Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-altix64-castor.sh	(revision 15366)
+++ 	(revision )
@@ -1,65 +1,0 @@
-#!/bin/bash
-set -eu
-#Step 1: unzip and install
-#Step 2: After Plapack implodes
-STEP=0
-
-if [ $STEP -eq 1 ]; then
-	#Some cleanup
-	rm -rf install petsc-2.3.2-p3 src
-	mkdir install src
-
-	#Download from ISSM server
-	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
-
-	#Untar and move petsc to install directory
-	tar -zxvf  petsc-2.3.2-p3.tar.gz
-	mv petsc-2.3.2-p3/* install/
-	rm -rf petsc-2.3.2-p3
-
-	#configure
-	cd install
-	./config/configure.py \
-		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-batch=1  \
-		--ISSM_ARCH=$ISSM_ARCH \
-		--PETSC_DIR=$PETSC_DIR   \
-		--with-debugging=no \
-		--with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \
-		--with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \
-		--with-mpi-lib=/usr/lib/libmpi.so \
-		--with-mpi-include=/usr/include  \
-		--with-mpi-shared=0 \
-		--download-mumps=yes \
-		--download-scalapack=yes \
-		--download-blacs=yes  \
-		--download-plapack=yes \
-		--FFLAGS=-I/usr/include \
-		--with-cc=icc \
-		--with-fc=ifort
-
-	echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc232/) =="
-	echo "== Then run STEP=2 =="
-fi
-if [ $STEP -eq 2 ]; then
-	cd install
-	./config/configure.py  \
-		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-batch=1  \
-		--ISSM_ARCH=$ISSM_ARCH \
-		--PETSC_DIR=$PETSC_DIR   \
-		--with-debugging=no \
-		--with-shared=0 COPTFLAGS=-O3 FOPTFLAGS=-O3 \
-		--with-blas-lapack-dir=/opt/intel/mkl/9.1.023 \
-		--with-mpi-lib=/usr/lib/libmpi.so \
-		--with-mpi-include=/usr/include  \
-		--with-mpi-shared=0 \
-		--download-mumps=yes \
-		--download-scalapack=yes \
-		--download-blacs=yes  \
-		--with-plapack-dir=$PETSC_DIR/externalpackages/PLAPACKR32-hg/$ISSM_ARCH \
-		--FFLAGS=-I/usr/include \
-		--with-cc=icc \
-		--with-fc=ifort
-	echo "== Follow PETSc's instructions"
-fi
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-cosmos.sh	(revision 15366)
+++ 	(revision )
@@ -1,36 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-2.3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
-
-#Untar and move petsc to install directory
-tar -zxvf  petsc-2.3.2-p3.tar.gz
-mv petsc-2.3.2-p3/* install/
-rm -rf petsc-2.3.2-p3
-
-#configure
-cd install
-PETSC_DIR=$ISSM_DIR/externalpackages/petsc/install
-./config/configure.py  \
-	--prefix=$PETSC_DIR \
-	--with-batch=1  \
-	--ISSM_ARCH=$ISSM_ARCH \
-	--PETSC_DIR=$PETSC_DIR   \
-	--with-debugging=no COPTFLAGS=-O3 FOPTFLAGS=-O3 \
-	--with-blas-lapack-dir=/opt/intel/mkl/10.0.5.025/ \
-	--with-mpi-dir=/opt/mpich/gm/intel10.1/  \
-	--download-mumps=yes \
-	--download-scalapack=yes \
-	--download-blacs=yes  \
-	--download-plapack=yes \
-	--FFLAGS=-I/usr/include  \
-	--with-mpi-shared=0
-
-#Compile petsc and install it
-make
-make install
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-linux64-astrid.sh	(revision 15366)
+++ 	(revision )
@@ -1,39 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-2.3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$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
-tar -zxvf  petsc-2.3.2-p3.tar.gz
-mv petsc-2.3.2-p3/* install/
-rm -rf petsc-2.3.2-p3
-
-#configure
-cd install
-./config/configure.py  \
-	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
-	--PETSC_ARCH=linux-gnu-amd64 \
-	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-fc=gfortran \
-	--with-debugging=1 \
-	--with-shared=0 \
-	--download-mumps=yes \
-	--download-scalapack=yes \
-	--download-blacs=yes \
-	--download-blas=yes \
-	--download-f-blas-lapack=yes \
-	--FFLAGS=-I$ISSM_DIR/externalpackages/mpich/install/include \
-	--download-plapack=yes \
-	--COPTFLAGS="-march=opteron -O2" \
-	--FOPTFLAGS="-march=opteron -O2" \
-	--CXXOPTFLAGS="-march=opteron -O2" 
-
-#Compile petsc and install it
-make
-make install
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-eric.sh	(revision 15366)
+++ 	(revision )
@@ -1,72 +1,0 @@
-#!/bin/bash
-set -eu
-#Step 1: unzip and install
-#Step 2: After MUMPS Crashes
-STEP=0
-
-if [ $STEP -eq 1 ]; then
-	#Some cleanup
-	rm -rf install petsc-2.3.2-p3 src
-	mkdir install src
-
-	#Download from ISSM server
-	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
-
-	#Untar and move petsc to install directory
-	tar -zxvf  petsc-2.3.2-p3.tar.gz
-	mv petsc-2.3.2-p3/* install/
-	rm -rf petsc-2.3.2-p3
-
-	#configure
-	cd install
-	./config/configure.py  \
-		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
-		--PETSC_ARCH=macosx-gnu \
-		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-fc=/usr/local/bin/gfortran \
-		--with-debugging=0 \
-		--with-shared=0 \
-		--download-mumps=yes \
-		--download-scalapack=yes \
-		--download-blacs=yes \
-		--download-blas=yes \
-		--download-f-blas-lapack=yes \
-		--FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -L$ISSM_DIR/externalpackages/mpich/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran  -fPIC -arch i386" \
-		--download-plapack=yes \
-		--CXXFLAGS=" -fPIC -arch i386" \
-		--CFLAGS=" -fPIC -arch i386" \
-		--with-pic \
-		--with-fc="gfortran -arch i386 " \
-		--LDFLAGS="-arch i386"
-	echo "== Fix MUMPS compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc232/) =="
-	echo "== Then run STEP=2 =="
-fi
-
-if [ $STEP -eq 2 ]; then
-	cd install
-	./config/configure.py  \
-		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
-		--PETSC_ARCH=macosx-gnu \
-		--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-fc=/usr/local/bin/gfortran \
-		--with-debugging=0 \
-		--with-shared=0 \
-		--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_DIR/externalpackages/mpich/install/include -L$ISSM_DIR/externalpackages/mpich/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran  -fPIC -arch i386" \
-		--download-plapack=yes \
-		--CXXFLAGS=" -fPIC -arch i386" \
-		--CFLAGS=" -fPIC -arch i386" \
-		--with-pic \
-		--with-fc="gfortran -arch i386 " \
-		--LDFLAGS="-arch i386"
-
-	#Compile petsc and install it
-	make
-	make install
-fi
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx32-ogive.sh	(revision 15366)
+++ 	(revision )
@@ -1,35 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-2.3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$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
-tar -zxvf  petsc-2.3.2-p3.tar.gz
-mv petsc-2.3.2-p3/* install/
-rm -rf petsc-2.3.2-p3
-
-#configure
-cd install
-./config/configure.py  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
-	--PETSC_ARCH=macosx-gnu \
-	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-fc=/usr/local/bin/gfortran \
-	--with-debugging=0 \
-	--with-shared=0 \
-	--download-mumps=yes \
-	--download-scalapack=yes \
-	--download-blacs=yes \
-	--download-blas=yes \
-	--download-f-blas-lapack=yes \
-	--FFLAGS="-I$ISSM_DIR/externalpackages/mpich/install/include -L$ISSM_DIR/externalpackages/mpich/install/lib -L/usr/local/bin -lmpich -lpmpich -lgfortran" \
-	--download-plapack=yes
-
-#Compile petsc and install it
-make
-make install
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh	(revision 15366)
+++ 	(revision )
@@ -1,35 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-2.3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$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
-tar -zxvf  petsc-2.3.2-p3.tar.gz
-mv petsc-2.3.2-p3/* src/
-rm -rf petsc-2.3.2-p3
-
-#configure
-cd src
-./config/configure.py \
-  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
-  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
-  --PETSC_ARCH=macosx-gnu \
-  --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
-  --with-debugging=0 \
-  --with-shared-libraries=0 \
-  --download-mumps=yes \
-  --download-scalapack=yes \
-  --download-blacs=yes \
-  --download-blas=yes \
-  --download-plapack=yes  \
-  --download-parmetis=yes \
-  --download-f-blas-lapack=yes 
-
-#Compile petsc and install it
-make
-make install
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-pleiades.sh	(revision 15366)
+++ 	(revision )
@@ -1,71 +1,0 @@
-#!/bin/bash
-set -eu
-#Step 1: unzip and install
-#Step 2: After Plapack implodes
-STEP=0
-
-if [ $STEP -eq 1 ]; then
-	#Some cleanup
-	rm -rf install petsc-2.3.2-p3 src
-	mkdir install src
-
-	#Download from ISSM server
-	$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
-
-	#Untar and move petsc to install directory
-	tar -zxvf  petsc-2.3.2-p3.tar.gz
-	mv petsc-2.3.2-p3/* install/
-	rm -rf petsc-2.3.2-p3
-
-	#configure
-	cd install
-	./config/configure.py  \
-		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-batch=1  \
-		--PETSC_ARCH=$ISSM_ARCH \
-		--PETSC_DIR=$PETSC_DIR   \
-		--with-debugging=no \
-		--with-shared=0 \
-		--with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \
-		--with-mpi-lib=/nasa/sgi/mpt/1.23.nas/lib64/libmpi.so \
-		--with-mpi-include=/nasa/sgi/mpt/1.23.nas/include  \
-		--with-mpi-shared=0 \
-		--download-mumps=yes \
-		--download-scalapack=yes \
-		--download-blacs=yes  \
-		--download-plapack=yes \
-		--FFLAGS=-I/usr/include \
-		--with-cc=icc \
-		--with-fc=ifort \
-		--COPTFLAGS=" -O3 -xS" \
-		--FOPTFLAGS=" -O3 -xS" \
-		--CXXOPTFLAGS=" -O3 -xS"
-
-	echo "== Fix Plapack compilation manually (http://issm.jpl.nasa.gov/installation/compilationtroubleshooting/petsc232/) =="
-	echo "== Then run STEP=2 =="
-fi
-if [ $STEP -eq 2 ]; then
-	cd install
-	./config/configure.py  \
-		--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-		--with-batch=1  \
-		--PETSC_ARCH=$ISSM_ARCH \
-		--PETSC_DIR=$PETSC_DIR   \
-		--with-debugging=no \
-		--with-shared=0 \
-		--with-blas-lapack-dir=/nasa/intel/mkl/10.0.011/ \
-		--with-mpi-lib=/nasa/sgi/mpt/1.23.nas/lib64/libmpi.so \
-		--with-mpi-include=/nasa/sgi/mpt/1.23.nas/include  \
-		--with-mpi-shared=0 \
-		--download-mumps=yes \
-		--download-scalapack=yes \
-		--download-blacs=yes  \
-		--with-plapack-dir=$PETSC_DIR/externalpackages/PLAPACKR32-hg/$ISSM_ARCH \
-		--FFLAGS=-I/usr/include \
-		--with-cc=icc \
-		--with-fc=ifort \
-		--COPTFLAGS=" -O3 -xS" \
-		--FOPTFLAGS=" -O3 -xS" \
-		--CXXOPTFLAGS=" -O3 -xS"
-	echo "== Follow PETSc's instructions"
-fi
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win32-eric.sh	(revision 15366)
+++ 	(revision )
@@ -1,29 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-2.3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-2.3.2-p3.tar.gz' 'petsc-2.3.2-p3.tar.gz'
-
-#Untar and move petsc to install directory
-tar -zxvf  petsc-2.3.2-p3.tar.gz
-mv petsc-2.3.2-p3/* install/
-rm -rf petsc-2.3.2-p3
-
-#configure
-cd install
-./config/configure.py  \
-	--with-parallel-no \
-	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-	--PETSC_ARCH=cygwin-intel \
-	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-debugging=0 \
-	--with-mpi=0 \
-	--download-c-blas-lapack=1
-
-#Compile petsc and install it
-make
-make install
Index: sm/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-win7.sh	(revision 15366)
+++ 	(revision )
@@ -1,29 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-2.3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$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
-tar -zxvf  petsc-2.3.2-p3.tar.gz
-mv petsc-2.3.2-p3/* install/
-rm -rf petsc-2.3.2-p3
-
-#configure
-cd install
-./config/configure.py  \
-	--with-parallel-no \
-	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-	--PETSC_ARCH=cygwin-intel \
-	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-debugging=0 \
-	--with-mpi=0 \
-	--download-c-blas-lapack=1
-
-#Compile petsc and install it
-make
-make install
Index: sm/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.1-linux64-astrid.sh	(revision 15366)
+++ 	(revision )
@@ -1,40 +1,0 @@
-#!/bin/bash
-set -eu
-
-#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=$ISSM_DIR/externalpackages/mpich/install \
- --PETSC_ARCH=linux-gnu-amd64 \
- --PETSC_DIR="$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$ISSM_DIR/externalpackages/mpich/install/include \
- --download-plapack=yes \
- --COPTFLAGS="-march=opteron -O2" \
- --FOPTFLAGS="-march=opteron -O2" \
- --CXXOPTFLAGS="-march=opteron -O2" \
- --with-pic=1
-
-#Compile petsc and install it
-make
-make install
Index: /issm/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh	(revision 15366)
+++ /issm/trunk-jpl/externalpackages/petsc/install-3.2-linux64.sh	(revision 15367)
@@ -18,5 +18,5 @@
 ./config/configure.py \
 	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-mpi-dir=$ISSM_DIR/externalpackages/mpich/install \
+	--with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
 	--with-clanguage=C++ \
 	--PETSC_ARCH=linux-gnu-amd64 \
Index: /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh	(revision 15366)
+++ /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh	(revision 15367)
@@ -4,5 +4,4 @@
 
 if [ $STEP -eq 1 ]; then
-	# Adapted from petsc 3.2. 
 	# Used Mercurial to get code
 	rm -rf src