
+	dnl python-numpy{{{
+	AC_ARG_WITH([python-numpy-dir],
+	  AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]),
+	  [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT=""]) 
+	AC_MSG_CHECKING(for python-numpy)
+	
+	if test -d "$PYTHON_NUMPY_ROOT"; then
+		dnl defaults
+		HAVE_PYTHON_NUMPY=yes
+		PYTHON_NUMPYINCL="-I$PYTHON_NUMPY_ROOT -I$PYTHON_NUMPY_ROOT/core/include/numpy"
+
+		AC_DEFINE([_HAVE_PYTHON_NUMPY_],[1],[with Python-Numpy in ISSM src])
+		AC_SUBST([PYTHON_NUMPYINCL])
+	else
+		HAVE_PYTHON_NUMPY=no
+	fi
+	AC_MSG_RESULT($HAVE_PYTHON_NUMPY)
+	dnl }}}
+	dnl chaco{{{
+	AC_ARG_WITH([chaco-dir],
+	  AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]),
+	  [CHACO_ROOT=$withval],[CHACO_ROOT=""]) 
+	AC_MSG_CHECKING(for chaco)
+	
+	if test -d "$CHACO_ROOT"; then
+
+		dnl defaults
+		HAVE_CHACO=yes
+		CHACOINCL=-I$CHACO_ROOT/include
+		CHACOLIB="-L$CHACO_ROOT/lib -lchacominusblas"
+
+		AC_DEFINE([_HAVE_CHACO_],[1],[with Chaco in ISSM src])
+		AC_SUBST([CHACOINCL])
+		AC_SUBST([CHACOLIB])
+
+	else
+		HAVE_CHACO=no
+	fi
+	AC_MSG_RESULT($HAVE_CHACO)
+	dnl }}}
+	dnl scotch{{{
+	AC_ARG_WITH([scotch-dir],
+	  AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]),
+	  [SCOTCH_ROOT=$withval],[SCOTCH_ROOT=""]) 
+	AC_MSG_CHECKING(for scotch)
+	
+	if test -d "$SCOTCH_ROOT"; then
+
+		dnl defaults
+		HAVE_SCOTCH=yes
+		SCOTCHINCL="-DNOFILEIO -I$SCOTCH_ROOT/include -DSCOTCH_VERSION=\\\"UNKNOWN\\\""
+		SCOTCHLIB="-L$SCOTCH_ROOT/lib -lnfioscotch -lnfioscotcherr -lnfioscotcherrexit -lscotchmetis"
+
+		AC_DEFINE([_HAVE_SCOTCH_],[1],[with Scotch in ISSM src])
+		AC_SUBST([SCOTCHINCL])
+		AC_SUBST([SCOTCHLIB])
+
+	else
+		HAVE_SCOTCH=no
+	fi
+	AC_MSG_RESULT($HAVE_SCOTCH)
+	dnl }}}
+	dnl adolc{{{
+	AC_ARG_WITH([adolc-dir],
+		AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]),
+		[ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) 
+	AC_MSG_CHECKING(for adolc)
+
+	if test "x$ADOLC_ROOT" = "xno"; then
+		HAVE_ADOLC=no
+	else
+		if test -d "$ADOLC_ROOT"; then
+
+			dnl defaults
+			HAVE_ADOLC=yes
+			ADOLCINCL="-I$ADOLC_ROOT/include"
+			ADOLCLIB="-L$ADOLC_ROOT/lib64 -ladolc"
+
+			AC_DEFINE([_HAVE_ADOLC_],[1],[with adolc in ISSM src])
+			AC_SUBST([ADOLCINCL])
+			AC_SUBST([ADOLCLIB])
+
+		else
+			echo  "Specified directory does not exist!"
+			exit 1
+		fi
+	fi
+	AM_CONDITIONAL([ADOLC], [test x$HAVE_ADOLC = xyes])
+	AC_MSG_RESULT($HAVE_ADOLC)
+	dnl }}}
+	dnl adolc-version{{{
+	AC_ARG_WITH([adolc-version],
+		AS_HELP_STRING([--with-adolc-version=number], [adolc version.]),
+		[ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) 
+	AC_MSG_CHECKING(for adolc-version) 
+
+	AC_DEFINE_UNQUOTED([_ADOLC_VERSION_],$ADOLC_VERSION,[ADOLC version])
+	AC_MSG_RESULT($ADOLC_VERSION)
+	dnl }}}
+	dnl adic2{{{
+	AC_ARG_WITH([adic2-dir],
+	  AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]),
+	  [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) 
+	AC_MSG_CHECKING(for adic2)
+
+	if test "x$ADIC2_ROOT" = "xno"; then
+		HAVE_ADIC2=no
+	else
+		if test -d "$ADIC2_ROOT"; then
+
+			dnl defaults
+			HAVE_ADIC2=yes
+			ADIC2INCL="-DADIC2_DENSE -I$ADIC2_ROOT/include -I$ADIC2_ROOT/share/runtime_dense/"
+			ADIC2LIB=""
+
+			AC_DEFINE([_HAVE_ADIC2_],[1],[with adic2 in ISSM src])
+			AC_SUBST([ADIC2INCL])
+			AC_SUBST([ADIC2LIB])
+
+		else
+			echo  "Specified directory does not exist!"
+			exit 1
+		fi
+	fi
+	AM_CONDITIONAL([ADIC2], [test x$HAVE_ADIC2 = xyes])
+	AC_MSG_RESULT($HAVE_ADIC2)
+	dnl }}}
+	dnl gsl{{{
+	AC_ARG_WITH([gsl-dir],
+	  AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]),
+	  [GSL_ROOT=$withval],[GSL_ROOT=""]) 
+	AC_MSG_CHECKING(for gsl)
+	
+	if test -d "$GSL_ROOT"; then
+
+		dnl defaults
+		HAVE_GSL=yes
+		GSLINCL="-I$GSL_ROOT/include"
+		GSLLIB="-dy -L$GSL_ROOT/lib -lgsl -lgslcblas -lm"
+
+		AC_DEFINE([_HAVE_GSL_],[1],[with gsl in ISSM src])
+		AC_SUBST([GSLINCL])
+		AC_SUBST([GSLLIB])
+
+	else
+		HAVE_GSL=no
+	fi
+	AM_CONDITIONAL([GSL], [test x$HAVE_GSL = xyes])
+	AC_MSG_RESULT($HAVE_GSL)
+	dnl }}}
+	dnl rose{{{
+	AC_ARG_WITH([rose-dir],
+	  AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]),
+	  [ROSE_ROOT=$withval],[ROSE_ROOT=""]) 
+	AC_MSG_CHECKING(for rose)
+	
+	if test -d "$ROSE_ROOT"; then
+
+		dnl defaults
+		HAVE_ROSE=yes
+		ROSEINCL="-I$ROSE_ROOT/include"
+		ROSELIB=""
+
+		AC_DEFINE([_HAVE_ROSE_],[1],[with rose in ISSM src])
+		AC_SUBST([ROSEINCL])
+		AC_SUBST([ROSELIB])
+
+	else
+		HAVE_ROSE=no
+	fi
+	AM_CONDITIONAL([ROSE], [test x$HAVE_ROSE = xyes])
+	AC_MSG_RESULT($HAVE_ROSE)
+	dnl }}}
+	dnl mpi{{{
+	AC_MSG_CHECKING(for mpi)
+	
+	AC_ARG_WITH([mpi-include],
+	  AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]),
+	  [MPI_INCLUDE=$withval],[MPI_INCLUDE=""])
+
+	AC_ARG_WITH([mpi-libdir],
+	  AS_HELP_STRING([--with-mpi-libdir=DIR],[mpi lib directory, necessary for parallel build]),
+	  [MPI_LIBDIR=$withval],[MPI_LIBDIR=""])
+
+	AC_ARG_WITH([mpi-libflags],
+	  AS_HELP_STRING([--with-mpi-libflags=LIBS],[mpi libraries to be used, necessary for parallel build]),
+	  [MPI_LIBFLAGS=$withval],[MPI_LIBFLAGS=""])
+
+	
+	if test -z "$MPI_INCLUDE" ; then
+		HAVE_MPI=no
+	else
+		HAVE_MPI=yes
+
+		dnl Processing for windows
+		if  test x$VENDOR = xintel-win7-32; then
+			MPI_LIBDIR=`cygpath -m $MPI_LIBDIR`
+			MPIINCL=`cygpath -m $MPI_INCLUDE`
+		elif test x$VENDOR = xintel-win7-64; then
+			MPI_LIBDIR=`cygpath -m $MPI_LIBDIR`
+			MPI_INCLUDE=`cygpath -m $MPI_INCLUDE`
+		fi
+
+		if test -z "$MPI_LIBDIR"; then
+			MPIINCL=-I"$MPI_INCLUDE"
+			MPILIB="$MPI_LIBFLAGS"
+		else
+			MPIINCL=-I"$MPI_INCLUDE"
+			MPILIB="-L$MPI_LIBDIR $MPI_LIBFLAGS"
+		fi
+		AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
+		AC_DEFINE([HAVE_MPI],[1],[Mpi Flag for Dakota (DO NOT REMOVE)])
+		AC_SUBST([MPIINCL])
+		AC_SUBST([MPILIB])
+	fi
+
+	AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes])
+	AC_MSG_RESULT($HAVE_MPI)
+	dnl }}}
+	dnl petsc{{{
+	AC_ARG_WITH([petsc-dir],
+	  AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]),
+	  [PETSC_ROOT=$withval],[PETSC_ROOT=""])
+		
+	if test -d "$PETSC_ROOT"; then
+		AC_MSG_CHECKING(for petsc version)
+		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_],$PETSC_MINOR,[PETSc version minor])
+		AC_MSG_RESULT($PETSC_MAJOR.$PETSC_MINOR)
+
+		PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' `
+		PETSC_RELEASE=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_RELEASE" | sed 's/#define PETSC_VERSION_RELEASE//' | sed 's/ //g'`
+
+		AC_MSG_CHECKING(whether petsc is the development version)
+		dnl if test x$PETSC_VERSION_DATE_HG = xunknown; then
+		if test "$PETSC_RELEASE" = "0"; then
+		   AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev])
+			AC_MSG_RESULT(yes)
+		else
+			AC_MSG_RESULT(no)
+		fi
+	fi
+	
+	AC_ARG_WITH([petsc-arch],
+	  AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch , necessary for parallel build]),
+	  [PETSC_ARCH=$withval],[PETSC_ARCH=""])
+
+	AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH)
+	
+	dnl To ge PETSc's libraries:
+	dnl cd externalpackages/petsc/src
+	dnl make getlinklibs
+	if test -d "$PETSC_ROOT"; then
+
+	 PETSCINCL=" -I$PETSC_ROOT/include"
+	 dnl Add other location (not needed anymore since at least PETSc 3.0)
+	 if test "x$PETSC_ARCH" != "x" && test -d "$PETSC_ROOT/$PETSC_ARCH/include"; then
+	  PETSCINCL+=" $PETSC_ROOT/$PETSC_ARCH/include"
+	 fi
+	 if test "x$PETSC_ARCH" != "x" && test -d "$PETSC_ROOT/include/$PETSC_ARCH"; then
+	  PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH"
+	 fi
+	
+	 case "${host_os}" in
+			*cygwin*)
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB=-Wl,/LIBPATH:`cygpath -w $PETSC_ROOT/lib`  -Wl,libpetscksp.lib  -Wl,libpetscdm.lib  -Wl,libpetscmat.lib  -Wl,libpetscvec.lib  -Wl,libpetscsnes.lib  -Wl,libpetscts.lib  -Wl,libmpiuni.lib  -Wl,libpetsc.lib
+			else
+				PETSCLIB="-L$PETSC_ROOT/lib  -Wl,libpetsc.lib"
+				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+="  -Wl,libmetis.lib"; fi
+			fi
+			;;
+			*linux*)
+			if test $PETSC_MAJOR -lt 3 ; then
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lmpiuni -lpetsc"
+			else
+				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc -ldl"
+				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi
+			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 $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi
+			fi
+			;;
+		esac
+		AC_DEFINE([_HAVE_PETSC_],[1],[with PETSc in ISSM src])
+		AC_SUBST([PETSCINCL])
+		AC_SUBST([PETSCLIB])
+		HAVE_PETSC=yes
+	else
+		HAVE_PETSC=no
+	fi
+	
+	AM_CONDITIONAL([PETSC], [test x$HAVE_PETSC = xyes])
+	AC_MSG_RESULT($HAVE_PETSC)
+	dnl }}}
+	dnl metis{{{
+	if test "$HAVE_PETSC" = "yes" && test "x$PETSC_MAJOR" = "x3" && test $PETSC_MINOR -ge 3; then
+
+		dnl in petsc >=3.3, metis is provided
+		HAVE_METIS="yes"
+		AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number])
+		AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src])
+	else
+		AC_ARG_WITH([metis-dir],
+		  AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]),
+		  [METIS_ROOT=$withval],[METIS_ROOT=""])
+
+		AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT)
+
+		if test -d "$METIS_ROOT"; then
+
+			dnl first figure out version of metis: does the VERSION file exist?
+			if test -e "$METIS_ROOT/VERSION"; then
+				METIS_VERSION=4
+			else
+				METIS_VERSION=5
+			fi
+
+			dnl defaults
+			HAVE_METIS=yes
+
+			if test "$METIS_VERSION" = "4" ; then
+					
+				METISINCL=-I"$METIS_ROOT/Lib" 
+				case "${host_os}" in
+					*cygwin*)
+					METISLIB="-L$METIS_ROOT -Wl,libmetis.lib"
+					;;
+					*linux*)
+					METISLIB=-L"$METIS_ROOT/ -lmetis"
+					;;
+					*darwin*)
+					METISLIB=-L"$METIS_ROOT/ -lmetis"
+					;;
+				esac
+
+					AC_DEFINE([_METIS_VERSION_],[4],[ Metis version number])
+			fi
+			if test "$METIS_VERSION" = "5" ; then
+		
+				case "${host_os}" in
+					*cygwin*)
+					METISLIB="-L$METIS_ROOT libmetis.lib"
+					;;
+					*linux*)
+					METISLIB=-L"$METIS_ROOT/lib -lmetis"
+					;;
+					*darwin*)
+					METISLIB=-L"$METIS_ROOT/lib -lmetis"
+					;;
+				esac
+
+				METISINCL=-I"$METIS_ROOT/include" 
+				AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number])
+			fi
+
+			AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src])
+			AC_SUBST([METISINCL])
+			AC_SUBST([METISLIB])
+		else
+			HAVE_METIS=no
+		fi
+		AC_MSG_RESULT($HAVE_METIS)
+	fi
+	AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes])
+	dnl }}}
+	dnl tao{{{
+	AC_ARG_WITH([tao-dir],
+		AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]),
+		[TAO_ROOT=$withval],[TAO_ROOT=""]) 
+	AC_MSG_CHECKING(for tao)
+
+	if test -d "$TAO_ROOT"; then
+
+	  HAVE_TAO=yes
+	  TAOINCL="-I$TAO_ROOT/ -I$TAO_ROOT/include -I$TAO_ROOT/bmake/ "
+	  TAOLIB="-L$TAO_ROOT/lib -ltao -lpetsc"
+
+	  AC_DEFINE([_HAVE_TAO_],[1],[with Tao in ISSM src])
+	  AC_SUBST([TAOINCL])
+	  AC_SUBST([TAOLIB])
+	else
+		HAVE_TAO=no
+	fi
+	AC_MSG_RESULT($HAVE_TAO)
+	dnl }}}
+	dnl slepc{{{
+	AC_ARG_WITH([slepc-dir],
+	  AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]),
+	  [SLEPC_ROOT=$withval],[SLEPC_ROOT=""])
+			  
+	AC_MSG_CHECKING(for slepc headers and libraries in $SLEPC_ROOT)
+	if test -d "$SLEPC_ROOT"; then
+		HAVE_SLEPC=yes
+		SLEPCINCL=-I"$SLEPC_ROOT/include"
+		SLEPCLIB=-L"$SLEPC_ROOT/lib/ -lslepc"
+
+		AC_DEFINE([_HAVE_SLEPC_],[1],[with Slepc in ISSM src])
+		AC_SUBST([SLEPCINCL])
+		AC_SUBST([SLEPCLIB])
+	else
+		HAVE_SLEPC=no
+	fi
+	AC_MSG_RESULT($HAVE_SLEPC)
+	dnl }}}
+	dnl shapelib{{{
+	AC_ARG_WITH([shapelib-dir],
+	  AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]),
+	  [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT=""])
+			  
+	AC_MSG_CHECKING(for shapelib headers and libraries in $SHAPELIB_ROOT)
+	if test -d "$SHAPELIB_ROOT"; then
+
+		dnl defaults
+		HAVE_SHAPELIB=yes
+		SHAPELIBINCL=-I"$SHAPELIB_ROOT/include"
+		SHAPELIBLIB=-L"$SHAPELIB_ROOT/lib/ -lshape"
+
+		AC_DEFINE([_HAVE_SHAPELIB_],[1],[with Shapelib in ISSM src])
+		AC_SUBST([SHAPELIBINCL])
+		AC_SUBST([SHAPELIBLIB])
+	else
+		HAVE_SHAPELIB=no
+	fi
+	AC_MSG_RESULT($HAVE_SHAPELIB)
+	dnl }}}
+	dnl scalapack{{{
+	AC_ARG_WITH([scalapack-dir],
+	  AS_HELP_STRING([--with-scalapack-dir=DIR],[scalapack root directory]),
+	  [SCALAPACK_ROOT=$withval],[SCALAPACK_ROOT=""])
+			  
+	AC_MSG_CHECKING(for scalapack headers and libraries in $SCALAPACK_ROOT)
+	if test -d "$SCALAPACK_ROOT"; then
+
+		dnl defaults
+		HAVE_SCALAPACK=yes
+		if test x$VENDOR = xintel-discover; then
+		 SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lmkl_scalapack_lp64"
+		else
+		 SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack"
+		fi
+
+		AC_DEFINE([_HAVE_SCALAPACK_],[1],[with Scalapack in ISSM src])
+		AC_SUBST([SCALAPACKLIB])
+	else
+		HAVE_SCALAPACK=no
+	fi
+	AC_MSG_RESULT($HAVE_SCALAPACK)
+	dnl }}}
+	dnl blas{{{
+	AC_ARG_WITH([blas-lapack-dir],
+	  AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]),
+	  [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT=""])
+			  
+	AC_MSG_CHECKING(for blas and lapack headers and libraries in $BLASLAPACK_ROOT)
+	if test -d "$BLASLAPACK_ROOT"; then
+
+		dnl defaults
+		HAVE_BLASLAPACK=yes
+		BLASLAPACKINCL=""
+	
+		if test x$VENDOR = xintel-discover; then
+		 BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lmkl_lapack -lmkl -lguide -lpthread"
+		else
+		dnl: branch on whether we are running on windows or linux.
+		case "${host_os}" in
+			*cygwin*)
+			BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib  -Wl,libf2clapack.lib"
+			;;
+			*linux*)
+			BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " 
+			;;
+			*darwin*)
+			BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " 
+			;;
+		esac
+		fi
+
+		AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src])
+		AC_SUBST([BLASLAPACKLIB])
+		AC_SUBST([BLASLAPACKINCL])
+	else
+		HAVE_BLASLAPACK=no
+	fi
+	AC_MSG_RESULT($HAVE_BLASLAPACK)
+	dnl }}}
+	dnl mkl{{{
+	AC_ARG_WITH([mkl-dir],
+	  AS_HELP_STRING([--with-mkl-dir=DIR],[mkl root directory]),
+	  [MKL_ROOT=$withval],[MKL_ROOT=""])
+			  
+	AC_MSG_CHECKING(for mkl headers and libraries in $MKL_ROOT)
+	if test -d "$MKL_ROOT"; then
+
+		dnl defaults
+		HAVE_MKL=yes
+		MKLINCL=""
+		if test x$VENDOR = xintel-pleiades; then
+		 MKLLIB=-L"$MKL_ROOT -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
+		else
+		 MKLLIB=-L"$MKL_ROOT -lmkl -lmkl_lapack -lmkl_scalapack_ilp64 -lmkl_blacs_sgimpt_ilp64 -lguide -lpthread"
+		fi
+		AC_DEFINE([_HAVE_MKL_],[1],[with mkl in ISSM src])
+		AC_SUBST([MKLLIB])
+		AC_SUBST([MKLINCL])
+	else
+		HAVE_MKL=no
+	fi
+	AC_MSG_RESULT($HAVE_MKL)
+	dnl }}}
+	dnl plapack{{{
+	AC_MSG_CHECKING(for plapack)
+	
+	AC_ARG_WITH([plapack-lib],
+	  AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]),
+	  [PLAPACK_LIB=$withval],[PLAPACK_LIB=""])
+	
+	AC_ARG_WITH([plapack-include],
+			  AS_HELP_STRING([--with-plapack-include = include],
+							 [plapack include ]),
+			  [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""])
+	  
+	if test -n "$PLAPACK_LIB"; then
+		if test -n "$PLAPACK_INCLUDE"; then
+		
+			dnl defaults
+			HAVE_PLAPACK=yes
+			PLAPACKINCL="$PLAPACK_INCLUDE"
+			PLAPACKLIB="$PLAPACK_LIB"
+
+			AC_DEFINE([_HAVE_PLAPACK_],[1],[with Plapack in ISSM src])
+			AC_SUBST([PLAPACKINCL])
+			AC_SUBST([PLAPACKLIB])
+		else
+			HAVE_PLAPACK=no
+		fi
+	else
+		HAVE_PLAPACK=no
+	fi
+	AC_MSG_RESULT($HAVE_PLAPACK)
+	dnl }}}
+	dnl mumps{{{
+	AC_ARG_WITH([mumps-dir],
+	  AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]),
+	  [MUMPS_ROOT=$withval],[MUMPS_ROOT=""])
+			  
+	AC_MSG_CHECKING(for mumps headers and libraries in $MUMPS_ROOT)
+	if test -d "$MUMPS_ROOT"; then
+
+		dnl defaults
+		HAVE_MUMPS=yes
+		MUMPSINCL=-I"$MUMPS_ROOT/include"
+		if test "$PETSC_MAJOR" = "2" ; then
+		MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lpord "
+		else
+		dnl MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis -lzmumps"
+		MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis"
+		fi
+
+		AC_DEFINE([_HAVE_MUMPS_],[1],[with Mumps in ISSM src])
+		AC_SUBST([MUMPSINCL])
+		AC_SUBST([MUMPSLIB])
+	else
+		HAVE_MUMPS=no
+	fi
+	AM_CONDITIONAL([MUMPS], [test x$HAVE_MUMPS = xyes])
+	AC_MSG_RESULT($HAVE_MUMPS)
+	dnl }}}
+	dnl blacs{{{
+	AC_ARG_WITH([blacs-dir],
+		AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]),
+			  [BLACS_ROOT=$withval],[BLACS_ROOT=""])
+			  
+	AC_MSG_CHECKING(for blacs headers and libraries in $BLACS_ROOT)
+	if test -d "$BLACS_ROOT"; then
+
+		dnl defaults
+		HAVE_BLACS=yes
+		BLACSINCL=""
+		if test x$VENDOR = xintel-discover; then
+		 BLACSLIB=-L"$BLACS_ROOT/ -lmkl_blacs_intelmpi_lp64"
+		else
+		 BLACSLIB=-L"$BLACS_ROOT/ -lblacs"
+		fi
+        
+		AC_DEFINE([_HAVE_BLACS_],[1],[with Blacs in ISSM src])
+		AC_SUBST([BLACSINCL])
+		AC_SUBST([BLACSLIB])
+	else
+		HAVE_BLACS=no
+	fi
+	AC_MSG_RESULT($HAVE_BLACS)
+	dnl }}}
+	dnl hypre{{{
+	AC_ARG_WITH([hypre-dir],
+	  AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]),
+			  [HYPRE_ROOT=$withval],[HYPRE_ROOT=""])
+			  
+	AC_MSG_CHECKING(for hypre headers and libraries in $HYPRE_ROOT)
+	if test -d "$HYPRE_ROOT"; then
+
+		dnl defaults
+		HAVE_HYPRE=yes
+		HYPREINCL=""
+		HYPRELIB=-L"$HYPRE_ROOT/lib -lHYPRE"
+        
+		AC_DEFINE([_HAVE_HYPRE_],[1],[with Blacs in ISSM src])
+		AC_SUBST([HYPREINCL])
+		AC_SUBST([HYPRELIB])
+	else
+		HAVE_HYPRE=no
+	fi
+	AC_MSG_RESULT($HAVE_HYPRE)
+	dnl }}}
+	dnl prometheus{{{
+		AC_ARG_WITH([prometheus-dir],
+					AS_HELP_STRING([--with-prometheus-dir=DIR],[prometheus root directory]),
+					[PROMETHEUS_ROOT=$withval],[PROMETHEUS_ROOT=""])
+
+		  AC_MSG_CHECKING(for prometheus headers and libraries in $PROMETHEUS_ROOT)
+		  if test -d "$PROMETHEUS_ROOT"; then
+
+			dnl defaults
+			  HAVE_PROMETHEUS=yes
+			  PROMETHEUSINCL=-I"$PROMETHEUS_ROOT/include"
+			  PROMETHEUSLIB=-L"$PROMETHEUS_ROOT/lib -lpromfei -lprometheus -lparmetis"
+
+			  AC_DEFINE([_HAVE_PROMETHEUS_],[1],[with Prometheus in ISSM src])
+			  AC_SUBST([PROMETHEUSINCL])
+			  AC_SUBST([PROMETHEUSLIB])
+		  else
+				HAVE_PROMETHEUS=no
+			fi
+			AC_MSG_RESULT($HAVE_PROMETHEUS)
+		dnl }}}
+dnl spai{{{
+	AC_ARG_WITH([spai-dir],
+				AS_HELP_STRING([--with-spai-dir=DIR],[spai root directory]),
+				[SPAI_ROOT=$withval],[SPAI_ROOT=""])
+
+	  AC_MSG_CHECKING(for spai headers and libraries in $SPAI_ROOT)
+	  if test -d "$SPAI_ROOT"; then
+
+		dnl defaults
+		  HAVE_SPAI=yes
+		  SPAIINCL=-I"$SPAI_ROOT/include"
+		  SPAILIB=-L"$SPAI_ROOT/lib -lspai"
+
+		  AC_DEFINE([_HAVE_SPAI_],[1],[with Spai in ISSM src])
+		  AC_SUBST([SPAIINCL])
+		  AC_SUBST([SPAILIB])
+	  else
+		HAVE_SPAI=no
+		  fi
+		  AC_MSG_RESULT($HAVE_SPAI)
+		  dnl }}}
+dnl superlu{{{ 
+	AC_ARG_WITH([superlu-dir],
+				AS_HELP_STRING([--with-superlu-dir=DIR],[superlu root directory]),
+				[SUPERLU_ROOT=$withval],[SUPERLU_ROOT=""])
+
+	  AC_MSG_CHECKING(for superlu headers and libraries in $SUPERLU_ROOT)
+	  if test -d "$SUPERLU_ROOT"; then
+
+		dnl defaults
+		  HAVE_SUPERLU=yes
+		  SUPERLUINCL=-I"$SUPERLU_ROOT/include"
+		  SUPERLULIB=-L"$SUPERLU_ROOT/lib -lsuperlu_4.3"
+
+		  AC_DEFINE([_HAVE_SUPERLU_],[1],[with Superlu in ISSM src])
+		  AC_SUBST([SUPERLUINCL])
+		  AC_SUBST([SUPERLULIB])
+	  else
+		HAVE_SUPERLU=no
+		  fi
+		  AC_MSG_RESULT($HAVE_SUPERLU)
+		  dnl }}}
+dnl spooles{{{ 
+	AC_ARG_WITH([spooles-dir],
+				AS_HELP_STRING([--with-spooles-dir=DIR],[spooles root directory]),
+				[SPOOLES_ROOT=$withval],[SPOOLES_ROOT=""])
+
+	  AC_MSG_CHECKING(for spooles headers and libraries in $SPOOLES_ROOT)
+	  if test -d "$SPOOLES_ROOT"; then
+
+		dnl defaults
+		  HAVE_SPOOLES=yes
+		  SPOOLESINCL=-I"$SPOOLES_ROOT/include"
+		  SPOOLESLIB=-L"$SPOOLES_ROOT/lib -lspooles"
+
+		  AC_DEFINE([_HAVE_SPOOLES_],[1],[with Spooles in ISSM src])
+		  AC_SUBST([SPOOLESINCL])
+		  AC_SUBST([SPOOLESLIB])
+	  else
+		HAVE_SPOOLES=no
+		  fi
+		  AC_MSG_RESULT($HAVE_SPOOLES)
+		  dnl }}}
+dnl pastix{{{ 
+	AC_ARG_WITH([pastix-dir],
+				AS_HELP_STRING([--with-pastix-dir=DIR],[pastix root directory]),
+				[PASTIX_ROOT=$withval],[PASTIX_ROOT=""])
+
+	  AC_MSG_CHECKING(for pastix headers and libraries in $PASTIX_ROOT)
+	  if test -d "$PASTIX_ROOT"; then
+
+		dnl defaults
+		  HAVE_PASTIX=yes
+		  PASTIXINCL=-I"$PASTIX_ROOT/include"
+		  PASTIXLIB=-L"$PASTIX_ROOT/lib -lpastix_XXbit_mpi_smp_nobubble_int32_simple_real_scotch_i686_pc_linux -lptscotch -lptscotcherr -lpastix"
+
+		  AC_DEFINE([_HAVE_PASTIX_],[1],[with Pastix in ISSM src])
+		  AC_SUBST([PASTIXINCL])
+		  AC_SUBST([PASTIXLIB])
+	  else
+		HAVE_PASTIX=no
+		  fi
+		  AC_MSG_RESULT($HAVE_PASTIX)
+		  dnl }}}
+	dnl ml{{{
+	AC_ARG_WITH([ml-dir],
+	  AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]),
+			  [ML_ROOT=$withval],[ML_ROOT=""])
+			  
+	AC_MSG_CHECKING(for ml headers and libraries in $ML_ROOT)
+	if test -d "$ML_ROOT"; then
+
+		dnl defaults
+		HAVE_ML=yes
+		MLINCL=-I"$ML_ROOT/include"
+		MLLIB=-L"$ML_ROOT/lib -lml"
+        
+		AC_DEFINE([_HAVE_ML_],[1],[with Blacs in ISSM src])
+		AC_SUBST([MLINCL])
+		AC_SUBST([MLLIB])
+	else
+		HAVE_ML=no
+	fi
+	AC_MSG_RESULT($HAVE_ML)
+	dnl }}}
+	dnl umfpack{{{
+		AC_ARG_WITH([umfpack-dir],
+		  AS_HELP_STRING([--with-umfpack-dir=DIR],[UMFPACK root directory]),
+					[UMFPACK_ROOT=$withval],[UMFPACK_ROOT=""])
+
+		AC_MSG_CHECKING(for UMFPACK headers and libraries in $UMFPACK_ROOT)
+		if test -d "$UMFPACK_ROOT"; then
+
+			dnl defaults
+			HAVE_UMFPACK=yes
+			UMFPACKINCL=""
+			UMFPACKLIB=-L"$UMFPACK_ROOT/lib -lumfpack -lumfpack.5.5.1"
+
+			AC_DEFINE([_HAVE_UMFPACK_],[1],[with UMFPACK in ISSM src])
+			AC_SUBST([UMFPACKINCL])
+			AC_SUBST([UMFPACKLIB])
+		else
+			HAVE_UMFPACK=no
+		fi
+		AC_MSG_RESULT($HAVE_UMFPACK)
+	dnl }}}
+dnl math{{{
+	AC_MSG_CHECKING(for math library)
+	AC_ARG_WITH([math-lib],
+	  AS_HELP_STRING([--with-math-lib = otions],[math options, for ex: "/usr/lib/libm.a]),
+	  [MATH_LIB=$withval],[MATH_LIB=""])
+
+	dnl check that --with-math-lib may have been provided
+	if test -n "$MATH_LIB" ; then
+		HAVE_MATH=yes
+		MATHLIB="$MATH_LIB"
+
+		AC_DEFINE([_HAVE_MATH_],[1],[with MATH in ISSM src])
+		AC_SUBST([MATHLIB])
+	fi
+	AC_MSG_RESULT(done)
+	dnl }}}
+	dnl fortran{{{
+	AC_ARG_WITH([fortran],
+		AS_HELP_STRING([--with-fortran = YES], [do we compile fortran code (default is yes)]),
+		[FORTRAN=$withval],[FORTRAN=yes]) 
+	AC_MSG_CHECKING(for fortran compilation)
+	if test "x$FORTRAN" = "xyes"; then
+		dnl defaults
+		HAVE_FORTRAN=yes
+
+		AC_DEFINE([_HAVE_FORTRAN_],[1],[with fortran capability])
+	else
+		HAVE_FORTRAN=no
+	fi
+	AM_CONDITIONAL([FORTRAN], [test x$FORTRAN = xyes])
+	AC_MSG_RESULT($FORTRAN)
+
+	if test "x$FORTRAN" = "xyes"; then
+		dnl fortran library  option
+		AC_MSG_CHECKING(for fortran library)
+		AC_ARG_WITH([fortran-lib],
+		  AS_HELP_STRING([--with-fortran-lib = options],[fortran options, for ex: "/usr/lib/gfortran.a]),
+			[FORTRAN_LIB=$withval],[FORTRAN_LIB=""])
+
+		dnl check that --with-fortran-lib may have been provided
+		if test -n "$FORTRAN_LIB" ; then
+			dnl check that library provided EXISTS!
+		   FORTRAN_DIR=$(echo $FORTRAN_LIB | sed -e "s/-L//g" | awk '{print $[1]}')
+			if test -d "$FORTRAN_DIR" || test -f "$FORTRAN_DIR"; then
+				FORTRANLIB="$FORTRAN_LIB"
+				AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src])
+				AC_SUBST([FORTRANLIB])
+			else
+			 if test "x$HAVE_MPI" = "xyes"; then
+				FORTRANLIB=$(mpif77 -print-file-name="libgfortran.a")
+				if test -f "$FORTRANLIB"; then
+					 AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist, MPI suggests the following library: $FORTRANLIB]);
+				fi
+			 fi
+				AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist!]);
+			fi
+		fi
+		AC_MSG_RESULT(done)
+	fi
+	dnl }}}
+	dnl graphics{{{
+	AC_MSG_CHECKING(for graphics library)
+	AC_ARG_WITH([graphics-lib],
+	  AS_HELP_STRING([--with-graphics-lib = options],[graphics options, for ex: "/usr/X11/lib/libX11.a]),
+	  [GRAPHICS_LIB=$withval],[GRAPHICS_LIB=""])
+
+	dnl check that --with-graphics-lib may have been provided
+	
+	if test -n "$GRAPHICS_LIB" ; then
+		dnl check that library provided EXISTS!
+		GRAPHICS_DIR=$(echo $GRAPHICS_LIB | sed -e "s/-L//g" | awk '{print $[1]}')
+		if test -d "$GRAPHICS_DIR" || test -f "$GRAPHICS_DIR"; then
+			HAVE_GRAPHICS=yes
+			GRAPHICSLIB="$GRAPHICS_LIB"
+			AC_DEFINE([_HAVE_GRAPHICS_],[1],[with GRAPHICS in ISSM src])
+			AC_SUBST([GRAPHICSLIB])
+		else
+			if test -f "$PETSC_ROOT/conf/petscvariables"; then
+				GRAPHICSLIB=$(cat $PETSC_ROOT/conf/petscvariables | grep X_LIB)
+				AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB) does not exist, PETSc suggests the following library: $GRAPHICSLIB]);
+			fi
+			AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB$) does not exist!]);
+		fi
+	fi
+	AC_MSG_RESULT(done)
+	dnl }}}
+
+	dnl Capabilities
+	dnl with-kml{{{
+	AC_ARG_WITH([kml],
+		AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is yes)]),
+		[KML=$withval],[KML=yes]) 
+	AC_MSG_CHECKING(for kml capability compilation)
+
+	if test "x$KML" = "xyes"; then
+		HAVE_KML=yes
+		AC_DEFINE([_HAVE_KML_],[1],[with kml capability])
+	else
+		HAVE_KML=no
+	fi
+	AM_CONDITIONAL([KML], [test x$HAVE_KML = xyes])
+	AC_MSG_RESULT($HAVE_KML)
+	dnl }}}
+	dnl with-kriging{{{
+	AC_ARG_WITH([kriging],
+		AS_HELP_STRING([--with-kriging = YES],[compile with kriging capabilities (default is yes)]),
+		[KRIGING=$withval],[KRIGING=yes]) 
+	AC_MSG_CHECKING(for kriging capability compilation)
+
+	if test "x$KRIGING" = "xyes"; then
+		HAVE_KRIGING=yes
+		AC_DEFINE([_HAVE_KRIGING_],[1],[with kriging capability])
+	else
+		HAVE_KRIGING=no
+	fi
+	AM_CONDITIONAL([KRIGING], [test x$HAVE_KRIGING = xyes])
+	AC_MSG_RESULT($HAVE_KRIGING)
+	dnl }}}
+	dnl with-steadystate{{{
+	AC_ARG_WITH([steadystate],
+		AS_HELP_STRING([--with-steadystate = YES],[compile with steadystate capabilities (default is yes)]),
+		[STEADYSTATE=$withval],[STEADYSTATE=yes]) 
+	AC_MSG_CHECKING(for steadystate capability compilation)
+
+	if test "x$STEADYSTATE" = "xyes"; then
+
+		dnl defaults
+		HAVE_STEADYSTATE=yes
+
+		AC_DEFINE([_HAVE_STEADYSTATE_],[1],[with steadystate capability])
+	else
+		HAVE_STEADYSTATE=no
+	fi
+	AM_CONDITIONAL([STEADYSTATE], [test x$HAVE_STEADYSTATE = xyes])
+	AC_MSG_RESULT($HAVE_STEADYSTATE)
+	dnl }}}
+	dnl with-transient{{{
+	AC_ARG_WITH([transient],
+		AS_HELP_STRING([--with-transient = YES], [compile with transient capabilities (default is yes)]),
+		[TRANSIENT=$withval],[TRANSIENT=yes]) 
+	AC_MSG_CHECKING(for transient capability compilation)
+
+	if test "x$TRANSIENT" = "xyes"; then
+
+		dnl defaults
+		HAVE_TRANSIENT=yes
+
+		AC_DEFINE([_HAVE_TRANSIENT_],[1],[with transient capability])
+	else
+		HAVE_TRANSIENT=no
+	fi
+	AM_CONDITIONAL([TRANSIENT], [test x$HAVE_TRANSIENT = xyes])
+	AC_MSG_RESULT($HAVE_TRANSIENT)
+	dnl }}}
+	dnl with-thermal{{{
+	AC_ARG_WITH([thermal],
+		AS_HELP_STRING([--with-thermal = YES], [compile with thermal capabilities (default is yes)]),
+		[THERMAL=$withval],[THERMAL=yes]) 
+	AC_MSG_CHECKING(for thermal capability compilation)
+
+	if test "x$THERMAL" = "xyes"; then
+
+		dnl defaults
+		HAVE_THERMAL=yes
+
+		AC_DEFINE([_HAVE_THERMAL_],[1],[with thermal capability])
+	else
+		HAVE_THERMAL=no
+	fi
+	AM_CONDITIONAL([THERMAL], [test x$HAVE_THERMAL = xyes])
+	AC_MSG_RESULT($HAVE_THERMAL)
+	dnl }}}
+	dnl with-prognostic{{{
+	AC_ARG_WITH([prognostic],
+		AS_HELP_STRING([--with-prognostic = YES], [compile with prognostic capabilities (default is yes)]),
+		[PROGNOSTIC=$withval],[PROGNOSTIC=yes]) 
+	AC_MSG_CHECKING(for prognostic capability compilation)
+
+	if test "x$PROGNOSTIC" = "xyes"; then
+
+		dnl defaults
+		HAVE_PROGNOSTIC=yes
+
+		AC_DEFINE([_HAVE_PROGNOSTIC_],[1],[with prognostic capability])
+	else
+		HAVE_PROGNOSTIC=no
+	fi
+	AM_CONDITIONAL([PROGNOSTIC], [test x$HAVE_PROGNOSTIC = xyes])
+	AC_MSG_RESULT($HAVE_PROGNOSTIC)
+	dnl }}}
+	dnl with-control{{{
+	AC_ARG_WITH([control],
+		AS_HELP_STRING([--with-control = YES], [compile with control capabilities (default is yes)]),
+		[CONTROL=$withval],[CONTROL=yes]) 
+	AC_MSG_CHECKING(for control capability compilation)
+
+	if test "x$CONTROL" = "xyes"; then
+
+		dnl defaults
+		HAVE_CONTROL=yes
+
+		AC_DEFINE([_HAVE_CONTROL_],[1],[with control capability])
+	else
+		HAVE_CONTROL=no
+	fi
+	AM_CONDITIONAL([CONTROL], [test x$HAVE_CONTROL = xyes])
+	AC_MSG_RESULT($HAVE_CONTROL)
+	dnl }}}
+	dnl with-hydrology{{{
+	AC_ARG_WITH([hydrology],
+		AS_HELP_STRING([--with-hydrology = YES], [compile with hydrology capabilities (default is yes)]),
+		[HYDROLOGY=$withval],[HYDROLOGY=yes]) 
+	AC_MSG_CHECKING(for hydrology capability compilation)
+
+	if test "x$HYDROLOGY" = "xyes"; then
+
+		dnl defaults
+		HAVE_HYDROLOGY=yes
+
+		AC_DEFINE([_HAVE_HYDROLOGY_],[1],[with hydrology capability])
+	else
+		HAVE_HYDROLOGY=no
+	fi
+	AM_CONDITIONAL([HYDROLOGY], [test x$HAVE_HYDROLOGY = xyes])
+	AC_MSG_RESULT($HAVE_HYDROLOGY)
+	dnl }}}
+	dnl with-diagnostic{{{
+	AC_ARG_WITH([diagnostic],
+		AS_HELP_STRING([--with-diagnostic = YES], [compile with diagnostic capabilities (default is yes)]),
+		[DIAGNOSTIC=$withval],[DIAGNOSTIC=yes]) 
+	AC_MSG_CHECKING(for diagnostic capability compilation)
+
+	if test "x$DIAGNOSTIC" = "xyes"; then
+
+		dnl defaults
+		HAVE_DIAGNOSTIC=yes
+
+		AC_DEFINE([_HAVE_DIAGNOSTIC_],[1],[with diagnostic capability])
+	else
+		HAVE_DIAGNOSTIC=no
+	fi
+	AM_CONDITIONAL([DIAGNOSTIC], [test x$HAVE_DIAGNOSTIC = xyes])
+	AC_MSG_RESULT($HAVE_DIAGNOSTIC)
+	dnl }}}
+	dnl with-balanced{{{
+	AC_ARG_WITH([balanced],
+		AS_HELP_STRING([--with-balanced = YES], [compile with balanced capabilities (default is yes)]),
+		[BALANCED=$withval],[BALANCED=yes]) 
+	AC_MSG_CHECKING(for balanced capability compilation)
+
+	if test "x$BALANCED" = "xyes"; then
+
+		dnl defaults
+		HAVE_BALANCED=yes
+
+		AC_DEFINE([_HAVE_BALANCED_],[1],[with balanced capability])
+	else
+		HAVE_BALANCED=no
+	fi
+	AM_CONDITIONAL([BALANCED], [test x$HAVE_BALANCED = xyes])
+	AC_MSG_RESULT($HAVE_BALANCED)
+	dnl }}}
+	dnl with-responses{{{
+	AC_ARG_WITH([responses],
+		AS_HELP_STRING([--with-responses = YES], [compile with responses capabilities (default is yes)]),
+		[RESPONSES=$withval],[RESPONSES=yes]) 
+	AC_MSG_CHECKING(for responses capability compilation)
+
+	if test "x$RESPONSES" = "xyes"; then
+
+		dnl defaults
+		HAVE_RESPONSES=yes
+
+		AC_DEFINE([_HAVE_RESPONSES_],[1],[with responses capability])
+	else
+		HAVE_RESPONSES=no
+	fi
+	AM_CONDITIONAL([RESPONSES], [test x$HAVE_RESPONSES = xyes])
+	AC_MSG_RESULT($HAVE_RESPONSES)
+	dnl }}}
+	dnl with-slope{{{
+	AC_ARG_WITH([slope],
+		AS_HELP_STRING([--with-slope = YES], [compile with slope capabilities (default is yes)]),
+		[SLOPE=$withval],[SLOPE=yes]) 
+	AC_MSG_CHECKING(for slope capability compilation)
+
+	if test "x$SLOPE" = "xyes"; then
+
+		dnl defaults
+		HAVE_SLOPE=yes
+
+		AC_DEFINE([_HAVE_SLOPE_],[1],[with slope capability])
+	else
+		HAVE_SLOPE=no
+	fi
+	AM_CONDITIONAL([SLOPE], [test x$HAVE_SLOPE = xyes])
+	AC_MSG_RESULT($HAVE_SLOPE)
+	dnl }}}
+	dnl with-groundingline{{{
+	AC_ARG_WITH([groundingline],
+		AS_HELP_STRING([--with-groundingline = YES], [compile with groundingline capabilities (default is yes)]),
+		[GROUNDINGLINE=$withval],[GROUNDINGLINE=yes]) 
+	AC_MSG_CHECKING(for groundingline capability compilation)
+
+	if test "x$GROUNDINGLINE" = "xyes"; then
+
+		dnl defaults
+		HAVE_GROUNDINGLINE=yes
+
+		AC_DEFINE([_HAVE_GROUNDINGLINE_],[1],[with groundingline capability])
+	else
+		HAVE_GROUNDINGLINE=no
+	fi
+	AM_CONDITIONAL([GROUNDINGLINE], [test x$HAVE_GROUNDINGLINE = xyes])
+	AC_MSG_RESULT($HAVE_GROUNDINGLINE)
+	dnl }}}
+	dnl with-rifts{{{
+	AC_ARG_WITH([rifts],
+		AS_HELP_STRING([--with-rifts = YES], [compile with rifts capabilities (default is yes)]),
+		[RIFTS=$withval],[RIFTS=yes]) 
+	AC_MSG_CHECKING(for rifts capability compilation)
+
+	if test "x$RIFTS" = "xyes"; then
+
+		dnl defaults
+		HAVE_RIFTS=yes
+
+		AC_DEFINE([_HAVE_RIFTS_],[1],[with rifts capability])
+	else
+		HAVE_RIFTS=no
+	fi
+	AM_CONDITIONAL([RIFTS], [test x$HAVE_RIFTS = xyes])
+	AC_MSG_RESULT($HAVE_RIFTS)
+	dnl }}}
+	dnl math77{{{
+	AC_ARG_WITH([math77-dir],
+		AS_HELP_STRING([--with-math77-dir=DIR], [math77 root directory.]),
+		[MATH77_ROOT=$withval],[MATH77_ROOT=""]) 
+	AC_MSG_CHECKING(for math77)
+
+	if test -d "$MATH77_ROOT"; then
+
+	  HAVE_MATH77=yes
+	  MATH77LIB="-L$MATH77_ROOT/ -lmath77"
+
+	  AC_DEFINE([_HAVE_MATH77_],[1],[with math77 in ISSM src])
+	  AC_SUBST([MATH77LIB])
+	else
+		HAVE_MATH77=no
+	fi
+	AC_MSG_RESULT($HAVE_MATH77)
+	dnl }}}
+	dnl with-gia{{{
+	AC_ARG_WITH([gia],
+		AS_HELP_STRING([--with-gia = YES], [compile with gia capabilities (default is yes)]),
+		[GIA=$withval],[GIA=no]) 
+	AC_MSG_CHECKING(for gia capability compilation)
+
+	if test "x$GIA" = "xyes"; then
+	  
+	  if test "x$HAVE_MATH77" = "xno"; then
+		  HAVE_GIA=no
+		  AC_MSG_ERROR([gia requires compilation of math77 library! Reconfigure with --with-math77 option on]);
+	  else
+		dnl defaults
+		HAVE_GIA=yes
+		AC_DEFINE([_HAVE_GIA_],[1],[with gia capability])
+	  fi
+
+	else
+		HAVE_GIA=no
+	fi
+	AM_CONDITIONAL([GIA], [test x$HAVE_GIA = xyes])
+	AC_MSG_RESULT($HAVE_GIA)
+	dnl }}}
+	dnl with-ios{{{
+	AC_ARG_WITH([ios],
+		AS_HELP_STRING([--with-ios = YES], [compile with iOS capabilities (default is no, alternatives are yes)]),
+		[IOS=$withval],[IOS=no]) 
+	AC_MSG_CHECKING(for iOS compilation)
+
+	if test "x$IOS" = "xyes"; then
+		dnl defaults
+		HAVE_IOS=yes
+
+		AC_DEFINE([_HAVE_IOS_],[1],[with android capability])
+	elif test "x$IOS" = "xno"; then
+		HAVE_IOS=no
+	else
+	  AC_MSG_ERROR([--with-ios should be either no or yes])
+	fi
+	AM_CONDITIONAL([IOS], [test x$HAVE_IOS != xno])
+	AC_MSG_RESULT($HAVE_IOS)
+	dnl }}}
+	dnl with-android{{{
+	AC_ARG_WITH([android],
+		AS_HELP_STRING([--with-android = EXE], [compile with android capabilities (default is no, alternatives are exe and jni)]),
+		[ANDROID=$withval],[ANDROID=no]) 
+	AC_MSG_CHECKING(for android capability compilation)
+
+	if test "x$ANDROID" = "xjni"; then
+
+		dnl defaults
+		HAVE_ANDROID=jni
+		AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability])
+		AC_DEFINE([_HAVE_ANDROID_JNI_],[1],[with android jni])
+	elif test "x$ANDROID" = "xexe"; then
+		dnl defaults
+		HAVE_ANDROID=exe
+
+		AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability])
+	elif test "x$ANDROID" = "xno"; then
+		HAVE_ANDROID=no
+	else
+	  AC_MSG_ERROR([--with-android should be either no, exe or jni])
+	fi
+	AM_CONDITIONAL([ANDROID], [test x$HAVE_ANDROID != xno])
+	AM_CONDITIONAL([ANDROIDJNI], [test x$HAVE_ANDROID = xjni])
+	AM_CONDITIONAL([ANDROIDEXE], [test x$HAVE_ANDROID = xexe])
+	AC_MSG_RESULT($HAVE_ANDROID)
+	dnl }}}
+	dnl with-android-ndk{{{
+	AC_ARG_WITH([android-ndk],
+	  AS_HELP_STRING([--with-android-ndk=DIR], [android-ndk root directory.]),
+	  [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) 
+	AC_MSG_CHECKING(with android ndk)
+	
+	if test -d "$ANDROID_NDK_ROOT"; then
+		dnl defaults
+		HAVE_ANDROID_NDK=yes
+		ANDROID_NDKINCL="-I$ANDROID_NDK_ROOT/arm-linux-android-install/sysroot/usr/include"
+
+		AC_DEFINE([_HAVE_ANDROID_NDK_],[1],[with android ndk in ISSM src])
+		AC_SUBST([ANDROID_NDKINCL])
+	else
+		HAVE_ANDROID_NDK=no
+	fi
+	AC_MSG_RESULT($HAVE_ANDROID_NDK)
+	dnl }}}
+	dnl with-3d{{{
+	AC_ARG_WITH([3d],
+		AS_HELP_STRING([--with-3d = YES], [compile with 3d capabilities (default is yes)]),
+		[THREED=$withval],[THREED=yes]) 
+	AC_MSG_CHECKING(for 3d capability compilation)
+
+	if test "x$THREED" = "xyes"; then
+
+		dnl defaults
+		HAVE_3D=yes
+
+		AC_DEFINE([_HAVE_3D_],[1],[with 3d capability])
+	else
+		HAVE_3D=no
+	fi
+	AM_CONDITIONAL([THREED], [test x$HAVE_3D = xyes])
+	AC_MSG_RESULT($HAVE_3D)
+	dnl }}}
+	dnl checks{{{
+	AC_MSG_CHECKING(consistency between all libraries)
+	
+	dnl check that if petsc is requested , mpi should be specified
+	if test "$HAVE_PETSC" = "yes" ; then
+		if test "$HAVE_MPI" = "NO";  then
+			AC_MSG_ERROR([petsc requires mpi!]);
+		fi
+	fi
+
+	dnl check that we have either python or matlab support if we compile the modules
+	if test "$MODULES_VALUE" = "yes"  && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then
+		AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]);
+	fi
+
+	dnl check that if we have MPI, we have metis
+	if test "$HAVE_METIS" = "yes"  && test "$HAVE_MPI" = "no" ; then
+	AC_MSG_ERROR([need mpi if using the metis partitioner!]);
+	fi
+
+	AC_MSG_RESULT(done)
+	dnl }}}
+
+	dnl other options
+	dnl optimization{{{
+	dnl bypass standard optimization -g -O2 ? 
+	AC_ARG_WITH([cxxoptflags],
+	  AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]),
+	  [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2"]) 
+	AC_MSG_CHECKING(for c++ optimization flags)
+	AC_SUBST([CXXOPTFLAGS])
+	AC_MSG_RESULT(done)
+
+	dnl }}}
+	dnl multithreading{{{
+	AC_ARG_WITH([numthreads],
+	  AS_HELP_STRING([--with-numthreads = NUMTHREADS_VALUE],[numthreads, default is 1. ]),
+	  [NUMTHREADS_VALUE=$withval],[NUMTHREADS_VALUE=1])
+	AC_MSG_CHECKING(for number of threads)
+	dnl defaults
+	MULTITHREADING=no
+	MULTITHREADINLIB=""
+	if test "$NUMTHREADS_VALUE" != "1"; then
+		
+		MULTITHREADINGLIB="-lpthread -lrt"
+		case "${host_os}" in
+		*cygwin*)
+		MULTITHREADINGLIB="-lpthread -lrt"
+		;;
+		*linux*)
+		MULTITHREADINGLIB="-lpthread -lrt"
+		;;
+		*darwin*)
+		MULTITHREADINGLIB="-lpthread"
+		;;
+		esac
+
+		AC_DEFINE([_MULTITHREADING_],[1],[with numthreads enabled])
+		AC_DEFINE_UNQUOTED([_NUMTHREADS_],[$NUMTHREADS_VALUE],[number of threads])
+	fi
+	AC_SUBST([MULTITHREADINGLIB])
+	AC_MSG_RESULT($NUMTHREADS_VALUE) 
+	dnl }}}
+	dnl 64bit {{{
+	AC_ARG_WITH([64bit-indices],
+	  AS_HELP_STRING([--with-64bit-indices = bool], [use 64 bit integers, default 0, ex: --with-64bit-indices=1]),
+	  [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) 
+	AC_MSG_CHECKING(for 64 bit indices)
+
+	if test "$USE_64BIT_INDICES" == "1"; then
+	AC_DEFINE([ISSM_USE_64BIT_INDICES],[1],[with 64 bits indices])
+	else
+	AC_DEFINE([ISSM_USE_64BIT_INDICES],[0],[with 64 bits indices])
+	fi
+	AC_MSG_RESULT($USE_64BIT_INDICES)
+	dnl }}}
+])
Index: /issm/trunk-jpl/packagers/ubuntu/issmpkg/templates/sampleControl
===================================================================
--- /issm/trunk-jpl/packagers/ubuntu/issmpkg/templates/sampleControl	(revision 16002)
+++ /issm/trunk-jpl/packagers/ubuntu/issmpkg/templates/sampleControl	(revision 16002)
@@ -0,0 +1,6 @@
+Package: issm-python
+Version: 1.1.3
+Architecture: amd64
+Depends: mpich2, petsc3.2-issm, metis4.0-issm, triangle-bin, libtriangle-dev, python2.7-dev, python-scipy, python-netcdf4, netcdf-bin, python-nose, libnetcdfc++4, hdf5-tools
+Maintainer: issm/jpl (issm@jpl.nasa.gov)
+Description: Ice Sheet System Model, ubuntu/debian package
Index: /issm/trunk-jpl/packagers/ubuntu/issmpkg/triangle.h.patch
===================================================================
--- /issm/trunk-jpl/packagers/ubuntu/issmpkg/triangle.h.patch	(revision 16002)
+++ /issm/trunk-jpl/packagers/ubuntu/issmpkg/triangle.h.patch	(revision 16002)
@@ -0,0 +1,12 @@
+250a251,257
+> /*Patch for ISSM*/
+> #ifndef REAL
+> typedef double REAL;
+> typedef void VOID;
+> #endif
+> /*End patch*/
+> 
+283c290
+< void triangulate(char *, struct triangulateio *, struct triangulateio *,
+---
+> extern "C" void triangulate(char *, struct triangulateio *, struct triangulateio *,