Index: /issm/trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh	(revision 18340)
+++ /issm/trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh	(revision 18340)
@@ -0,0 +1,47 @@
+#!/bin/bash
+set -eu
+
+#Note of caution:  stop after boostrap phase, and run 
+#bjam --debug-configuration, to figure out which paths boost is using to include 
+#python. make sure everyone of these paths is covered by python. If not, just make 
+#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY 
+#to get the boost library to include python support without doing that. 
+
+#Some cleanup
+rm -rf install boost_1_55_0 src
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz'
+
+#Untar 
+tar -zxvf  boost_1_55_0.tar.gz
+
+#Move boost into install directory
+mv boost_1_55_0/* src
+rm -rf boost_1_55_0
+
+#patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
+#patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
+#patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch
+#patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch
+#patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch
+
+#Configure and compile
+cd src 
+./bootstrap.sh \
+	--prefix="$ISSM_DIR/externalpackages/boost/install" \
+	--with-python=python2.7 \
+	--with-python-root="$ISSM_DIR/externalpackages/python/install" \
+	--with-toolset=intel-linux
+
+#Compile boost
+# Need gcc with iconv installed in a location that has been added to your path
+./b2 toolset=intel-linux cxxflags=-static-libstdc++ linkflags=-static-libstdc++ threading=multi install
+#./bjam install
+
+#./b2 toolset=clang cxxflags=-stdlib=libstdc++ linkflags=-stdlib=libstdc++ -j2 variant=release link=static threading=multi instal
+
+#put bjam into install also: 
+mkdir ../install/bin
+cp bjam ../install/bin
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch	(revision 18340)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.pfe.patch	(revision 18340)
@@ -0,0 +1,6 @@
+156c153,155
+< # TODO: Can't this be integrated into the following logic?
+---
+> # TODO: Can't this be integrated into the following logic?
+> set(BLAS_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
+> set(LAPACK_LIBS "-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread")
Index: /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh	(revision 18340)
+++ /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh	(revision 18340)
@@ -0,0 +1,51 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf Dakota
+rm -rf src 
+rm -rf build 
+rm -rf install 
+mkdir src build install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz'
+
+#Untar 
+tar -zxvf dakota-5.3.1-public-src.tar.gz
+
+#Move Dakota to src directory
+mv dakota-5.3.1.src/* src
+rm -rf dakota-5.3.1.src
+
+#Set up Dakota cmake variables and config
+export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
+export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
+cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
+patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.patch
+patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch
+patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.pfe.patch
+
+#Apply patches
+patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch
+patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch
+patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch
+patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch
+patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch
+
+#Configure dakota
+cd $DAK_BUILD
+cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC
+cd ..
+
+#Compile and install dakota
+cd $DAK_BUILD
+if [ $# -eq 0 ];
+then
+	make
+	make install
+else
+	make -j $1
+	make -j $1 install
+fi
+cd ..
Index: sm/trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16	(revision 18339)
+++ 	(revision )
@@ -1,61 +1,0 @@
-#!/bin/bash
-
-#Some cleanup
-rm -rf install petsc-3.4.2 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz'
-
-#Untar and move petsc to install directory
-tar -zxvf  petsc-3.4.2.tar.gz
-mv petsc-3.4.2/* src/
-rm -rf petsc-3.4.2
-
-#configure
-cd src
-./config/configure.py \
- --prefix="$ISSM_DIR/externalpackages/petsc/install" \
- --PETSC_ARCH="$ISSM_ARCH" \
- --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
- --with-batch=1  \
- --with-debugging=0 \
- --with-shared-libraries=1 \
- --known-mpi-shared-libraries=1 \
- --with-mpi=1 \
- --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
- --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
- --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
- --download-scalapack=yes \
- --download-blacs=yes \
- --download-mumps=yes \
- --download-metis=yes \
- --download-parmetis=yes \
- --download-trilinos=yes \
- --download-euclid=yes \
- --download-hypre=yes \
- --COPTFLAGS="-lmpi -O3" \
- --FOPTFLAGS="-lmpi -O3" \
- --CXXOPTFLAGS="-lmpi -O3"
-
-#prepare script to reconfigure petsc
-cat > script.queue << EOF
-#PBS -S /bin/bash
-#PBS -l select=1:ncpus=1:model=wes 
-#PBS -l walltime=200 
-#PBS -W group_list=s1010
-#PBS -m e 
-
-. /usr/share/modules/init/bash 
-module load comp-intel/2012.0.032
-module load mpi-sgi/mpt.2.06rp16
-
-export PATH="$PATH:." 
-export MPI_GROUP_MAX=64 
-mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
-EOF
-
-#print instructions
-echo "== Now: cd src/ "
-echo "== qsub -q devel script.queue "
-echo "== Then run reconfigure script generated by PETSc and follow instructions"
Index: /issm/trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh	(revision 18340)
+++ /issm/trunk-jpl/externalpackages/petsc/install-3.4-pleiades-intel2012.0.032-mpt.2.06rp16.sh	(revision 18340)
@@ -0,0 +1,61 @@
+#!/bin/bash
+
+#Some cleanup
+rm -rf install petsc-3.4.2 src
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.4.2.tar.gz' 'petsc-3.4.2.tar.gz'
+
+#Untar and move petsc to install directory
+tar -zxvf  petsc-3.4.2.tar.gz
+mv petsc-3.4.2/* src/
+rm -rf petsc-3.4.2
+
+#configure
+cd src
+./config/configure.py \
+ --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+ --PETSC_ARCH="$ISSM_ARCH" \
+ --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+ --with-batch=1  \
+ --with-debugging=0 \
+ --with-shared-libraries=1 \
+ --known-mpi-shared-libraries=1 \
+ --with-mpi=1 \
+ --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
+ --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
+ --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
+ --download-scalapack=yes \
+ --download-blacs=yes \
+ --download-mumps=yes \
+ --download-metis=yes \
+ --download-parmetis=yes \
+ --download-trilinos=yes \
+ --download-euclid=yes \
+ --download-hypre=yes \
+ --COPTFLAGS="-lmpi -O3" \
+ --FOPTFLAGS="-lmpi -O3" \
+ --CXXOPTFLAGS="-lmpi -O3"
+
+#prepare script to reconfigure petsc
+cat > script.queue << EOF
+#PBS -S /bin/bash
+#PBS -l select=1:ncpus=1:model=wes 
+#PBS -l walltime=200 
+#PBS -W group_list=s1010
+#PBS -m e 
+
+. /usr/share/modules/init/bash 
+module load comp-intel/2012.0.032
+module load mpi-sgi/mpt.2.06rp16
+
+export PATH="$PATH:." 
+export MPI_GROUP_MAX=64 
+mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
+EOF
+
+#print instructions
+echo "== Now: cd src/ "
+echo "== qsub -q devel script.queue "
+echo "== Then run reconfigure script generated by PETSc and follow instructions"
Index: /issm/trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh	(revision 18340)
+++ /issm/trunk-jpl/externalpackages/petsc/install-3.5-pleiades-intel2012.0.032-mpt.2.06rp16.sh	(revision 18340)
@@ -0,0 +1,62 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf install petsc-3.5.1 src
+mkdir install src
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.5.1.tar.gz' 'petsc-3.5.1.tar.gz'
+
+#Untar and move petsc to install directory
+tar -zxvf  petsc-3.5.1.tar.gz
+mv petsc-3.5.1/* src/
+rm -rf petsc-3.5.1
+
+#configure
+cd src
+./config/configure.py \
+  --prefix="$ISSM_DIR/externalpackages/petsc/install" \
+  --PETSC_ARCH="$ISSM_ARCH" \
+  --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
+  --with-batch=1  \
+  --with-debugging=0 \
+  --with-shared-libraries=1 \
+  --known-mpi-shared-libraries=1 \
+  --with-mpi=1 \
+  --with-mpi-lib="/nasa/sgi/mpt/2.06rp16/lib/libmpi.so" \
+  --with-mpi-include="/nasa/sgi/mpt/2.06rp16/include" \
+  --with-blas-lapack-dir="/nasa/intel/Compiler/2012.0.032/composer_xe_2011_sp1/mkl/lib/intel64" \
+  --download-scalapack=yes \
+  --download-mumps=yes \
+  --download-metis=yes \
+  --download-parmetis=yes \
+  --download-trilinos=yes \
+  --download-euclid=yes \
+  --download-hypre=yes \
+  --COPTFLAGS="-lmpi -O3" \
+  --FOPTFLAGS="-lmpi -O3" \
+  --CXXOPTFLAGS="-lmpi -O3"
+
+#prepare script to reconfigure petsc
+cat > script.queue << EOF
+#PBS -S /bin/bash
+#PBS -l select=1:ncpus=1:model=wes 
+#PBS -l walltime=200 
+#PBS -W group_list=s1010
+#PBS -m e 
+
+. /usr/share/modules/init/bash 
+module load comp-intel/2012.0.032
+module load math/intel_mkl_64_10.0.011
+module load mpi-sgi/mpt.2.06rp16
+
+export PATH="$PATH:." 
+export MPI_GROUP_MAX=64 
+mpiexec -np 1 ./conftest-linux-gnu-ia64-intel.py
+EOF
+
+#print instructions
+echo "== Now: cd src/ "
+echo "== qsub -q devel script.queue "
+echo "== Then run reconfigure script generated by PETSc and follow instructions"