Index: issm/trunk/README
===================================================================
--- issm/trunk/README	(revision 12331)
+++ issm/trunk/README	(revision 12332)
@@ -23,5 +23,5 @@
 ------------------------------------------------------------------------------
 
-Website: ttp://issm.jpl.nasa.gov/ for additional information.
+Website: http://issm.jpl.nasa.gov/ for additional information.
 
 ------------------------------------------------------------------------------
Index: issm/trunk/configs/config-altix64-castor.sh
===================================================================
--- issm/trunk/configs/config-altix64-castor.sh	(revision 12331)
+++ issm/trunk/configs/config-altix64-castor.sh	(revision 12332)
@@ -1,3 +1,3 @@
 #!/bin/csh
 
-./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/usr/include  --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so
+./configure --prefix=$ISSM_DIR --with-serial=no --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=/usr/include  --with-mpi-lib="-L/usr/lib -lmpi" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-mkl-dir=/opt/intel/mkl/9.1.023/lib/64 --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH --with-graphics-lib=/usr/X11R6/lib/libX11.so
Index: issm/trunk/configs/config-arm-linux.sh
===================================================================
--- issm/trunk/configs/config-arm-linux.sh	(revision 12332)
+++ issm/trunk/configs/config-arm-linux.sh	(revision 12332)
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+./configure \
+	--prefix=$ISSM_DIR \
+    --host="arm-linux" \
+	--without-modules \
+    CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \
+    GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc \
+    CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++ \
+	--with-vendor=arm-linux \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\
+    --without-fortran-lib
Index: issm/trunk/configs/config-cosmos.sh
===================================================================
--- issm/trunk/configs/config-cosmos.sh	(revision 12331)
+++ issm/trunk/configs/config-cosmos.sh	(revision 12332)
@@ -1,3 +1,3 @@
 #!/bin/csh
 
-./configure --prefix=$ISSM_TIER --with-serial=no --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include  --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm  -lpthread  -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/  --with-plapack-dir="-L$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/$ISSM_ARCH  --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so
+./configure --prefix=$ISSM_DIR --with-serial=no --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=/opt/mpich/gm/intel10.1/include  --with-mpi-lib="-L/opt/mpich/gm/intel10.1/lib -lmpich -L/usr/local/gm/lib/ -lgm  -lpthread  -lrt" --with-petsc-arch=$ISSM_ARCH --with-mkl-dir=/opt/intel/mkl/10.0.5.025/lib/32/  --with-plapack-dir="-L$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH  --with-vendor=intel-linux --with-graphics-lib=/usr/X11R6/lib/libX11.so
Index: issm/trunk/configs/config-discover.sh
===================================================================
--- issm/trunk/configs/config-discover.sh	(revision 12332)
+++ issm/trunk/configs/config-discover.sh	(revision 12332)
@@ -0,0 +1,24 @@
+#!/bin/csh
+
+#PETSc 3.2
+#MPI /usr/local/intel/mpi/3.2.2.006/lib64/
+
+./configure \
+ --prefix=$ISSM_DIR \
+ --with-modules=no \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-mpi-include="/usr/local/intel/mpi/3.2.2.006/include64/" \
+ --with-mpi-lib="-L/usr/local/intel/mpi/3.2.2.006/lib64/ -lmpi -lmpi_ilp64 -lmpiif" \
+ --with-petsc-arch=$ISSM_ARCH \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+ --with-mkl-dir=/usr/local/intel/mkl/10.1.2.024/ \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-graphics-lib=/usr/lib64/libX11.so \
+ --with-cxxoptflags="-O3 -xS" \
+ --with-vendor=intel-linux
Index: issm/trunk/configs/config-greenplanet.sh
===================================================================
--- issm/trunk/configs/config-greenplanet.sh	(revision 12331)
+++ issm/trunk/configs/config-greenplanet.sh	(revision 12332)
@@ -5,19 +5,19 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
- --with-serial=no \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
+ --prefix=$ISSM_DIR \
+ --with-modules=no \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
  --with-mpi-include="/sopt/mpi/openmpi-1.5.4_psm/intel/include/" \
  --with-mpi-lib="-L/sopt/mpi/openmpi-1.5.4_psm/intel/lib/ -lmpi -lmpi_f77" \
  --with-petsc-arch=$ISSM_ARCH \
- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
  --with-mkl-dir=/opt/intel/mkl/10.2.4.032/ \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
  --with-graphics-lib=/usr/lib64/libX11.so \
  --with-cxxoptflags="-O3 -xS" \
Index: issm/trunk/configs/config-linux64-ad.sh
===================================================================
--- issm/trunk/configs/config-linux64-ad.sh	(revision 12332)
+++ issm/trunk/configs/config-linux64-ad.sh	(revision 12332)
@@ -0,0 +1,18 @@
+#!/bin/sh
+
+./configure \
+	--prefix=$ISSM_DIR \
+	--without-modules\
+	--with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\
+	--without-thermal \
+	--without-control \
+	--without-hydrology \
+	--without-diagnostic \
+	--without-balanced \
+	--without-responses \
+	--without-slope \
+	--without-rifts \
+	--without-steadystate \
+	--without-transient \
+	--without-3d \
+	--without-groundingline
Index: issm/trunk/configs/config-linux64-astrid-ad.sh
===================================================================
--- issm/trunk/configs/config-linux64-astrid-ad.sh	(revision 12331)
+++ issm/trunk/configs/config-linux64-astrid-ad.sh	(revision 12332)
@@ -2,22 +2,22 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
+ --prefix=$ISSM_DIR \
  --with-serial=no\
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \
  --with-petsc-arch=$ISSM_ARCH \
- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
  --with-graphics-lib=/usr/lib64/libX11.so \
  --with-cxxoptflags="-march=opteron -O2" \
  --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \
- --with-rose-dir=$ISSM_TIER/externalpackages/rose/install/ \
- --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \
+ --with-rose-dir=$ISSM_DIR/externalpackages/rose/install/ \
+ --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \
  --with-numthreads=24 \
  --without-thermal \
Index: issm/trunk/configs/config-linux64-astrid-mpich1.0.sh
===================================================================
--- issm/trunk/configs/config-linux64-astrid-mpich1.0.sh	(revision 12332)
+++ issm/trunk/configs/config-linux64-astrid-mpich1.0.sh	(revision 12332)
@@ -0,0 +1,31 @@
+#!/bin/sh
+
+#External packages versions:
+#petsc 3.1 or 3.2
+#mpich 1.0.2
+
+./configure \
+ --prefix=$ISSM_DIR \
+ --with-matlab-dir=$MATLAB_DIR \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \
+ --with-petsc-arch=$ISSM_ARCH \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \
+ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
+ --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \
+ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \
+ --with-graphics-lib=/usr/lib64/libX11.so \
+ --with-cxxoptflags="-march=opteron -O2" \
+ --with-numthreads=32 \
+ --enable-debugging
Index: issm/trunk/configs/config-linux64-astrid-mpich1.4.sh
===================================================================
--- issm/trunk/configs/config-linux64-astrid-mpich1.4.sh	(revision 12331)
+++ 	(revision )
@@ -1,31 +1,0 @@
-#!/bin/sh
-
-#External packages versions:
-#petsc 3.1 or 3.2
-#mpich 1.4
-
-./configure \
- --prefix=$ISSM_TIER \
- --with-matlab-dir=$MATLAB_DIR \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \
- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \
- --with-petsc-arch=$ISSM_ARCH \
- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \
- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \
- --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \
- --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \
- --with-graphics-lib=/usr/lib64/libX11.so \
- --with-cxxoptflags="-march=opteron -O2" \
- --with-numthreads=32 \
- --enable-debugging
Index: issm/trunk/configs/config-linux64-astrid-petsc2.sh
===================================================================
--- issm/trunk/configs/config-linux64-astrid-petsc2.sh	(revision 12331)
+++ issm/trunk/configs/config-linux64-astrid-petsc2.sh	(revision 12332)
@@ -5,3 +5,3 @@
 #mpich 1.0.2
 
-./configure --prefix=$ISSM_TIER --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_TIER/externalpackages/scotch/install --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_TIER/externalpackages/shapelib/install\
+./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH -lPLAPACK" --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/$ISSM_ARCH/INCLUDE" --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3/$ISSM_ARCH --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so --with-cxxoptflags="-march=opteron -O2" --with-numthreads=32 --with-scotch-dir=$ISSM_DIR/externalpackages/scotch/install --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install --enable-debugging --with-shapelib-dir=$ISSM_DIR/externalpackages/shapelib/install\
Index: issm/trunk/configs/config-linux64-astrid.sh
===================================================================
--- issm/trunk/configs/config-linux64-astrid.sh	(revision 12331)
+++ issm/trunk/configs/config-linux64-astrid.sh	(revision 12332)
@@ -3,26 +3,27 @@
 #External packages versions:
 #petsc 3.1 or 3.2
-#mpich 1.0.2
+#mpich 1.4
 
 ./configure \
- --prefix=$ISSM_TIER \
+ --prefix=$ISSM_DIR \
  --with-matlab-dir=$MATLAB_DIR \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-tao-dir=$ISSM_TIER/externalpackages/tao/install \
- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich " \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl " \
  --with-petsc-arch=$ISSM_ARCH \
- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \
- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \
- --with-shapelib-dir="$ISSM_TIER/externalpackages/shapelib/install" \
+ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \
+ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
+ --with-shapelib-dir="$ISSM_DIR/externalpackages/shapelib/install" \
  --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \
  --with-graphics-lib=/usr/lib64/libX11.so \
@@ -30,2 +31,3 @@
  --with-numthreads=32 \
  --enable-debugging
+ #--with-serial=no \
Index: issm/trunk/configs/config-linux64-murdo-ad.sh
===================================================================
--- issm/trunk/configs/config-linux64-murdo-ad.sh	(revision 12331)
+++ issm/trunk/configs/config-linux64-murdo-ad.sh	(revision 12332)
@@ -2,23 +2,23 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
+ --prefix=$ISSM_DIR \
  --with-serial=no\
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \
  --with-petsc-arch=$ISSM_ARCH \
- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-hypre-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-ml-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-ml-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
  --with-graphics-lib=/usr/lib64/libX11.so \
  --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\
  --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lg2c  /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortran.a" \
- --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \
+ --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \
 --with-numthreads=24 \
  --without-thermal \
Index: issm/trunk/configs/config-linux64-murdo-nopetsc.sh
===================================================================
--- issm/trunk/configs/config-linux64-murdo-nopetsc.sh	(revision 12331)
+++ issm/trunk/configs/config-linux64-murdo-nopetsc.sh	(revision 12332)
@@ -2,26 +2,26 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \
+ --prefix=$ISSM_DIR \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \
  --with-matlab-dir=$MATLAB_DIR \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib \
  --with-graphics-lib=/usr/lib64/libX11.so \
- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \
- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \
+ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \
+ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
  --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\
  --with-numthreads=18 \
  --enable-debugging \
- --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install
+ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install
  
  
-# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
+# --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
 # --with-petsc-arch=$ISSM_ARCH \
-# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
-# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+# --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+# --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+# --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+# --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+# --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+# --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
Index: issm/trunk/configs/config-linux64-murdo.sh
===================================================================
--- issm/trunk/configs/config-linux64-murdo.sh	(revision 12331)
+++ issm/trunk/configs/config-linux64-murdo.sh	(revision 12332)
@@ -2,24 +2,24 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
+ --prefix=$ISSM_DIR \
  --with-matlab-dir=$MATLAB_DIR \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
- --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \
  --with-petsc-arch=$ISSM_ARCH \
- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \
- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \
+ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
  --with-graphics-lib=/usr/lib64/libX11.so \
  --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\
  --with-numthreads=18 \
- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
  --enable-debugging
  
Index: issm/trunk/configs/config-linux64-ubuntu64.sh
===================================================================
--- issm/trunk/configs/config-linux64-ubuntu64.sh	(revision 12332)
+++ issm/trunk/configs/config-linux64-ubuntu64.sh	(revision 12332)
@@ -0,0 +1,26 @@
+#!/bin/sh
+
+./configure \
+ --prefix=$ISSM_DIR \
+ --with-matlab-dir=$MATLAB_DIR \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich -lmpl -ldl" \
+ --with-petsc-arch=$ISSM_ARCH \
+ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \
+ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
+ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\
+ --with-fortran-lib="-lgfortran"\
+ --with-numthreads=8 \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+ --enable-debugging
+ 
+ 
Index: issm/trunk/configs/config-macosx32-mathieu.sh
===================================================================
--- issm/trunk/configs/config-macosx32-mathieu.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx32-mathieu.sh	(revision 12332)
@@ -10,19 +10,19 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 	--with-fortran-lib="/usr/local/lib/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
Index: issm/trunk/configs/config-macosx32-ogive.sh
===================================================================
--- issm/trunk/configs/config-macosx32-ogive.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx32-ogive.sh	(revision 12332)
@@ -5,19 +5,19 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
Index: issm/trunk/configs/config-macosx64-ad.sh
===================================================================
--- issm/trunk/configs/config-macosx64-ad.sh	(revision 12332)
+++ issm/trunk/configs/config-macosx64-ad.sh	(revision 12332)
@@ -0,0 +1,18 @@
+#!/bin/sh
+
+./configure \
+	--prefix=$ISSM_DIR \
+	--without-modules\
+	--with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install\
+	--without-thermal \
+	--without-control \
+	--without-hydrology \
+	--without-diagnostic \
+	--without-balanced \
+	--without-responses \
+	--without-slope \
+	--without-rifts \
+	--without-steadystate \
+	--without-transient \
+	--without-3d \
+	--without-groundingline
Index: issm/trunk/configs/config-macosx64-gsl.sh
===================================================================
--- issm/trunk/configs/config-macosx64-gsl.sh	(revision 12332)
+++ issm/trunk/configs/config-macosx64-gsl.sh	(revision 12332)
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+./configure \
+	--prefix=$ISSM_DIR \
+	--without-modules\
+	--with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install
+	#--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install 
+    #--without-fortran-lib
Index: issm/trunk/configs/config-macosx64-helene.sh
===================================================================
--- issm/trunk/configs/config-macosx64-helene.sh	(revision 12332)
+++ issm/trunk/configs/config-macosx64-helene.sh	(revision 12332)
@@ -0,0 +1,26 @@
+#!/bin/sh
+
+#petsc 3.2
+#mpich 1.4
+
+./configure \
+	--prefix=$ISSM_DIR \
+	--with-matlab-dir=$MATLAB_DIR \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a" \
+	--with-petsc-arch=$ISSM_ARCH \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
+	--with-math-lib="/usr/lib/libm.dylib" \
+	--with-graphics-lib="/usr/X11/lib/libX11.dylib" \
+	--with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5  -O3 -DNDEBUG -w "\
+	--with-numthreads=8
Index: issm/trunk/configs/config-macosx64-larour-ad.sh
===================================================================
--- issm/trunk/configs/config-macosx64-larour-ad.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-larour-ad.sh	(revision 12332)
@@ -6,17 +6,17 @@
 ./configure \
 	--with-serial=no\
-	--prefix=$ISSM_TIER \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--prefix=$ISSM_DIR \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--without-blas-lapack-dir \
-	--with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \
+	--with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
 	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
 	--with-math-lib="/usr/lib/libm.dylib" \
 	--with-graphics-lib="/usr/X11/lib/libX11.dylib" \
 	--with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5  -O3 -DNDEBUG -w "\
-	--with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \
-	--with-adolc-dir=$ISSM_TIER/externalpackages/adolc/install/ \
+	--with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \
+	--with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install/ \
 	--with-numthreads=8 \
 	--without-thermal \
@@ -34,10 +34,10 @@
  
 #--without-prognostic \
-#--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
+#--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
 #--with-petsc-arch=$ISSM_ARCH \
-#--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-#--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-#--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-#--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-#--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-#--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+#--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+#--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+#--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+#--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+#--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+#--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
Index: issm/trunk/configs/config-macosx64-larour-bothapis.sh
===================================================================
--- issm/trunk/configs/config-macosx64-larour-bothapis.sh	(revision 12332)
+++ issm/trunk/configs/config-macosx64-larour-bothapis.sh	(revision 12332)
@@ -0,0 +1,33 @@
+#!/bin/sh
+
+#petsc 3.2
+#mpich 1.4
+
+pythonversion=2.7
+
+./configure \
+	--prefix=$ISSM_DIR \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-matlab-dir=$MATLAB_DIR \
+	--with-python-dir=$ISSM_DIR/externalpackages/python/install\
+	--with-python-version=$pythonversion \
+	--with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
+	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
+	--with-math-lib="/usr/lib/libm.dylib" \
+	--with-graphics-lib="/usr/X11/lib/libX11.dylib" \
+	--with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5  -O3 -DNDEBUG -w "\
+	--with-numthreads=8 \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-petsc-arch=$ISSM_ARCH \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ 
+	#--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	#--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \
Index: issm/trunk/configs/config-macosx64-larour-nopetsc.sh
===================================================================
--- issm/trunk/configs/config-macosx64-larour-nopetsc.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-larour-nopetsc.sh	(revision 12332)
@@ -1,28 +1,15 @@
 #!/bin/sh
 
-#petsc 3.2
-#mpich 1.4
+pythonversion=3.2
 
 ./configure \
-	--prefix=$ISSM_TIER \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \
-	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
+	--with-python-dir=$ISSM_DIR/externalpackages/python/install\
+	--with-python-version=$pythonversion \
+	--with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
 	--with-math-lib="/usr/lib/libm.dylib" \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \
 	--with-graphics-lib="/usr/X11/lib/libX11.dylib" \
 	--with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5  -O3 -DNDEBUG -w "\
-	--with-numthreads=8 \
-	--with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install
-#	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-#	--with-petsc-arch=$ISSM_ARCH \
-#	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-#	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-#	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-#	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-#	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ 
-#   --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+	--with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install
Index: issm/trunk/configs/config-macosx64-larour-python.sh
===================================================================
--- issm/trunk/configs/config-macosx64-larour-python.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-larour-python.sh	(revision 12332)
@@ -5,12 +5,12 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-python-dir=$ISSM_TIER/externalpackages/python/install\
-	--with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
-	--with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \
+	--prefix=$ISSM_DIR \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-python-dir=$ISSM_DIR/externalpackages/python/install\
+	--with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
 	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
@@ -18,12 +18,12 @@
 	--with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5  -O3 -DNDEBUG -w "\
 	--with-numthreads=8 \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ 
-	#--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	#--with-boost-dir=$ISSM_TIER/externalpackages/boost/install/ \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ 
+	#--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	#--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \
Index: issm/trunk/configs/config-macosx64-larour.sh
===================================================================
--- issm/trunk/configs/config-macosx64-larour.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-larour.sh	(revision 12332)
@@ -5,11 +5,11 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
-	--with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
 	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
@@ -17,11 +17,11 @@
 	--with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5  -O3 -DNDEBUG -w "\
 	--with-numthreads=8 \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ 
-	#--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ 
+	#--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
Index: issm/trunk/configs/config-macosx64-mathieu.sh
===================================================================
--- issm/trunk/configs/config-macosx64-mathieu.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-mathieu.sh	(revision 12332)
@@ -5,19 +5,19 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 	--with-fortran-lib="/usr/local/lib/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
Index: issm/trunk/configs/config-macosx64-nicole.sh
===================================================================
--- issm/trunk/configs/config-macosx64-nicole.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-nicole.sh	(revision 12332)
@@ -5,21 +5,21 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \
-	--with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \
+	--with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
 	--with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
Index: issm/trunk/configs/config-macosx64-ogive.sh
===================================================================
--- issm/trunk/configs/config-macosx64-ogive.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-ogive.sh	(revision 12332)
@@ -9,19 +9,19 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 	--with-fortran-lib="/usr/local/gfortran/lib/x86_64/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
Index: issm/trunk/configs/config-macosx64-sophie.sh
===================================================================
--- issm/trunk/configs/config-macosx64-sophie.sh	(revision 12331)
+++ issm/trunk/configs/config-macosx64-sophie.sh	(revision 12332)
@@ -9,19 +9,19 @@
 
 ./configure \
-	--prefix=$ISSM_TIER \
+	--prefix=$ISSM_DIR \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
-	--with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
-	--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  \
-	--with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include  \
-	--with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include  \
+	--with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \
 	--with-petsc-arch=$ISSM_ARCH \
-	--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \
-	--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
-	--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \
-	--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
-	--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+	--with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/include/ " \
+	--with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 	--with-fortran-lib="/sw/usr/local/lib/x86_64/libgfortran.a" \
 	--with-math-lib="/usr/lib/libm.dylib" \
Index: issm/trunk/configs/config-pleiades-petsc2.sh
===================================================================
--- issm/trunk/configs/config-pleiades-petsc2.sh	(revision 12331)
+++ issm/trunk/configs/config-pleiades-petsc2.sh	(revision 12332)
@@ -2,19 +2,19 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
- --with-serial=no \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
+ --prefix=$ISSM_DIR \
+ --with-modules=no \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
  --with-mpi-include=/nasa/sgi/mpt/1.25/include \
  --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \
  --with-petsc-arch=$ISSM_ARCH \
- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
  --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
  --with-graphics-lib=/usr/lib64/libX11.so \
  --with-cxxoptflags="-O3 -xS" \
Index: issm/trunk/configs/config-pleiades.sh
===================================================================
--- issm/trunk/configs/config-pleiades.sh	(revision 12331)
+++ issm/trunk/configs/config-pleiades.sh	(revision 12332)
@@ -2,19 +2,20 @@
 
 ./configure \
- --prefix=$ISSM_TIER \
- --with-serial=no \
- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \
- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \
- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \
+ --prefix=$ISSM_DIR \
+ --with-modules=no \
+ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \
+ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+ --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \
  --with-mpi-include=/nasa/sgi/mpt/1.25/include \
  --with-mpi-lib="-L/nasa/sgi/mpt/1.25/lib/ -lmpi -lpthread -lgfortran" \
  --with-petsc-arch=$ISSM_ARCH \
- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \
+ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
  --with-mkl-dir=/nasa/intel/mkl/10.0.011/lib/64/ \
- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \
- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \
- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \
+ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \
+ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \
+ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \
  --with-graphics-lib=/usr/lib64/libX11.so \
  --with-cxxoptflags="-O3 -xS" \
Index: issm/trunk/configs/config-win32-eric.sh
===================================================================
--- issm/trunk/configs/config-win32-eric.sh	(revision 12331)
+++ issm/trunk/configs/config-win32-eric.sh	(revision 12332)
@@ -4,3 +4,3 @@
 #get configure.sh to pick up the intel compiler 
 
-./configure --prefix=$ISSM_TIER --with-parallel=no --with-vendor=intel-win  --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install  --with-petsc-arch=$ISSM_ARCH  --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH
+./configure --prefix=$ISSM_DIR --with-parallel=no --with-vendor=intel-win  --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  --with-petsc-arch=$ISSM_ARCH  --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/f2cblaslapack/$ISSM_ARCH
Index: issm/trunk/configs/config-win7-32.sh
===================================================================
--- issm/trunk/configs/config-win7-32.sh	(revision 12331)
+++ issm/trunk/configs/config-win7-32.sh	(revision 12332)
@@ -2,15 +2,15 @@
 
 #Dos style path needed for the windows sdk 7.1 cl compiler: 
-ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"`
+ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"`
 
 #get configure.sh to pick up the win7 Visual Studio compiler 
-./configure --prefix=$ISSM_TIER \
+./configure --prefix=$ISSM_DIR \
 	--with-vendor=intel-win7-32  \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \
-	--with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \
-	--with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \
+	--with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \
+	--with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \
+	--with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \
 	--with-petsc-arch=$ISSM_ARCH  \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/  \
-	--with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \
-	--with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" 
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/  \
+	--with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \
+	--with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni" 
Index: issm/trunk/configs/config-win7-64.sh
===================================================================
--- issm/trunk/configs/config-win7-64.sh	(revision 12331)
+++ issm/trunk/configs/config-win7-64.sh	(revision 12332)
@@ -2,15 +2,15 @@
 
 #Dos style path needed for the windows sdk 7.1 cl compiler: 
-ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"`
+ISSM_DIR_WIN=`cygpath -m "$ISSM_DIR"`
 
 #get configure.sh to pick up the win7 Visual Studio compiler 
-./configure --prefix=$ISSM_TIER \
+./configure --prefix=$ISSM_DIR \
 	--with-vendor=intel-win7-64  \
 	--with-matlab-dir=$MATLAB_DIR \
-	--with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \
-	--with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \
-	--with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \
+	--with-triangle-dir="$ISSM_DIR_WIN/externalpackages/triangle/install" \
+	--with-metis-dir="$ISSM_DIR_WIN/externalpackages/metis/install" \
+	--with-petsc-dir="$ISSM_DIR_WIN/externalpackages/petsc/install" \
 	--with-petsc-arch=$ISSM_ARCH  \
-	--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/  \
-	--with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \
-	--with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" 
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/lib/  \
+	--with-mpi-lib="$ISSM_DIR_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \
+	--with-mpi-include="$ISSM_DIR_WIN/externalpackages/petsc/install/include/mpiuni" 
Index: issm/trunk/configure.ac
===================================================================
--- issm/trunk/configure.ac	(revision 12331)
+++ issm/trunk/configure.ac	(revision 12332)
@@ -2,5 +2,5 @@
 
 #AUTOCONF
-AC_INIT([ISSM],[4.1],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure
+AC_INIT([ISSM],[4.2],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure
 AC_CONFIG_AUX_DIR([./aux-config])         #Put config files in aux-config
 AC_CONFIG_MACRO_DIR([m4])                 #m4 macros are located in m4
@@ -36,6 +36,10 @@
 AC_CONFIG_FILES([Makefile
 			src/Makefile
-			src/c/Makefile
-			src/mex/Makefile
+			src/c/Makefile 
+			src/py/Makefile
+			src/py/model/Makefile
+			src/modules/Makefile
+			src/modules/python/Makefile
+			src/modules/matlab/Makefile
 			src/m/Makefile
 			bin/Makefile])
Index: issm/trunk/cron/configs/linux64_daily
===================================================================
--- issm/trunk/cron/configs/linux64_daily	(revision 12331)
+++ issm/trunk/cron/configs/linux64_daily	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full paths)
-ISSM_DIR="/path/to/issm"
-ISSM_TIER="/path/to/issm/cron/trunk-jpl"
+ISSM_DIR="/path/to/issm/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -72,5 +71,5 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
 SKIPMAIL="no"
 
Index: issm/trunk/cron/configs/linux64_nightly
===================================================================
--- issm/trunk/cron/configs/linux64_nightly	(revision 12331)
+++ issm/trunk/cron/configs/linux64_nightly	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full paths)
-ISSM_DIR="/path/to/issm"
-ISSM_TIER="/path/to/issm/cron/trunk-jpl"
+ISSM_DIR="/path/to/issm/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -72,5 +71,5 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
 SKIPMAIL="no"
 
Index: issm/trunk/cron/configs/macosx64_daily
===================================================================
--- issm/trunk/cron/configs/macosx64_daily	(revision 12331)
+++ issm/trunk/cron/configs/macosx64_daily	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full path)
-ISSM_DIR="/path/to/issm/"
-ISSM_TIER="/path/to/issm/trunk-jpl/cron/trunk-jpl"
+ISSM_DIR="/path/to/issm/trunk-jpl/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -72,5 +71,5 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
 SKIPMAIL="no"
 
Index: issm/trunk/cron/configs/macosx64_nightly
===================================================================
--- issm/trunk/cron/configs/macosx64_nightly	(revision 12331)
+++ issm/trunk/cron/configs/macosx64_nightly	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full path)
-ISSM_DIR="/path/to/issm/"
-ISSM_TIER="/path/to/issm/trunk-jpl/cron/trunk-jpl"
+ISSM_DIR="/path/to/issm/trunk-jpl/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -72,5 +71,5 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
 SKIPMAIL="no"
 
Index: issm/trunk/cron/configs/win732
===================================================================
--- issm/trunk/cron/configs/win732	(revision 12331)
+++ issm/trunk/cron/configs/win732	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full path)
-ISSM_DIR="/cygdrive/c/issm"
-ISSM_TIER="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl"
+ISSM_DIR="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -16,5 +15,5 @@
 
 #MATLAB path
-MATLAB_PATH="C:/MATLAB/R2011b32/"
+MATLAB_PATH="C:/MATLAB/R2012a/"
 
 #COMPILATION CONFIGURATION FILE
@@ -32,5 +31,5 @@
 # - "none"     leave ISSM as is in its directory
 #              ->skip to section 3
-ISSM_INSTALLATION="none"
+ISSM_INSTALLATION="checkout"
 
 #SVN repository
@@ -38,5 +37,5 @@
 
 #execution path used for parallel runs
-EXECUTION_PATH="/cygdrive/c/issm/ExecutionNightlyRun"
+EXECUTION_PATH="/cygdrive/c/issm-uci/ExecutionNightlyRun"
 
 #-----------------------------------#
@@ -49,6 +48,6 @@
 # - "none"    leave external packages as is
 #             ->skip to section 4
-ISSM_EXTERNALPACKAGES="none"
-EXTERNALPACKAGESDIR="/cygdrive/c/issm/trunk-jpl/externalpackages"
+ISSM_EXTERNALPACKAGES="link"
+EXTERNALPACKAGESDIR="/cygdrive/c/issm-uci/trunk-jpl/externalpackages"
 
 #List of external pakages to be installed
@@ -66,5 +65,5 @@
 # - "yes" compile ISSM
 # - "no"  do not compile ISSM
-ISSM_COMPILATION="no"
+ISSM_COMPILATION="yes"
 
 #----------------------#
@@ -73,9 +72,9 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
-SKIPMAIL="no"
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
+SKIPMAIL="yes"
 
 #Sender email address
-EMAIL_ADRESS="eric.larour@jpl.nasa.gov"
+EMAIL_ADRESS="eric.larour@gmail.com"
 
 #------------------------#
@@ -85,5 +84,5 @@
 #number of cpus used in ISSM installation and compilation (one is usually
 #safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=8
+NUMCPUS_INSTALL=1
 
 #number of cpus used in the nightly runs.
@@ -95,8 +94,8 @@
 #ex: "'id',[101 102 103]"
 
-NROPTIONS="'benchmark','all'"
+NROPTIONS="'benchmark',102:2:120"
 
 #------------------------#
 # 7: Matlab#
 #------------------------#
-MATLABBIN=/cygdrive/c/MATLAB/R2011b32/bin/matlab
+MATLABBIN=/cygdrive/c/MATLAB/R2012a/bin/matlab
Index: issm/trunk/cron/configs/win764
===================================================================
--- issm/trunk/cron/configs/win764	(revision 12331)
+++ issm/trunk/cron/configs/win764	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full path)
-ISSM_DIR="/cygdrive/c/issm"
-ISSM_TIER="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl"
+ISSM_DIR="/cygdrive/c/issm/trunk-jpl/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -73,5 +72,5 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
 SKIPMAIL="no"
 
Index: issm/trunk/cron/configs/winxp32
===================================================================
--- issm/trunk/cron/configs/winxp32	(revision 12331)
+++ issm/trunk/cron/configs/winxp32	(revision 12332)
@@ -6,6 +6,5 @@
 
 #ISSM main directory (full path)
-ISSM_DIR="C:/home/issm/trunk-jpl"
-ISSM_TIER="C:/home/issm/trunk-jpl/cron/trunk-jpl"
+ISSM_DIR="C:/home/issm/trunk-jpl/cron/trunk-jpl"
 
 #ISSM Architecture
@@ -66,5 +65,5 @@
 
 #Mail delivery. If SKIPMAIL="no", the html nightly run report will be
-#sent to the adresses present in $ISSM_TIER/cron/mailinglist.
+#sent to the adresses present in $ISSM_DIR/cron/mailinglist.
 SKIPMAIL="no"
 
Index: issm/trunk/cron/nightlyrun.sh
===================================================================
--- issm/trunk/cron/nightlyrun.sh	(revision 12331)
+++ issm/trunk/cron/nightlyrun.sh	(revision 12332)
@@ -65,5 +65,4 @@
 #Export ISSM_* variables{{{1
 export ISSM_DIR
-export ISSM_TIER
 export ISSM_ARCH
 #}}}
@@ -90,5 +89,5 @@
 
 	#only update ISSM
-	cd $ISSM_TIER
+	cd $ISSM_DIR
 	svn update
 
@@ -109,9 +108,9 @@
 #Create cluster's settings{{{1
 #create simpler  cluster.rc file, with only the cluster we are interested in.
-cd $ISSM_TIER/test/NightlyRun/
+cd $ISSM_DIR/test/NightlyRun/
 if [ "$MACHINE" = "win7" ]; then
 	cat << END > $HOST_NAME"_settings.m"
 cluster.login='$USER';
-cluster.codepath='`cygpath -m $ISSM_TIER/bin`';
+cluster.codepath='`cygpath -m $ISSM_DIR/bin`';
 cluster.executionpath='`cygpath -m $EXECUTION_PATH`';
 END
@@ -119,8 +118,8 @@
 	cat << END > $HOST_NAME"_settings.m"
 cluster.login='$USER';
-cluster.codepath='$ISSM_TIER/bin';
+cluster.codepath='$ISSM_DIR/bin';
 cluster.executionpath='$EXECUTION_PATH';
 END
-   cat << END > $ISSM_TIER/externalpackages/matlab/install.sh
+   cat << END > $ISSM_DIR/externalpackages/matlab/install.sh
 #!/bin/bash
 rm -rf install
@@ -131,5 +130,5 @@
 #}}}
 #Source environment variables with new matlab path {{{1
-cd $ISSM_TIER/etc
+cd $ISSM_DIR/etc
 source environment.sh MATLAB_DIR=$MATLAB_PATH
 #}}}
@@ -138,5 +137,5 @@
 then
 	
-	cd $ISSM_TIER/externalpackages
+	cd $ISSM_DIR/externalpackages
 	#number of packages: 
 	numpackages=`echo $EXTERNALPACKAGES | wc -w`
@@ -156,5 +155,5 @@
 
 	#erase externapackages, and link with externalpackages_dir
-	cd $ISSM_TIER
+	cd $ISSM_DIR
 	rm -rf externalpackages
 	cp -Rf $EXTERNALPACKAGESDIR ./
@@ -164,5 +163,5 @@
 
 	#erase externapackages, and link with externalpackages_dir
-	cd $ISSM_TIER
+	cd $ISSM_DIR
 	rm -rf externalpackages
 	ln -s  $EXTERNALPACKAGESDIR  .
@@ -186,5 +185,5 @@
 then
 
-	cd $ISSM_TIER
+	cd $ISSM_DIR
 	make clean
 	make distclean
@@ -214,7 +213,7 @@
 #Prepare run
 #create softlink to startup {{{1
-cd $ISSM_TIER/test/NightlyRun/
+cd $ISSM_DIR/test/NightlyRun/
 rm startup.m #in case it alreade exists
-cp $ISSM_TIER/startup.m .
+cp $ISSM_DIR/startup.m .
 #}}}
 #Create nightlylog directory and info.log {{{1
@@ -222,7 +221,7 @@
 INSTALL_TIME=$(timer)
 ELAPSED_INSTALL=$(timer $START_TIME)
-rm -rf $ISSM_TIER/nightlylog
-mkdir  $ISSM_TIER/nightlylog
-cat << END > $ISSM_TIER/nightlylog/info.log
+rm -rf $ISSM_DIR/nightlylog
+mkdir  $ISSM_DIR/nightlylog
+cat << END > $ISSM_DIR/nightlylog/info.log
 today:     $(echo $TODAY)
 user:      $(echo $USER)
@@ -245,7 +244,7 @@
 #on Matlab and windows machines, we'll need a windows style path:  {{{
 if [ "$MACHINE" = "win7" ]; then
-	MATLAB_TIER=`cygpath -m $ISSM_TIER`
+	MATLAB_TIER=`cygpath -m $ISSM_DIR`
 else 
-	MATLAB_TIER=$ISSM_TIER
+	MATLAB_TIER=$ISSM_DIR
 fi
 #}}}
@@ -254,5 +253,5 @@
 do
 	#Launch matlab and the nightly run script
-	cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF
+	cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF
 	warning off %necessary to avoid a info.log of several Go for parallel runs
 	try,
@@ -263,5 +262,4 @@
 		echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
 	else
-		#echo "runme('id',[101 102]);" 
 		echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
 	fi
@@ -271,5 +269,5 @@
 		message=getReport(me)
 		directory=strsplit(pwd,'/');
-		fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at');
+		fid=fopen([issmdir '/nightlylog/matlaberror.log'], 'at');
 		fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
 		fprintf(fid,'%s',message);
@@ -281,5 +279,5 @@
 
 	#Start run from nightlylog directory
-	cd $ISSM_TIER/nightlylog/
+	cd $ISSM_DIR/nightlylog/
 
 	MATLABBIN=$MATLAB_PATH/bin/matlab
@@ -298,5 +296,5 @@
 #}}}
 #concatenate all reports {{{1
-cd $ISSM_TIER/nightlylog/
+cd $ISSM_DIR/nightlylog/
 cp matlab_log1.log  matlab_log.log
 for (( i=2;i<=$NUMCPUS_RUN;i++ ))
@@ -315,5 +313,5 @@
 ELAPSED_RUN=$(timer $INSTALL_TIME)
 ELAPSED_TOTAL=$(timer $START_TIME)
-cat << END >>  $ISSM_TIER/nightlylog/info.log
+cat << END >>  $ISSM_DIR/nightlylog/info.log
 elapsed_run:   $(echo $ELAPSED_RUN)
 elapsed_total: $(echo $ELAPSED_TOTAL)
@@ -324,7 +322,7 @@
 #Send Report
 #Build html report {{{1
-cd $ISSM_TIER/nightlylog/
+cd $ISSM_DIR/nightlylog/
 sh ../scripts/report.sh
-echo "html report located in $ISSM_TIER/nightlylog/report.html"
+echo "html report located in $ISSM_DIR/nightlylog/report.html"
 #}}}
 #send mail if requested                  (SKIPMAIL) {{{1
@@ -332,14 +330,14 @@
 then
 	echo "sending report..."
-	source $ISSM_TIER/cron/mailinglist
+	source $ISSM_DIR/cron/mailinglist
 	for i in `echo $MAILINGLIST`; do
 
 		if [ "$MACHINE" = "win7" ]
 		then
-			email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" -n "ISSM Nightly run" -f echo $EMAIL_ADRESS $i < $ISSM_TIER/nightlylog/report.html
+			email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" -n "ISSM Nightly run" -f echo $EMAIL_ADRESS $i < $ISSM_DIR/nightlylog/report.html
 		else 
 			if [ "$MACHINE" = "astrid" ]
 			then
-cat - $ISSM_TIER/nightlylog/report.html <<HERE | /usr/lib/sendmail  -oi -t
+cat - $ISSM_DIR/nightlylog/report.html <<HERE | /usr/lib/sendmail  -oi -t
 From: "ISSM Nightly run" <$EMAIL_ADRESS>
 To: $i
@@ -349,5 +347,5 @@
 HERE
 		else
-cat - $ISSM_TIER/nightlylog/report.html <<HERE | /usr/sbin/sendmail  -oi -t
+cat - $ISSM_DIR/nightlylog/report.html <<HERE | /usr/sbin/sendmail  -oi -t
 From: "ISSM Nightly run" <$EMAIL_ADRESS>
 To: $i
Index: issm/trunk/etc/environment.csh
===================================================================
--- issm/trunk/etc/environment.csh	(revision 12331)
+++ issm/trunk/etc/environment.csh	(revision 12332)
@@ -1,4 +1,4 @@
-#ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
-source $ISSM_TIER/etc/environment_variables.csh
+#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
+source $ISSM_DIR/etc/environment_variables.csh
 
 #Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables 
@@ -10,8 +10,8 @@
 
 #CRON utilities
-setenv PATH {$PATH}:{$ISSM_TIER}/cron
+setenv PATH {$PATH}:{$ISSM_DIR}/cron
 
 #SCRIPTS utilities
-setenv PATH {$PATH}:{$ISSM_TIER}/scripts
+setenv PATH {$PATH}:{$ISSM_DIR}/scripts
 
 #MATLAB
@@ -110,9 +110,9 @@
 #AUTOCONF
 setenv AUTOCONF_DIR {$AUTOCONF_DIR}
-setenv PATH {$PATH}:{$AUTOCONF_DIR}/bin
+setenv PATH {$AUTOCONF_DIR}/bin:{$PATH}
 
 #AUTOMAKE
 setenv AUTOMAKE_DIR {$AUTOMAKE_DIR}
-setenv PATH {$PATH}:{$AUTOMAKE_DIR}/bin
+setenv PATH {$AUTOMAKE_DIR}/bin:{$PATH}
 
 #BORLAND
Index: issm/trunk/etc/environment.sh
===================================================================
--- issm/trunk/etc/environment.sh	(revision 12331)
+++ issm/trunk/etc/environment.sh	(revision 12332)
@@ -1,10 +1,10 @@
-#ISSM_TIER and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
+#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
 
 #Windows compilers: 
 if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
-	source $ISSM_TIER/externalpackages/windows/windows_environment.sh
+	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
 fi
 
-source $ISSM_TIER/etc/environment_variables.sh
+source $ISSM_DIR/etc/environment_variables.sh
 
 #Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them after exporting the variables
@@ -16,8 +16,8 @@
 
 #CRON utilities
-PATH="$PATH:$ISSM_TIER/cron"
+PATH="$PATH:$ISSM_DIR/cron"
 
 #scripts
-PATH="$PATH:$ISSM_TIER/scripts"
+PATH="$PATH:$ISSM_DIR/scripts"
 
 ##MATLAB
@@ -137,5 +137,5 @@
 #export INTEL_DIR
 #PATH="$PATH:$INTEL_DIR"
-#source $ISSM_TIER/externalpackages/intel/intel.sh
+#source $ISSM_DIR/externalpackages/intel/intel.sh
 
 #SDK
@@ -215,5 +215,5 @@
 #APPSCAN
 export PATH="$PATH:$APPSCAN_DIR/install/bin"
-export PATH="$PATH:$APPSCAN_DIR/bin"]
+export PATH="$PATH:$APPSCAN_DIR/bin"
 
 #CPPCHECK
@@ -242,6 +242,6 @@
 export PATH="$PATH:$ANDROID_NDK_DIR/"
 
-#ANDROID_DEV_DIR
-export ANDROID_DEV_DIR
+#ANDROID_DIR
+export ANDROID_DIR
 
 #ANDROID_SDK
@@ -253,4 +253,6 @@
 #GSL
 export PATH="$PATH:$GSL_DIR/bin"
+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GSL_DIR/lib"
+export LD_RUN_PATH="$LD_RUN_PATH:$GSL_DIR/lib"
 
 #GMAKE
@@ -259,7 +261,11 @@
 #PYTHON
 export PATH="$PYTHON_DIR/bin:$PATH"
-export PYTHONPATH="$PYTHONPATH:$ISSM_TIER/src/mex"
-export LD_LIBRARY_PATH=$ISSM_TIER/src/mex:$LD_LIBRARY_PATH
+export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python"
+export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$LD_LIBRARY_PATH
+export PYTHONSTARTUP
 
 #MODELE
 export PATH="$MODELE_DIR/src/exec:$PATH"
+
+#GIT
+export PATH="$PATH:$GIT_DIR/install/bin"
Index: issm/trunk/etc/environment_variables.csh
===================================================================
--- issm/trunk/etc/environment_variables.csh	(revision 12331)
+++ issm/trunk/etc/environment_variables.csh	(revision 12332)
@@ -1,77 +1,77 @@
 #
 #
-#This routine can only be run if the ISSM_TIER variable has been correctly set!
+#This routine can only be run if the ISSM_DIR variable has been correctly set!
 #
 #
 
 #MATLAB
-set MATLAB_DIR={$ISSM_TIER}/externalpackages/matlab/install
+set MATLAB_DIR={$ISSM_DIR}/externalpackages/matlab/install
 
 #MPI
-set MPI_DIR={$ISSM_TIER}/externalpackages/mpich2/install
+set MPI_DIR={$ISSM_DIR}/externalpackages/mpich2/install
 
 #PETSC
-set PETSC_DIR={$ISSM_TIER}/externalpackages/petsc/install
+set PETSC_DIR={$ISSM_DIR}/externalpackages/petsc/install
 
 #SLEPC
-set SLEPC_DIR={$ISSM_TIER}/externalpackages/slepc/install
+set SLEPC_DIR={$ISSM_DIR}/externalpackages/slepc/install
 
 #Dakota
-set DAKOTA_DIR={$ISSM_TIER}/externalpackages/dakota/install
+set DAKOTA_DIR={$ISSM_DIR}/externalpackages/dakota/install
 
 #Qhull
-set QHULL_DIR={$ISSM_TIER}/externalpackages/qhull/install
+set QHULL_DIR={$ISSM_DIR}/externalpackages/qhull/install
 
 #Doxygen
-set DOXYGEN_DIR={$ISSM_TIER}/externalpackages/doxygen/install
+set DOXYGEN_DIR={$ISSM_DIR}/externalpackages/doxygen/install
 
 #MTOC
-set MTOC_DIR={$ISSM_TIER}/externalpackages/mtoc/install
+set MTOC_DIR={$ISSM_DIR}/externalpackages/mtoc/install
 
 #Triangle
-set TRIANGLE_DIR={$ISSM_TIER}/externalpackages/triangle/install
+set TRIANGLE_DIR={$ISSM_DIR}/externalpackages/triangle/install
 
 #METIS
-set METIS_DIR={$ISSM_TIER}/externalpackages/metis/install
+set METIS_DIR={$ISSM_DIR}/externalpackages/metis/install
 
 #BLAS
-set BLAS_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/fblaslapack
+set BLAS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack
 
 #LAPACK
-set LAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH
+set LAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH
 
 #SCALAPACK
-set SCALAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH
+set SCALAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH
 
 #PLAPACK
-set PLAPACK_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32
+set PLAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32
 
 #BLACS
-set BLACS_DIR={$ISSM_TIER}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH
+set BLACS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH
 
 #sowing
-set SOWING_DIR={$ISSM_TIER}/externalpackages/sowing/install
+set SOWING_DIR={$ISSM_DIR}/externalpackages/sowing/install
 
 #YAMS
-set YAMS_DIR={$ISSM_TIER}/externalpackages/yams/install
+set YAMS_DIR={$ISSM_DIR}/externalpackages/yams/install
 
 #TEX2IM
-set TEX2IM_DIR={$ISSM_TIER}/externalpackages/tex2im/install
+set TEX2IM_DIR={$ISSM_DIR}/externalpackages/tex2im/install
 
 #Chaco
-set CHACO_DIR={$ISSM_TIER}/externalpackages/chaco/install
+set CHACO_DIR={$ISSM_DIR}/externalpackages/chaco/install
 
 #MeshPart
-set MESHPART_DIR={$ISSM_TIER}/externalpackages/meshpart/install
+set MESHPART_DIR={$ISSM_DIR}/externalpackages/meshpart/install
 
 #SCOTCH
-set SCOTCH_DIR={$ISSM_TIER}/externalpackages/scotch/install
+set SCOTCH_DIR={$ISSM_DIR}/externalpackages/scotch/install
 
 #Development packages
 #automake
-set AUTOMAKE_DIR={$ISSM_TIER}/externalpackages/automake/install
+set AUTOMAKE_DIR={$ISSM_DIR}/externalpackages/automake/install
 
 #autoconf
-set AUTOCONF_DIR={$ISSM_TIER}/externalpackages/autoconf/install
+set AUTOCONF_DIR={$ISSM_DIR}/externalpackages/autoconf/install
 
 #borland
@@ -79,6 +79,6 @@
 
 #ssh
-set SSH_DIR={$ISSM_TIER}/externalpackages/ssh
+set SSH_DIR={$ISSM_DIR}/externalpackages/ssh
 
 #valgrind
-set VALGRIND_DIR={$ISSM_TIER}/externalpackages/valgrind/install/bin
+set VALGRIND_DIR={$ISSM_DIR}/externalpackages/valgrind/install/bin
Index: issm/trunk/etc/environment_variables.sh
===================================================================
--- issm/trunk/etc/environment_variables.sh	(revision 12331)
+++ issm/trunk/etc/environment_variables.sh	(revision 12332)
@@ -1,83 +1,83 @@
 #
 #
-#This routine can only be run if the ISSM_TIER variable has been correctly set!
+#This routine can only be run if the ISSM_DIR variable has been correctly set!
 #
 #
 
 #MATLAB
-MATLAB_DIR="$ISSM_TIER/externalpackages/matlab/install"
+MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
 
 #MPI
-MPI_DIR="$ISSM_TIER/externalpackages/mpich2/install"
+MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
 
 #PETSC
-PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install"
+PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
 
 #SLEPC
-SLEPC_DIR="$ISSM_TIER/externalpackages/slepc/install"
+SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
 
 #Dakota
-DAKOTA_DIR="$ISSM_TIER/externalpackages/dakota/install"
+DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
 
 #Qhull
-QHULL_DIR="$ISSM_TIER/externalpackages/qhull/install"
+QHULL_DIR="$ISSM_DIR/externalpackages/qhull/install"
 
 #Doxygen
-DOXYGEN_DIR="$ISSM_TIER/externalpackages/doxygen/install"
+DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
 
 #MTOC
-MTOC_DIR="$ISSM_TIER/externalpackages/mtoc/install"
+MTOC_DIR="$ISSM_DIR/externalpackages/mtoc/install"
 
 #Triangle
-TRIANGLE_DIR="$ISSM_TIER/externalpackages/triangle/install"
+TRIANGLE_DIR="$ISSM_DIR/externalpackages/triangle/install"
 
 #METIS
-METIS_DIR="$ISSM_TIER/externalpackages/metis/install"
+METIS_DIR="$ISSM_DIR/externalpackages/metis/install"
 
 #BLAS
-BLAS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack"
+BLAS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack"
 
 #LAPACK
-LAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH"
+LAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH"
 
 #SCALAPACK
-SCALAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH"
+SCALAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH"
 
 #PLAPACK
-PLAPACK_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32"
+PLAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32"
 
 #BLACS
-BLACS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH"
+BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH"
 
 #sowing
-SOWING_DIR="$ISSM_TIER/externalpackages/sowing/install"
+SOWING_DIR="$ISSM_DIR/externalpackages/sowing/install"
 
 #BLACS
-BLACS_DIR="$ISSM_TIER/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH"
+BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH"
 
 #YAMS
-YAMS_DIR="$ISSM_TIER/externalpackages/yams/install"
+YAMS_DIR="$ISSM_DIR/externalpackages/yams/install"
 
 #BAMG
-BAMG_DIR="$ISSM_TIER/externalpackages/bamg/install"
+BAMG_DIR="$ISSM_DIR/externalpackages/bamg/install"
 
 #Chaco
-CHACO_DIR="$ISSM_TIER/externalpackages/chaco/install"
+CHACO_DIR="$ISSM_DIR/externalpackages/chaco/install"
 
 #MeshPart
-MESHPART_DIR="$ISSM_TIER/externalpackages/meshpart/install"
+MESHPART_DIR="$ISSM_DIR/externalpackages/meshpart/install"
 
 #SCOTCH
-SCOTCH_DIR="$ISSM_TIER/externalpackages/scotch/install"
+SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install"
 
 #Development packages
 #automake
-AUTOMAKE_DIR="$ISSM_TIER/externalpackages/automake/install"
+AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install"
 
 #libtool
-LIBTOOL_DIR="$ISSM_TIER/externalpackages/libtool/install"
+LIBTOOL_DIR="$ISSM_DIR/externalpackages/libtool/install"
 
 #autoconf
-AUTOCONF_DIR="$ISSM_TIER/externalpackages/autoconf/install"
+AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install"
 
 #borland
@@ -88,5 +88,5 @@
 
 #TEX2IM			 
-TEX2IM_DIR="$ISSM_TIER/externalpackages/tex2im/install" 
+TEX2IM_DIR="$ISSM_DIR/externalpackages/tex2im/install" 
 
 #sdk
@@ -94,40 +94,40 @@
 
 #ssh 
-SSH_DIR="$ISSM_TIER/externalpackages/ssh"
+SSH_DIR="$ISSM_DIR/externalpackages/ssh"
 
 #valgrind
-VALGRIND_DIR="$ISSM_TIER/externalpackages/valgrind/install/bin"
+VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin"
 
 #graphviz
-GRAPHVIZ_DIR="$ISSM_TIER/externalpackages/graphviz/install/bin"
+GRAPHVIZ_DIR="$ISSM_DIR/externalpackages/graphviz/install/bin"
 
 #cppcheck
-CPPCHECK_DIR="$ISSM_TIER/externalpackages/cppcheck/install"
+CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
 
 #gdal
-GDAL_DIR="$ISSM_TIER/externalpackages/gdal/install"
+GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
 
 #mercurial
-MERCURIAL_DIR="$ISSM_TIER/externalpackages/mercurial/install"
+MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
 
 #boost
-BOOST_DIR="$ISSM_TIER/externalpackages/boost/install"
-BOOSTROOT="$ISSM_TIER/externalpackages/boost/install"
+BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
+BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
 
 #OpenAnalysis
-OPENANALYSISROOT="$ISSM_TIER/externalpackages/openanalysis/install"
+OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
 
 #xerces
-XERCESROOT="$ISSM_TIER/externalpackages/xerces/install"
-XERCESCROOT="$ISSM_TIER/externalpackages/xerces/src"
+XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
+XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
 
 #xaifBooster
-XAIFBOOSTERROOT="$ISSM_TIER/externalpackages/xaifbooster/"
-XAIF_DIR="$ISSM_TIER/externalpackages/xaifbooster/xaifBooster"
-XAIFBOOSTER_HOME="$ISSM_TIER/externalpackages/xaifbooster/xaifBooster"
+XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/"
+XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
+XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
 PLATFORM=x86-Linux
 
 #angel
-ANGELROOT="$ISSM_TIER/externalpackages/angel/angel"
+ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
 
 #java
@@ -135,63 +135,68 @@
 
 #bbftp
-BBFTP_DIR="$ISSM_TIER/externalpackages/bbftp/install"
+BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
 
 #adic2
-ADIC_DIR="$ISSM_TIER/externalpackages/adic/install"
+ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
 
 #colpack
-COLPACK_DIR="$ISSM_TIER/externalpackages/colpack/install"
+COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
 
 #eclipse
-ECLIPSE_DIR="$ISSM_TIER/externalpackages/eclipse/install"
+ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
 
 #flaim
-FLAIM_DIR="$ISSM_TIER/externalpackages/flaim/install"
+FLAIM_DIR="$ISSM_DIR/externalpackages/flaim/install"
 
 #appscan
-APPSCAN_DIR="$ISSM_TIER/externalpackages/appscan"
+APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan"
 
 #cppcheck
-CPPCHECK_DIR="$ISSM_TIER/externalpackages/cppcheck/install"
+CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
 
 #rats
-RATS_DIR="$ISSM_TIER/externalpackages/rats/install"
+RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
 
 #dyson
-DYSON_DIR="$ISSM_TIER/externalpackages/dyson/"
+DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
 
 #cmake
-CMAKE_DIR="$ISSM_TIER/externalpackages/cmake/install"
+CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
 
 #shapelib
-SHAPELIB_DIR="$ISSM_TIER/externalpackages/shapelib/install"
+SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
 
 #cccl
-CCCL_DIR="$ISSM_TIER/externalpackages/cccl/install"
+CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
 
 #packagemaker
-PACKAGEMAKER_DIR="$ISSM_TIER/externalpackages/packagemaker/install"
+PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
+
+#android-dev-dir
+ANDROID_DIR="$ISSM_DIR/externalpackages/android"
 
 #android-ndk
-ANDROID_NDK_DIR="$ISSM_TIER/externalpackages/android-ndk/install"
-
-#android-dev-dir
-ANDROID_DEV_DIR="$ISSM_TIER/externalpackages/android-dev-dir"
+ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
 
 #android-sdk
-ANDROID_SDK_DIR="$ISSM_TIER/externalpackages/android-sdk/install-sdk"
+ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk"
 
 #android-ant
-ANDROID_ANT_DIR="$ISSM_TIER/externalpackages/android-sdk/install-ant"
+ANDROID_ANT_DIR="$ANDROID_DIR/android-sdk/install-ant"
 
 #gsl
-GSL_DIR="$ISSM_TIER/externalpackages/gsl/install"
+GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
 
 #gnu make
-GMAKE_DIR="$ISSM_TIER/externalpackages/gmake/install"
+GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
 
 #PYTHON
-PYTHON_DIR="$ISSM_TIER/externalpackages/python/install"
+PYTHON_DIR="$ISSM_DIR/externalpackages/python/install"
+PYTHONSTARTUP="$ISSM_DIR/startup.py"
 
 #MODELE
-MODELE_DIR="$ISSM_TIER/externalpackages/modelE"
+MODELE_DIR="$ISSM_DIR/externalpackages/modelE"
+
+
+#GIT
+GIT_DIR="$ISSM_DIR/externalpackages/git"
Index: issm/trunk/externalpackages/adic/install.sh
===================================================================
--- issm/trunk/externalpackages/adic/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/adic/install.sh	(revision 12332)
@@ -19,11 +19,11 @@
 cd build
 ../source/configure \
-	--with-rose=$ISSM_TIER/externalpackages/rose/install \
-	--with-openanalysis=$ISSM_TIER/externalpackages/openanalysis/openanalysis/x86_64-Linux \
-	--with-boost=$ISSM_TIER/externalpackages/boost/install \
-	--with-xerces=$ISSM_TIER/externalpackages/xerces/src \
-	--with-xaifbooster=$ISSM_TIER/externalpackages/xaifbooster/xaifBooster \
-	--with-colpack=$ISSM_TIER/externalpackages/colpack/install\
-	--prefix=$ISSM_TIER/externalpackages/adic/install 
+	--with-rose=$ISSM_DIR/externalpackages/rose/install \
+	--with-openanalysis=$ISSM_DIR/externalpackages/openanalysis/openanalysis/x86_64-Linux \
+	--with-boost=$ISSM_DIR/externalpackages/boost/install \
+	--with-xerces=$ISSM_DIR/externalpackages/xerces/src \
+	--with-xaifbooster=$ISSM_DIR/externalpackages/xaifbooster/xaifBooster \
+	--with-colpack=$ISSM_DIR/externalpackages/colpack/install\
+	--prefix=$ISSM_DIR/externalpackages/adic/install 
 if [ -z $1 ]; then
 	make
Index: issm/trunk/externalpackages/adolc/install.sh
===================================================================
--- issm/trunk/externalpackages/adolc/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/adolc/install.sh	(revision 12332)
@@ -5,4 +5,7 @@
 #Some cleanup
 rm -rf install ADOL-C-2.2.0 src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz'
 
 #Create install directories
@@ -20,5 +23,5 @@
 
 ./configure \
-	--prefix=$ISSM_TIER/externalpackages/adolc/install \
+	--prefix=$ISSM_DIR/externalpackages/adolc/install \
 	--enable-sparse \
 	--enable-docexa \
Index: issm/trunk/externalpackages/android/android-ndk/install.sh
===================================================================
--- issm/trunk/externalpackages/android/android-ndk/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/android/android-ndk/install.sh	(revision 12332)
@@ -0,0 +1,24 @@
+#This installs the Android NDK (Native Development Kit)
+#which is needed for the compilation of C/C++ code into the 
+#native architecture of the Android device.
+
+#The android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 file was downloaded 
+#from the android developer website: 
+
+#Cleanup the install
+rm -rf install
+rm -rf $ANDROID_DIR/arm-linux-android-4.0
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-ndk-r7b-darwin-x86.tar.bz2' 'dummy.tar.bz2'
+
+# Install Android SDK and NDK.
+bunzip2 dummy.tar.bz2
+tar -xvf dummy.tar
+rm -rf dummy.tar dummy.tar.bz2
+
+#Move to install
+mv android-ndk-r7b install
+
+#Create Standalone Development Directory
+$ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-5 --install-dir=$ANDROID_DIR/arm-linux-android-4.0
Index: issm/trunk/externalpackages/android/android-sdk/install.sh
===================================================================
--- issm/trunk/externalpackages/android/android-sdk/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/android/android-sdk/install.sh	(revision 12332)
@@ -0,0 +1,87 @@
+#This installs the Android SDK (Software Development Kit)
+#which is needed for the compilation of the Java project. 
+
+step=3;
+
+#Different steps here. 
+#1: install sdk, ant and sdk tools
+#2: install an emulator.
+#3: test the emulator
+#4: cleanup
+
+present_dir=`pwd`;
+default_droid="Android-4.0"
+sd_card="issm-sdcard"
+
+if [[ $step == "1" ]]; then
+
+	#Cleanup the install
+	rm -rf install-sdk install-ant
+
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/android-sdk-r16-macosx.zip' 'android-sdk-r16-macosx.zip'
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/apache-ant-1.8.2-bin.zip' 'apache-ant-1.8.2-bin.zip'
+
+	# Install Android SDK and NDK.
+	unzip -o android-sdk-r16-macosx.zip
+	unzip -o apache-ant-1.8.2-bin.zip
+
+	#Move to install
+	mv android-sdk-macosx install-sdk
+	mv apache-ant-1.8.2 install-ant
+
+	#Post_install configuration: 
+	#We need specific settings for specific platforms, for the SDK to 
+	#function properly
+
+	#For now, we need to install:  
+	#android sdk platform tools  
+	#and a specific android api: API 15
+	#Note: API 15 corresponds to Android 4.0.3
+
+	cd install-sdk/tools/ && source ./android update sdk -t platform-tools,android-15,android-14,system-image --no-ui
+
+fi
+
+if [[ $step == "2" ]]; then
+
+	#Once this is done, we need to install an emulator. Location will default to ~/.android/avd, 
+	#which we will move to $ISSM_DIR/externalpackages/android-emulators.  
+	#For now, it's called: Android-4.0.3
+
+	#Here we delete the Android-4.0.3 device if it already exists.
+	cd $present_dir/install-sdk/tools
+
+    if [ -e $ANDROID_DIR/android-emulators/$default_droid ] 
+    then
+        echo "Deleting previously created device: $default_droid"
+	    ./android delete avd -n $default_droid
+    fi
+
+	#Android will prompt the user to specify hardware emulation options. For now, default
+	#default settings will suffice. Press 'enter' to take default settings or enter 'no'.
+
+	./android create avd -f -n $default_droid -t 1 -p $ANDROID_DIR/android-emulators/$default_droid --abi armeabi-v7a
+    echo "Creating an SD Card"
+    ./mksdcard -l $sd_card 2G $ANDROID_DIR/android-emulators/$sd_card.img
+fi
+
+if [[ $step == "3" ]]; then
+    #Here we will start up our default emulator to test that it is working properly.
+    #Once the device has booted we will use the Android Debug Bridge tool to gain
+    #a terminal in our device.
+
+	cd $present_dir/install-sdk/tools
+	./emulator -avd $default_droid -sdcard $ANDROID_DIR/android-emulators/$sd_card.img &
+
+    cd ../platform-tools
+    ./adb wait-for-device shell mount -o rw,remount -t yaffs2 /dev/block/mtdblock1 /system
+    #./adb wait-for-device shell
+    ./adb push $ISSM_TIER/src/c/issm.exe /data/issm.exe
+    ./adb shell chmod 777 /data/issm.exe
+    ./adb shell /data/issm.exe
+fi
+
+if [[ $step == "4" ]]; then
+	rm -rf install-sdk install-ant
+fi
Index: issm/trunk/externalpackages/autoconf/install.sh
===================================================================
--- issm/trunk/externalpackages/autoconf/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/autoconf/install.sh	(revision 12332)
@@ -4,9 +4,12 @@
 rm -rf install autoconf-2.68 src
 
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.68.tar.gz' 'autoconf-2.68.tar.gz'
+
 #Create install directories
 mkdir install
 
 #Untar 
-tar -zxvf  autoconf-2.68.tar.gz
+tar -zxvf autoconf-2.68.tar.gz
 
 #Move autoconf into src directory
@@ -15,5 +18,5 @@
 #Compile autoconf
 cd src 
-./configure --prefix="$ISSM_TIER/externalpackages/autoconf/install" 
+./configure --prefix="$ISSM_DIR/externalpackages/autoconf/install" 
 make  
 make install
Index: issm/trunk/externalpackages/automake/install.sh
===================================================================
--- issm/trunk/externalpackages/automake/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/automake/install.sh	(revision 12332)
@@ -3,4 +3,7 @@
 #Some cleanup
 rm -rf install automake-1.11.3 src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.11.3.tar.gz' 'automake-1.11.3.tar.gz'
 
 #Create install directories
@@ -13,5 +16,5 @@
 #Compile automake
 cd src 
-./configure --prefix="$ISSM_TIER/externalpackages/automake/install" 
+./configure --prefix="$ISSM_DIR/externalpackages/automake/install" 
 make  
 make install
Index: issm/trunk/externalpackages/bbftp/install.sh
===================================================================
--- issm/trunk/externalpackages/bbftp/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/bbftp/install.sh	(revision 12332)
@@ -3,4 +3,7 @@
 #Some cleanup
 rm -rf src install bbftp-client-3.2.0
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/bbftp-client-3.2.0.tar.gz' 'bbftp-client-3.2.0.tar.gz'
 
 #Create install directories
@@ -19,5 +22,5 @@
 #Configure and compile
 cd bbftpc
-./configure --prefix=$ISSM_TIER/externalpackages/bbftp/install
+./configure --prefix=$ISSM_DIR/externalpackages/bbftp/install
 make
 make install
Index: issm/trunk/externalpackages/blas/configs/linux64/make.inc
===================================================================
--- issm/trunk/externalpackages/blas/configs/linux64/make.inc	(revision 12332)
+++ issm/trunk/externalpackages/blas/configs/linux64/make.inc	(revision 12332)
@@ -0,0 +1,34 @@
+####################################################################
+#  BLAS make include file.                                         #
+#  March 2007                                                      #
+####################################################################
+#
+SHELL = /bin/sh
+#
+#  The machine (platform) identifier to append to the library names
+#
+PLAT = _LINUX
+#  
+#  Modify the FORTRAN and OPTS definitions to refer to the
+#  compiler and desired compiler options for your machine.  NOOPT
+#  refers to the compiler options desired when NO OPTIMIZATION is
+#  selected.  Define LOADER and LOADOPTS to refer to the loader and 
+#  desired load options for your machine.
+#
+FORTRAN  = gfortran
+OPTS     = -fPIC -O3
+DRVOPTS  = $(OPTS)
+NOOPT    =
+LOADER   = gfortran
+LOADOPTS =
+#
+#  The archiver and the flag(s) to use when building archive (library)
+#  If you system has no ranlib, set RANLIB = echo.
+#
+ARCH     = ar
+ARCHFLAGS= cr
+RANLIB   = ranlib
+#
+#  The location and name of the Reference BLAS library.
+#
+BLASLIB      = blas$(PLAT).a
Index: issm/trunk/externalpackages/blas/install-linux64.sh
===================================================================
--- issm/trunk/externalpackages/blas/install-linux64.sh	(revision 12332)
+++ issm/trunk/externalpackages/blas/install-linux64.sh	(revision 12332)
@@ -0,0 +1,28 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src install BLAS blas.tgz
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/blas.tgz' 'blas.tgz'
+
+#Untar 
+tar -zxvf  blas.tgz
+
+#Move blas into install directory
+mv BLAS/* src
+rm -rf BLAS
+
+#install
+cd src 
+cp ../configs/linux64/make.inc ./
+make 
+
+#Compile 
+cd ../install
+mkdir lib
+cd lib
+cp ../../src/*.a .
+ln -s blas_LINUX.a blas.a
+ln -s blas_LINUX.a libblas.a
Index: issm/trunk/externalpackages/boost/install.sh
===================================================================
--- issm/trunk/externalpackages/boost/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/boost/install.sh	(revision 12332)
@@ -7,9 +7,10 @@
 #to get the boost library to include python support without doing that. 
 
-
-
 #Some cleanup
 rm -rf install boost_1_49_0 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_49_0.tar.gz' 'boost_1_49_0.tar.gz'
 
 #Untar 
@@ -22,7 +23,7 @@
 cd src 
 ./bootstrap.sh \
-	--prefix="$ISSM_TIER/externalpackages/boost/install" \
+	--prefix="$ISSM_DIR/externalpackages/boost/install" \
 	--with-python=python3.2 \
-	--with-python-root="$ISSM_TIER/externalpackages/python/install" 
+	--with-python-root="$ISSM_DIR/externalpackages/python/install" 
 
 #Compile boost
Index: issm/trunk/externalpackages/bsdtar/install-win7.sh
===================================================================
--- issm/trunk/externalpackages/bsdtar/install-win7.sh	(revision 12331)
+++ issm/trunk/externalpackages/bsdtar/install-win7.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install src libarchive-3.0.3
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libarchive-3.0.3.tar.gz' 'libarchive-3.0.3.tar.gz'
 
 #Untar 
@@ -13,5 +16,5 @@
 
 cd src 
-./configure --prefix="$ISSM_TIER/externalpackages/bsdtar/install" 
+./configure --prefix="$ISSM_DIR/externalpackages/bsdtar/install" 
 make
 make install
Index: issm/trunk/externalpackages/cccl/install-win7.orig.sh
===================================================================
--- issm/trunk/externalpackages/cccl/install-win7.orig.sh	(revision 12331)
+++ issm/trunk/externalpackages/cccl/install-win7.orig.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install cccl-0.03
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cccl-0.03.tar.gz' 'cccl-0.03.tar.gz'
 
 #Untar 
@@ -15,5 +18,5 @@
 
 #Compile
-./configure --prefix="$ISSM_TIER/externalpackages/cccl/install"
+./configure --prefix="$ISSM_DIR/externalpackages/cccl/install"
 
 make
Index: issm/trunk/externalpackages/cccl/issm/cccl
===================================================================
--- issm/trunk/externalpackages/cccl/issm/cccl	(revision 12331)
+++ issm/trunk/externalpackages/cccl/issm/cccl	(revision 12332)
@@ -74,4 +74,17 @@
     esac
 	;;
+	-fPIC)
+	#do nothing
+	;;
+	-g)
+	#do nothing
+	;;
+	-pthread)
+	#do nothing
+	;;
+	-fno-omit-frame-pointer)
+	#do nothing
+	;;
+
 	*)
 		#do nothing
@@ -83,4 +96,7 @@
     shift
 done
+			
+#Some default options:
+opts="$opts /nologo"
 
 #echo "$prog $opts"
Index: issm/trunk/externalpackages/chaco/install.sh
===================================================================
--- issm/trunk/externalpackages/chaco/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/chaco/install.sh	(revision 12332)
@@ -6,4 +6,7 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Chaco-2.2.tar.gz' 'Chaco-2.2.tar.gz'
 
 # Untar 
Index: issm/trunk/externalpackages/cmake/install.sh
===================================================================
--- issm/trunk/externalpackages/cmake/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/cmake/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install cmake-2.8.5
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cmake-2.8.5.tar.gz' 'cmake-2.8.5.tar.gz'
 
 #Untar 
@@ -14,5 +17,5 @@
 #Compile cmake
 cd install 
-./bootstrap --prefix=$ISSM_TIER/externalpackages/cmake/install
+./bootstrap --prefix=$ISSM_DIR/externalpackages/cmake/install
 if [ -z $1 ]; then
 	make
Index: issm/trunk/externalpackages/colpack/install.sh
===================================================================
--- issm/trunk/externalpackages/colpack/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/colpack/install.sh	(revision 12332)
@@ -3,4 +3,7 @@
 #Erase install
 rm -rf install  src ColPack
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ColPack-1.0.3.tar.gz' 'ColPack-1.0.3.tar.gz'
 
 #install directory
Index: issm/trunk/externalpackages/cppcheck/install.sh
===================================================================
--- issm/trunk/externalpackages/cppcheck/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/cppcheck/install.sh	(revision 12332)
@@ -5,4 +5,6 @@
 mkdir src
 
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/cppcheck-1.48.tar' 'cppcheck-1.48.tar'
 tar -xvf cppcheck-1.48.tar
 
@@ -17,4 +19,4 @@
 	make -j $1
 fi  
-make install PREFIX=$ISSM_TIER/externalpackages/cppcheck/install
+make install PREFIX=$ISSM_DIR/externalpackages/cppcheck/install
 cd ..
Index: issm/trunk/externalpackages/dace/install.sh
===================================================================
--- issm/trunk/externalpackages/dace/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/dace/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install dace
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dace.zip' 'dace.zip'
 
 #uncompress
Index: issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh
===================================================================
--- issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh	(revision 12331)
+++ issm/trunk/externalpackages/dakota/install-altix64-cosmos.sh	(revision 12332)
@@ -9,4 +9,7 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
 
 #Untar 
@@ -29,5 +32,5 @@
 cd src
 ./configure \ 
-	--prefix="$ISSM_TIER/externalpackages/dakota/install" \
+	--prefix="$ISSM_DIR/externalpackages/dakota/install" \
 	--without-graphics  \
 	--with-pic \
Index: issm/trunk/externalpackages/dakota/install-discover.sh
===================================================================
--- issm/trunk/externalpackages/dakota/install-discover.sh	(revision 12332)
+++ issm/trunk/externalpackages/dakota/install-discover.sh	(revision 12332)
@@ -0,0 +1,99 @@
+#!/bin/bash
+
+#Get number of cpus
+NUMCPUS=$1;
+
+#Some cleanup
+rm -rf Dakota
+rm -rf src
+rm -rf install
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
+
+#Untar 
+tar -zxvf  Dakota_4_3.src.tar.gz
+
+#Move Dakota to src directory
+mv Dakota/* src
+rm -rf Dakota
+
+#Apply patches
+patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch
+patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch
+patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch
+patch src/src/NonDSampling.C ./NonDSampling.C.patch
+patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch
+patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch    #  source not even used?
+#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch
+
+#Configure dakota
+cd src
+./configure \
+--prefix="$ISSM_DIR/externalpackages/dakota/install/" \
+--without-graphics  \
+--with-pic \
+--disable-mpi \
+--with-blas="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \
+--with-lapack="-L/usr/local/intel/mkl/10.1.2.024/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread"
+cd ..
+
+#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages 
+#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC 
+#flag to the compilation.
+cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' >  temp
+mv temp ./src/methods/NCSUOpt/Makefile
+
+cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp
+mv temp ./src/methods/acro/packages/pebbl/src/Makefile
+
+cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2  -fPIC/g' > temp
+mv temp ./src/methods/hopspack/src-nappspack/Makefile
+
+cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp
+mv temp  ./src/methods/hopspack/src-cddlib/Makefile
+
+cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp
+mv temp  ./src/methods/hopspack/src-shared/Makefile
+
+cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2  -fPIC/g' > temp
+mv temp  ./src/methods/hopspack/src-shared/Makefile
+
+cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp
+mv temp  ./src/methods/hopspack/src-conveyor/Makefile
+
+cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2  -fPIC/g' > temp
+mv temp ./src/methods/hopspack/src-appspack/Makefile
+
+cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp
+mv temp ./src/methods/acro/packages/colin/src/Makefile
+
+cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp
+mv temp ./src/methods/acro/packages/coliny/src/Makefile
+
+cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp
+mv temp  ./src/methods/acro/packages/tpl/3po/Makefile
+
+cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp
+mv temp  ./src/methods/acro/packages/tpl/3po/Makefile
+
+cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp
+mv temp  ./src/packages/ampl/Makefile
+
+#Compile and install dakota
+cd src
+if [ -z $NUMCPUS ];
+then
+	make
+	make install
+else
+	make -j $NUMCPUS
+	make -j $NUMCPUS install
+fi
+cd ..
+
+#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing!
+cd install/lib
+mv libamplsolver.a libamplsolver.a.bak
+ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a
Index: issm/trunk/externalpackages/dakota/install-linux64-astrid.sh
===================================================================
--- issm/trunk/externalpackages/dakota/install-linux64-astrid.sh	(revision 12331)
+++ issm/trunk/externalpackages/dakota/install-linux64-astrid.sh	(revision 12332)
@@ -9,4 +9,7 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
 
 #Untar 
@@ -29,5 +32,5 @@
 cd src
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/dakota/install" \
+	--prefix="$ISSM_DIR/externalpackages/dakota/install" \
 	--without-graphics  \
 	--with-pic \
Index: issm/trunk/externalpackages/dakota/install-linux64-murdo.sh
===================================================================
--- issm/trunk/externalpackages/dakota/install-linux64-murdo.sh	(revision 12331)
+++ issm/trunk/externalpackages/dakota/install-linux64-murdo.sh	(revision 12332)
@@ -9,4 +9,7 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
 
 #Untar 
@@ -29,5 +32,5 @@
 cd src
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/dakota/install" \
+	--prefix="$ISSM_DIR/externalpackages/dakota/install" \
 	--without-graphics  \
 	--with-pic \
Index: issm/trunk/externalpackages/dakota/install-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/dakota/install-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/dakota/install-macosx64.sh	(revision 12332)
@@ -9,4 +9,7 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
 
 #Untar 
@@ -29,10 +32,10 @@
 cd src
 ./configure \
-   --prefix="$ISSM_TIER/externalpackages/dakota/install" \
+   --prefix="$ISSM_DIR/externalpackages/dakota/install" \
    --without-graphics  \
    --with-pic \
    --disable-mpi \
-   --with-blas="-L$ISSM_TIER/externalpackages/petsc/install/lib -lfblas " \
-   --with-lapack="-L$ISSM_TIER/externalpackages/petsc/install/lib -lflapack -lPLAPACK "
+   --with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \
+   --with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack -lPLAPACK "
 cd ..
 
Index: issm/trunk/externalpackages/dakota/install-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/dakota/install-pleiades.sh	(revision 12331)
+++ issm/trunk/externalpackages/dakota/install-pleiades.sh	(revision 12332)
@@ -9,4 +9,7 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
 
 #Untar 
@@ -29,5 +32,5 @@
 cd src
 ./configure \ 
-	--prefix="$ISSM_TIER/externalpackages/dakota/install" \
+	--prefix="$ISSM_DIR/externalpackages/dakota/install" \
 	--without-graphics  \
 	--with-pic \
Index: issm/trunk/externalpackages/distribute/install.sh
===================================================================
--- issm/trunk/externalpackages/distribute/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/distribute/install.sh	(revision 12332)
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://python-distribute.org/distribute_setup.py' 'distribute_setup.py'
+python distribute_setup.py
Index: issm/trunk/externalpackages/doxygen/install.sh
===================================================================
--- issm/trunk/externalpackages/doxygen/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/doxygen/install.sh	(revision 12332)
@@ -8,5 +8,5 @@
 
 #Configure doxygen
-cd install && ./configure --prefix "$ISSM_TIER/externalpackages/doxygen/install"
+cd install && ./configure --prefix "$ISSM_DIR/externalpackages/doxygen/install"
 if [ -z $1 ]; then
 	make
Index: issm/trunk/externalpackages/findbugs/install.sh
===================================================================
--- issm/trunk/externalpackages/findbugs/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/findbugs/install.sh	(revision 12332)
@@ -5,4 +5,6 @@
 mkdir install
 
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/findbugs-1.3.9.tar.gz' 'findbugs-1.3.9.tar.gz'
 tar -zxvf findbugs-1.3.9.tar.gz 
 
Index: issm/trunk/externalpackages/freetype/install.sh
===================================================================
--- issm/trunk/externalpackages/freetype/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/freetype/install.sh	(revision 12332)
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src
+rm -rf install
+rm -rf freetype-2.4.9
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/freetype-2.4.9.tar.gz' 'freetype-2.4.9.tar.gz'
+
+#Untar 
+tar -zxvf  freetype-2.4.9.tar.gz
+
+#Move freetype into src directory
+mv freetype-2.4.9/* src
+rm -rf freetype-2.4.9
+
+#Configure freetype
+cd src
+sudo ./configure 
+
+#Compile and install freetype
+if [ -z $1 ]; then
+	sudo make
+else
+	sudo make -j $1
+fi
+sudo make install
Index: issm/trunk/externalpackages/gdal/install.sh
===================================================================
--- issm/trunk/externalpackages/gdal/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/gdal/install.sh	(revision 12332)
@@ -6,4 +6,7 @@
 rm -rf gdal-1.6.0
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz'
 
 #Untar 
@@ -17,5 +20,5 @@
 cd src
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/gdal/install" \
+	--prefix="$ISSM_DIR/externalpackages/gdal/install" \
 	--without-python \
 	--with-netcdf=no \
Index: issm/trunk/externalpackages/gdaltokmz/install.sh
===================================================================
--- issm/trunk/externalpackages/gdaltokmz/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/gdaltokmz/install.sh	(revision 12332)
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdaltokmz-1.0.tar.gz' 'gdaltokmz-1.0.tar.gz'
Index: issm/trunk/externalpackages/git/install.sh
===================================================================
--- issm/trunk/externalpackages/git/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/git/install.sh	(revision 12332)
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src install git-1.7.10.2
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/git-1.7.10.2.tar.gz' 'git-1.7.10.2.tar.gz'
+
+#Untar 
+tar -zxvf  git-1.7.10.2.tar.gz
+
+#Move git into install directory
+mv git-1.7.10.2/* src
+rm -rf git-1.7.10.2
+
+#install
+cd src 
+./configure  --prefix="$ISSM_DIR/externalpackages/git/install"
+	
+#Compile
+make install
Index: issm/trunk/externalpackages/gmake/install.sh
===================================================================
--- issm/trunk/externalpackages/gmake/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/gmake/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install src make-3.82
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/make-3.82.tar.gz' 'make-3.82.tar.gz'
 
 #Untar 
@@ -16,5 +19,5 @@
 
 #Configure and compile: 
-./configure --prefix=$ISSM_TIER/externalpackages/gmake/install
+./configure --prefix=$ISSM_DIR/externalpackages/gmake/install
 
 if [ -z $1 ]; then
Index: issm/trunk/externalpackages/graphviz/install.sh
===================================================================
--- issm/trunk/externalpackages/graphviz/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/graphviz/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/graphviz-2.24.0.tar.gz' 'graphviz-2.24.0.tar.gz'
 
 #Untar 
@@ -14,5 +17,5 @@
 #Configure dakota
 cd src
-./configure --prefix="$ISSM_TIER/externalpackages/graphviz/install"
+./configure --prefix="$ISSM_DIR/externalpackages/graphviz/install"
 cd ..
 
Index: issm/trunk/externalpackages/gsl/install-android-4.0.sh
===================================================================
--- issm/trunk/externalpackages/gsl/install-android-4.0.sh	(revision 12332)
+++ issm/trunk/externalpackages/gsl/install-android-4.0.sh	(revision 12332)
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src install gsl-1.15
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz'
+
+#Untar 
+tar -zxvf  gsl-1.15.tar.gz
+
+#Move gsl into src directory
+mv gsl-1.15/* src
+rm -rf gsl-1.15
+
+#Configure gsl
+cd src
+
+./configure \
+    CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc\
+    LD=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ld\
+    AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar\
+    RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib\
+    NM=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-nm\
+    OBJ_EXT=o\
+    LIB_EXT=a\
+    --host="arm-linux"\
+	--prefix="$ISSM_DIR/externalpackages/gsl/install" 
+
+#Compile gsl
+if [ -z $1 ]; then
+	make
+else
+	make -j $1
+fi
+
+make install
Index: issm/trunk/externalpackages/gsl/install-linux64-murdo.sh
===================================================================
--- issm/trunk/externalpackages/gsl/install-linux64-murdo.sh	(revision 12331)
+++ 	(revision )
@@ -1,26 +1,0 @@
-#!/bin/bash
-
-#Some cleanup
-rm -rf src install gsl-1.15
-mkdir src install
-
-#Untar 
-tar -zxvf  gsl-1.15.tar.gz
-
-#Move gsl into src directory
-mv gsl-1.15/* src
-rm -rf gsl-1.15
-
-#Configure gsl
-cd src
-
-./configure \
-	--prefix="$ISSM_TIER/externalpackages/gsl/install" 
-
-#Compile gsl
-if [ -z $1 ]; then
-	make
-else
-	make -j $1
-fi
-make install 
Index: issm/trunk/externalpackages/gsl/install-linux64.sh
===================================================================
--- issm/trunk/externalpackages/gsl/install-linux64.sh	(revision 12332)
+++ issm/trunk/externalpackages/gsl/install-linux64.sh	(revision 12332)
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src install gsl-1.15
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz'
+
+#Untar 
+tar -zxvf  gsl-1.15.tar.gz
+
+#Move gsl into src directory
+mv gsl-1.15/* src
+rm -rf gsl-1.15
+
+#Configure gsl
+cd src
+
+./configure \
+	--prefix="$ISSM_DIR/externalpackages/gsl/install" 
+
+#Compile gsl
+if [ -z $1 ]; then
+	make
+else
+	make -j $1
+fi
+make install 
Index: issm/trunk/externalpackages/gsl/install-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/gsl/install-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/gsl/install-macosx64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install gsl-1.15
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz'
 
 #Untar 
@@ -18,5 +21,5 @@
 
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/gsl/install" 
+	--prefix="$ISSM_DIR/externalpackages/gsl/install" 
 
 #Compile gsl
Index: issm/trunk/externalpackages/gsl/install-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/gsl/install-pleiades.sh	(revision 12332)
+++ issm/trunk/externalpackages/gsl/install-pleiades.sh	(revision 12332)
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src install gsl-1.15
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz'
+
+#Untar 
+tar -zxvf  gsl-1.15.tar.gz
+
+#Move gsl into src directory
+mv gsl-1.15/* src
+rm -rf gsl-1.15
+
+#Configure gsl
+cd src
+
+./configure \
+	--prefix="$ISSM_DIR/externalpackages/gsl/install" 
+
+#Compile gsl
+if [ -z $1 ]; then
+	make
+else
+	make -j $1
+fi
+make install 
Index: issm/trunk/externalpackages/gslib/install.sh
===================================================================
--- issm/trunk/externalpackages/gslib/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/gslib/install.sh	(revision 12332)
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf install
+mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gslib90_ls.tar.gz' 'gslib90_ls.tar.gz'
+
+#Untar 
+tar -zxvf  gslib90_ls.tar.gz
+
+#Move gslib into install directory
+mv gslib90/* install
+rm -rf gslib90
+
+#Change compiler to gfortran
+cd install
+cat Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak
+mv Makefile.bak Makefile
+cat gslib/Makefile | sed -e "s/FC=g95/FC=gfortran/g" > Makefile.bak
+mv Makefile.bak gslib/Makefile
+make 
Index: issm/trunk/externalpackages/ipython/install.sh
===================================================================
--- issm/trunk/externalpackages/ipython/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/ipython/install.sh	(revision 12332)
@@ -0,0 +1,22 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src
+rm -rf install
+rm -rf ipython-0.12
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ipython-0.12.tar.gz' 'ipython-0.12.tar.gz'
+
+#Untar 
+tar -zxvf  ipython-0.12.tar.gz
+
+#Move ipython into src directory
+mv ipython-0.12/* src
+rm -rf ipython-0.12
+
+#install  ipython
+cd src
+python setup.py build
+python setup.py install
Index: issm/trunk/externalpackages/kml/install.sh
===================================================================
--- issm/trunk/externalpackages/kml/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/kml/install.sh	(revision 12332)
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/kml_shapefile.zip' 'kml_shapefile.zip'
Index: issm/trunk/externalpackages/lapack/configs/linux64/make.inc
===================================================================
--- issm/trunk/externalpackages/lapack/configs/linux64/make.inc	(revision 12332)
+++ issm/trunk/externalpackages/lapack/configs/linux64/make.inc	(revision 12332)
@@ -0,0 +1,71 @@
+####################################################################
+#  LAPACK make include file.                                       #
+#  LAPACK, Version 3.4.0                                           #
+#  April 2012                                                   #
+####################################################################
+#
+SHELL = /bin/sh
+#  
+#  Modify the FORTRAN and OPTS definitions to refer to the
+#  compiler and desired compiler options for your machine.  NOOPT
+#  refers to the compiler options desired when NO OPTIMIZATION is
+#  selected.  Define LOADER and LOADOPTS to refer to the loader and 
+#  desired load options for your machine.
+#
+FORTRAN  = gfortran 
+OPTS     = -fPIC -O2
+DRVOPTS  = $(OPTS)
+NOOPT    = -O0
+LOADER   = gfortran
+LOADOPTS =
+#
+# Timer for the SECOND and DSECND routines
+#
+# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME
+#TIMER    = EXT_ETIME
+# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME_
+# TIMER    = EXT_ETIME_
+# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL FUNCTION ETIME
+TIMER    = INT_ETIME
+# If your Fortran compiler does not provide etime (like Nag Fortran Compiler, etc...)
+# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME
+# TIMER    = INT_CPU_TIME
+# If neither of this works...you can use the NONE value... In that case, SECOND and DSECND will always return 0
+# TIMER     = NONE
+#
+#  Configuration LAPACKE: Native C interface to LAPACK
+#  To generate LAPACKE library: type 'make lapackelib'
+#  Configuration file: turned off (default)
+#  Complex types: C99 (default)
+#  Name pattern: mixed case (default)
+#  (64-bit) Data model: LP64 (default)
+#
+# CC is the C compiler, normally invoked with options CFLAGS.
+#
+CC = gcc
+CFLAGS = -O3
+#
+#  The archiver and the flag(s) to use when building archive (library)
+#  If you system has no ranlib, set RANLIB = echo.
+#
+ARCH     = ar
+ARCHFLAGS= cr
+RANLIB   = ranlib
+#
+#  Location of the extended-precision BLAS (XBLAS) Fortran library
+#  used for building and testing extended-precision routines.  The
+#  relevant routines will be compiled and XBLAS will be linked only if
+#  USEXBLAS is defined.
+#
+# USEXBLAS    = Yes
+XBLASLIB     =
+# XBLASLIB    = -lxblas
+#
+#  The location of the libraries to which you will link.  (The 
+#  machine-specific, optimized BLAS library should be used whenever
+#  possible.)
+#
+BLASLIB      = ../../librefblas.a
+LAPACKLIB    = liblapack.a
+TMGLIB       = libtmglib.a
+LAPACKELIB   = liblapacke.a
Index: issm/trunk/externalpackages/lapack/install-linux64.sh
===================================================================
--- issm/trunk/externalpackages/lapack/install-linux64.sh	(revision 12332)
+++ issm/trunk/externalpackages/lapack/install-linux64.sh	(revision 12332)
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src install lapack-3.4.1 lapack-3.4.1.tgz
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/lapack-3.4.1.tgz' 'lapack-3.4.1.tgz'
+
+#Untar 
+tar -zxvf  lapack-3.4.1.tgz
+
+#Move lapack into install directory
+mv lapack-3.4.1/* src
+rm -rf lapack-3.4.1
+
+#install
+cd src 
+cp ../configs/linux64/make.inc ./
+
+#Compile and install lapack
+if [ -z $1 ]; then
+	make lib
+else
+	make -j $1 lib
+fi
+
+#Compile 
+cd ../install
+mkdir lib
+cd lib
+cp ../../src/liblapack.a .
Index: issm/trunk/externalpackages/latex2rtf/install.sh
===================================================================
--- issm/trunk/externalpackages/latex2rtf/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/latex2rtf/install.sh	(revision 12332)
@@ -3,4 +3,7 @@
 #Some cleanup
 rm -rf latex2rtf-2.0.0 cfg install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/latex2rtf-2.0.0.tar.gz' 'latex2rtf-2.0.0.tar.gz'
 
 #untar 
@@ -10,4 +13,4 @@
 #Compile
 cd install
-export PREFIX="$ISSM_TIER/externalpackages/latex2rtf/install/"
+export PREFIX="$ISSM_DIR/externalpackages/latex2rtf/install/"
 make
Index: issm/trunk/externalpackages/libermate/install.sh
===================================================================
--- issm/trunk/externalpackages/libermate/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/libermate/install.sh	(revision 12332)
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf install
+rm -rf libermate-0.4
+mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libermate-0.4.tgz' 'libermate-0.4.tgz'
+
+#Untar 
+tar -zxvf  libermate-0.4.tgz
+
+#Move libermate into install directory
+mv libermate-0.4/* install
+rm -rf libermate-0.4
Index: issm/trunk/externalpackages/libpng/install.sh
===================================================================
--- issm/trunk/externalpackages/libpng/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/libpng/install.sh	(revision 12332)
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src
+rm -rf install
+rm -rf libpng-1.5.10
+mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libpng-1.5.10.tar.gz' 'libpng-1.5.10.tar.gz'
+
+#Untar 
+tar -zxvf  libpng-1.5.10.tar.gz
+
+#Move libpng into src directory
+mv libpng-1.5.10/* src
+rm -rf libpng-1.5.10
+
+#Configure libpng
+cd src
+sudo ./configure 
+
+#Compile and install libpng
+if [ -z $1 ]; then
+	sudo make
+else
+	sudo make -j $1
+fi
+sudo make install
Index: issm/trunk/externalpackages/libtool/install.sh
===================================================================
--- issm/trunk/externalpackages/libtool/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/libtool/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install libtool-2.2.6b src
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.2.6b.tar.gz' 'libtool-2.2.6b.tar.gz'
 
 #Untar 
@@ -13,5 +16,5 @@
 #Compile libtool
 cd src 
-./configure --prefix="$ISSM_TIER/externalpackages/libtool/install" 
+./configure --prefix="$ISSM_DIR/externalpackages/libtool/install" 
 make  
 make install
Index: issm/trunk/externalpackages/m2html/install.sh
===================================================================
--- issm/trunk/externalpackages/m2html/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/m2html/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install m2html
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/m2html.zip' 'm2html.zip'
 
 #uncompress
Index: issm/trunk/externalpackages/matplotlib/install-osx.sh
===================================================================
--- issm/trunk/externalpackages/matplotlib/install-osx.sh	(revision 12332)
+++ issm/trunk/externalpackages/matplotlib/install-osx.sh	(revision 12332)
@@ -0,0 +1,10 @@
+#/bin/bash
+pythonversion=2.7
+PYTHON=python${pythonversion}
+
+git clone https://github.com/matplotlib/matplotlib
+mv matplotlib src
+mkdir deps
+cd src
+make -f make.osx PREFIX=$ISSM_DIR/externalpackages/matplotlib/deps PYVERSION=$pythonversion fetch deps mpl_install_std
+${PYTHON} -c "import matplotlib; print 'Installed matplotlib', matplotlib.__version__, matplotlib.__file__"
Index: issm/trunk/externalpackages/matplotlib/install.sh
===================================================================
--- issm/trunk/externalpackages/matplotlib/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/matplotlib/install.sh	(revision 12332)
@@ -0,0 +1,7 @@
+#/bin/bash
+
+git clone https://github.com/matplotlib/matplotlib
+mv matplotlib src
+cd src
+python setup.py build
+python setup.py install
Index: issm/trunk/externalpackages/mercurial/install.sh
===================================================================
--- issm/trunk/externalpackages/mercurial/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/mercurial/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install mercurial-1.7.3
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mercurial-1.7.3.tar.gz' 'mercurial-1.7.3.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/configs/4.0/discover/Makefile.in.patch
===================================================================
--- issm/trunk/externalpackages/metis/configs/4.0/discover/Makefile.in.patch	(revision 12332)
+++ issm/trunk/externalpackages/metis/configs/4.0/discover/Makefile.in.patch	(revision 12332)
@@ -0,0 +1,10 @@
+3c3,5
+< CC = cc
+---
+> CC = icc
+> OBJ_EXT=o
+> LIB_EXT=a
+6c8
+< OPTFLAGS = -O2 
+---
+> OPTFLAGS = -DLINUX -fPIC
Index: issm/trunk/externalpackages/metis/install-4.0-altix64.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-altix64.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-altix64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-cosmos.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-cosmos.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-cosmos.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-discover.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-discover.sh	(revision 12332)
+++ issm/trunk/externalpackages/metis/install-4.0-discover.sh	(revision 12332)
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf install metis-4.0
+mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
+
+#Untar 
+tar -zxvf  metis-4.0.tar.gz
+
+#Move metis into install directory
+mv metis-4.0/* install
+rm -rf metis-4.0
+
+#Apply patches
+cd install 
+patch -p1 < ../metis-4.0.patch
+patch Makefile.in ../configs/4.0/discover/Makefile.in.patch
+
+#Compile
+make
Index: issm/trunk/externalpackages/metis/install-4.0-greenplanet.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-greenplanet.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-greenplanet.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-linux64.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-linux64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-macosx32.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-macosx32.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-macosx32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-macosx64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-pleiades.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-pleiades.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-win32.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-win32.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-win32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-4.0-win7.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-4.0-win7.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-4.0-win7.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install metis-4.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-4.0.tar.gz' 'metis-4.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/metis/install-5.0.1-linux64.sh
===================================================================
--- issm/trunk/externalpackages/metis/install-5.0.1-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/metis/install-5.0.1-linux64.sh	(revision 12332)
@@ -5,4 +5,7 @@
 rm -rf install metis-5.0.1
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/metis-5.0.1.tar.gz' 'metis-5.0.1.tar.gz'
 
 #Untar 
@@ -17,4 +20,4 @@
 
 #Compile metis
-make config prefix="$ISSM_TIER/externalpackages/metis/install"
+make config prefix="$ISSM_DIR/externalpackages/metis/install"
 make install
Index: issm/trunk/externalpackages/modelE/install.sh
===================================================================
--- issm/trunk/externalpackages/modelE/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/modelE/install.sh	(revision 12332)
@@ -6,4 +6,7 @@
 rm -rf src install  modelE_AR5_branch
 mkdir src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/modelE_AR5_branch.2012.03.13_10.12.21.tgz' 'modelE_AR5_branch.2012.03.13_10.12.21.tgz'
 
 #Untar 
Index: issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.0.2-altix64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.0.2p1
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz'
 
 #Untar 
@@ -18,5 +21,5 @@
 export FFLAGS="$FFLAGS -fPIC"
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/mpich2/install" \
 	--enable-sharedlibs=gcc \
 	--enable-f91=gfortran 
Index: issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.0.2-linux64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.0.2p1
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz'
 
 #Untar 
@@ -18,5 +21,5 @@
 export FFLAGS="$FFLAGS -fPIC"
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/mpich2/install" \
 	--enable-sharedlibs=gcc \
 	--enable-f91=gfortran 
Index: issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.0.2-macosx32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.0.2p1
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz'
 
 #Untar 
@@ -17,5 +20,5 @@
 export CFLAGS=" -m32"
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/mpich2/install" \
 	--enable-f91=gfortran \
 	--enable-sharedlibs=osx-gcc
Index: issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.0.2-win32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.0.2p1
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.0.2p1.tar.gz' 'mpich2-1.0.2p1.tar.gz'
 
 #Untar 
@@ -17,5 +20,5 @@
 export CFLAGS="$CFLAGS -fPIC"
 export FFLAGS="$FFLAGS -fPIC"
-./configure --prefix="$ISSM_TIER/externalpackages/mpich2/install" 
+./configure --prefix="$ISSM_DIR/externalpackages/mpich2/install" 
 
 #Apply Patch to examples
Index: issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.4-linux64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.4
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz'
 
 #Untar 
@@ -17,5 +20,5 @@
 export FFLAGS="$FFLAGS -fPIC"
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/mpich2/install" \
 	--enable-shared \
 	--enable-sharedlibs=gcc \
Index: issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.4-macosx32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.4
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz'
 
 #Untar 
@@ -19,5 +22,5 @@
 export CPPFLAGS=" -arch i386"
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/mpich2/install" \
 	--enable-f91=gfortran \
 	--enable-sharedlibs=osx-gcc \
Index: issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/mpich2/install-1.4-macosx64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install mpich2-1.4
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich2-1.4.tar.gz' 'mpich2-1.4.tar.gz'
 
 #Untar 
@@ -19,5 +22,5 @@
 export CXXFLAGS=" -arch x86_64"
 ./configure \
-	--prefix="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/mpich2/install" \
 	--enable-f91 \
 	--enable-sharedlibs=osx-gcc \
Index: issm/trunk/externalpackages/ncview/install.sh
===================================================================
--- issm/trunk/externalpackages/ncview/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/ncview/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ncview-1.93g.tar.gz' 'ncview-1.93g.tar.gz'
 
 #Untar 
@@ -15,9 +18,9 @@
 cd install
 ./configure \
-	--prefix "$ISSM_TIER/externalpackages/ncview/install" \
+	--prefix "$ISSM_DIR/externalpackages/ncview/install" \
 	--x-libraries=/usr/X11/lib/ \
 	--x-includes=/usr/X11/include/ \
-	--with-netcdf_incdir="$ISSM_TIER/externalpackages/netcdf/install/include/" \
-	--with-netcdf_libdir="$ISSM_TIER/externalpackages/netcdf/install/lib/"
+	--with-netcdf_incdir="$ISSM_DIR/externalpackages/netcdf/install/include/" \
+	--with-netcdf_libdir="$ISSM_DIR/externalpackages/netcdf/install/lib/"
 
 make
Index: issm/trunk/externalpackages/netcdf/install.sh
===================================================================
--- issm/trunk/externalpackages/netcdf/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/netcdf/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install netcdf-4.0.1
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/netcdf-4.0.1.tar.gz' 'netcdf-4.0.1.tar.gz'
 
 #Untar 
@@ -15,5 +18,5 @@
 #Configure and compile
 cd install
-./configure  --prefix="$ISSM_TIER/externalpackages/netcdf/install" 
+./configure  --prefix="$ISSM_DIR/externalpackages/netcdf/install" 
 if [ -z $1 ]; then
 	make
Index: issm/trunk/externalpackages/nose/install-macosx64sh
===================================================================
--- issm/trunk/externalpackages/nose/install-macosx64sh	(revision 12331)
+++ issm/trunk/externalpackages/nose/install-macosx64sh	(revision 12332)
@@ -1,10 +1,29 @@
-#/bin/bash
-#Install Python3 nose module
+#!/bin/bash
+#Install Python nose module
 
-rm -rf py3k
+pythonversion=2
+	
+rm -rf src 
 
-svn checkout http://python-nose.googlecode.com/svn/branches/py3k
-cd py3k
+if [[ $pythonversion == "3" ]];then
 
-python3.2 ./setup.py build
-python3.2 ./setup.py install
+	svn checkout http://python-nose.googlecode.com/svn/branches/py3k
+	mv py3k src
+
+	cd src
+	python ./setup.py build
+	python ./setup.py install
+fi
+
+if [[ $pythonversion == "2" ]];then
+
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/nose-1.1.2.tar.gz' 'nose-1.1.2.tar.gz'
+	tar -zxvf  nose-1.1.2.tar.gz
+	mv nose-1.1.2 src
+	rm -rf nose-1.1.2
+
+	cd src
+	python ./setup.py build
+	python ./setup.py install
+fi
Index: issm/trunk/externalpackages/octave/install.sh
===================================================================
--- issm/trunk/externalpackages/octave/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/octave/install.sh	(revision 12332)
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+#Some cleanup
+version=3.6.1
+rm -rf src install octave-$version octave-$version.tar.gz
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/octave-$version.tar.gz" "octave-$version.tar.gz"
+
+#Untar 
+tar -zxvf  octave-$version.tar.gz
+
+#Move octave into install directory
+mv octave-$version/* src
+rm -rf octave-$version
+
+#install
+cd src 
+
+exit
+make 
+
+#Compile 
+cd ../install
+mkdir lib
+cd lib
+cp ../../src/*.a .
+ln -s octave_LINUX.a octave.a
+ln -s octave_LINUX.a liboctave.a
Index: issm/trunk/externalpackages/oofem/install.sh
===================================================================
--- issm/trunk/externalpackages/oofem/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/oofem/install.sh	(revision 12332)
@@ -5,4 +5,7 @@
 rm -rf oofem-2.0
 mkdir src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/oofem-2.0.tar.gz' 'oofem-2.0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/pcre/install.sh
===================================================================
--- issm/trunk/externalpackages/pcre/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/pcre/install.sh	(revision 12332)
@@ -5,4 +5,7 @@
 rm -rf pcre-8.21
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pcre-8.21.tar.gz' 'pcre-8.21.tar.gz'
 
 #Untar and move python into install directory
@@ -13,5 +16,5 @@
 #Configure doxygen
 cd install 
-./configure --prefix "$ISSM_TIER/externalpackages/python/install"
+./configure --prefix "$ISSM_DIR/externalpackages/python/install"
 make
 make install
Index: issm/trunk/externalpackages/petsc/install-2.3.2-altix64-castor.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-altix64-castor.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-altix64-castor.sh	(revision 12332)
@@ -9,4 +9,7 @@
 	mkdir install src
 
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
+
 	#Untar and move petsc to install directory
 	tar -zxvf  petsc-2.3.2-p3.tar.gz
@@ -17,5 +20,5 @@
 	cd install
 	./config/configure.py \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-batch=1  \
 		--ISSM_ARCH=$ISSM_ARCH \
@@ -41,5 +44,5 @@
 	cd install
 	./config/configure.py  \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-batch=1  \
 		--ISSM_ARCH=$ISSM_ARCH \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-cosmos.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-cosmos.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-cosmos.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-2.3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
 
 #Untar and move petsc to install directory
@@ -12,5 +15,5 @@
 #configure
 cd install
-PETSC_DIR=$ISSM_TIER/externalpackages/petsc/install
+PETSC_DIR=$ISSM_DIR/externalpackages/petsc/install
 ./config/configure.py  \
 	--prefix=$PETSC_DIR \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-linux64-astrid.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-linux64-astrid.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-linux64-astrid.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-2.3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
 
 #Untar and move petsc to install directory
@@ -13,8 +16,8 @@
 cd install
 ./config/configure.py  \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 	--PETSC_ARCH=linux-gnu-amd64 \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
 	--with-fc=gfortran \
 	--with-debugging=1 \
@@ -25,5 +28,5 @@
 	--download-blas=yes \
 	--download-f-blas-lapack=yes \
-	--FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \
+	--FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \
 	--download-plapack=yes \
 	--COPTFLAGS="-march=opteron -O2" \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-eric.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-eric.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-eric.sh	(revision 12332)
@@ -9,4 +9,7 @@
 	mkdir install src
 
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
+
 	#Untar and move petsc to install directory
 	tar -zxvf  petsc-2.3.2-p3.tar.gz
@@ -17,8 +20,8 @@
 	cd install
 	./config/configure.py  \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-		--with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+		--with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 		--PETSC_ARCH=macosx-gnu \
-		--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \
+		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-fc=/usr/local/bin/gfortran \
 		--with-debugging=0 \
@@ -29,5 +32,5 @@
 		--download-blas=yes \
 		--download-f-blas-lapack=yes \
-		--FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran  -fPIC -arch i386" \
+		--FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran  -fPIC -arch i386" \
 		--download-plapack=yes \
 		--CXXFLAGS=" -fPIC -arch i386" \
@@ -43,17 +46,17 @@
 	cd install
 	./config/configure.py  \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-		--with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+		--with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 		--PETSC_ARCH=macosx-gnu \
-		--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \
+		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-fc=/usr/local/bin/gfortran \
 		--with-debugging=0 \
 		--with-shared=0 \
-		--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3  \
+		--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/MUMPS_4.6.3  \
 		--download-scalapack=yes \
 		--download-blacs=yes \
 		--download-blas=yes \
 		--download-f-blas-lapack=yes \
-		--FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran  -fPIC -arch i386" \
+		--FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran  -fPIC -arch i386" \
 		--download-plapack=yes \
 		--CXXFLAGS=" -fPIC -arch i386" \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-2.3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
 
 #Untar and move petsc to install directory
@@ -12,8 +15,8 @@
 #configure
 cd install
-./config/configure.py  --prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+./config/configure.py  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 	--PETSC_ARCH=macosx-gnu \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
 	--with-fc=/usr/local/bin/gfortran \
 	--with-debugging=0 \
@@ -24,5 +27,5 @@
 	--download-blas=yes \
 	--download-f-blas-lapack=yes \
-	--FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \
+	--FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \
 	--download-plapack=yes
 
Index: issm/trunk/externalpackages/petsc/install-2.3.2-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-macosx64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-2.3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
 
 #Untar and move petsc to install directory
@@ -13,8 +16,8 @@
 cd src
 ./config/configure.py \
-  --prefix="$ISSM_TIER/externalpackages/petsc/install" \
-  --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
   --PETSC_ARCH=macosx-gnu \
-  --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \
+  --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \
   --with-debugging=0 \
   --with-shared-libraries=0 \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-pleiades.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-pleiades.sh	(revision 12332)
@@ -9,4 +9,7 @@
 	mkdir install src
 
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
+
 	#Untar and move petsc to install directory
 	tar -zxvf  petsc-2.3.2-p3.tar.gz
@@ -17,5 +20,5 @@
 	cd install
 	./config/configure.py  \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-batch=1  \
 		--PETSC_ARCH=$ISSM_ARCH \
@@ -44,5 +47,5 @@
 	cd install
 	./config/configure.py  \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-batch=1  \
 		--PETSC_ARCH=$ISSM_ARCH \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-win32-eric.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-win32-eric.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-win32-eric.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-2.3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
 
 #Untar and move petsc to install directory
@@ -14,7 +17,7 @@
 ./config/configure.py  \
 	--with-parallel-no \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 	--PETSC_ARCH=cygwin-intel \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
 	--with-debugging=0 \
 	--with-mpi=0 \
Index: issm/trunk/externalpackages/petsc/install-2.3.2-win7.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-2.3.2-win7.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-2.3.2-win7.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-2.3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
 
 #Untar and move petsc to install directory
@@ -14,7 +17,7 @@
 ./config/configure.py  \
 	--with-parallel-no \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 	--PETSC_ARCH=cygwin-intel \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
 	--with-debugging=0 \
 	--with-mpi=0 \
Index: issm/trunk/externalpackages/petsc/install-3.1-altix64-castor.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-altix64-castor.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-altix64-castor.sh	(revision 12332)
@@ -9,4 +9,7 @@
 	mkdir install src
 
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
+
 	#Untar and move petsc to install directory
 	tar -zxvf  petsc-3.1-p7.tar.gz
@@ -17,6 +20,6 @@
 	cd src
 	./config/configure.py \
-	  --prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	  --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	  --ISSM_ARCH=$ISSM_ARCH \
 	  --with-debugging=no \
@@ -41,6 +44,6 @@
 	cd src
 	./config/configure.py \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-		--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 		--with-batch=1  \
 		--ISSM_ARCH=$ISSM_ARCH \
Index: issm/trunk/externalpackages/petsc/install-3.1-cosmos.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-cosmos.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-cosmos.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-3.1-p7 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
 
 #Untar and move petsc to install directory
@@ -13,6 +16,6 @@
 cd src
 ./config/configure.py \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	--with-batch=1  \
 	--ISSM_ARCH=$ISSM_ARCH \
Index: issm/trunk/externalpackages/petsc/install-3.1-linux64-astrid.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-linux64-astrid.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-linux64-astrid.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-3.1-p7 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
 
 #Untar and move petsc to install directory
@@ -13,8 +16,8 @@
 cd src
 ./config/configure.py \
- --prefix="$ISSM_TIER/externalpackages/petsc/install" \
- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
  --PETSC_ARCH=linux-gnu-amd64 \
- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
  --with-debugging=0 \
  --with-shared=0 \
@@ -25,5 +28,5 @@
  --download-f-blas-lapack=yes \
  --download-parmetis=yes \
- --FFLAGS=-I$ISSM_TIER/externalpackages/mpich2/install/include \
+ --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \
  --download-plapack=yes \
  --COPTFLAGS="-march=opteron -O2" \
Index: issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-macosx32-mathieu.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-3.1-p7 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
 
 #Untar and move petsc to install directory
@@ -13,8 +16,8 @@
 cd src
 ./config/configure.py  \
- --prefix="$ISSM_TIER/externalpackages/petsc/install" \
- --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
  --PETSC_ARCH=macosx-gnu \
- --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
  --with-debugging=0 \
  --with-shared=0 \
@@ -25,5 +28,5 @@
  --download-f-blas-lapack=yes \
  --download-plapack=yes \
- --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \
+ --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \
  --COPTFLAGS="-march=opteron -O2 -arch i386" \
  --FOPTFLAGS="-march=opteron -O2 -arch i386" \
Index: issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-macosx32-ogive.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-3.1-p7 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
 
 #Untar and move petsc to install directory
@@ -13,7 +16,7 @@
 cd src
 ./config/configure.py \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
-	--with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 	--PETSC_ARCH=macosx-gnu \
 	--with-fc=/usr/local/bin/gfortran \
@@ -30,5 +33,5 @@
 	--FOPTFLAGS="-march=opteron -O2 " \
 	--CXXOPTFLAGS="-march=opteron -O2 " \
-	--FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -L$ISSM_TIER/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " 
+	--FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -L$ISSM_DIR/externalpackages/mpich2/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran " 
 
 #Compile petsc and install it
Index: issm/trunk/externalpackages/petsc/install-3.1-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-pleiades.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-pleiades.sh	(revision 12332)
@@ -9,4 +9,7 @@
 	mkdir install src
 
+	#Download from ISSM server
+	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
+
 	#Untar and move petsc to install directory
 	tar -zxvf  petsc-3.1-p7.tar.gz
@@ -17,8 +20,8 @@
 	cd src
 	./config/configure.py \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-batch=1  \
 		--PETSC_ARCH="$ISSM_ARCH" \
-		--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 		--with-debugging=no \
 		--with-shared=0 \
@@ -44,8 +47,8 @@
 	cd src
 	./config/configure.py \
-	 --prefix="$ISSM_TIER/externalpackages/petsc/install" \
+	 --prefix="$ISSM_DIR/externalpackages/petsc/install" \
 	 --with-batch=1  \
 	 --PETSC_ARCH="$ISSM_ARCH" \
-	 --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	 --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	 --with-debugging=no \
 	 --with-shared=0 \
@@ -57,5 +60,5 @@
 	 --download-scalapack=yes \
 	 --download-blacs=yes  \
-	 --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \
+	 --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \
 	 --download-parmetis=yes \
 	 --FFLAGS=-I/usr/include \
Index: issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh	(revision 12332)
+++ issm/trunk/externalpackages/petsc/install-3.1-ubuntu64.sh	(revision 12332)
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf install petsc-3.1-p7 src
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
+
+#Untar and move petsc to install directory
+tar -zxvf  petsc-3.1-p7.tar.gz
+mv petsc-3.1-p7/* src/
+rm -rf petsc-3.1-p7
+
+#configure
+cd src
+./config/configure.py \
+ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+ --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
+ --PETSC_ARCH=linux-gnu\
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-debugging=0 \
+ --with-shared=0 \
+ --download-mumps=yes \
+ --download-scalapack=yes \
+ --download-blacs=yes \
+ --download-blas=yes \
+ --download-f-blas-lapack=yes \
+ --download-parmetis=yes \
+ --FFLAGS=-I$ISSM_DIR/externalpackages/mpich2/install/include \
+ --download-plapack=yes \
+ --COPTFLAGS="-O2" \
+ --FOPTFLAGS="-O2" \
+ --CXXOPTFLAGS="-O2" \
+ --with-pic=1
+
+#Compile petsc and install it
+make
+make install
Index: issm/trunk/externalpackages/petsc/install-3.1-win7.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.1-win7.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.1-win7.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-3.1-p7 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.1-p7.tar.gz' 'petsc-3.1-p7.tar.gz'
 
 #Untar and move petsc to install directory
@@ -14,7 +17,7 @@
 ./config/configure.py  \
 	--with-parallel-no \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 	--PETSC_ARCH=cygwin-intel \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	--with-debugging=0 \
 	--with-mpi=0 \
@@ -26,8 +29,8 @@
 
 #./config/configure.py  \
-# --prefix="$ISSM_TIER/externalpackages/petsc/install" \
-# --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+# --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+# --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 # --PETSC_ARCH=macosx-gnu \
-# --with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+# --with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 # --with-debugging=0 \
 # --with-shared=0 \
@@ -38,5 +41,5 @@
 # --download-f-blas-lapack=yes \
 # --download-plapack=yes \
-# --FFLAGS="-I$ISSM_TIER/externalpackages/mpich2/install/include -arch i386" \
+# --FFLAGS="-I$ISSM_DIR/externalpackages/mpich2/install/include -arch i386" \
 # --COPTFLAGS="-march=opteron -O2 -arch i386" \
 # --FOPTFLAGS="-march=opteron -O2 -arch i386" \
Index: issm/trunk/externalpackages/petsc/install-3.2-discover.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.2-discover.sh	(revision 12332)
+++ issm/trunk/externalpackages/petsc/install-3.2-discover.sh	(revision 12332)
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+#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" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+	--PETSC_ARCH="$ISSM_ARCH" \
+	--with-batch=1 \
+	--with-debugging=0 \
+	--with-shared-libraries=0 \
+	--known-mpi-shared-libraries=1 \
+	--with-mpi-dir=/usr/local/intel/mpi/3.2.2.006/lib64 \
+	--with-blas-lapack-dir=/usr/local/intel/mkl/10.1.2.024/lib/64/ \
+	--download-mumps=yes \
+	--download-scalapack=yes \
+	--download-blacs=yes \
+	--download-plapack=yes \
+	--download-parmetis=yes \
+	--with-pic=1
+
+echo "== Follow PETSc's instructions"
Index: issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.2-greenplanet.sh	(revision 12332)
@@ -4,4 +4,7 @@
 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
@@ -13,6 +16,6 @@
 cd src
 ./config/configure.py \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	--PETSC_ARCH="$ISSM_ARCH" \
 	--with-batch=1 \
Index: issm/trunk/externalpackages/petsc/install-3.2-linux64.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.2-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.2-linux64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install petsc-3.2-p3 src
 mkdir install src
+
+#Download from ISSM server
+$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
@@ -13,9 +16,9 @@
 cd src
 ./config/configure.py \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--with-mpi-dir=$ISSM_TIER/externalpackages/mpich2/install \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich2/install \
 	--with-clanguage=C++ \
 	--PETSC_ARCH=linux-gnu-amd64 \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	--with-debugging=0 \
 	--with-shared-libraries=0 \
Index: issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.2-macosx64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 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
@@ -13,8 +16,8 @@
 cd src
 ./config/configure.py \
-  --prefix="$ISSM_TIER/externalpackages/petsc/install" \
-  --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
   --PETSC_ARCH=macosx-gnu \
-  --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \
+  --with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \
   --with-debugging=0 \
   --with-shared-libraries=0 \
Index: issm/trunk/externalpackages/petsc/install-3.2-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-3.2-pleiades.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-3.2-pleiades.sh	(revision 12332)
@@ -2,5 +2,5 @@
 #Step 1: unzip and install
 #Step 2: After Plapack implodes
-STEP=2
+STEP=1
 
 if [ $STEP -eq 1 ]; then
@@ -8,4 +8,7 @@
 	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
@@ -17,8 +20,8 @@
 	cd src
 	./config/configure.py \
-		--prefix="$ISSM_TIER/externalpackages/petsc/install" \
+		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
 		--with-batch=1  \
 		--PETSC_ARCH="$ISSM_ARCH" \
-		--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 		--with-debugging=0 \
 		--with-shared-libraries=0 \
@@ -38,5 +41,5 @@
 		--CXXOPTFLAGS=" -O3 -xS" \
 		--with-pic=1
-	echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc31/) =="
+	echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/documentation/faq/petsc32/) =="
 	echo "== Then run STEP=2 =="
 fi
@@ -44,8 +47,8 @@
 	cd src
 	./config/configure.py \
-	 --prefix="$ISSM_TIER/externalpackages/petsc/install" \
+	 --prefix="$ISSM_DIR/externalpackages/petsc/install" \
 	 --with-batch=1  \
 	 --PETSC_ARCH="$ISSM_ARCH" \
-	 --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	 --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	 --with-debugging=0 \
 	 --with-shared-libraries=0 \
@@ -57,5 +60,5 @@
 	 --download-scalapack=yes \
 	 --download-blacs=yes  \
-	 --with-plapack-dir=$ISSM_TIER/externalpackages/petsc/src/$ISSM_ARCH \
+	 --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/src/$ISSM_ARCH \
 	 --download-parmetis=yes \
 	 --FFLAGS=-I/usr/include \
@@ -66,4 +69,19 @@
 	 --CXXOPTFLAGS=" -O3 -xS" \
 	 --with-pic=1
+	 cat > src/script.queue << EOF
+#PBS -S /bin/bash
+#PBS -q debug 
+#PBS -l select=1:ncpus=1:model=har 
+#PBS -l walltime=200 
+#PBS -W group_list=s1010 
+#PBS -m e 
+. /usr/share/modules/init/bash 
+module load comp-intel/11.1.046 
+module load mpi/mpt.1.25 
+module load math/intel_mkl_64_10.0.011 
+export PATH="$PATH:." 
+export MPI_GROUP_MAX=64 
+mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
+EOF
 	echo "== Follow PETSc's instructions"
 fi
Index: issm/trunk/externalpackages/petsc/install-dev-linux64.sh
===================================================================
--- issm/trunk/externalpackages/petsc/install-dev-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/petsc/install-dev-linux64.sh	(revision 12332)
@@ -6,4 +6,5 @@
 	# Adapted from petsc 3.2. 
 	# Used Mercurial to get code
+	rm -rf src
 	hg clone http://petsc.cs.iit.edu/petsc/petsc-dev src
 	cd src
@@ -25,11 +26,12 @@
 
 if [ $STEP -eq 2 ]; then
+	rm -rf install
 	cd src
 	./config/configure.py \
-	--prefix="$ISSM_TIER/externalpackages/petsc/install" \
-	--with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \
+	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
+	--with-mpi-dir="$ISSM_DIR/externalpackages/mpich2/install" \
 	--with-clanguage=C++ \
 	--PETSC_ARCH=linux-gnu-amd64 \
-	--PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \
+	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
 	--with-debugging=0 \
 	--with-shared-libraries=0 \
@@ -42,4 +44,5 @@
 	--download-plapack=yes \
 	--download-parmetis=yes \
+	--download-spai=yes \
 	--with-pic=1
 
Index: issm/trunk/externalpackages/polygonclipper/install.sh
===================================================================
--- issm/trunk/externalpackages/polygonclipper/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/polygonclipper/install.sh	(revision 12332)
@@ -3,4 +3,7 @@
 #Some cleanup
 rm -rf install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/PolygonClipper.zip' 'PolygonClipper.zip'
 
 #install
Index: issm/trunk/externalpackages/pyclips/install.sh
===================================================================
--- issm/trunk/externalpackages/pyclips/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/pyclips/install.sh	(revision 12332)
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf install
+rm -rf pyclips-1.0.7.348
+mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/pyclips-1.0.7.348.tar.gz' 'pyclips-1.0.7.348.tar.gz'
+
+#Untar 
+tar -zxvf  pyclips-1.0.7.348.tar.gz
+
+#Move pyclips into install directory
+mv pyclips/* install
+rm -rf pyclips
+
+#install
+cd install
+python setup.py build
+sudo python setup.py install
Index: issm/trunk/externalpackages/python/install-linux64-astrid.sh
===================================================================
--- issm/trunk/externalpackages/python/install-linux64-astrid.sh	(revision 12332)
+++ issm/trunk/externalpackages/python/install-linux64-astrid.sh	(revision 12332)
@@ -0,0 +1,43 @@
+#!/bin/bash
+#wget http://python.org/ftp/python/version/Python-version.tgz
+
+#version=3.2.2
+version=2.7.2
+
+#Some cleanup
+rm -rf install src
+rm -rf Python-$version
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz
+
+#exports
+export CC
+
+#Untar and move python into install directory
+tar -zxvf  Python-$version.tgz
+mv Python-$version/* src
+rm -rf Python-$version
+
+#Configure doxygen
+cd src 
+./configure --prefix="$ISSM_DIR/externalpackages/python/install" 
+
+if [ -z $1 ]; then
+	make
+else
+	make -j $1
+fi
+make install
+
+#Some modifications to be done in case version is 3.2: 
+if [[ $version == "3.2.2" ]]; then 
+	cd install/bin
+	ln -s python3.2 python 
+	cd ../
+	ln -s Python.framework/Versions/3.2/include/python3.2m include
+	ln -s Python.framework/Versions/3.2/lib/ lib
+
+
+fi
Index: issm/trunk/externalpackages/python/install-macosx-lion.sh
===================================================================
--- issm/trunk/externalpackages/python/install-macosx-lion.sh	(revision 12332)
+++ issm/trunk/externalpackages/python/install-macosx-lion.sh	(revision 12332)
@@ -0,0 +1,42 @@
+#!/bin/bash
+#wget http://python.org/ftp/python/version/Python-version.tgz
+
+#version=3.2.2
+version=2.7.2
+
+#Some cleanup
+rm -rf install src
+rm -rf Python-$version
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz
+
+#exports
+export CC
+
+#Untar and move python into install directory
+tar -zxvf  Python-$version.tgz
+mv Python-$version/* src
+rm -rf Python-$version
+
+#Configure doxygen
+cd src 
+./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install"
+if [ -z $1 ]; then
+	make
+else
+	make -j $1
+fi
+make install
+
+#Some modifications to be done in case version is 3.2: 
+if [[ $version == "3.2.2" ]]; then 
+	cd install/bin
+	ln -s python3.2 python 
+	cd ../
+	ln -s Python.framework/Versions/3.2/include/python3.2m include
+	ln -s Python.framework/Versions/3.2/lib/ lib
+
+
+fi
Index: issm/trunk/externalpackages/python/install-macosx-snowleopard.sh
===================================================================
--- issm/trunk/externalpackages/python/install-macosx-snowleopard.sh	(revision 12332)
+++ issm/trunk/externalpackages/python/install-macosx-snowleopard.sh	(revision 12332)
@@ -0,0 +1,41 @@
+#!/bin/bash
+#wget http://python.org/ftp/python/version/Python-version.tgz
+
+#version=3.2.2
+version=2.7.2
+
+#Some cleanup
+rm -rf install src
+rm -rf Python-$version
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-$version.tgz Python-$version.tgz
+
+#exports
+export CC
+export MACOSX_DEPLOYMENT_TARGET=10.6
+
+#Untar and move python into install directory
+tar -zxvf  Python-$version.tgz
+mv Python-$version/* src
+rm -rf Python-$version
+
+#Configure doxygen
+cd src 
+./configure --prefix="$ISSM_DIR/externalpackages/python/install" --enable-framework="$ISSM_DIR/externalpackages/python/install" --enable-universalsdk --with-universal-archs="32-bit"
+if [ -z $1 ]; then
+	make
+else
+	make -j $1
+fi
+make install
+
+#Some modifications to be done in case version is 3.2: 
+if [[ $version == "3.2.2" ]]; then 
+	cd install/bin
+	ln -s python3.2 python 
+	cd ../
+	ln -s Python.framework/Versions/3.2/include/python3.2m include
+	ln -s Python.framework/Versions/3.2/lib/ lib
+fi
Index: issm/trunk/externalpackages/python/install.sh
===================================================================
--- issm/trunk/externalpackages/python/install.sh	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-#!/bin/bash
-#wget http://python.org/ftp/python/version/Python-version.tgz
-
-version=3.2.2
-#version=2.7.2
-
-#Some cleanup
-rm -rf install src
-rm -rf Python-$version
-mkdir install src
-
-#exports
-export CC
-
-#Untar and move python into install directory
-tar -zxvf  Python-$version.tgz
-mv Python-$version/* src
-rm -rf Python-$version
-
-#Configure doxygen
-cd src 
-./configure --prefix="$ISSM_TIER/externalpackages/python/install" --enable-framework="$ISSM_TIER/externalpackages/python/install"
-if [ -z $1 ]; then
-	make
-else
-	make -j $1
-fi
-make install
-
-#Some modifications to be done in case version is 3.2: 
-if [[ $version == "3.2.2" ]]; then 
-	cd install/bin
-	ln -s python3.2 python 
-	cd ../
-	ln -s Python.framework/Versions/3.2/include/python3.2m include
-	ln -s Python.framework/Versions/3.2/lib/ lib
-
-
-fi
Index: issm/trunk/externalpackages/qhull/install.sh
===================================================================
--- issm/trunk/externalpackages/qhull/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/qhull/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf src install qhull-2003.1
 mkdir src install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/qhull-2003.1.tar.gz' 'qhull-2003.1.tar.gz'
 
 #Untar 
@@ -15,5 +18,5 @@
 #Configure qhull
 cd src
-./configure --prefix="$ISSM_TIER/externalpackages/qhull/install"
+./configure --prefix="$ISSM_DIR/externalpackages/qhull/install"
 make
 make install
Index: issm/trunk/externalpackages/rats/install.sh
===================================================================
--- issm/trunk/externalpackages/rats/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/rats/install.sh	(revision 12332)
@@ -3,4 +3,7 @@
 #Erase install
 rm -rf install  src rats-2.3
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/rats-2.3.tar.gz' 'rats-2.3.tar.gz'
 
 #install directory
@@ -12,5 +15,5 @@
 #compile
 cd src
-./configure --prefix=$ISSM_TIER/externalpackages/rats/install
+./configure --prefix=$ISSM_DIR/externalpackages/rats/install
 make
 make install
Index: issm/trunk/externalpackages/readline/install.sh
===================================================================
--- issm/trunk/externalpackages/readline/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/readline/install.sh	(revision 12332)
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf src
+rm -rf readline-6.2.2
+mkdir src 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/readline-6.2.2.tar.gz' 'readline-6.2.2.tar.gz'
+
+#Untar 
+tar -zxvf  readline-6.2.2.tar.gz
+
+#Move readline into src directory
+mv readline-6.2.2/* src
+rm -rf readline-6.2.2
+
+$install
+cd src
+python setup.py install
Index: issm/trunk/externalpackages/rose/install.sh
===================================================================
--- issm/trunk/externalpackages/rose/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/rose/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf source build install
 mkdir install source build
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/rose-0.9.5a-13219.tar.gz' 'rose-0.9.5a-13219.tar.gz'
 
 #Untar 
@@ -15,7 +18,7 @@
 cd build
 ../source/configure \
-	--prefix=$ISSM_TIER/externalpackages/rose/install \
-	--with-boost=$ISSM_TIER/externalpackages/boost/install\
-	--srcdir=$ISSM_TIER/externalpackages/rose/source
+	--prefix=$ISSM_DIR/externalpackages/rose/install \
+	--with-boost=$ISSM_DIR/externalpackages/boost/install\
+	--srcdir=$ISSM_DIR/externalpackages/rose/source
 
 if [ -z $1 ]; then
Index: issm/trunk/externalpackages/satstress/install.sh
===================================================================
--- issm/trunk/externalpackages/satstress/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/satstress/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install SatStress-0.1.2
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/SatStress-0.1.2.tar.gz' 'SatStress-0.1.2.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/scipy/README
===================================================================
--- issm/trunk/externalpackages/scipy/README	(revision 12331)
+++ issm/trunk/externalpackages/scipy/README	(revision 12332)
@@ -1,2 +1,2 @@
 You will find instructions on scipy at: 
-http://www.scipy.org/Installing_SciPy/Mac_OS_X#head-ba1926aec910a9a1deaf9eff99e38ee23103a3b3
+http://www.scipy.org/Installing_SciPy/Mac_OS_X
Index: issm/trunk/externalpackages/scipy/install-linux64.sh
===================================================================
--- issm/trunk/externalpackages/scipy/install-linux64.sh	(revision 12332)
+++ issm/trunk/externalpackages/scipy/install-linux64.sh	(revision 12332)
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+#1: install numpy
+#2 install scipy
+#3 erase
+install=2
+
+
+export CC="gcc -fPIC"
+export CXX="g++ -fPIC"
+export F77="gfortran -fPIC"
+export FC="gfortran -fPIC"
+export FFLAGS=-ff2c
+
+
+if [[ $install == "1" ]];then 
+
+	#download numpy first
+
+	export GIT_SSL_NO_VERIFY=true 
+	git clone https://github.com/numpy/numpy.git
+
+	#install numpy
+	cd numpy
+	python setup.py build
+	python setup.py install
+
+	
+elif [[ $install == "2" ]];then 
+	
+	#download scipy
+	export GIT_SSL_NO_VERIFY=true 
+	git clone https://github.com/scipy/scipy.git
+
+	#install scipy
+	cd scipy
+	export  BLAS_SRC=$ISSM_DIR/externalpackages/blas/install/lib
+	export  BLAS=$ISSM_DIR/externalpackages/blas/install/lib
+	export  LAPACK_SRC=$ISSM_DIR/externalpackages/lapack/install/lib
+	export  LAPACK=$ISSM_DIR/externalpackages/lapack/install/lib
+
+	python setup.py build
+	python setup.py install
+
+elif [[ $install == "3" ]];then 
+	rm -rf numpy scipy
+else 
+	echo "Choice not covered"
+fi
Index: issm/trunk/externalpackages/scipy/install-macosx-lion.sh
===================================================================
--- issm/trunk/externalpackages/scipy/install-macosx-lion.sh	(revision 12332)
+++ issm/trunk/externalpackages/scipy/install-macosx-lion.sh	(revision 12332)
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+#1: install numpy
+#2 install scipy
+#3 erase
+install=2
+
+
+export CC=gcc
+export CXX=g++
+export FFLAGS=-ff2c
+
+
+if [[ $install == "1" ]];then 
+
+	#download numpy first
+	git clone https://github.com/numpy/numpy.git
+
+	#install numpy
+	cd numpy
+	python setup.py build
+	python setup.py install
+
+	
+elif [[ $install == "2" ]];then 
+	
+	#download scipy
+	git clone https://github.com/scipy/scipy.git
+
+	#install scipy
+	cd scipy
+	python setup.py build
+	python setup.py install
+
+elif [[ $install == "3" ]];then 
+	rm -rf numpy scipy
+else 
+	echo "Choice not covered"
+fi
Index: issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh
===================================================================
--- issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh	(revision 12332)
+++ issm/trunk/externalpackages/scipy/install-macosx-snowleopard.sh	(revision 12332)
@@ -0,0 +1,41 @@
+#!/bin/bash
+PYVERSION=2.7
+PYTHON=python${PYVERSION}
+
+#1: install numpy
+#2 install scipy
+#3 erase
+install=2
+
+export CC=/usr/bin/gcc-4.0
+export CXX=/usr/bin/g++-4.0
+
+if [[ $install == "1" ]];then 
+
+	#download numpy first
+	git clone https://github.com/numpy/numpy.git
+
+	#install numpy
+	cd numpy
+	python setup.py build
+	python setup.py install
+	cd ..
+	${PYTHON} -c "import numpy; print 'Installed NumPy', numpy.__version__"
+	
+elif [[ $install == "2" ]];then 
+	
+	#download scipy
+	git clone https://github.com/scipy/scipy.git
+
+	#install scipy
+	cd scipy
+	python setup.py build
+	python setup.py install
+	cd ..
+	${PYTHON} -c "import scipy; print 'Installed SciPy', scipy.__version__"
+
+elif [[ $install == "3" ]];then 
+	rm -rf numpy scipy
+else 
+	echo "Choice not covered"
+fi
Index: issm/trunk/externalpackages/scipy/install-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/scipy/install-macosx64.sh	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-#!/bin/bash
-
-#1: install numpy
-#2 install scipy
-#3 erase
-install=2
-
-
-export CC=gcc
-export CXX=g++
-export FFLAGS=-ff2c
-
-
-if [[ $install == "1" ]];then 
-
-	#download numpy first
-	git clone https://github.com/numpy/numpy.git
-
-	#install numpy
-	cd numpy
-	python3.2 setup.py build
-	python3.2 setup.py install
-
-	
-elif [[ $install == "2" ]];then 
-	
-	#download scipy
-	git clone https://github.com/scipy/scipy.git
-
-	#install scipy
-	cd scipy
-	python3.2 setup.py build
-	python3.2 setup.py install
-
-elif [[ $install == "3" ]];then 
-	rm -rf numpy scipy
-else 
-	echo "Choice not covered"
-fi
Index: issm/trunk/externalpackages/scotch/install.sh
===================================================================
--- issm/trunk/externalpackages/scotch/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/scotch/install.sh	(revision 12332)
@@ -8,4 +8,7 @@
 # Create src and install directories
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/scotch_5.1.6.tar.gz' 'scotch_5.1.6.tar.gz'
 
 # Untar 
Index: issm/trunk/externalpackages/shapelib/install.sh
===================================================================
--- issm/trunk/externalpackages/shapelib/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/shapelib/install.sh	(revision 12332)
@@ -6,4 +6,8 @@
 rm -rf install 
 mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shapelib-1.2.10.tar.gz' 'shapelib-1.2.10.tar.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/shape_eg_data.zip' 'shape_eg_data.zip'
 
 # Untar 
Index: issm/trunk/externalpackages/slepc/install.sh
===================================================================
--- issm/trunk/externalpackages/slepc/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/slepc/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install slepc-2.3.2
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/slepc-2.3.2.tgz' 'slepc-2.3.2.tgz'
 
 #Untar 
Index: issm/trunk/externalpackages/swig/install.sh
===================================================================
--- issm/trunk/externalpackages/swig/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/swig/install.sh	(revision 12332)
@@ -5,4 +5,7 @@
 rm -rf swig-2.0.4
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/swig-2.0.4.tar.gz' 'swig-2.0.4.tar.gz'
 
 #Untar and move python into install directory
@@ -13,14 +16,14 @@
 #Copy pcre prototype in include directory
 cd install 
-#cp $ISSM_TIER/externalpackages/pcre/install/pcre.h  ./Source/Include/
-#cp $ISSM_TIER/externalpackages/pcre/install/.libs/*  ./Source/Include/
-export CFLAGS="$CFLAGS -I$ISSM_TIER/externalpackages/pcre/install"
-export LDFLAGS="-L$ISSM_TIER/externalpackages/pcre/install/.libs/"
+#cp $ISSM_DIR/externalpackages/pcre/install/pcre.h  ./Source/Include/
+#cp $ISSM_DIR/externalpackages/pcre/install/.libs/*  ./Source/Include/
+export CFLAGS="$CFLAGS -I$ISSM_DIR/externalpackages/pcre/install"
+export LDFLAGS="-L$ISSM_DIR/externalpackages/pcre/install/.libs/"
 export LIBS="-lpcre"
 #Configure doxygen
 ./configure \
- --prefix="$ISSM_TIER/externalpackages/python/install" \
- --with-pcre-prefix="$ISSM_TIER/externalpackages/pcre/install" \
- --with-pcre-exec-prefix="$ISSM_TIER/externalpackages/pcre/install"
+ --prefix="$ISSM_DIR/externalpackages/python/install" \
+ --with-pcre-prefix="$ISSM_DIR/externalpackages/pcre/install" \
+ --with-pcre-exec-prefix="$ISSM_DIR/externalpackages/pcre/install"
 make 
 make install
Index: issm/trunk/externalpackages/tao/install.sh
===================================================================
--- issm/trunk/externalpackages/tao/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/tao/install.sh	(revision 12332)
@@ -7,4 +7,7 @@
 mkdir install
 
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tao-2.0-p3.tar.gz' 'tao-2.0-p3.tar.gz'
+
 #Untar 
 tar -zxvf  tao-2.0-p3.tar.gz
@@ -14,5 +17,5 @@
 rm -rf tao-2.0-p3
 cd install
-export TAO_DIR="$ISSM_TIER/externalpackages/tao/install/"
+export TAO_DIR="$ISSM_DIR/externalpackages/tao/install/"
 
 #petsc needs to be compiled with --with-clanguage=C++
Index: issm/trunk/externalpackages/tex2im/install.sh
===================================================================
--- issm/trunk/externalpackages/tex2im/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/tex2im/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/tex2im-1.8.tar.gz' 'tex2im-1.8.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/configs/android/android-4.0/configure.make
===================================================================
--- issm/trunk/externalpackages/triangle/configs/android/android-4.0/configure.make	(revision 12331)
+++ issm/trunk/externalpackages/triangle/configs/android/android-4.0/configure.make	(revision 12332)
@@ -11,8 +11,8 @@
 
 ANDROID_BIN=$(ISSM_TIER)/src/android/tmp/android-14-toolchain/bin
-CC=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-gcc
-AR=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-ar
-RANLIB=$(ANDROID_DEV_DIR)/tmp/android-linux-4.0/bin/arm-linux-androideabi-ranlib
-CSWITCHES = $(CFLAGS)  -I/usr/X11R6/include -L/usr/X11R6/lib -I$(MATLAB_DIR)/extern/include -fPIC -I$(MATLAB_DIR)/include
+CC=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc
+AR=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-ar
+RANLIB=$(ANDROID_DIR)/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib
+CSWITCHES = $(CFLAGS)
 TRILIBDEFS = -DTRILIBRARY
 OBJ_EXT=o
Index: issm/trunk/externalpackages/triangle/install-altix64.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-altix64.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-altix64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-android-4.0.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-android-4.0.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-android-4.0.sh	(revision 12332)
@@ -4,8 +4,10 @@
 matlab=0
 
-
 #Some cleanup 
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-linux64.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-linux64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-macosx32.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-macosx32.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-macosx32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-macosx64.sh	(revision 12332)
@@ -8,4 +8,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-pleiades.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-pleiades.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-pleiades.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-win32.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-win32.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-win32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/install-win7.sh
===================================================================
--- issm/trunk/externalpackages/triangle/install-win7.sh	(revision 12331)
+++ issm/trunk/externalpackages/triangle/install-win7.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install triangle
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/triangle.zip' 'triangle.zip'
 
 #Untar 
Index: issm/trunk/externalpackages/triangle/triangle.c.patch.python
===================================================================
--- issm/trunk/externalpackages/triangle/triangle.c.patch.python	(revision 12331)
+++ issm/trunk/externalpackages/triangle/triangle.c.patch.python	(revision 12332)
@@ -5,6 +5,6 @@
 >  * double precision activation in exactinit(); The rest is not changed. 
 >  * We also created the ice_makefile to compile Triangle into a library. */
-> #include <mat.h>
-> #include <matrix.h>
+> /* #include <mat.h>
+> #include <matrix.h> */
 > #define ANSI_DECLARATORS
 > #define NO_TIMER
Index: issm/trunk/externalpackages/valgrind/install-altix64.sh
===================================================================
--- issm/trunk/externalpackages/valgrind/install-altix64.sh	(revision 12331)
+++ issm/trunk/externalpackages/valgrind/install-altix64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install valgrind-3.7.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2'
 
 #Untar 
@@ -14,5 +17,5 @@
 #configure
 cd install
-./configure --prefix="$ISSM_TIER/externalpackages/valgrind/install"
+./configure --prefix="$ISSM_DIR/externalpackages/valgrind/install"
 
 #Compile valgrind
Index: issm/trunk/externalpackages/valgrind/install-linux64.sh
===================================================================
--- issm/trunk/externalpackages/valgrind/install-linux64.sh	(revision 12331)
+++ issm/trunk/externalpackages/valgrind/install-linux64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install valgrind-3.7.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2'
 
 #Untar 
@@ -14,5 +17,5 @@
 #configure
 cd install
-./configure  --prefix="$ISSM_TIER/externalpackages/valgrind/install"
+./configure  --prefix="$ISSM_DIR/externalpackages/valgrind/install"
 
 #Compile valgrind
Index: issm/trunk/externalpackages/valgrind/install-macosx32.sh
===================================================================
--- issm/trunk/externalpackages/valgrind/install-macosx32.sh	(revision 12331)
+++ issm/trunk/externalpackages/valgrind/install-macosx32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install valgrind-3.7.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2'
 
 #Untar 
@@ -14,5 +17,5 @@
 #configure
 cd install
-./configure  --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only32bit
+./configure  --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only32bit
 
 #Compile valgrind
Index: issm/trunk/externalpackages/valgrind/install-macosx64.sh
===================================================================
--- issm/trunk/externalpackages/valgrind/install-macosx64.sh	(revision 12331)
+++ issm/trunk/externalpackages/valgrind/install-macosx64.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install valgrind-3.7.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2'
 
 #Untar 
@@ -14,5 +17,5 @@
 #configure
 cd install
-./configure  --prefix="$ISSM_TIER/externalpackages/valgrind/install" --enable-only64bit
+./configure  --prefix="$ISSM_DIR/externalpackages/valgrind/install" --enable-only64bit
 
 #Compile valgrind
Index: issm/trunk/externalpackages/valgrind/install-win32.sh
===================================================================
--- issm/trunk/externalpackages/valgrind/install-win32.sh	(revision 12331)
+++ issm/trunk/externalpackages/valgrind/install-win32.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install valgrind-3.7.0
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/valgrind-3.7.0.tar.bz2' 'valgrind-3.7.0.tar.bz2'
 
 #Untar 
@@ -14,5 +17,5 @@
 #configure
 cd install
-./configure  --prefix="$ISSM_TIER/externalpackages/valgrind/install"
+./configure  --prefix="$ISSM_DIR/externalpackages/valgrind/install"
 
 #Compile valgrind
Index: issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim
===================================================================
--- issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim	(revision 12331)
+++ issm/trunk/externalpackages/vim/addons/vim/syntax/c.vim	(revision 12332)
@@ -547,4 +547,10 @@
 syn keyword cType QuadTree
 syn keyword cType SetOfE4
+syn keyword cType Variogram
+syn keyword cType GaussianVariogram
+syn keyword cType ExponentialVariogram
+syn keyword cType SphericalVariogram
+syn keyword cType Quadtree
+syn keyword cType Observation
 "ISSM's objects end
 
@@ -686,4 +692,8 @@
 syn keyword cConstant SettingsResultsAsPatchesEnum
 syn keyword cConstant SettingsWaitonlockEnum
+syn keyword cConstant DebugPetscProfilingEnum
+syn keyword cConstant PetscProfilingCurrentMemEnum
+syn keyword cConstant PetscProfilingCurrentFlopsEnum
+syn keyword cConstant PetscProfilingSolutionTimeEnum
 syn keyword cConstant SteadystateMaxiterEnum
 syn keyword cConstant SteadystateNumRequestedOutputsEnum
@@ -701,6 +711,7 @@
 syn keyword cConstant ThermalIsenthalpyEnum
 syn keyword cConstant ThicknessEnum
+syn keyword cConstant TimesteppingStartTimeEnum
+syn keyword cConstant TimesteppingFinalTimeEnum
 syn keyword cConstant TimesteppingCflCoefficientEnum
-syn keyword cConstant TimesteppingFinalTimeEnum
 syn keyword cConstant TimesteppingTimeAdaptEnum
 syn keyword cConstant TimesteppingTimeStepEnum
@@ -764,4 +775,5 @@
 syn keyword cConstant BoolInputEnum
 syn keyword cConstant BoolParamEnum
+syn keyword cConstant ContourEnum
 syn keyword cConstant ControlInputEnum
 syn keyword cConstant DatasetInputEnum
@@ -904,4 +916,5 @@
 syn keyword cConstant P1Enum
 syn keyword cConstant P1DGEnum
+syn keyword cConstant SaveResultsEnum
 syn keyword cConstant BoolElementResultEnum
 syn keyword cConstant BoolExternalResultEnum
@@ -918,4 +931,5 @@
 syn keyword cConstant PetscVecExternalResultEnum
 syn keyword cConstant StringExternalResultEnum
+syn keyword cConstant StepEnum
 syn keyword cConstant TimeEnum
 syn keyword cConstant TriaP1ElementResultEnum
Index: issm/trunk/externalpackages/vim/install.sh
===================================================================
--- issm/trunk/externalpackages/vim/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/vim/install.sh	(revision 12332)
@@ -5,4 +5,7 @@
 rm -rf vim72
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/vim-7.2.tar.bz2' 'vim-7.2.tar.bz2'
 
 #Untar 
@@ -19,5 +22,5 @@
 cd src/src 
 ./configure \
-	--prefix "$ISSM_TIER/externalpackages/vim/install" \
+	--prefix "$ISSM_DIR/externalpackages/vim/install" \
 	--with-gcc "/usr/bin/gcc"
 
Index: issm/trunk/externalpackages/windows/InstallInstructions.txt
===================================================================
--- issm/trunk/externalpackages/windows/InstallInstructions.txt	(revision 12331)
+++ issm/trunk/externalpackages/windows/InstallInstructions.txt	(revision 12332)
@@ -42,4 +42,5 @@
 python: Python language interpreter
 unzip
+cygrunsrv
 
 
@@ -144,9 +145,15 @@
 
 How to setup a Cron job? 
-Download exim and cron from cygwin setup. Run exim-config (don't forget to launch your cygwin terminal as
-Administrator). If asked for a daemon name, type ntsec. Also, if cron complains about sendmail,
-symlink /usr/lib/sendmail to /usr/sbin/sendmail.  Then link /usr/sbin/sendmail
-to /usr/bin/exim. Alternatively, if you have an smtp server, you can download and configure
-ssmtp.  Run ssmtp-config
-as Administrator and link /usr/sbin/sendmail to /usr/bin/ssmtp. After the email has been configured,
-run cron-config as Administrator.
+First, make sure you downloaded cygrunsrv, otherwise the cron setup will only work on a per-session 
+basis! Also, make sure that you have an email correctly setup.  In particular, cron relies on the
+/usr/sbin/sendmail script. If it does not exist, cron will not send emails. Most email management 
+systems will create this script, but you need to check on it. 
+Run cron-config  and fill up the questions. For daemon name, type ntsec. 
+Be careful, make sure that you are running your terminal as Administrator, 
+otherwise your settings will be only user-based. 
+How to setup email? 
+
+Preferred way is through ssmtp. Download it on cygwin, and type ssmtp-config.  If the ssmtp 
+daemon does not create /usr/sbin/sendmail, be sure to create a symlink from the email client 
+to the latter file. Be careful, make sure that you are running your terminal as Administrator, 
+otherwise your settings will be only user-based. 
Index: issm/trunk/externalpackages/windows/configs/sdk7.1.win7-32.sh
===================================================================
--- issm/trunk/externalpackages/windows/configs/sdk7.1.win7-32.sh	(revision 12331)
+++ issm/trunk/externalpackages/windows/configs/sdk7.1.win7-32.sh	(revision 12332)
@@ -1,37 +1,37 @@
 declare -x ALLUSERSPROFILE="C:\\ProgramData"
-declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319"
-declare -x COMMONPROGRAMFILES="C:\\Program Files (x86)\\Common Files"
+declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319"
+declare -x COMMONPROGRAMFILES="C:\\Program Files\\Common Files"
 declare -x COMSPEC="C:\\Windows\\system32\\cmd.exe"
-declare -x CommandPromptType="Cross"
-declare -x CommonProgramW6432="C:\\Program Files\\Common Files"
+declare -x CommandPromptType="Native"
 declare -x Configuration="Debug"
 declare -x FP_NO_HOST_CHECK="NO"
 declare -x FrameworkVersion="v4.0.30319"
 declare -x HOMEDRIVE="C:"
-declare -x INCLUDE="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\INCLUDE;"
+declare -x INCLUDE="C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;"
 declare -x INFOPATH="/usr/local/info:/usr/share/info:/usr/info:"
 declare -x LANG="en_US.UTF-8"
-declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\LIB;"
-declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;"
+declare -x LIB="C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;"
+declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files\\Microsoft Visual Studio 10.0\\VC\\Lib;"
 declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:"
-declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b32/runtime/win32:/cygdrive/c/MATLAB/R2011b32/bin:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/c/MATLAB/R2011b/bin:/cygdrive/c/Program Files (x86)/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/DTS/Binn:/cygdrive/c/Program Files/Microsoft Network Monitor 3"
+declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/MATLAB/R2012a/runtime/win32:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit"
 declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC"
+declare -x PRINTER="137.78.140.129#:1"
 declare -x PROCESSOR_ARCHITECTURE="x86"
-declare -x PROCESSOR_ARCHITEW6432="AMD64"
-declare -x PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 42 Stepping 7, GenuineIntel"
+declare -x PROCESSOR_IDENTIFIER="x86 Family 6 Model 42 Stepping 7, GenuineIntel"
 declare -x PROCESSOR_LEVEL="6"
 declare -x PROCESSOR_REVISION="2a07"
-declare -x PROGRAMFILES="C:\\Program Files (x86)"
+declare -x PROGRAMFILES="C:\\Program Files"
 declare -x PSModulePath="C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\"
 declare -x PUBLIC="C:\\Users\\Public"
 declare -x PlatformToolset="Windows7.1SDK"
 declare -x ProgramData="C:\\ProgramData"
-declare -x ProgramW6432="C:\\Program Files"
 declare -x SHELL="/bin/bash"
 declare -x SYSTEMDRIVE="C:"
 declare -x SYSTEMROOT="C:\\Windows"
+declare -x TARGET_CPU="x86"
 declare -x TARGET_PLATFORM="WIN7"
 declare -x TERM="cygwin"
-declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\"
+declare -x ToolsVersion="4.0"
+declare -x VS100COMNTOOLS="C:\\Program Files\\Microsoft Visual Studio 10.0\\Common7\\Tools\\"
 declare -x WINDIR="C:\\Windows"
 declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\"
Index: issm/trunk/externalpackages/windows/configs/sdk7.1.win7-64.sh
===================================================================
--- issm/trunk/externalpackages/windows/configs/sdk7.1.win7-64.sh	(revision 12331)
+++ issm/trunk/externalpackages/windows/configs/sdk7.1.win7-64.sh	(revision 12332)
@@ -13,7 +13,6 @@
 declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib\\X64;"
 declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework64\\v3.5;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;"
-declare -x LOCALAPPDATA="C:\\Users\\schlegel\\AppData\\Local"
 declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:"
-declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/b/MATLAB/R2011b/bin:/cygdrive/c/MATLAB/R2011b/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include"
+declare -x PATH="/usr/local/bin:/usr/bin:/usr/include:/cygdrive/c/cygwin/usr/bin:/cygdrive/c/cygwin/usr/include:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2012a/runtime/win64:/cygdrive/c/MATLAB/R2012a/bin:/cygdrive/c/MATLAB/R2012a/extern/include:/cygdrive/c/MATLAB/R2011a/runtime/win64:/cygdrive/c/MATLAB/R2011a/bin:/cygdrive/c/MATLAB/R2011a/extern/include"
 declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC"
 declare -x PROCESSOR_ARCHITECTURE="x86"
@@ -41,6 +40,4 @@
 declare -x TMP="/tmp"
 declare -x ToolsVersion="4.0"
-declare -x USER="schlegel"
-declare -x USERNAME="schlegel"
 declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\"
 declare -x WINDIR="C:\\Windows"
Index: issm/trunk/externalpackages/windows/install.sh
===================================================================
--- issm/trunk/externalpackages/windows/install.sh	(revision 12332)
+++ issm/trunk/externalpackages/windows/install.sh	(revision 12332)
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/win7.sdk7.1.exe' 'win7.sdk7.1.exe'
Index: issm/trunk/externalpackages/windows/windows_environment.sh
===================================================================
--- issm/trunk/externalpackages/windows/windows_environment.sh	(revision 12331)
+++ issm/trunk/externalpackages/windows/windows_environment.sh	(revision 12332)
@@ -2,5 +2,5 @@
 
 #Where are the configuration files for each compiler: 
-config_dir="$ISSM_TIER/externalpackages/windows/configs"
+config_dir="$ISSM_DIR/externalpackages/windows/configs"
 
 #your choise of compiler: 
@@ -10,5 +10,15 @@
 # 4: intel compiler on WinXP
 
-compiler=2;
+#Determine OS version using uname: 
+version=`uname -s | grep 64`
+if [[ $version == "" ]];then
+	compiler=1
+else
+	compiler=2
+fi
+
+#If you want to override and use intel compilers: 
+#compiler=3;
+
 
 #source corresponding environment variables: 
@@ -24,5 +34,5 @@
 fi
 
-#finally, out of ISSM_TIER, we need to create an ISSM_TIER_WIN variable for Matlab to pick up on.
-ISSM_TIER_WIN=`cygpath -m $ISSM_TIER`
-export ISSM_TIER_WIN
+#finally, out of ISSM_DIR, we need to create an ISSM_DIR_WIN variable for Matlab to pick up on.
+ISSM_DIR_WIN=`cygpath -m $ISSM_DIR`
+export ISSM_DIR_WIN
Index: issm/trunk/externalpackages/xerces/install.sh
===================================================================
--- issm/trunk/externalpackages/xerces/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/xerces/install.sh	(revision 12332)
@@ -4,4 +4,7 @@
 rm -rf install xerces-c-src_2_8_0 src
 mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/xerces-c-src_2_8_0.tar.gz' 'xerces-c-src_2_8_0.tar.gz'
 
 #Untar 
Index: issm/trunk/externalpackages/yams/install.sh
===================================================================
--- issm/trunk/externalpackages/yams/install.sh	(revision 12331)
+++ issm/trunk/externalpackages/yams/install.sh	(revision 12332)
@@ -4,4 +4,9 @@
 rm -rf install
 mkdir install
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/yams2-linux.gz' 'yams2-linux.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/yams2-osx.gz' 'yams2-osx.gz'
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/yams2-win.exe' 'yams2-win.exe'
 
 #loop over the binaries
Index: issm/trunk/m4/issm_options.m4
===================================================================
--- issm/trunk/m4/issm_options.m4	(revision 12331)
+++ issm/trunk/m4/issm_options.m4	(revision 12332)
@@ -13,31 +13,15 @@
 	fi
 	dnl }}}
-	dnl Serial build {{{
-	AC_ARG_WITH([serial],
-		AS_HELP_STRING([--with-serial = value],[serial compilation. ]),
-		[SERIAL_VALUE=$withval],[SERIAL_VALUE="yes"])
-	AC_MSG_CHECKING(for serial compilation)
-	AM_CONDITIONAL([NOSERIAL], [test $SERIAL_VALUE = no])
-	AM_CONDITIONAL([SERIAL], [test $SERIAL_VALUE = yes])
-	AC_MSG_RESULT($SERIAL_VALUE) 
-	dnl }}}
-	dnl Parallel build {{{
-	AC_ARG_WITH([parallel],
-		AS_HELP_STRING([--with-parallel = value], [parallel compilation. ]),
-		[PARALLEL_VALUE=$withval],[PARALLEL_VALUE="yes"])
-	AC_MSG_CHECKING(for parallel compilation)
-	AM_CONDITIONAL([NOPARALLEL], [test $PARALLEL_VALUE = no])
-	AM_CONDITIONAL([PARALLEL], [test $PARALLEL_VALUE = yes])
-	AC_MSG_RESULT($PARALLEL_VALUE) 
+	dnl Modules build {{{
+	AC_ARG_WITH([modules],
+		AS_HELP_STRING([--with-modules = value],[modules compilation. ]),
+		[MODULES_VALUE=$withval],[MODULES_VALUE="yes"])
+	AC_MSG_CHECKING(for modules compilation)
+	AM_CONDITIONAL([MODULES], [test $MODULES_VALUE = yes])
+	AC_MSG_RESULT($MODULES_VALUE) 
+	dnl }}}
+	dnl Extensions{{{
 	ISSMEXT=".exe"
 	AC_SUBST([ISSMEXT])
-	dnl }}}
-	dnl Serial or Parallel check {{{
-	dnl Check that at least serial or parallel builds have been requested!
-	if test "$SERIAL_VALUE" != "yes" ; then
-		if test "$PARALLEL_VALUE" != "yes"; then
-			AC_MSG_ERROR([cannot request --with-serial=no and --with-parallel=no at the same time!])
-		fi
-	fi
 	dnl }}}
 
@@ -81,5 +65,11 @@
 			export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ "
 			export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ "
-		else
+		elif test $VENDOR = arm-linux; then
+			export CC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc
+			export GCC=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-gcc
+			export CXX=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-g++
+			export AR=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ar
+			export RANLIB=$ANDROID_DIR/arm-linux-android-4.0/bin/arm-linux-androideabi-ranlib
+        else
 		AC_MSG_ERROR([unknow compiler vendor!])
 		fi
@@ -92,8 +82,8 @@
 	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.]),
+		AS_HELP_STRING([--with-matlab-dir=DIR], [matlab root directory. necessary for serial build.]),
 		[MATLAB_ROOT=$withval],[MATLAB_ROOT=""]) 
 
-	AC_MSG_CHECKING([wether Matlab is enabled])
+	AC_MSG_CHECKING([whether matlab is enabled])
 	if test -d "$MATLAB_ROOT"; then
 		HAVE_MATLAB=yes
@@ -109,5 +99,5 @@
 	dnl 2. if matlab is provided, get version number
 	if test x$HAVE_MATLAB = xyes; then
-		AC_MSG_CHECKING([for Matlab version])
+		AC_MSG_CHECKING([for matlab version])
 		MATLAB_VERSION=""
 
@@ -172,5 +162,5 @@
 
 		dnl 3. Get Matlab libraries
-		AC_MSG_CHECKING(for Matlab headers and libraries in $MATLAB_ROOT)
+		AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT)
 		MATLABINCL=-I"$MATLAB_ROOT/extern/include";
 		
@@ -217,6 +207,6 @@
 		AC_SUBST([MATLABINCL])
 		AC_SUBST([MEX])
-		WRAPPEREXT=$MEXEXT
-		AC_SUBST([WRAPPEREXT])
+		MATLABWRAPPEREXT=$MEXEXT
+		AC_SUBST([MATLABWRAPPEREXT])
 		AC_SUBST([MEXLIB]) 
 		AC_SUBST([MEXLINK])
@@ -225,7 +215,7 @@
 	dnl triangle {{{
 	AC_ARG_WITH([triangle-dir],
-			  AS_HELP_STRING([--with-triangle-dir = DIR], [triangle root directory. necessary for serial build]),
+			  AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory. necessary for serial build]),
 			 [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT=""]) 
-	AC_MSG_CHECKING(for Triangle headers and libraries)
+	AC_MSG_CHECKING(for triangle headers and libraries)
 
 	if test -d "$TRIANGLE_ROOT"; then
@@ -266,7 +256,7 @@
 	dnl dakota{{{
 	AC_ARG_WITH([dakota-dir],
-	  AS_HELP_STRING([--with-dakota-dir = DIR], [dakota root directory. necessary for serial build]),
+	  AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory. necessary for serial build]),
 	  [DAKOTA_ROOT=$withval],[DAKOTA_ROOT=""]) 
-	AC_MSG_CHECKING(for Dakota)
+	AC_MSG_CHECKING(for dakota)
 	
 	if test -d "$DAKOTA_ROOT"; then
@@ -299,7 +289,7 @@
 	dnl boost{{{
 	AC_ARG_WITH([boost-dir],
-	  AS_HELP_STRING([--with-boost-dir = DIR], [boost root directory.]),
+	  AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]),
 	  [BOOST_ROOT=$withval],[BOOST_ROOT=""]) 
-	AC_MSG_CHECKING(for Boost)
+	AC_MSG_CHECKING(for boost)
 	
 	if test -d "$BOOST_ROOT"; then
@@ -320,7 +310,7 @@
 	dnl python{{{
 	AC_ARG_WITH([python-dir],
-	  AS_HELP_STRING([--with-python-dir = DIR], [python root directory.]),
+	  AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]),
 	  [PYTHON_ROOT=$withval],[PYTHON_ROOT=""]) 
-	AC_MSG_CHECKING(for Python)
+	AC_MSG_CHECKING(for python)
 	
 	if test -d "$PYTHON_ROOT"; then
@@ -328,5 +318,5 @@
 		HAVE_PYTHON=yes
 		PYTHONINCL=-I$PYTHON_ROOT/include
-		PYTHONLIB="-L$PYTHON_ROOT/lib -lpython3.2"
+		PYTHONLIB="-L$PYTHON_ROOT/lib -lpython$PYTHONVERSION"
 		PYTHONEXT=.so
 		PYTHONLINK="-dynamiclib"
@@ -335,6 +325,6 @@
 		AC_SUBST([PYTHONINCL])
 		AC_SUBST([PYTHONLIB])
-		WRAPPEREXT=$PYTHONEXT
-		AC_SUBST([WRAPPEREXT])
+		PYTHONWRAPPEREXT=$PYTHONEXT
+		AC_SUBST([PYTHONWRAPPEREXT])
 		AC_SUBST([PYTHONLINK])
 	else
@@ -343,10 +333,30 @@
 	AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes])
 	AC_MSG_RESULT($HAVE_PYTHON)
+
+	dnl python-version
+	HAVE_PYTHON3="no"
+	if test x$HAVE_PYTHON = xyes; then
+		AC_ARG_WITH([python-version],
+		  AS_HELP_STRING([--with-python-version = PYTHONVERSION],[python version.]),
+		  [PYTHONVERSION=$withval],[PYTHONVERSION=""])
+		AC_MSG_CHECKING(for python version)
+
+		dnl recover major: 
+		PYTHON_MAJOR=${PYTHONVERSION%.*}
+
+		if test x$PYTHON_MAJOR = x3; then
+			dnl are we running python 3?
+			HAVE_PYTHON3="yes"
+		fi
+		AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major])
+		AC_MSG_RESULT($PYTHON_MAJOR)
+	fi
+	AM_CONDITIONAL([PYTHON3], [test x$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.]),
+	  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)
+	AC_MSG_CHECKING(for python-numpy)
 	
 	if test -d "$PYTHON_NUMPY_ROOT"; then
@@ -364,7 +374,7 @@
 	dnl chaco{{{
 	AC_ARG_WITH([chaco-dir],
-	  AS_HELP_STRING([--with-chaco-dir = DIR], [chaco root directory.]),
+	  AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]),
 	  [CHACO_ROOT=$withval],[CHACO_ROOT=""]) 
-	AC_MSG_CHECKING(for Chaco)
+	AC_MSG_CHECKING(for chaco)
 	
 	if test -d "$CHACO_ROOT"; then
@@ -386,7 +396,7 @@
 	dnl scotch{{{
 	AC_ARG_WITH([scotch-dir],
-	  AS_HELP_STRING([--with-scotch-dir = DIR], [scotch root directory.]),
+	  AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]),
 	  [SCOTCH_ROOT=$withval],[SCOTCH_ROOT=""]) 
-	AC_MSG_CHECKING(for Scotch)
+	AC_MSG_CHECKING(for scotch)
 	
 	if test -d "$SCOTCH_ROOT"; then
@@ -408,7 +418,7 @@
 	dnl adolc{{{
 	AC_ARG_WITH([adolc-dir],
-		AS_HELP_STRING([--with-adolc-dir = DIR], [adolc root directory.]),
+		AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]),
 		[ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) 
-	AC_MSG_CHECKING(for ADOLC)
+	AC_MSG_CHECKING(for adolc)
 
 	if test "x$ADOLC_ROOT" = "xno"; then
@@ -436,7 +446,7 @@
 	dnl adic2{{{
 	AC_ARG_WITH([adic2-dir],
-	  AS_HELP_STRING([--with-adic2-dir = DIR], [adic2 root directory.]),
+	  AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]),
 	  [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) 
-	AC_MSG_CHECKING(for ADIC2)
+	AC_MSG_CHECKING(for adic2)
 
 	if test "x$ADIC2_ROOT" = "xno"; then
@@ -464,7 +474,7 @@
 	dnl gsl{{{
 	AC_ARG_WITH([gsl-dir],
-	  AS_HELP_STRING([--with-gsl-dir = DIR], [gsl root directory.]),
+	  AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]),
 	  [GSL_ROOT=$withval],[GSL_ROOT=""]) 
-	AC_MSG_CHECKING(for Gsl)
+	AC_MSG_CHECKING(for gsl)
 	
 	if test -d "$GSL_ROOT"; then
@@ -487,7 +497,7 @@
 	dnl rose{{{
 	AC_ARG_WITH([rose-dir],
-	  AS_HELP_STRING([--with-rose-dir = DIR], [rose root directory.]),
+	  AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]),
 	  [ROSE_ROOT=$withval],[ROSE_ROOT=""]) 
-	AC_MSG_CHECKING(for Rose)
+	AC_MSG_CHECKING(for rose)
 	
 	if test -d "$ROSE_ROOT"; then
@@ -510,10 +520,10 @@
 	dnl metis{{{
 	AC_ARG_WITH([metis-dir],
-	  AS_HELP_STRING([--with-metis-dir = DIR],[metis root directory. necessary for serial build]),
+	  AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]),
 	  [METIS_ROOT=$withval],[METIS_ROOT=""])
 
 	if test -d "$METIS_ROOT"; then
 
-		AC_MSG_CHECKING(for Metis headers and libraries in $METIS_ROOT)
+		AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT)
 
 		dnl first figure out version of metis: does the VERSION file exist?
@@ -568,10 +578,5 @@
 		HAVE_METIS=no
 	fi
-
-	if test $HAVE_METIS = no; then
-		AC_MSG_ERROR([--with-metis-dir  missing. Metis is needed to run ISSM]);
-	else
-		AC_MSG_RESULT($HAVE_METIS)
-	fi
+	AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes])
 	dnl }}}
 	dnl mpi{{{
@@ -582,5 +587,5 @@
 	
 	AC_ARG_WITH([mpi-include],
-	  AS_HELP_STRING([--with-mpi-include = DIR],[mpi include directory, necessary for parallel build]),
+	  AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]),
 	  [MPI_INCLUDE=$withval],[MPI_INCLUDE=""])
 	
@@ -591,4 +596,5 @@
 			HAVE_MPI=no
 		else
+			HAVE_MPI=yes
 			MPIINCL=-I"$MPI_INCLUDE/"
 			AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
@@ -598,13 +604,14 @@
 		fi
 	fi
-	AC_MSG_RESULT(done)
+	AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes])
+	AC_MSG_RESULT($HAVE_MPI)
 	dnl }}}
 	dnl petsc{{{
 	AC_ARG_WITH([petsc-dir],
-	  AS_HELP_STRING([--with-petsc-dir = DIR],[PETSc root directory, necessary for parallel build]),
+	  AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]),
 	  [PETSC_ROOT=$withval],[PETSC_ROOT=""])
 		
 	if test -d "$PETSC_ROOT"; then
-		AC_MSG_CHECKING(for PETSc version)
+		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'`
@@ -614,5 +621,5 @@
 
 		PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' `
-		AC_MSG_CHECKING(wether PETSc is the development version)
+		AC_MSG_CHECKING(whether petsc is the development version)
 		if test x$PETSC_VERSION_DATE_HG = xunknown; then
 			AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev])
@@ -624,8 +631,8 @@
 	
 	AC_ARG_WITH([petsc-arch],
-	  AS_HELP_STRING([--with-petsc-arch = DIR],[PETSc arch , necessary for parallel build]),
+	  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)
+	AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH)
 	
 	if test -d "$PETSC_ROOT"; then
@@ -671,7 +678,7 @@
 	dnl tao{{{
 	AC_ARG_WITH([tao-dir],
-		AS_HELP_STRING([--with-tao-dir = DIR], [tao root directory.]),
+		AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]),
 		[TAO_ROOT=$withval],[TAO_ROOT=""]) 
-	AC_MSG_CHECKING(for Tao)
+	AC_MSG_CHECKING(for tao)
 
 	if test -d "$TAO_ROOT"; then
@@ -689,33 +696,10 @@
 	AC_MSG_RESULT($HAVE_TAO)
 	dnl }}}
-	dnl mpiuni{{{
-	dnl when running in serial mode, MPI must be ignored, and set to internal petsc mpiuni: 
-	if test "$PARALLEL_VALUE" = "no" ; then
-		HAVE_MPI=yes
-		MPIINCL=-I"$PETSC_ROOT/include/mpiuni"
-
-		case "${host_os}" in
-			*cygwin*)
-			dnl MPILIB="-link -LIBPATH:\"$PETSC_ROOT/$PETSC_ARCH/lib\" -LIBPATH:\"$PETSC_ROOT/lib\" -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libmpiuni.lib"
-			;;
-			*linux*)
-			MPILIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lmpiuni"
-			;;
-			*darwin*)
-			MPILIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -L$PETSC_ROOT/lib/$PETSC_ARCH -lmpiuni"
-			;;
-		esac
-								  
-		AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
-		AC_SUBST([MPIINCL])
-		AC_SUBST([MPILIB])
-	fi
-	dnl }}}
 	dnl slepc{{{
 	AC_ARG_WITH([slepc-dir],
-	  AS_HELP_STRING([--with-slepc-dir = DIR],[slepc root directory]),
+	  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)
+	AC_MSG_CHECKING(for slepc headers and libraries in $SLEPC_ROOT)
 	if test -d "$SLEPC_ROOT"; then
 		HAVE_SLEPC=yes
@@ -733,8 +717,8 @@
 	dnl shapelib{{{
 	AC_ARG_WITH([shapelib-dir],
-	  AS_HELP_STRING([--with-shapelib-dir = DIR], [shapelib root directory]),
+	  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)
+	AC_MSG_CHECKING(for shapelib headers and libraries in $SHAPELIB_ROOT)
 	if test -d "$SHAPELIB_ROOT"; then
 
@@ -754,8 +738,8 @@
 	dnl scalapack{{{
 	AC_ARG_WITH([scalapack-dir],
-	  AS_HELP_STRING([--with-scalapack-dir = DIR],[scalapack root directory]),
+	  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)
+	AC_MSG_CHECKING(for scalapack headers and libraries in $SCALAPACK_ROOT)
 	if test -d "$SCALAPACK_ROOT"; then
 
@@ -773,8 +757,8 @@
 	dnl blas{{{
 	AC_ARG_WITH([blas-lapack-dir],
-	  AS_HELP_STRING([--with-blas-lapack-dir = DIR],[blas-lapack root directory]),
+	  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)
+	AC_MSG_CHECKING(for blas and lapack headers and libraries in $BLASLAPACK_ROOT)
 	if test -d "$BLASLAPACK_ROOT"; then
 
@@ -806,5 +790,5 @@
 	dnl mkl{{{
 	AC_ARG_WITH([mkl-dir],
-	  AS_HELP_STRING([--with-mkl-dir = DIR],[mkl root directory]),
+	  AS_HELP_STRING([--with-mkl-dir=DIR],[mkl root directory]),
 	  [MKL_ROOT=$withval],[MKL_ROOT=""])
 			  
@@ -825,8 +809,9 @@
 	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_MSG_CHECKING(for Plapack libraries)
 	
 	AC_ARG_WITH([plapack-include],
@@ -834,5 +819,4 @@
 							 [plapack include ]),
 			  [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""])
-	AC_MSG_CHECKING(for Plapack headers)
 	  
 	if test -n "$PLAPACK_LIB"; then
@@ -857,8 +841,8 @@
 	dnl mumps{{{
 	AC_ARG_WITH([mumps-dir],
-	  AS_HELP_STRING([--with-mumps-dir = DIR],[mumps root directory]),
+	  AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]),
 	  [MUMPS_ROOT=$withval],[MUMPS_ROOT=""])
 			  
-	AC_MSG_CHECKING(for Mumps headers and libraries in $MUMPS_ROOT)
+	AC_MSG_CHECKING(for mumps headers and libraries in $MUMPS_ROOT)
 	if test -d "$MUMPS_ROOT"; then
 
@@ -882,8 +866,8 @@
 	dnl blacs{{{
 	AC_ARG_WITH([blacs-dir],
-		AS_HELP_STRING([--with-blacs-dir = DIR],[blacs root directory]),
+		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)
+	AC_MSG_CHECKING(for blacs headers and libraries in $BLACS_ROOT)
 	if test -d "$BLACS_ROOT"; then
 
@@ -903,8 +887,8 @@
 	dnl hypre{{{
 	AC_ARG_WITH([hypre-dir],
-	  AS_HELP_STRING([--with-hypre-dir = DIR],[hypre root directory]),
+	  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)
+	AC_MSG_CHECKING(for hypre headers and libraries in $HYPRE_ROOT)
 	if test -d "$HYPRE_ROOT"; then
 
@@ -924,8 +908,8 @@
 	dnl ml{{{
 	AC_ARG_WITH([ml-dir],
-	  AS_HELP_STRING([--with-ml-dir = DIR],[ml root directory]),
+	  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)
+	AC_MSG_CHECKING(for ml headers and libraries in $ML_ROOT)
 	if test -d "$ML_ROOT"; then
 
@@ -960,19 +944,34 @@
 	dnl }}}
 	dnl fortran{{{
-	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
+	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
-		FORTRANLIB="$FORTRAN_LIB"
-
-		AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src])
-		AC_SUBST([FORTRANLIB])
-	fi
-	AC_MSG_RESULT(done)
+
+		AC_DEFINE([_HAVE_FORTRAN_],[1],[with fortran capability])
+	else
+		HAVE_FORTRAN=no
+	fi
+	AM_CONDITIONAL([FORTRAN], [test x$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
+			FORTRANLIB="$FORTRAN_LIB"
+			AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src])
+			AC_SUBST([FORTRANLIB])
+		fi
+		AC_MSG_RESULT(done)
+	fi
 	dnl }}}
 	dnl graphics{{{
@@ -1229,5 +1228,5 @@
 	AC_MSG_CHECKING(consistency between all libraries)
 	
-	dnl check that if petsc is requested in parallel, mpi should be specified
+	dnl check that if petsc is requested , mpi should be specified
 	if test "$HAVE_PETSC" = "yes" ; then
 		if test "$HAVE_MPI" = "NO";  then
@@ -1236,15 +1235,22 @@
 	fi
 
-	dnl check that we have either python or matlab support if we only compile serially
-	if test "$PARALLEL_VALUE" = "no"  && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then
-		AC_MSG_ERROR([need at least python or matlab support to compile only in serial mode!]);
-	fi
-
-	dnl check that we don't have with-matlab and with-python at the same time
-	if test "$HAVE_PYTHON" = "yes" ; then
-		if test "$HAVE_MATLAB" = "yes";  then
-			AC_MSG_ERROR([cannot create matlab and python wrappers simultaneously! Please choose one or the other.]);
-		fi
-	fi
+	dnl check that we have either python or matlab support if we compile the modules
+	if test "$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 we have python version if python compile is specified
+	if test "$HAVE_PYTHON" = "yes"  && test "$PYTHONVERSION" = "" ; then
+	AC_MSG_ERROR([need python-version if python compile is required!]);
+	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)
@@ -1257,5 +1263,5 @@
 	  AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]),
 	  [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2"]) 
-	AC_MSG_CHECKING(for C++ optimization flags)
+	AC_MSG_CHECKING(for c++ optimization flags)
 	AC_SUBST([CXXOPTFLAGS])
 	AC_MSG_RESULT(done)
Index: issm/trunk/scripts/DownloadExternalPackage.py
===================================================================
--- issm/trunk/scripts/DownloadExternalPackage.py	(revision 12332)
+++ issm/trunk/scripts/DownloadExternalPackage.py	(revision 12332)
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+# -*- coding: ISO-8859-1 -*-
+
+import os,sys
+import urllib
+
+#Check inputs
+if(len(sys.argv)!=3): raise NameError('usage: ./DownloadExternalPackage.py URL localfile')
+
+url=sys.argv[1];
+localFile=sys.argv[2]
+
+#Remove file if it already exists
+if os.path.exists(localFile):
+	print "File "+ localFile +" already exists and will not be downloaded..."
+	sys.exit()
+
+#Try to download from url
+httpfail=-1
+try:
+	print "Fetching %s" % localFile
+	urllib.urlretrieve(url,localFile)
+	httpfail=0
+except Exception, e:
+	httpfail=1
+
+#Error message in case it failed
+if (httpfail):
+	failureMessage = '''
+===========================================================================
+Unable to download package %s from: %s
+* If URL specified manually - perhaps there is a typo?
+* If your network is disconnected - please reconnect 
+* Alternatively, you can download the above URL manually
+===========================================================================
+''' % (localFile,url)
+	raise RuntimeError(failureMessage)
Index: issm/trunk/scripts/GenerateReferences.sh
===================================================================
--- issm/trunk/scripts/GenerateReferences.sh	(revision 12331)
+++ issm/trunk/scripts/GenerateReferences.sh	(revision 12332)
@@ -16,5 +16,5 @@
 \begin{document}
 \nocite{$CITE}
-\bibliography{$ISSM_DIR/publications/bibtex/references}
+\bibliography{$JPL_SVN/publications/bibtex/references}
 \end{document}
 END
@@ -29,5 +29,5 @@
 mv references.bak2 references.bbl
 echo "Converting to rtf"
-$ISSM_TIER/externalpackages/latex2rtf/install/latex2rtf -P $ISSM_TIER/externalpackages/latex2rtf/install/cfg/ references
+$ISSM_DIR/externalpackages/latex2rtf/install/latex2rtf -P $ISSM_DIR/externalpackages/latex2rtf/install/cfg/ references
 
 #Remove all but rtf file
Index: issm/trunk/scripts/archive.sh
===================================================================
--- issm/trunk/scripts/archive.sh	(revision 12331)
+++ issm/trunk/scripts/archive.sh	(revision 12332)
@@ -10,5 +10,5 @@
 
 #Cleanup code 
-cd $ISSM_TIER
+cd $ISSM_DIR
 make clean
 make distclean
@@ -18,5 +18,5 @@
 
 #Create tar file, with today's date in the title;
-cd $ISSM_TIER/..
+cd $ISSM_DIR/..
 today=`today_date`
-tar zcvf issm-3.0-$today.tar.gz  `basename $ISSM_TIER`
+tar zcvf issm-3.0-$today.tar.gz  `basename $ISSM_DIR`
Index: issm/trunk/scripts/automakererun.sh
===================================================================
--- issm/trunk/scripts/automakererun.sh	(revision 12331)
+++ issm/trunk/scripts/automakererun.sh	(revision 12332)
@@ -4,8 +4,8 @@
 
 
- ACLOCAL="$ISSM_TIER/externalpackages/automake/install/bin/aclocal"
-AUTOCONF="$ISSM_TIER/externalpackages/autoconf/install/bin/autoconf"
-AUTOHEAD="$ISSM_TIER/externalpackages/autoconf/install/bin/autoheader"
-AUTOMAKE="$ISSM_TIER/externalpackages/automake/install/bin/automake"
+ ACLOCAL="$ISSM_DIR/externalpackages/automake/install/bin/aclocal"
+AUTOCONF="$ISSM_DIR/externalpackages/autoconf/install/bin/autoconf"
+AUTOHEAD="$ISSM_DIR/externalpackages/autoconf/install/bin/autoheader"
+AUTOMAKE="$ISSM_DIR/externalpackages/automake/install/bin/automake"
 
 echo "removing config.cach"
Index: issm/trunk/scripts/cloc2html.py
===================================================================
--- issm/trunk/scripts/cloc2html.py	(revision 12331)
+++ issm/trunk/scripts/cloc2html.py	(revision 12332)
@@ -4,6 +4,6 @@
 import sys, re, os
 
-ISSM_TIER=os.getenv('ISSM_TIER');
-if(not ISSM_TIER): raise NameError('ISSM_TIER undefined')
+ISSM_DIR=os.getenv('ISSM_DIR');
+if(not ISSM_DIR): raise NameError('ISSM_DIR undefined')
 
 infile  = open('temp','r')
Index: issm/trunk/scripts/convertmatlabclasses.py
===================================================================
--- issm/trunk/scripts/convertmatlabclasses.py	(revision 12331)
+++ issm/trunk/scripts/convertmatlabclasses.py	(revision 12332)
@@ -4,8 +4,8 @@
 
 #get names of all directories to process
-ISSM_TIER=os.getenv('ISSM_TIER');
-if(not ISSM_TIER): raise NameError('ISSM_TIER undefined')
-newclassesdir = ISSM_TIER + '/src/m/classes/'
-oldclassesdir = ISSM_TIER + '/src/m/oldclasses/'
+ISSM_DIR=os.getenv('ISSM_DIR');
+if(not ISSM_DIR): raise NameError('ISSM_DIR undefined')
+newclassesdir = ISSM_DIR + '/src/m/classes/'
+oldclassesdir = ISSM_DIR + '/src/m/oldclasses/'
 
 #make new directory
Index: issm/trunk/scripts/dailyrun.sh
===================================================================
--- issm/trunk/scripts/dailyrun.sh	(revision 12331)
+++ issm/trunk/scripts/dailyrun.sh	(revision 12332)
@@ -54,15 +54,15 @@
 #Prepare run
 #Windows hack for startup.m {{{1
-#windows environments: ISSM_TIER_WIN variable not correctly picked up when using 
-#the cron job. just get startup to take the ISSM_TIER variable as the pwd:
+#windows environments: ISSM_DIR_WIN variable not correctly picked up when using 
+#the cron job. just get startup to take the ISSM_DIR variable as the pwd:
 if [ "$OS" = "winxp32" ]
 then
-	cat startup.m | sed 's/clear status/clear status; ISSM_TIER=pwd;/g' > startup.m.bak
+	cat startup.m | sed 's/clear status/clear status; ISSM_DIR=pwd;/g' > startup.m.bak
 	mv startup.m.bak startup.m
 fi
 #}}}
 #create softlink to startup {{{1
-cd $ISSM_TIER/test/NightlyRun/
-ln -s $ISSM_TIER/startup.m .
+cd $ISSM_DIR/test/NightlyRun/
+ln -s $ISSM_DIR/startup.m .
 #}}}
 #Create dailylog directory and info.log {{{1
@@ -70,7 +70,7 @@
 INSTALL_TIME=$(timer)
 ELAPSED_INSTALL=$(timer $START_TIME)
-rm -rf $ISSM_TIER/dailylog
-mkdir  $ISSM_TIER/dailylog
-cat << END > $ISSM_TIER/dailylog/info.log
+rm -rf $ISSM_DIR/dailylog
+mkdir  $ISSM_DIR/dailylog
+cat << END > $ISSM_DIR/dailylog/info.log
 today:     $(echo $TODAY)
 user:      $(echo $USER)
@@ -95,8 +95,8 @@
 do
 	#Launch matlab and the daily run script
-	cat > $ISSM_TIER/dailylog/matlab_run$i.m << EOF
+	cat > $ISSM_DIR/dailylog/matlab_run$i.m << EOF
 	warning off %necessary to avoid a info.log of several Go for parallel runs
 	try,
-	cd $ISSM_TIER/test/NightlyRun
+	cd $ISSM_DIR/test/NightlyRun
 	startup;
 	$(if [ "$NROPTIONS" = ""  ]
@@ -111,5 +111,5 @@
 		directory=strsplit(pwd,'/');
 		message=getReport(me)
-		fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at');
+		fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at');
 		fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
 		fprintf(fid,'%s',message);
@@ -121,5 +121,5 @@
 
 	#Start run from dailylog directory
-	cd $ISSM_TIER/dailylog/
+	cd $ISSM_DIR/dailylog/
 
 	#Start test
@@ -132,5 +132,5 @@
 #}}}
 #concatenate all reports {{{1
-cd $ISSM_TIER/dailylog/
+cd $ISSM_DIR/dailylog/
 mv matlab_log1.log  matlab_log.log
 for (( i=2;i<=$NUMCPUS_RUN;i++ ))
@@ -149,5 +149,5 @@
 ELAPSED_RUN=$(timer $INSTALL_TIME)
 ELAPSED_TOTAL=$(timer $START_TIME)
-cat << END >>  $ISSM_TIER/dailylog/info.log
+cat << END >>  $ISSM_DIR/dailylog/info.log
 elapsed_run:   $(echo $ELAPSED_RUN)
 elapsed_total: $(echo $ELAPSED_TOTAL)
@@ -158,7 +158,7 @@
 #Send Report
 #Build html report {{{1
-cd $ISSM_TIER/dailylog/
+cd $ISSM_DIR/dailylog/
 sh ../scripts/report.sh
-ln -s $ISSM_TIER/dailylog/report.html $INIT_PATH
-echo "html report located in $ISSM_TIER/dailylog/report.html and $INIT_PATH/report.html"
+ln -s $ISSM_DIR/dailylog/report.html $INIT_PATH
+echo "html report located in $ISSM_DIR/dailylog/report.html and $INIT_PATH/report.html"
 #}}}
Index: issm/trunk/scripts/getloc.sh
===================================================================
--- issm/trunk/scripts/getloc.sh	(revision 12331)
+++ issm/trunk/scripts/getloc.sh	(revision 12332)
@@ -1,12 +1,12 @@
 #!/bin/bash
 #get number of lines of code
-cloc-1.55.pl $ISSM_TIER/src $ISSM_TIER/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp
+cloc-1.55.pl $ISSM_DIR/src $ISSM_DIR/m4 --exclude-dir=.svn --exclude-ext=exp --exclude-lang=make --out=temp
 cat temp
 ./cloc2html.py
 rm temp
 
-cat $ISSM_TIER/src/dox/issm.dox | sed '/<table/,//d' > input1
-cat $ISSM_TIER/src/dox/issm.dox | sed '1,/<\/table>/d' > input2
-cat input1 temp.html input2 > $ISSM_TIER/src/dox/issm.dox
+cat $ISSM_DIR/src/dox/issm.dox | sed '/<table/,//d' > input1
+cat $ISSM_DIR/src/dox/issm.dox | sed '1,/<\/table>/d' > input2
+cat input1 temp.html input2 > $ISSM_DIR/src/dox/issm.dox
 rm input1 input2 temp.html
 
@@ -19,10 +19,10 @@
 #OLDER MANUAL VESION
 #get Matlab number of lines
-cd $ISSM_TIER/src/m
+cd $ISSM_DIR/src/m
 M_LOC=$(find . -name "*.m" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}');
 echo "Matlab code: $M_LOC"
 
 #get C/CPP number of lines
-cd $ISSM_TIER/src
+cd $ISSM_DIR/src
 CPP_LOC=$(find . -name "*.cpp" -exec wc -l '{}' \; | awk '{ sum += $1 } END { print sum}');
 echo "C++    code: $CPP_LOC"
Index: issm/trunk/scripts/issmconfiguration.sh
===================================================================
--- issm/trunk/scripts/issmconfiguration.sh	(revision 12331)
+++ issm/trunk/scripts/issmconfiguration.sh	(revision 12332)
@@ -7,6 +7,6 @@
 presendir=`pwd`
 
-if test -d "$ISSM_TIER/configs" ; then
-	cd $ISSM_TIER/configs
+if test -d "$ISSM_DIR/configs" ; then
+	cd $ISSM_DIR/configs
 	LIST=`ls`
 	
@@ -40,5 +40,5 @@
 	echo ""
 
-	cd $ISSM_TIER 
+	cd $ISSM_DIR 
 	source ./scripts/automakererun.sh 
 	source configs/$configurename
@@ -56,3 +56,3 @@
 
 
-#alias aut='a=`pwd` && cd $ISSM_TIER && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh'
+#alias aut='a=`pwd` && cd $ISSM_DIR && ./scripts/automakererun.sh && ./configs/config-macosx64-larour-nopetsc.sh'
Index: issm/trunk/scripts/mail
===================================================================
--- issm/trunk/scripts/mail	(revision 12332)
+++ issm/trunk/scripts/mail	(revision 12332)
@@ -0,0 +1,158 @@
+#!/bin/sh
+
+# This is a shell script to emulate the standard mail(1) aka mailx(1)
+# aka Mail(1) tool usage for sending emails. This shell script is not
+# a client for checking or reading mail. Also, this version of mail
+# does not touch any mail boxes.
+
+# Copyright (c) 2003 by Jeremy C. Reed
+# This software is provided "as is" without any warranties. You may
+# redistribute and use this source, with or without modification,
+# as long as you include this copyright and disclaimer.
+
+# To do: some switches to consider:
+# -v  display details of delivery
+# -E  do not send empty messages
+# -c  send carbon copies to users
+# -b  send blind carbon copies
+
+# todo: test if read can read in long enough lines
+# some shells may have limit of 256 characters per read?
+ 
+SENDMAIL=sendmail  # set to path of your sendmail(8) command
+SENDMAIL_ARGS="-t -i" # -i is so dot doesn't terminate message
+                      # -t is to get recipients from headers
+
+unset subject
+unset to_addr
+dontsendempty=0
+
+about ()
+{
+  echo "This is mailx.sh version 0.03. This is simple, shell script"
+  echo "to implement mailx(1) functionality for sending mail. It does"
+  echo "not provide an interface for checking or reading email messages."
+  echo
+
+  # maybe do this without forking a command
+  mailname=$( basename $0 )
+
+  if [ -n "$1" ] ; then
+    echo "$mailname: $1" 1>&2
+  fi
+
+  echo "Usage: $mailname [-s subject] to-addr ..." 1>&2
+
+  if [ -n "$1" ] ; then
+    if [ -n "$2" ] ; then 
+      exit $2
+    fi
+    exit 100
+  fi
+
+  exit 0
+}
+
+if [ $# -eq 0 ] ; then
+  about "Sorry, this is not a mail reader." 1
+fi
+
+while [ -n "$1" ] ; do
+  case "$1" in
+  -*)
+      if [ "$1" = "-s" ] ; then
+        if [ -z "$2" ] ; then
+          about "The \"-s\" option requires an argument." 4
+        fi
+        subject="$2"
+        shift
+      elif [ "$1" = "-u" -o "$1" = "-f" ] ; then
+        about "Sorry, this is not a mail reader." 2
+#      elif [ "$1" = "-E" ] ; then
+# this probably needs to have entire message saved to temp file first
+#        dontsendempty=1
+      else
+#        about "unknown option -- $1" 3
+        about "Switch \"$1\" is not implemented." 3
+      fi
+      ;;
+  *)  if [ -n "$to_addr" ] ; then
+        to_addr="${to_addr}, $1"
+      else
+        to_addr="$1"
+      fi
+      ;;
+  esac
+  shift
+done
+
+
+if [ -t 0 ] ; then   # no piped in standard input
+  if [ -z "$subject" ] ; then
+    echo -n "Subject: "
+    OLD_IFS=$IFS
+    IFS=""
+    read -r subject
+    IFS=$OLD_IFS
+  fi
+fi
+
+if [ -z "$to_addr" ] ; then
+  about "No recipients specified." 6
+#  about "You must specify recipients." 6
+fi
+
+# generate SMTP headers
+
+# mail(1) doesn't seem to set date
+#date +"Date: %a, %e %b %G %T %z"
+## maybe pipe though sed to get rid of extra space
+## before single digit day of month?
+
+{
+# if [ -n "$to_addr" ] ; then
+echo "To: ${to_addr}"
+# fi
+
+if [ -n "$subject" ] ; then
+  echo "Subject: $subject"
+fi
+
+# end of headers
+echo ""
+
+# output
+line_count=0
+OLD_IFS=$IFS
+IFS=""
+while read -r line ; do
+  # finish if manual, non-piped input is a period on a line by itself
+  if [ "$line" = "." -a -t 0 ] ; then
+      break
+  fi
+  echo "$line"
+  line_count=$(( line_count + 1 ))
+done
+
+IFS=$OLD_IFS
+
+if [ -t 0 ] ; then   # no piped in standard input
+  echo "EOT" 1>&2
+fi
+
+# later add switch to not send mail by exiting
+if [ "$line_count" -eq 0 ] ; then
+#  if [ "$dontsendempty" -eq 1 ] ; then
+# todo this, have it save to temp file and then send to sendmail as needed
+#    # No message, so just exit cleanly
+#    exit 0
+#  fi
+  if [ -z "$subject" ] ; then
+    echo "No message, no subject; hope that's ok" 1>&2
+  else
+    echo "Null message body; hope that's ok" 1>&2
+  fi
+fi
+
+} | $SENDMAIL $SENDMAIL_ARGS
+
Index: issm/trunk/scripts/report.sh
===================================================================
--- issm/trunk/scripts/report.sh	(revision 12331)
+++ issm/trunk/scripts/report.sh	(revision 12332)
@@ -49,5 +49,5 @@
 
 #create some variables
-if [ $(ls -1 $ISSM_TIER/bin | wc -l) -le 20 ];
+if [ $(ls -1 $ISSM_DIR/bin | wc -l) -le 20 ];
 then
 	IS_INSTALL=0
Index: issm/trunk/scripts/run.sh
===================================================================
--- issm/trunk/scripts/run.sh	(revision 12331)
+++ issm/trunk/scripts/run.sh	(revision 12332)
@@ -6,6 +6,6 @@
 MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8
 #create softlink to startup {{{1
-cd $ISSM_TIER/test/NightlyRun/
-ln -s $ISSM_TIER/startup.m .
+cd $ISSM_DIR/test/NightlyRun/
+ln -s $ISSM_DIR/startup.m .
 #}}}
 
@@ -14,8 +14,8 @@
 do
 	#Launch matlab and the daily run script
-	cat > $ISSM_TIER/dailylog/matlab_run$i.m << EOF
+	cat > $ISSM_DIR/dailylog/matlab_run$i.m << EOF
 	warning off %necessary to avoid a daily.log of several Go for parallel runs
 	try,
-		cd $ISSM_TIER/test/NightlyRun
+		cd $ISSM_DIR/test/NightlyRun
 		startup;
 		$(if [ "$NROPTIONS" = ""  ]
@@ -30,5 +30,5 @@
 		directory=strsplit(pwd,'/');
 		message=getReport(me)
-		fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at');
+		fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at');
 		fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
 		fprintf(fid,'%s',message);
@@ -39,5 +39,5 @@
 
 	#Start run from dailylog directory
-	cd $ISSM_TIER/dailylog/
+	cd $ISSM_DIR/dailylog/
 
 	#Start test
Index: issm/trunk/scripts/windowsbuild.sh
===================================================================
--- issm/trunk/scripts/windowsbuild.sh	(revision 12331)
+++ issm/trunk/scripts/windowsbuild.sh	(revision 12332)
@@ -11,5 +11,5 @@
 today=`today_date`
 
-cd $ISSM_TIER/bin
+cd $ISSM_DIR/bin
 
 #Filter out .svn files
Index: issm/trunk/startup.m
===================================================================
--- issm/trunk/startup.m	(revision 12331)
+++ issm/trunk/startup.m	(revision 12332)
@@ -11,35 +11,35 @@
 lastwarn(''); 
 
-%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN
+%Recover ISSM_DIR , or if on a Windows machine, ISSM_DIR_WIN
 if ~ispc,
-	ISSM_TIER=getenv('ISSM_TIER');
+	ISSM_DIR=getenv('ISSM_DIR');
 else
-	ISSM_TIER=getenv('ISSM_TIER_WIN');
-	%ISSM_TIER='';
+	ISSM_DIR=getenv('ISSM_DIR_WIN');
+	%ISSM_DIR='';
 end
-if (isempty(ISSM_TIER)),
-	error('''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!');
+if (isempty(ISSM_DIR)),
+	error('''ISSM_DIR'' environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!');
 end
 
 %Now add all issm code paths necessary to run issm smoothly. 
 %We capture the error output, so that we can warn the user to update 
-%the variable ISSM_TIER in this file, in case it is not correctly setup. 
+%the variable ISSM_DIR in this file, in case it is not correctly setup. 
 
 %ISSM path
-addpath([ISSM_TIER '/src/m/utils/']); %loads recursivepath
-addpath([ISSM_TIER '/bin']);
-addpath(recursivepath([ISSM_TIER '/src/m']));
-addpath(recursivepath([ISSM_TIER '/externalpackages/scotch']));
-addpath(recursivepath([ISSM_TIER '/externalpackages/canos']));
-addpath(recursivepath([ISSM_TIER '/externalpackages/kml']));
-addpath(recursivepath([ISSM_TIER '/externalpackages/export_fig']));
-addpath(recursivepath([ISSM_TIER '/externalpackages/googleearthtoolbox']));
-addpath(recursivepath([ISSM_TIER '/externalpackages/cm_and_cb_utilities']));
+addpath([ISSM_DIR '/src/m/utils/']); %loads recursivepath
+addpath([ISSM_DIR '/bin']);
+addpath(recursivepath([ISSM_DIR '/src/m']));
+addpath(recursivepath([ISSM_DIR '/externalpackages/scotch']));
+addpath(recursivepath([ISSM_DIR '/externalpackages/canos']));
+addpath(recursivepath([ISSM_DIR '/externalpackages/kml']));
+addpath(recursivepath([ISSM_DIR '/externalpackages/export_fig']));
+addpath(recursivepath([ISSM_DIR '/externalpackages/googleearthtoolbox']));
+addpath(recursivepath([ISSM_DIR '/externalpackages/cm_and_cb_utilities']));
 
-clear ISSM_TIER;
+clear ISSM_DIR;
 
 %Check on any warning messages that might indicate that the paths were not correct. 
 if ~isempty(lastwarn),
-	fprintf('\n  Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n');
+	fprintf('\n  Error trying to setup ''ISSM'' code paths. Try and update the ISSM_DIR variable in your .cshrc or .bashrc!\n');
 	fprintf('  ''ISSM'' will not  work at all until this is resolved\n\n');
 else
Index: issm/trunk/startup.py
===================================================================
--- issm/trunk/startup.py	(revision 12331)
+++ issm/trunk/startup.py	(revision 12332)
@@ -5,27 +5,30 @@
 #  before handing over the prompt to the user if the environment variable
 #  PYTHONSTARTUP is defined:
-#  export PYTHONSTARTUP=$ISSM_TIER/startup.py
+#  export PYTHONSTARTUP=$ISSM_DIR/startup.py
 #  This startup script should be run by users before trying to use ISSM.
 
 import os,sys
 
- 
-#First check we are running python 3 at least 
-if sys.version_info[0] < 3:
-	print("ISSM can only work in Python 3. Exiting python")
-	sys.exit(1)
-
-#Recover ISSM_TIER, ISSM_DIR  and USERNAME
-ISSM_TIER=os.getenv('ISSM_TIER')
+#Recover ISSM_DIR and USERNAME
+ISSM_DIR=os.getenv('ISSM_DIR')
 USERNAME =os.getenv('USER')
-if(ISSM_TIER==None):
-	raise NameError('"ISSM_TIER" environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!')
+if(ISSM_DIR==None):
+	raise NameError('"ISSM_DIR" environment variable is empty! You should define ISSM_DIR in your .cshrc or .bashrc!')
 
 #Now add all issm code paths necessary to run issm smoothly. 
 #We capture the error output, so that we can warn the user to update 
-#the variable ISSM_TIER in this file, in case it is not correctly setup. 
+#the variable ISSM_DIR in this file, in case it is not correctly setup. 
 
 #ISSM path. Go through src/py and load everything we find  that looks like a python file
-for root,dirs,files in os.walk(ISSM_TIER+ '/src/py'):
+for root,dirs,files in os.walk(ISSM_DIR+ '/src/py'):
+	for file in files:
+		if file.find(".py") != -1:
+			if file.find(".pyc") == -1:
+				#add to path 
+				sys.path.append(root)
+				file=os.path.splitext(file)[0]
+				#__import__(file)
+
+for root,dirs,files in os.walk(ISSM_DIR+ '/src/m'):
 	for file in files:
 		if file.find(".py") != -1:
@@ -36,5 +39,5 @@
 				#__import__(file)
 				
-sys.path.append(ISSM_TIER + '/src/mex')
+sys.path.append(ISSM_DIR + '/src/modules/python')
 
 #Deal with scipy import: 
@@ -79,5 +82,6 @@
 from miscellaneous import *
 from private import *
-from TriMesh import *
+from triangle import *
+from setmask import *
 
 #}}}
Index: issm/trunk/test/NightlyRun/runme.m
===================================================================
--- issm/trunk/test/NightlyRun/runme.m	(revision 12331)
+++ issm/trunk/test/NightlyRun/runme.m	(revision 12332)
@@ -30,6 +30,6 @@
 %      md=runme('id',102,'procedure','model');
 
-%Get ISSM_TIER variable
-ISSM_TIER=issmtier();
+%Get ISSM_DIR variable
+ISSM_DIR=issmdir();
 
 %Check inputs
@@ -168,5 +168,5 @@
 					message=getReport(me2);
 					if strcmpi(output,'nightly')
-						fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at');
+						fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at');
 						fprintf(fid,'%s',message);
 						fprintf(fid,'\n------------------------------------------------------------------\n');
@@ -174,5 +174,5 @@
 						disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname));
 					elseif strcmpi(output,'daily');
-						fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at');
+						fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at');
 						fprintf(fid,'%s',message);
 						fprintf(fid,'\n------------------------------------------------------------------\n');
@@ -193,5 +193,5 @@
 		message=getReport(me);
 		if strcmpi(output,'nightly')
-			fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at');
+			fid=fopen([ISSM_DIR '/nightlylog/matlaberror.log'], 'at');
 			fprintf(fid,'%s',message);
 			fprintf(fid,'\n------------------------------------------------------------------\n');
@@ -199,5 +199,5 @@
 			disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A'));
 		elseif strcmpi(output,'daily');
-			fid=fopen([ISSM_TIER '/dailylog/matlaberror.log'], 'at');
+			fid=fopen([ISSM_DIR '/dailylog/matlaberror.log'], 'at');
 			fprintf(fid,'%s',message);
 			fprintf(fid,'\n------------------------------------------------------------------\n');
Index: issm/trunk/test/NightlyRun/test101.m
===================================================================
--- issm/trunk/test/NightlyRun/test101.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test101.py
===================================================================
--- issm/trunk/test/NightlyRun/test101.py	(revision 12331)
+++ 	(revision )
@@ -1,6 +1,0 @@
-from model import *
-from TriMesh import *
-
-md=model()
-[a,b,c,d,e]=TriMesh('../Exp/Square.exp',15000.0**2.0,True)
-print(a,b,c,d,e)
Index: issm/trunk/test/NightlyRun/test102.py
===================================================================
--- issm/trunk/test/NightlyRun/test102.py	(revision 12332)
+++ issm/trunk/test/NightlyRun/test102.py	(revision 12332)
@@ -0,0 +1,9 @@
+from model import *
+from triangle import *
+from setmask import *
+from parameterize import *
+
+md=model();
+md=triangle(md,'../Exp/Square.exp',50000);
+md=setmask(md,'all','');
+md=parameterize(md,'../Par/SquareShelfConstrained.py')
Index: issm/trunk/test/NightlyRun/test103.m
===================================================================
--- issm/trunk/test/NightlyRun/test103.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test105.m
===================================================================
--- issm/trunk/test/NightlyRun/test105.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test107.m
===================================================================
--- issm/trunk/test/NightlyRun/test107.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,2);
-md.cluster=none;
-md=setflowequation(md,'stokes','all');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test109.m
===================================================================
--- issm/trunk/test/NightlyRun/test109.m	(revision 12331)
+++ 	(revision )
@@ -1,13 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test111.m
===================================================================
--- issm/trunk/test/NightlyRun/test111.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=meshconvert(md);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.prognostic.stabilization=3;
-md.prognostic.spcthickness=md.geometry.thickness;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test113.m
===================================================================
--- issm/trunk/test/NightlyRun/test113.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md=extrude(md,5,3);
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test115.m
===================================================================
--- issm/trunk/test/NightlyRun/test115.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.timestepping.time_step=0;
-md.cluster=none;
-md=solve(md,ThermalSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.ThermalSolution.Temperature),...
-	(md.results.ThermalSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test117.m
===================================================================
--- issm/trunk/test/NightlyRun/test117.m	(revision 12331)
+++ 	(revision )
@@ -1,19 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test119.m
===================================================================
--- issm/trunk/test/NightlyRun/test119.m	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-
-
-
-
-
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test121.m
===================================================================
--- issm/trunk/test/NightlyRun/test121.m	(revision 12331)
+++ 	(revision )
@@ -1,45 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test123.m
===================================================================
--- issm/trunk/test/NightlyRun/test123.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,SurfaceSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'SurfaceSlopeX','SurfaceSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeX),...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test125.m
===================================================================
--- issm/trunk/test/NightlyRun/test125.m	(revision 12331)
+++ 	(revision )
@@ -1,15 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,SurfaceSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'SurfaceSlopeX','SurfaceSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeX),...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test127.m
===================================================================
--- issm/trunk/test/NightlyRun/test127.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BedSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'BedSlopeX','BedSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.BedSlopeSolution.BedSlopeX),...
-	(md.results.BedSlopeSolution.BedSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test129.m
===================================================================
--- issm/trunk/test/NightlyRun/test129.m	(revision 12331)
+++ 	(revision )
@@ -1,15 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BedSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'BedSlopeX','BedSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.BedSlopeSolution.BedSlopeX),...
-	(md.results.BedSlopeSolution.BedSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test131.m
===================================================================
--- issm/trunk/test/NightlyRun/test131.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-%Add boundary conditions on thickness on the border
-pos=find(md.mesh.vertexonboundary);
-md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.BalancethicknessSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test133.m
===================================================================
--- issm/trunk/test/NightlyRun/test133.m	(revision 12331)
+++ 	(revision )
@@ -1,17 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,5,1);
-%Add boundary conditions on thickness on the border
-pos=find(md.mesh.vertexonboundary);
-md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.BalancethicknessSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test135.m
===================================================================
--- issm/trunk/test/NightlyRun/test135.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=meshconvert(md);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md.balancethickness.stabilization=3;
-md.initialization.vy=md.initialization.vy+400;
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.BalancethicknessSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test139.m
===================================================================
--- issm/trunk/test/NightlyRun/test139.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.timestepping.time_step=0;
-md.cluster=none;
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md=solve(md,EnthalpySolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Enthalpy','Waterfraction','Temperature'};
-field_tolerances={1e-13,1e-10,1e-13};
-field_values={...
-	(md.results.EnthalpySolution.Enthalpy),...
-	(md.results.EnthalpySolution.Waterfraction),...
-	(md.results.EnthalpySolution.Temperature),...
-	};
Index: issm/trunk/test/NightlyRun/test141.m
===================================================================
--- issm/trunk/test/NightlyRun/test141.m	(revision 12331)
+++ 	(revision )
@@ -1,30 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md.cluster=none;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md.thermal.isenthalpy=1;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Enthalpy1','Waterfraction1','Temperature1',...
-	'Enthalpy2','Waterfraction2','Temperature2',...
-	'Enthalpy3','Waterfraction3','Temperature3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Enthalpy),...
-	(md.results.TransientSolution(1).Waterfraction),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(2).Enthalpy),...
-	(md.results.TransientSolution(2).Waterfraction),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(3).Enthalpy),...
-	(md.results.TransientSolution(3).Waterfraction),...
-	(md.results.TransientSolution(3).Temperature),...
-	};
Index: issm/trunk/test/NightlyRun/test143.m
===================================================================
--- issm/trunk/test/NightlyRun/test143.m	(revision 12331)
+++ 	(revision )
@@ -1,53 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelfConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md.thermal.isenthalpy=1;
-md.thermal.stabilization=2;
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','Waterfraction1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','Waterfraction2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','Waterfraction3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-						1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-						1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).Enthalpy),...
-	(md.results.TransientSolution(1).Waterfraction),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).Enthalpy),...
-	(md.results.TransientSolution(2).Waterfraction),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).Enthalpy),...
-	(md.results.TransientSolution(3).Waterfraction),...
-	};
Index: issm/trunk/test/NightlyRun/test201.m
===================================================================
--- issm/trunk/test/NightlyRun/test201.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test203.m
===================================================================
--- issm/trunk/test/NightlyRun/test203.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test205.m
===================================================================
--- issm/trunk/test/NightlyRun/test205.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test207.m
===================================================================
--- issm/trunk/test/NightlyRun/test207.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,2);
-md.cluster=none;
-md=setflowequation(md,'stokes','all');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test209.m
===================================================================
--- issm/trunk/test/NightlyRun/test209.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','penalties');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test211.m
===================================================================
--- issm/trunk/test/NightlyRun/test211.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.timestepping.time_step=0;
-md.cluster=none;
-md=solve(md,ThermalSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.ThermalSolution.Temperature),...
-	(md.results.ThermalSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test213.m
===================================================================
--- issm/trunk/test/NightlyRun/test213.m	(revision 12331)
+++ 	(revision )
@@ -1,23 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature1','MeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test215.m
===================================================================
--- issm/trunk/test/NightlyRun/test215.m	(revision 12331)
+++ 	(revision )
@@ -1,33 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test217.m
===================================================================
--- issm/trunk/test/NightlyRun/test217.m	(revision 12331)
+++ 	(revision )
@@ -1,45 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test219.m
===================================================================
--- issm/trunk/test/NightlyRun/test219.m	(revision 12331)
+++ 	(revision )
@@ -1,45 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test221.m
===================================================================
--- issm/trunk/test/NightlyRun/test221.m	(revision 12331)
+++ 	(revision )
@@ -1,48 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'stokes','all');
-md.diagnostic.reltol=NaN;
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,...
-						1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,...
-						1e-08,1e-08,1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test223.m
===================================================================
--- issm/trunk/test/NightlyRun/test223.m	(revision 12331)
+++ 	(revision )
@@ -1,33 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'MaterialsRheologyBbar'};
-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.MaterialsRheologyBbar),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test225.m
===================================================================
--- issm/trunk/test/NightlyRun/test225.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'MaterialsRheologyBbar'};
-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.MaterialsRheologyB),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test227.m
===================================================================
--- issm/trunk/test/NightlyRun/test227.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'MaterialsRheologyBbar'};
-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.MaterialsRheologyB),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test229.m
===================================================================
--- issm/trunk/test/NightlyRun/test229.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'stokes','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'MaterialsRheologyBbar'};
-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.MaterialsRheologyB),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test233.m
===================================================================
--- issm/trunk/test/NightlyRun/test233.m	(revision 12331)
+++ 	(revision )
@@ -1,69 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-%redo the parameter file for this special shelf. 
-%constant thickness, constrained (vy=0) flow into an icefront, 
-%from 0 m/yr at the grounding line.
-
-%tighten
-md.diagnostic.restol=10^-4;
-
-%needed later
-ymin=min(md.mesh.y);
-ymax=max(md.mesh.y);
-xmin=min(md.mesh.x);
-xmax=max(md.mesh.x);
-
-di=md.materials.rho_ice/md.materials.rho_water;
-
-h=1000;
-md.geometry.thickness=h*ones(md.mesh.numberofvertices,1);
-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-
-%Initial velocity and pressure
-md.initialization.vx=zeros(md.mesh.numberofvertices,1);
-md.initialization.vy=zeros(md.mesh.numberofvertices,1);
-md.initialization.vz=zeros(md.mesh.numberofvertices,1);
-md.initialization.pressure=zeros(md.mesh.numberofvertices,1);
-
-%Materials
-md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1);
-md.materials.rheology_B=paterson(md.initialization.temperature);
-md.materials.rheology_n=3*ones(md.mesh.numberofelements,1);
-
-%Boundary conditions:
-md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1);
-md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1);
-md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1);
-
-%constrain flanks to 0 normal velocity
-pos=find(md.mesh.x==xmin | md.mesh.x==xmax);
-md.diagnostic.spcvx(pos)=0;
-md.diagnostic.spcvz(pos)=NaN;
-
-%constrain grounding line to 0 velocity
-pos=find(md.mesh.y==ymin);
-md.diagnostic.spcvx(pos)=0;
-md.diagnostic.spcvy(pos)=0;
-
-%icefront
-nodeonicefront=zeros(md.mesh.numberofvertices,1);
-pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:);
-diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
-md.diagnostic.icefront=diagnostic.icefront;
-
-md=solve(md,DiagnosticSolutionEnum);
-
-%create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292.
-%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3;
-%vy_c=ey_c.*md.mesh.y*md.constants.yts;
-
-%Fields and tolerances to track changes
-field_names     ={'Vy'};
-field_tolerances={1e-13};
-field_values={(md.results.DiagnosticSolution.Vy)};
Index: issm/trunk/test/NightlyRun/test235.m
===================================================================
--- issm/trunk/test/NightlyRun/test235.m	(revision 12331)
+++ 	(revision )
@@ -1,92 +1,0 @@
-md=squaremesh(model,1000000,1000000,5,5);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-%redo the parameter file for this special shelf. 
-%constant thickness, constrained (vy=0) flow into an icefront, 
-%from 0 m/yr at the grounding line.
-
-%needed later
-ymin=min(md.mesh.y);
-ymax=max(md.mesh.y);
-xmin=min(md.mesh.x);
-xmax=max(md.mesh.x);
-
-di=md.materials.rho_ice/md.materials.rho_water;
-
-h=1000;
-md.geometry.thickness=h*ones(md.mesh.numberofvertices,1);
-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-
-%Initial velocity and pressure
-md.initialization.vx=zeros(md.mesh.numberofvertices,1);
-md.initialization.vy=zeros(md.mesh.numberofvertices,1);
-md.initialization.vz=zeros(md.mesh.numberofvertices,1);
-md.initialization.pressure=zeros(md.mesh.numberofvertices,1);
-
-%Materials
-md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1);
-md.materials.rheology_B=paterson(md.initialization.temperature);
-md.materials.rheology_n=3*ones(md.mesh.numberofelements,1);
-
-%Boundary conditions:
-md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1);
-md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1);
-md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1);
-
-%constrain flanks to 0 normal velocity
-pos=find(md.mesh.x==xmin | md.mesh.x==xmax);
-md.diagnostic.spcvx(pos)=0;
-md.diagnostic.spcvz(pos)=NaN;
-
-%constrain grounding line to 0 velocity
-pos=find(md.mesh.y==ymin);
-md.diagnostic.spcvx(pos)=0;
-md.diagnostic.spcvy(pos)=0;
-
-%icefront
-nodeonicefront=zeros(md.mesh.numberofvertices,1);
-pos=find(md.mesh.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:);
-diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
-md.diagnostic.icefront=diagnostic.icefront;
-
-%partitioning
-md.qmu.numberofpartitions=md.mesh.numberofvertices;
-md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions);
-md.qmu.partition=md.qmu.partition-1;
-
-%Dakota options
-%variables
-md.qmu.variables.rheology_B=normal_uncertain('scaled_MaterialsRheologyB',1,.5);
-
-%responses
-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-
-%method
-md.qmu.method     =dakota_method('nond_l');
-
-%parameters
-md.qmu.params.direct=true;
-md.qmu.params.analysis_driver='diagnostic';
-md.qmu.params.evaluation_concurrency=1;
-md.qmu.params.interval_type='forward';
-
-%imperative! 
-md.diagnostic.reltol=10^-10; %tighten for qmu analysese
-md.qmu.isdakota=1;
-
-%solve
-md=solve(md,DiagnosticSolutionEnum,'overwrite','y');
-
-%Fields and tolerances to track changes
-md=tres(md,'dakota');
-md.results.dakota.importancefactors=importancefactors(md,'scaled_MaterialsRheologyB','MaxVel')';
-field_names     ={'importancefactors'};
-field_tolerances={1e-10};
-field_values={...
-         md.results.dakota.importancefactors,...
-	};
Index: issm/trunk/test/NightlyRun/test237.m
===================================================================
--- issm/trunk/test/NightlyRun/test237.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test239.m
===================================================================
--- issm/trunk/test/NightlyRun/test239.m	(revision 12331)
+++ 	(revision )
@@ -1,17 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',120000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,2,1);
-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test241.m
===================================================================
--- issm/trunk/test/NightlyRun/test241.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',120000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,2,1);
-md.diagnostic.viscosity_overshoot=0.0;
-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test243.m
===================================================================
--- issm/trunk/test/NightlyRun/test243.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.prognostic.hydrostatic_adjustment='Incremental';
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test245.m
===================================================================
--- issm/trunk/test/NightlyRun/test245.m	(revision 12331)
+++ 	(revision )
@@ -1,35 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50;
-md.cluster=none;
-md.prognostic.hydrostatic_adjustment='Incremental';
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test247.m
===================================================================
--- issm/trunk/test/NightlyRun/test247.m	(revision 12331)
+++ 	(revision )
@@ -1,46 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.prognostic.hydrostatic_adjustment='Incremental';
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test249.m
===================================================================
--- issm/trunk/test/NightlyRun/test249.m	(revision 12331)
+++ 	(revision )
@@ -1,47 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50;
-md.cluster=none;
-md.prognostic.hydrostatic_adjustment='Incremental';
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test251.m
===================================================================
--- issm/trunk/test/NightlyRun/test251.m	(revision 12331)
+++ 	(revision )
@@ -1,35 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.timestepping.time_adapt=1;
-md.timestepping.final_time=10;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test253.m
===================================================================
--- issm/trunk/test/NightlyRun/test253.m	(revision 12331)
+++ 	(revision )
@@ -1,49 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.timestepping.time_adapt=1;
-md.timestepping.final_time=10;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,...
-						1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,...
-						1e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test255.m
===================================================================
--- issm/trunk/test/NightlyRun/test255.m	(revision 12331)
+++ 	(revision )
@@ -1,64 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-md.timestepping.time_step=1;
-md.settings.output_frequency=1;
-md.timestepping.final_time=4;
-
-%Set up transient
-smb = ones(md.mesh.numberofvertices,1)*3.6;
-smb=[ smb smb*-1 ];
-
-md.surfaceforcings.mass_balance= smb;
-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3];
-md.transient.isthermal=0;
-
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ...
-	'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ...
-	'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', ...
-	'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4'};
-field_tolerances={1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-	1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-	1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-	1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
-
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(4).Vx),...
-	(md.results.TransientSolution(4).Vy),...
-	(md.results.TransientSolution(4).Vel),...
-	(md.results.TransientSolution(4).Pressure),...
-	(md.results.TransientSolution(4).Bed),...
-	(md.results.TransientSolution(4).Surface),...
-	(md.results.TransientSolution(4).Thickness),...
-	(md.results.TransientSolution(4).SurfaceforcingsMassBalance),...
-	};
Index: issm/trunk/test/NightlyRun/test257.m
===================================================================
--- issm/trunk/test/NightlyRun/test257.m	(revision 12331)
+++ 	(revision )
@@ -1,64 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-md.timestepping.time_step=1;
-md.settings.output_frequency=1;
-md.timestepping.final_time=4;
-
-%Set up transient
-smb = ones(md.mesh.numberofvertices,1)*3.6;
-smb=[ smb smb*2 ];
-
-md.surfaceforcings.mass_balance= smb;
-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3];
-md.transient.isthermal=0;
-
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ...
-	'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ...
-	'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', ...
-	'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4'};
-field_tolerances={1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-	1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-	1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-	1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
-
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(4).Vx),...
-	(md.results.TransientSolution(4).Vy),...
-	(md.results.TransientSolution(4).Vel),...
-	(md.results.TransientSolution(4).Pressure),...
-	(md.results.TransientSolution(4).Bed),...
-	(md.results.TransientSolution(4).Surface),...
-	(md.results.TransientSolution(4).Thickness),...
-	(md.results.TransientSolution(4).SurfaceforcingsMassBalance),...
-	};
Index: issm/trunk/test/NightlyRun/test259.m
===================================================================
--- issm/trunk/test/NightlyRun/test259.m	(revision 12331)
+++ 	(revision )
@@ -1,69 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',350000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-md.timestepping.time_step=1;
-md.settings.output_frequency=1;
-md.timestepping.final_time=4;
-
-%Set up transient
-smb = ones(md.mesh.numberofvertices,1)*3.6;
-smb=[ smb smb*-1 ];
-
-md.surfaceforcings.mass_balance= smb;
-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3];
-md.transient.isthermal=0;
-
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ...
-	'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ...
-	'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3',...
-	'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceMassbalance4'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(4).Vx),...
-	(md.results.TransientSolution(4).Vy),...
-	(md.results.TransientSolution(4).Vz),...
-	(md.results.TransientSolution(4).Vel),...
-	(md.results.TransientSolution(4).Pressure),...
-	(md.results.TransientSolution(4).Bed),...
-	(md.results.TransientSolution(4).Surface),...
-	(md.results.TransientSolution(4).Thickness),...
-	(md.results.TransientSolution(4).SurfaceforcingsMassBalance),...
-	};
Index: issm/trunk/test/NightlyRun/test261.m
===================================================================
--- issm/trunk/test/NightlyRun/test261.m	(revision 12331)
+++ 	(revision )
@@ -1,69 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',350000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-md.timestepping.time_step=1;
-md.settings.output_frequency=1;
-md.timestepping.final_time=4;
-
-%Set up transient
-smb = ones(md.mesh.numberofvertices,1)*3.6;
-smb=[ smb smb*2 ];
-
-md.surfaceforcings.mass_balance= smb;
-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3];
-md.transient.isthermal=0;
-
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', ...
-	'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', ...
-	'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3',...
-	'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceMassbalance4'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).SurfaceforcingsMassBalance),...
-	(md.results.TransientSolution(4).Vx),...
-	(md.results.TransientSolution(4).Vy),...
-	(md.results.TransientSolution(4).Vz),...
-	(md.results.TransientSolution(4).Vel),...
-	(md.results.TransientSolution(4).Pressure),...
-	(md.results.TransientSolution(4).Bed),...
-	(md.results.TransientSolution(4).Surface),...
-	(md.results.TransientSolution(4).Thickness),...
-	(md.results.TransientSolution(4).SurfaceforcingsMassBalance),...
-	};
Index: issm/trunk/test/NightlyRun/test263.m
===================================================================
--- issm/trunk/test/NightlyRun/test263.m	(revision 12331)
+++ 	(revision )
@@ -1,28 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.thermal.spctemperature=[md.thermal.spctemperature, md.thermal.spctemperature+5, md.thermal.spctemperature+10, md.thermal.spctemperature+15; 1.5 2.5 3.5 4];
-md.timestepping.time_step=1;
-md.timestepping.final_time=4;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3','Temperature4','BasalforcingsMeltingRate4'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(4).Temperature),...
-	(md.results.TransientSolution(4).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test265.m
===================================================================
--- issm/trunk/test/NightlyRun/test265.m	(revision 12331)
+++ 	(revision )
@@ -1,62 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.thermal.spctemperature=[md.thermal.spctemperature, md.thermal.spctemperature+5; 1 2];
-md.timestepping.time_step=0.5;
-md.timestepping.final_time=2;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3',...
-					   'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','Temperature4','BasalforcingsMeltingRate4'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ...
-						1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ...
-						1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09, ...
-						1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(4).Vx),...
-	(md.results.TransientSolution(4).Vy),...
-	(md.results.TransientSolution(4).Vz),...
-	(md.results.TransientSolution(4).Vel),...
-	(md.results.TransientSolution(4).Pressure),...
-	(md.results.TransientSolution(4).Bed),...
-	(md.results.TransientSolution(4).Surface),...
-	(md.results.TransientSolution(4).Thickness),...
-	(md.results.TransientSolution(4).Temperature),...
-	(md.results.TransientSolution(4).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test267.m
===================================================================
--- issm/trunk/test/NightlyRun/test267.m	(revision 12331)
+++ 	(revision )
@@ -1,72 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'all','');
-md=parameterize(md,'../Par/SquareShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=generic('name',oshostname(),'np',3);
-
-md.timestepping.time_step=1;
-md.settings.output_frequency=1;
-md.timestepping.final_time=4;
-
-smb = ones(md.mesh.numberofvertices,1)*3.6;
-smb=[ smb smb*-1 ];
-
-md.surfaceforcings.mass_balance= smb;
-md.surfaceforcings.mass_balance(end+1,:)=[1.5 3];
-md.transient.isthermal=0;
-%Dakota options
-
-%partitioning
-md.qmu.numberofpartitions=20;
-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on');
-md.qmu.partition=md.qmu.partition-1;
-
-%variables
-md.qmu.variables.surface_mass_balance=normal_uncertain('scaled_SurfaceforcingsMassBalance',1,0.1);
-
-%responses
-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.IceVolume=response_function('IceVolume',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.massFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-
-%mass flux profiles
-md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'};
-md.qmu.mass_flux_profile_directory=pwd;
-
-%%  nond_sampling study
-md.qmu.method=dakota_method('nond_samp');
-md.qmu.method(end)=dmeth_params_set(md.qmu.method(end),'seed',1234,'samples',20,'sample_type','lhs');
-
-%parameters
-md.qmu.params.direct=true;
-md.qmu.params.analysis_driver='';
-md.qmu.params.analysis_components='';
-md.qmu.params.evaluation_concurrency=1;
-md.qmu.params.interval_type='forward';
-md.qmu.isdakota=1;
-
-md.diagnostic.reltol=10^-5; %tighten for qmu analyses
-md.transient.requested_outputs=IceVolumeEnum();
-
-%solve
-md=solve(md,TransientSolutionEnum,'overwrite','y');
-md=tres(md,'dakota');
-
-%Fields and tolerances to track changes
-md.results.dakota.importancefactors=[];
-for i=1:8,
-	md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean];
-end
-for i=1:8,
-	md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev];
-end
-field_names     ={'importancefactors'};
-field_tolerances={1e-11};
-field_values={...
-         md.results.dakota.importancefactors,...
-	};
Index: issm/trunk/test/NightlyRun/test301.m
===================================================================
--- issm/trunk/test/NightlyRun/test301.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test303.m
===================================================================
--- issm/trunk/test/NightlyRun/test303.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'hutter','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test305.m
===================================================================
--- issm/trunk/test/NightlyRun/test305.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'hutter','../Exp/SquareHalfRight.exp','fill','macayeal');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test307.m
===================================================================
--- issm/trunk/test/NightlyRun/test307.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test309.m
===================================================================
--- issm/trunk/test/NightlyRun/test309.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,5,2);
-md=setflowequation(md,'hutter','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test311.m
===================================================================
--- issm/trunk/test/NightlyRun/test311.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,4,2);
-md=setflowequation(md,'hutter','../Exp/SquareHalfRight.exp','fill','macayeal');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test313.m
===================================================================
--- issm/trunk/test/NightlyRun/test313.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test315.m
===================================================================
--- issm/trunk/test/NightlyRun/test315.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md.cluster=none;
-md=setflowequation(md,'stokes','all');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test317.m
===================================================================
--- issm/trunk/test/NightlyRun/test317.m	(revision 12331)
+++ 	(revision )
@@ -1,13 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test319.m
===================================================================
--- issm/trunk/test/NightlyRun/test319.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=meshconvert(md);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.prognostic.stabilization=3;
-md.prognostic.spcthickness=md.geometry.thickness;
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test321.m
===================================================================
--- issm/trunk/test/NightlyRun/test321.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md=extrude(md,5,0.5);
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test323.m
===================================================================
--- issm/trunk/test/NightlyRun/test323.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.timestepping.time_step=0;
-md.cluster=none;
-md=solve(md,ThermalSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.ThermalSolution.Temperature),...
-	(md.results.ThermalSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test325.m
===================================================================
--- issm/trunk/test/NightlyRun/test325.m	(revision 12331)
+++ 	(revision )
@@ -1,19 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test327.m
===================================================================
--- issm/trunk/test/NightlyRun/test327.m	(revision 12331)
+++ 	(revision )
@@ -1,37 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'hutter','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1',...
-						'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2',...
-						'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test329.m
===================================================================
--- issm/trunk/test/NightlyRun/test329.m	(revision 12331)
+++ 	(revision )
@@ -1,47 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,5,1.2);
-md=setflowequation(md,'hutter','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-10,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test331.m
===================================================================
--- issm/trunk/test/NightlyRun/test331.m	(revision 12331)
+++ 	(revision )
@@ -1,33 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test333.m
===================================================================
--- issm/trunk/test/NightlyRun/test333.m	(revision 12331)
+++ 	(revision )
@@ -1,47 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-						1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-						1e-9,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test335.m
===================================================================
--- issm/trunk/test/NightlyRun/test335.m	(revision 12331)
+++ 	(revision )
@@ -1,23 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,4,1);
-md=setflowequation(md,'hutter','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'};
-
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13
-};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test337.m
===================================================================
--- issm/trunk/test/NightlyRun/test337.m	(revision 12331)
+++ 	(revision )
@@ -1,33 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=0*2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.FrictionCoefficient),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test339.m
===================================================================
--- issm/trunk/test/NightlyRun/test339.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.FrictionCoefficient),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test341.m
===================================================================
--- issm/trunk/test/NightlyRun/test341.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[102*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.FrictionCoefficient),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test343.m
===================================================================
--- issm/trunk/test/NightlyRun/test343.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'stokes','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[104*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.FrictionCoefficient),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test345.m
===================================================================
--- issm/trunk/test/NightlyRun/test345.m	(revision 12331)
+++ 	(revision )
@@ -1,35 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.timestepping.time_adapt=1;
-md.timestepping.final_time=600;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test347.m
===================================================================
--- issm/trunk/test/NightlyRun/test347.m	(revision 12331)
+++ 	(revision )
@@ -1,49 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,4,1.2);
-md=setflowequation(md,'hutter','all');
-md.cluster=none;
-md.timestepping.time_adapt=1;
-md.timestepping.final_time=500;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'};
-					   %'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-%	(md.results.TransientSolution(3).Vx),...
-%	(md.results.TransientSolution(3).Vy),...
-%	(md.results.TransientSolution(3).Vz),...
-%	(md.results.TransientSolution(3).Vel),...
-%	(md.results.TransientSolution(3).Pressure),...
-%	(md.results.TransientSolution(3).Bed),...
-%	(md.results.TransientSolution(3).Surface),...
-%	(md.results.TransientSolution(3).Thickness),...
-%	(md.results.TransientSolution(3).Temperature),...
-%	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test349.m
===================================================================
--- issm/trunk/test/NightlyRun/test349.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md.timestepping.time_step=0;
-md.cluster=none;
-md=solve(md,EnthalpySolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Enthalpy','Waterfraction','Temperature'};
-field_tolerances={1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.EnthalpySolution.Enthalpy),...
-	(md.results.EnthalpySolution.Waterfraction),...
-	(md.results.EnthalpySolution.Temperature),...
-	};
Index: issm/trunk/test/NightlyRun/test351.m
===================================================================
--- issm/trunk/test/NightlyRun/test351.m	(revision 12331)
+++ 	(revision )
@@ -1,30 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md.cluster=none;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md.thermal.isenthalpy=1;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Enthalpy1','Waterfraction1','Temperature1',...
-	'Enthalpy2','Waterfraction2','Temperature2',...
-	'Enthalpy3','Waterfraction3','Temperature3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Enthalpy),...
-	(md.results.TransientSolution(1).Waterfraction),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(2).Enthalpy),...
-	(md.results.TransientSolution(2).Waterfraction),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(3).Enthalpy),...
-	(md.results.TransientSolution(3).Waterfraction),...
-	(md.results.TransientSolution(3).Temperature),...
-	};
Index: issm/trunk/test/NightlyRun/test353.m
===================================================================
--- issm/trunk/test/NightlyRun/test353.m	(revision 12331)
+++ 	(revision )
@@ -1,55 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'','');
-md=parameterize(md,'../Par/SquareSheetConstrained.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md.initialization.temperature(:)=272;
-md.thermal.spctemperature(find(md.mesh.vertexonsurface))=272;
-md.thermal.isenthalpy=1;
-md.basalforcings.geothermalflux(:)=5;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','Enthalpy1','Waterfraction1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','Enthalpy2','Waterfraction2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','Enthalpy3','Waterfraction3'};
-field_tolerances={1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-						1e-09,1e-09,1e-10,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,...
-						1e-09,5e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).Enthalpy),...
-	(md.results.TransientSolution(1).Waterfraction),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).Enthalpy),...
-	(md.results.TransientSolution(2).Waterfraction),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).Enthalpy),...
-	(md.results.TransientSolution(3).Waterfraction),...
-	};
Index: issm/trunk/test/NightlyRun/test401.m
===================================================================
--- issm/trunk/test/NightlyRun/test401.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test403.m
===================================================================
--- issm/trunk/test/NightlyRun/test403.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,4,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test405.m
===================================================================
--- issm/trunk/test/NightlyRun/test405.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test407.m
===================================================================
--- issm/trunk/test/NightlyRun/test407.m	(revision 12331)
+++ 	(revision )
@@ -1,17 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'stokes','all');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test409.m
===================================================================
--- issm/trunk/test/NightlyRun/test409.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','penalties');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test411.m
===================================================================
--- issm/trunk/test/NightlyRun/test411.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,4,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,ThermalSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.ThermalSolution.Temperature),...
-	(md.results.ThermalSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test413.m
===================================================================
--- issm/trunk/test/NightlyRun/test413.m	(revision 12331)
+++ 	(revision )
@@ -1,19 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,4,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test415.m
===================================================================
--- issm/trunk/test/NightlyRun/test415.m	(revision 12331)
+++ 	(revision )
@@ -1,33 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test417.m
===================================================================
--- issm/trunk/test/NightlyRun/test417.m	(revision 12331)
+++ 	(revision )
@@ -1,45 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','penalties');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', ...
-					   'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'};
-field_tolerances={1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05,1e-05};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(3).Vx),...
-	(md.results.TransientSolution(3).Vy),...
-	(md.results.TransientSolution(3).Vz),...
-	(md.results.TransientSolution(3).Vel),...
-	(md.results.TransientSolution(3).Pressure),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).Temperature),...
-	(md.results.TransientSolution(3).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test419.m
===================================================================
--- issm/trunk/test/NightlyRun/test419.m	(revision 12331)
+++ 	(revision )
@@ -1,22 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13
-};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test421.m
===================================================================
--- issm/trunk/test/NightlyRun/test421.m	(revision 12331)
+++ 	(revision )
@@ -1,21 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test423.m
===================================================================
--- issm/trunk/test/NightlyRun/test423.m	(revision 12331)
+++ 	(revision )
@@ -1,45 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',300000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-%partitioning
-md.qmu.numberofpartitions=md.mesh.numberofvertices;
-md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions);
-md.qmu.partition=md.qmu.partition-1;
-md.qmu.isdakota=1;
-
-%Dakota options
-%variables
-md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01);
-md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,.01);
-%md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,.01*ones(md.qmu.numberofpartitions,1));
-
-%responses
-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-
-%method
-md.qmu.method     =dakota_method('nond_l');
-
-%parameters
-md.qmu.params.direct=true;
-md.qmu.params.analysis_driver='diagnostic';
-md.qmu.params.evaluation_concurrency=1;
-md.qmu.params.interval_type='forward';
-
-
-%imperative! 
-md.diagnostic.reltol=10^-5; %tighten for qmu analysese
-
-%solve
-md=solve(md,DiagnosticSolutionEnum,'overwrite','y');
-
-%Fields and tolerances to track changes
-md=tres(md,'dakota');
-md.results.dakota.importancefactors=importancefactors(md,'scaled_FrictionCoefficient','MaxVel')';
-field_names     ={'importancefactors'};
-field_tolerances={1e-10};
-field_values={...
-         md.results.dakota.importancefactors,...
-	};
Index: issm/trunk/test/NightlyRun/test425.m
===================================================================
--- issm/trunk/test/NightlyRun/test425.m	(revision 12331)
+++ 	(revision )
@@ -1,45 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-%Dakota options
-
-%partitioning
-md.qmu.numberofpartitions=20;
-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on');
-md.qmu.partition=md.qmu.partition-1;
-
-%variables
-md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01);
-md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,0.01);
-
-%responses
-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-
-%method
-md.qmu.method     =dakota_method('nond_l');
-
-%parameters
-md.qmu.params.direct=true;
-md.qmu.params.analysis_driver='diagnostic';
-md.qmu.params.evaluation_concurrency=1;
-md.qmu.params.interval_type='forward';
-
-
-%imperative!
-md.diagnostic.reltol=10^-5; %tighten for qmu analyses
-md.qmu.isdakota=1;
-
-%solve
-md=solve(md,DiagnosticSolutionEnum,'overwrite','y');
-
-%Fields and tolerances to track changes
-md=tres(md,'dakota');
-md.results.dakota.importancefactors=importancefactors(md,'scaled_FrictionCoefficient','MaxVel')';
-field_names     ={'importancefactors'};
-field_tolerances={1e-10};
-field_values={...
-         md.results.dakota.importancefactors,...
-	};
Index: issm/trunk/test/NightlyRun/test427.m
===================================================================
--- issm/trunk/test/NightlyRun/test427.m	(revision 12331)
+++ 	(revision )
@@ -1,71 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.materials.rho_ice=10^7; %involved in the mass flux, make it easy
-md.geometry.thickness(:)=1; %make it easy
-
-%constrain all velocities to 1 m/yr, in the y-direction
-md.diagnostic.spcvx(:)=0;
-md.diagnostic.spcvy(:)=1;
-md.diagnostic.spcvz(:)=0;
-
-%Dakota options
-
-%partitioning
-md.qmu.numberofpartitions=20;
-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on');
-md.qmu.partition=md.qmu.partition-1;
-
-%variables
-md.qmu.variables.drag_coefficient=normal_uncertain('scaled_FrictionCoefficient',1,0.01);
-
-%responses
-md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux1=response_function('indexed_MassFlux_1',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux2=response_function('indexed_MassFlux_2',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux3=response_function('indexed_MassFlux_3',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux4=response_function('indexed_MassFlux_4',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux5=response_function('indexed_MassFlux_5',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux6=response_function('indexed_MassFlux_6',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-md.qmu.responses.MassFlux7=response_function('indexed_MassFlux_7',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-
-%mass flux profiles
-md.qmu.mass_flux_profiles={'../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'};
-md.qmu.mass_flux_profile_directory=pwd;
-
-%method
-md.qmu.method     =dakota_method('nond_l');
-
-%parameters
-md.qmu.params.direct=true;
-md.qmu.params.analysis_driver='diagnostic';
-md.qmu.params.evaluation_concurrency=1;
-md.qmu.params.interval_type='forward';
-md.qmu.isdakota=1;
-md.diagnostic.reltol=10^-5; %tighten for qmu analyses
-
-%solve
-md=solve(md,DiagnosticSolutionEnum,'overwrite','y');
-md=tres(md,'dakota');
-
-%Fields and tolerances to track changes
-
-%ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr
-%we recover those mass fluxes through the mean of the response.
-%also, we recover the max velo, which should be 1m/yr. 
-%we put all that data in the importancefactors, which we will use to test for success.
-%also, check that the stddev are 0.
-md.results.dakota.importancefactors=[];
-for i=1:8,
-	md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).mean];
-end
-for i=1:8,
-	md.results.dakota.importancefactors=[md.results.dakota.importancefactors md.results.dakota.dresp_out(i).stddev];
-end
-field_names     ={'importancefactors'};
-field_tolerances={1e-11};
-field_values={...
-         md.results.dakota.importancefactors,...
-	};
Index: issm/trunk/test/NightlyRun/test429.m
===================================================================
--- issm/trunk/test/NightlyRun/test429.m	(revision 12331)
+++ 	(revision )
@@ -1,38 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',170000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.timestepping.time_step=0;
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.SteadystateSolution.Gradient1),...
-	md.results.SteadystateSolution.J,...
-	(md.results.SteadystateSolution.FrictionCoefficient),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate)
-};
Index: issm/trunk/test/NightlyRun/test431.m
===================================================================
--- issm/trunk/test/NightlyRun/test431.m	(revision 12331)
+++ 	(revision )
@@ -1,38 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',170000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[102*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1);
-md.timestepping.time_step=0;
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'};
-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06};
-field_values={...
-	(md.results.SteadystateSolution.Gradient1),...
-	md.results.SteadystateSolution.J,...
-	(md.results.SteadystateSolution.FrictionCoefficient),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate)
-};
Index: issm/trunk/test/NightlyRun/test435.m
===================================================================
--- issm/trunk/test/NightlyRun/test435.m	(revision 12331)
+++ 	(revision )
@@ -1,21 +1,0 @@
-%test partitioning, and partition averaging
-md=triangle(model,'../Exp/Square.exp',30000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-%partitioning
-md.qmu.numberofpartitions=100;
-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions);
-md.qmu.partition=md.qmu.partition-1;
-
-vector=(1:1:md.mesh.numberofvertices)';
-vector_on_partition=AreaAverageOntoPartition(md,vector);
-vector_on_nodes=vector_on_partition(md.qmu.partition+1);
-
-field_names     ={'vector_on_nodes'};
-field_tolerances={1e-11};
-field_values={...
-         vector_on_nodes,...
-	};
Index: issm/trunk/test/NightlyRun/test437.m
===================================================================
--- issm/trunk/test/NightlyRun/test437.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'macayeal','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','tiling');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test439.m
===================================================================
--- issm/trunk/test/NightlyRun/test439.m	(revision 12331)
+++ 	(revision )
@@ -1,49 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',200000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-%partitioning
-md.qmu.numberofpartitions=10;
-md=partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions);
-md.qmu.partition=md.qmu.partition-1;
-md.qmu.isdakota=1;
-
-%Dakota options
-%variables
-md.qmu.variables.rho_ice=normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01);
-
-%responses
-md.qmu.responses.MaxVel=response_function('scaled_Thickness',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]);
-
-%method
-md.qmu.method     =dakota_method('nond_l');
-
-%parameters
-md.qmu.params.direct=true;
-md.qmu.params.analysis_driver='diagnostic';
-md.qmu.params.evaluation_concurrency=1;
-md.qmu.params.interval_type='forward';
-
-
-%imperative! 
-md.diagnostic.reltol=10^-5; %tighten for qmu analysese
-
-%solve
-md=solve(md,DiagnosticSolutionEnum,'overwrite','y');
-md=tres(md,'dakota');
-
-%test on thickness
-h=zeros(md.qmu.numberofpartitions,1);
-for i=1:md.qmu.numberofpartitions,
-	h(i)=md.qmu.results.dresp_out(i).mean;
-end
-
-%project onto grid
-thickness=h(md.qmu.partition+1);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-11};
-field_values={thickness};
Index: issm/trunk/test/NightlyRun/test441.m
===================================================================
--- issm/trunk/test/NightlyRun/test441.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn','coupling','tiling');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test443.m
===================================================================
--- issm/trunk/test/NightlyRun/test443.m	(revision 12331)
+++ 	(revision )
@@ -1,19 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','tiling');
-md.cluster=none;
-md.diagnostic.reltol=0.4;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-06,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test445.m
===================================================================
--- issm/trunk/test/NightlyRun/test445.m	(revision 12331)
+++ 	(revision )
@@ -1,37 +1,0 @@
-radius=1e6;
-shelfextent=2e5;
-
-md=roundmesh(model,radius,200000);
-%fix center node to 0,0
-rad=sqrt(md.mesh.x.^2+md.mesh.y.^2);
-pos=find(rad==min(rad));
-md.mesh.x(pos)=0; md.mesh.y(pos)=0; %the closest node to the center is changed to be exactly at the center
-xelem=md.mesh.x(md.mesh.elements)*[1;1;1]/3;
-yelem=md.mesh.y(md.mesh.elements)*[1;1;1]/3;
-rad=sqrt(xelem.^2+yelem.^2);
-flags=zeros(md.mesh.numberofelements,1);
-pos=find(rad>=(radius-shelfextent));
-flags(pos)=1;
-md=setmask(md,flags,''); 
-md=parameterize(md,'../Par/RoundSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-
-md.transient.isthermal=0;
-md.transient.isprognostic=0;
-md.transient.isdiagnostic=0;
-md.transient.isgroundingline=1;
-
-%test different grounding line dynamics
-md.groundingline.migration='AgressiveMigration';
-md=solve(md,TransientSolutionEnum);
-element_on_iceshelf_agressive=(md.results.TransientSolution.MaskElementonfloatingice);
-
-md.groundingline.migration='SoftMigration';
-md=solve(md,TransientSolutionEnum);
-element_on_iceshelf_soft=(md.results.TransientSolution.MaskElementonfloatingice);
-
-%Fields and tolerances to track changes
-field_names     ={'ElementOnIceShelfAgressive','ElementOnIceShelfSoft'};
-field_tolerances={1e-13,1e-13};
-field_values={element_on_iceshelf_agressive,element_on_iceshelf_soft};
Index: issm/trunk/test/NightlyRun/test447.m
===================================================================
--- issm/trunk/test/NightlyRun/test447.m	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.initialization.vx(:)=0;
-md.initialization.vy(:)=0;
-md.initialization.vel(:)=0;
-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.thickness(:)=1000;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-md.surfaceforcings.mass_balance(:)=100;
-md.transient.isdiagnostic=0;
-md.transient.isgroundingline=1;
-md.groundingline.migration='AgressiveMigration';
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Bed1','Surface1','Thickness1','Floatingice1',...
-	'Bed2','Surface2','Thickness2','Floatingice2',...
-	'Bed3','Surface3','Thickness3','Floatingice3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).MaskElementonfloatingice),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).MaskElementonfloatingice),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).MaskElementonfloatingice),...
-	};
Index: issm/trunk/test/NightlyRun/test448.m
===================================================================
--- issm/trunk/test/NightlyRun/test448.m	(revision 12331)
+++ issm/trunk/test/NightlyRun/test448.m	(revision 12332)
@@ -3,5 +3,4 @@
 md=parameterize(md,'../Par/SquareSheetShelf.par');
 md=setflowequation(md,'macayeal','all');
-md.cluster=none;
 md.initialization.vx(:)=0;
 md.initialization.vy(:)=0;
Index: issm/trunk/test/NightlyRun/test449.m
===================================================================
--- issm/trunk/test/NightlyRun/test449.m	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.initialization.vx(:)=0;
-md.initialization.vy(:)=0;
-md.initialization.vel(:)=0;
-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.thickness(:)=1300;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-md.surfaceforcings.mass_balance(:)=-150;
-md.transient.isdiagnostic=0;
-md.transient.isgroundingline=1;
-md.groundingline.migration='SoftMigration';
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Bed1','Surface1','Thickness1','Floatingice1',...
-	'Bed2','Surface2','Thickness2','Floatingice2',...
-	'Bed3','Surface3','Thickness3','Floatingice3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).MaskElementonfloatingice),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).MaskElementonfloatingice),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).MaskElementonfloatingice),...
-	};
Index: issm/trunk/test/NightlyRun/test450.m
===================================================================
--- issm/trunk/test/NightlyRun/test450.m	(revision 12331)
+++ issm/trunk/test/NightlyRun/test450.m	(revision 12332)
@@ -3,5 +3,4 @@
 md=parameterize(md,'../Par/SquareSheetShelf.par');
 md=setflowequation(md,'macayeal','all');
-md.cluster=none;
 md.initialization.vx(:)=0;
 md.initialization.vy(:)=0;
Index: issm/trunk/test/NightlyRun/test451.m
===================================================================
--- issm/trunk/test/NightlyRun/test451.m	(revision 12331)
+++ 	(revision )
@@ -1,42 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',350000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md.cluster=none;
-md.initialization.vx(:)=0;
-md.initialization.vy(:)=0;
-md.initialization.vel(:)=0;
-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.thickness(:)=1000;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-md.surfaceforcings.mass_balance(:)=100;
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-
-md.transient.isdiagnostic=0;
-md.transient.isgroundingline=1;
-md.groundingline.migration='AgressiveMigration';
-
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Bed1','Surface1','Thickness1','Floatingice1',...
-	'Bed2','Surface2','Thickness2','Floatingice2',...
-	'Bed3','Surface3','Thickness3','Floatingice3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).MaskElementonfloatingice),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).MaskElementonfloatingice),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).MaskElementonfloatingice),...
-	};
Index: issm/trunk/test/NightlyRun/test452.m
===================================================================
--- issm/trunk/test/NightlyRun/test452.m	(revision 12331)
+++ issm/trunk/test/NightlyRun/test452.m	(revision 12332)
@@ -2,5 +2,4 @@
 md=setmask(md,'../Exp/SquareShelf.exp','');
 md=parameterize(md,'../Par/SquareSheetShelf.par');
-md.cluster=none;
 md.initialization.vx(:)=0;
 md.initialization.vy(:)=0;
Index: issm/trunk/test/NightlyRun/test453.m
===================================================================
--- issm/trunk/test/NightlyRun/test453.m	(revision 12331)
+++ 	(revision )
@@ -1,41 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md.initialization.vx(:)=0;
-md.initialization.vy(:)=0;
-md.initialization.vel(:)=0;
-md.geometry.bed=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.bathymetry=-700-abs(md.mesh.y-500000)/1000;
-md.geometry.thickness(:)=1300;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-
-md.surfaceforcings.mass_balance(:)=-150;
-md.transient.isdiagnostic=0;
-md.transient.isgroundingline=1;
-md.groundingline.migration='SoftMigration';
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Bed1','Surface1','Thickness1','Floatingice1',...
-	'Bed2','Surface2','Thickness2','Floatingice2',...
-	'Bed3','Surface3','Thickness3','Floatingice3'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13,...
-	1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).MaskElementonfloatingice),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).MaskElementonfloatingice),...
-	(md.results.TransientSolution(3).Bed),...
-	(md.results.TransientSolution(3).Surface),...
-	(md.results.TransientSolution(3).Thickness),...
-	(md.results.TransientSolution(3).MaskElementonfloatingice),...
-	};
Index: issm/trunk/test/NightlyRun/test455.m
===================================================================
--- issm/trunk/test/NightlyRun/test455.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=setflowequation(md,'macayeal','all');
-md.diagnostic.isnewton=1;
-md.diagnostic.restol=0.0001;
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test457.m
===================================================================
--- issm/trunk/test/NightlyRun/test457.m	(revision 12331)
+++ 	(revision )
@@ -1,20 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,5,1);
-md=setflowequation(md,'pattyn','all');
-md.diagnostic.isnewton=1;
-md.diagnostic.restol=0.0001;
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test459.m
===================================================================
--- issm/trunk/test/NightlyRun/test459.m	(revision 12331)
+++ 	(revision )
@@ -1,19 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',180000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'stokes','all');
-md.diagnostic.isnewton=1;
-md.diagnostic.restol=0.0001;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test461.m
===================================================================
--- issm/trunk/test/NightlyRun/test461.m	(revision 12331)
+++ 	(revision )
@@ -1,24 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md.thermal.isenthalpy=1;
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'};
-field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.Waterfraction),...
-	(md.results.SteadystateSolution.Enthalpy),...
-	};
Index: issm/trunk/test/NightlyRun/test463.m
===================================================================
--- issm/trunk/test/NightlyRun/test463.m	(revision 12331)
+++ 	(revision )
@@ -1,24 +1,0 @@
-md=triangle(model,'../Exp/Square.exp',150000);
-md=setmask(md,'../Exp/SquareShelf.exp','');
-md=parameterize(md,'../Par/SquareSheetShelf.par');
-md=extrude(md,3,2);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md.thermal.isenthalpy=1;
-md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1);
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'};
-field_tolerances={1e-09,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.Waterfraction),...
-	(md.results.SteadystateSolution.Enthalpy),...
-	};
Index: issm/trunk/test/NightlyRun/test501.m
===================================================================
--- issm/trunk/test/NightlyRun/test501.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',20000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test503.m
===================================================================
--- issm/trunk/test/NightlyRun/test503.m	(revision 12331)
+++ 	(revision )
@@ -1,18 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',20000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,0.9);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test505.m
===================================================================
--- issm/trunk/test/NightlyRun/test505.m	(revision 12331)
+++ 	(revision )
@@ -1,17 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',20000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,0.9);
-md=setflowequation(md,'stokes','all');
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy),...
-	(md.results.DiagnosticSolution.Vz),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Pressure),...
-	};
Index: issm/trunk/test/NightlyRun/test507.m
===================================================================
--- issm/trunk/test/NightlyRun/test507.m	(revision 12331)
+++ 	(revision )
@@ -1,26 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',20000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test509.m
===================================================================
--- issm/trunk/test/NightlyRun/test509.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'};
-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test511.m
===================================================================
--- issm/trunk/test/NightlyRun/test511.m	(revision 12331)
+++ 	(revision )
@@ -1,35 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,2,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,...
-						1e-12,1e-12,1e-12,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test513.m
===================================================================
--- issm/trunk/test/NightlyRun/test513.m	(revision 12331)
+++ 	(revision )
@@ -1,35 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,2,1);
-md=setflowequation(md,'stokes','all');
-md.cluster=none;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-%The thickness wants to be lower than 1 so we contrain it to 1
-field_names     ={'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', ...
-				      'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2'};
-field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08};
-field_values={...
-	(md.results.TransientSolution(1).Vx),...
-	(md.results.TransientSolution(1).Vy),...
-	(md.results.TransientSolution(1).Vz),...
-	(md.results.TransientSolution(1).Vel),...
-	(md.results.TransientSolution(1).Pressure),...
-	(md.results.TransientSolution(1).Bed),...
-	(md.results.TransientSolution(1).Surface),...
-	(md.results.TransientSolution(1).Thickness),...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Vx),...
-	(md.results.TransientSolution(2).Vy),...
-	(md.results.TransientSolution(2).Vz),...
-	(md.results.TransientSolution(2).Vel),...
-	(md.results.TransientSolution(2).Pressure),...
-	(md.results.TransientSolution(2).Bed),...
-	(md.results.TransientSolution(2).Surface),...
-	(md.results.TransientSolution(2).Thickness),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test515.m
===================================================================
--- issm/trunk/test/NightlyRun/test515.m	(revision 12331)
+++ 	(revision )
@@ -1,22 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,4,1.1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13
-};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test517.m
===================================================================
--- issm/trunk/test/NightlyRun/test517.m	(revision 12331)
+++ 	(revision )
@@ -1,22 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13
-};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test519.m
===================================================================
--- issm/trunk/test/NightlyRun/test519.m	(revision 12331)
+++ 	(revision )
@@ -1,22 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',20000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,2,1);
-md=setflowequation(md,'stokes','all');
-md.cluster=none;
-md.timestepping.time_step=0;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06
-};
-field_values={...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test521.m
===================================================================
--- issm/trunk/test/NightlyRun/test521.m	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',10000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-
-%impose hydrostatic equilibrium (required by Stokes)
-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness;
-md.geometry.surface=md.geometry.bed+md.geometry.thickness;
-md=extrude(md,3,1);
-md=setflowequation(md,'stokes','all');
-md=modelextract(md,md.mask.elementonfloatingice);
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'MaterialsRheologyBbar'};
-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10^8*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'MaterialsRheologyB' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10,1e-10};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.MaterialsRheologyB),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test523.m
===================================================================
--- issm/trunk/test/NightlyRun/test523.m	(revision 12331)
+++ 	(revision )
@@ -1,34 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',20000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-
-md.cluster=none;
-md=solve(md,DiagnosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy'};
-field_tolerances={1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11,1e-11};
-field_values={...
-	(md.results.DiagnosticSolution.Gradient1),...
-	md.results.DiagnosticSolution.J,...
-	(md.results.DiagnosticSolution.FrictionCoefficient),...
-	(md.results.DiagnosticSolution.Pressure),...
-	(md.results.DiagnosticSolution.Vel),...
-	(md.results.DiagnosticSolution.Vx),...
-	(md.results.DiagnosticSolution.Vy)
-};
Index: issm/trunk/test/NightlyRun/test525.m
===================================================================
--- issm/trunk/test/NightlyRun/test525.m	(revision 12331)
+++ 	(revision )
@@ -1,39 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'FrictionCoefficient'};
-md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1);
-md.inversion.nsteps=2;
-md.inversion.cost_functions=[103*ones(md.inversion.nsteps,1)  501*ones(md.inversion.nsteps,1)];
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,2); md.inversion.cost_functions_coefficients(:,2)=2*10^-7;
-md.inversion.gradient_scaling=3*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1);
-md.inversion.vx_obs=md.initialization.vx; md.inversion.vy_obs=md.initialization.vy;
-md.timestepping.time_step=0;
-
-md.thermal.penalty_lock=5;
-md.cluster=none;
-md=solve(md,SteadystateSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'FrictionCoefficient' 'Pressure' 'Vel' 'Vx' 'Vy' 'Vz' 'Temperature' 'BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13};
-field_values={...
-	(md.results.SteadystateSolution.Gradient1),...
-	md.results.SteadystateSolution.J,...
-	(md.results.SteadystateSolution.FrictionCoefficient),...
-	(md.results.SteadystateSolution.Pressure),...
-	(md.results.SteadystateSolution.Vel),...
-	(md.results.SteadystateSolution.Vx),...
-	(md.results.SteadystateSolution.Vy),...
-	(md.results.SteadystateSolution.Vz),...
-	(md.results.SteadystateSolution.Temperature),...
-	(md.results.SteadystateSolution.BasalforcingsMeltingRate)
-};
Index: issm/trunk/test/NightlyRun/test529.m
===================================================================
--- issm/trunk/test/NightlyRun/test529.m	(revision 12331)
+++ 	(revision )
@@ -1,22 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.thermal.stabilization=2;
-md.transient.isdiagnostic=0;
-md.transient.isprognostic=0;
-md.transient.isthermal=1;
-md.transient.isgroundingline=0;
-md=solve(md,TransientSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature1','BasalforcingsMeltingRate1', ...
-				      'Temperature2','BasalforcingsMeltingRate2'};
-field_tolerances={1e-13,1e-9,1e-13,1e-9};
-field_values={...
-	(md.results.TransientSolution(1).Temperature),...
-	(md.results.TransientSolution(1).BasalforcingsMeltingRate),...
-	(md.results.TransientSolution(2).Temperature),...
-	(md.results.TransientSolution(2).BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test531.m
===================================================================
--- issm/trunk/test/NightlyRun/test531.m	(revision 12331)
+++ 	(revision )
@@ -1,17 +1,0 @@
-md=triangle(model,'../Exp/Pig.exp',30000);
-md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp');
-md=parameterize(md,'../Par/Pig.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'pattyn','all');
-md.thermal.stabilization=2;
-md.timestepping.time_step=0;
-md.thermal.penalty_threshold=40;
-md=solve(md,ThermalSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Temperature','BasalforcingsMeltingRate'};
-field_tolerances={1e-13,1e-12};
-field_values={...
-	(md.results.ThermalSolution.Temperature),...
-	(md.results.ThermalSolution.BasalforcingsMeltingRate),...
-	};
Index: issm/trunk/test/NightlyRun/test601.m
===================================================================
--- issm/trunk/test/NightlyRun/test601.m	(revision 12331)
+++ 	(revision )
@@ -1,13 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test603.m
===================================================================
--- issm/trunk/test/NightlyRun/test603.m	(revision 12331)
+++ 	(revision )
@@ -1,16 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=meshconvert(md);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-md.prognostic.stabilization=3;
-md.prognostic.spcthickness=md.geometry.thickness;
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test605.m
===================================================================
--- issm/trunk/test/NightlyRun/test605.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=extrude(md,6,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,PrognosticSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.PrognosticSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test607.m
===================================================================
--- issm/trunk/test/NightlyRun/test607.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,SurfaceSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'SurfaceSlopeX','SurfaceSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeX),...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test609.m
===================================================================
--- issm/trunk/test/NightlyRun/test609.m	(revision 12331)
+++ 	(revision )
@@ -1,15 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=extrude(md,5,1.5);
-md=setflowequation(md,'pattyn','all');
-md.cluster=none;
-md=solve(md,SurfaceSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'SurfaceSlopeX','SurfaceSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeX),...
-	(md.results.SurfaceSlopeSolution.SurfaceSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test611.m
===================================================================
--- issm/trunk/test/NightlyRun/test611.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BedSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'BedSlopeX','BedSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.BedSlopeSolution.BedSlopeX),...
-	(md.results.BedSlopeSolution.BedSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test613.m
===================================================================
--- issm/trunk/test/NightlyRun/test613.m	(revision 12331)
+++ 	(revision )
@@ -1,15 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=extrude(md,2,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BedSlopeSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'BedSlopeX','BedSlopeY'};
-field_tolerances={1e-13,1e-13};
-field_values={...
-	(md.results.BedSlopeSolution.BedSlopeX),...
-	(md.results.BedSlopeSolution.BedSlopeY),...
-	};
Index: issm/trunk/test/NightlyRun/test615.m
===================================================================
--- issm/trunk/test/NightlyRun/test615.m	(revision 12331)
+++ 	(revision )
@@ -1,13 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.BalancethicknessSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test617.m
===================================================================
--- issm/trunk/test/NightlyRun/test617.m	(revision 12331)
+++ 	(revision )
@@ -1,15 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=meshconvert(md);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-md.balancethickness.stabilization=3;
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.BalancethicknessSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test619.m
===================================================================
--- issm/trunk/test/NightlyRun/test619.m	(revision 12331)
+++ 	(revision )
@@ -1,14 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=extrude(md,3,1);
-md=setflowequation(md,'macayeal','all');
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Thickness'};
-field_tolerances={1e-13};
-field_values={...
-	(md.results.BalancethicknessSolution.Thickness),...
-	};
Index: issm/trunk/test/NightlyRun/test621.m
===================================================================
--- issm/trunk/test/NightlyRun/test621.m	(revision 12331)
+++ 	(revision )
@@ -1,31 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.nsteps=2;
-md.prognostic.stabilization=1;
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'BalancethicknessThickeningRate'};
-md.inversion.thickness_obs=md.geometry.thickness;
-md.inversion.min_parameters=-50*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=50*ones(md.mesh.numberofvertices,1);
-md.inversion.cost_functions=201*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10/md.constants.yts*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1);
-
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'BalancethicknessThickeningRate' 'Thickness'};
-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12};
-field_values={...
-	(md.results.BalancethicknessSolution.Gradient1),...
-	md.results.BalancethicknessSolution.J,...
-	(md.results.BalancethicknessSolution.BalancethicknessThickeningRate),...
-	(md.results.BalancethicknessSolution.Thickness)
-};
Index: issm/trunk/test/NightlyRun/test623.m
===================================================================
--- issm/trunk/test/NightlyRun/test623.m	(revision 12331)
+++ 	(revision )
@@ -1,32 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=meshconvert(md);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-
-%control parameters
-md.inversion.nsteps=2;
-md.balancethickness.stabilization=3;
-md.inversion.iscontrol=1;
-md.inversion.control_parameters={'BalancethicknessThickeningRate'};
-md.inversion.thickness_obs=md.geometry.thickness;
-md.inversion.min_parameters=-50*ones(md.mesh.numberofvertices,1);
-md.inversion.max_parameters=50*ones(md.mesh.numberofvertices,1);
-md.inversion.cost_functions=201*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.gradient_scaling=10/md.constants.yts*ones(md.inversion.nsteps,1);
-md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1);
-
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient' 'Misfits' 'BalancethicknessThickeningRate' 'Thickness'};
-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12};
-field_values={...
-	(md.results.BalancethicknessSolution.Gradient1),...
-	md.results.BalancethicknessSolution.J,...
-	(md.results.BalancethicknessSolution.BalancethicknessThickeningRate),...
-	(md.results.BalancethicknessSolution.Thickness)
-};
Index: issm/trunk/test/NightlyRun/test625.m
===================================================================
--- issm/trunk/test/NightlyRun/test625.m	(revision 12331)
+++ 	(revision )
@@ -1,40 +1,0 @@
-md=triangle(model,'../Exp/79North.exp',10000);
-md=meshconvert(md);
-md=setmask(md,'../Exp/79NorthShelf.exp','');
-md=parameterize(md,'../Par/79North.par');
-md=setflowequation(md,'macayeal','all');
-
-%Ice sheet only
-md=modelextract(md,md.mask.elementongroundedice);
-pos=find(md.mesh.vertexonboundary);
-md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
-
-%control parameters
-md.inversion.thickness_obs=md.geometry.thickness;
-md.inversion.iscontrol=1;
-md.inversion.thickness_obs=md.geometry.thickness;
-md.inversion.nsteps=2;
-md.inversion.control_parameters={'Vx' 'Vy'};
-md.balancethickness.stabilization=1;
-md.inversion.gradient_scaling=[10/md.constants.yts*ones(md.inversion.nsteps,1) 10/md.constants.yts*ones(md.inversion.nsteps,1)];
-md.inversion.min_parameters=[-2000*ones(md.mesh.numberofvertices,1) -2000*ones(md.mesh.numberofvertices,1)];
-md.inversion.max_parameters=[+2000*ones(md.mesh.numberofvertices,1) +2000*ones(md.mesh.numberofvertices,1)];
-md.inversion.cost_functions=201*ones(md.inversion.nsteps,1);
-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1);
-md.inversion.maxiter_per_step=4*ones(md.inversion.nsteps,1);
-md.inversion.step_threshold=0.99*ones(md.inversion.nsteps,1);
-
-md.cluster=none;
-md=solve(md,BalancethicknessSolutionEnum);
-
-%Fields and tolerances to track changes
-field_names     ={'Gradient1' 'Gradient2' 'Misfits' 'Vx' 'Vy' 'Thickness'};
-field_tolerances={1e-12,1e-12,1e-12,1e-12,1e-12,1e-12};
-field_values={...
-	(md.results.BalancethicknessSolution.Gradient1),...
-	(md.results.BalancethicknessSolution.Gradient2),...
-	md.results.BalancethicknessSolution.J,...
-	(md.results.BalancethicknessSolution.Vx),...
-	(md.results.BalancethicknessSolution.Vy),...
-	(md.results.BalancethicknessSolution.Thickness)
-};
Index: issm/trunk/test/Par/SquareShelfConstrained.py
===================================================================
--- issm/trunk/test/Par/SquareShelfConstrained.py	(revision 12332)
+++ issm/trunk/test/Par/SquareShelfConstrained.py	(revision 12332)
@@ -0,0 +1,59 @@
+from numpy import *
+from verbose import *
+import scipy.io as matio
+import InterpFromMeshToMesh2d as im
+from   paterson import  *
+
+#Start defining model parameters here
+#Geometry
+hmin = 300.
+hmax = 1000.
+ymin = min(md.mesh.y)
+ymax = max(md.mesh.y)
+
+md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin)
+md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness;
+md.geometry.surface = md.geometry.bed+md.geometry.thickness
+
+#Initial velocity 
+mat=matio.loadmat('../Data/SquareShelfConstrained.data')
+#deal with 'F' oriented matlab matrices!
+index=mat['index'].astype(float)
+index=reshape(index.T,(len(index),3),order='F')
+
+md.initialization.vx = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vx'], md.mesh.x, md.mesh.y)
+md.initialization.vy = im.InterpFromMeshToMesh2d(index, mat['x'], mat['y'], mat['vy'], md.mesh.x, md.mesh.y)
+md.initialization.vz = zeros(md.mesh.numberofvertices)
+md.initialization.pressure = zeros(md.mesh.numberofvertices)
+#Materials
+md.initialization.temperature = (273.-20)*ones(md.mesh.numberofvertices)
+md.materials.rheology_B = paterson(md.initialization.temperature)
+md.materials.rheology_n = 3.*ones(md.mesh.numberofelements)
+#Surface mass balance and basal melting
+md.surfaceforcings.mass_balance = 10.*ones(md.mesh.numberofvertices)
+md.basalforcings.melting_rate = 5.*ones(md.mesh.numberofvertices)
+#Friction
+pos = nonzero(md.mask.elementonfloatingice)
+md.friction.coefficient = 20.*ones(md.mesh.numberofvertices)
+md.friction.coefficient[md.mesh.elements[pos,:].astype(int)-1] =0.
+md.friction.p = ones(md.mesh.numberofelements)
+md.friction.q = ones(md.mesh.numberofelements)
+#Numerical parameters
+md.diagnostic.viscosity_overshoot = 0.0
+md.prognostic.stabilization = 1.
+md.thermal.stabilization = 1.
+md.verbose = verbose()
+md.settings.waitonlock = 30.
+md.diagnostic.restol = 0.05
+md.diagnostic.reltol = 0.05
+md.steadystate.reltol = 0.05
+md.diagnostic.abstol = nan
+md.timestepping.time_step = 1.
+md.timestepping.final_time = 3.
+#Deal with boundary conditions:
+md = SetIceShelfBC(md)
+#Change name so that no test have the same name
+A = dbstack
+if length(A) > 2.:
+    md.miscellaneous.name = A[2].file[0:0-2.]
+
