Index: sm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh	(revision 21688)
+++ 	(revision )
@@ -1,103 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf Dakota
-rm -rf src
-rm -rf install
-mkdir src install
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
-
-#Untar 
-tar -zxvf  Dakota_4_3.src.tar.gz
-
-#Move Dakota to src directory
-mv Dakota/* src
-rm -rf Dakota
-
-#Apply patches
-patch src/src/ParallelLibrary.C configs/4.2/ParallelLibrary.C.patch
-patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch
-patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch
-patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch
-patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch
-patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch
-
-#Configure dakota
-cd src
-./configure \
---prefix="$ISSM_DIR/externalpackages/dakota/install/" \
---without-graphics  \
---with-pic \
---disable-mpi \
---with-blas="-L$ISSM_DIR/externalpackages/petsc/install/lib -lfblas " \
---with-lapack="-L$ISSM_DIR/externalpackages/petsc/install/lib -lflapack "
-
-#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \
-#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread"
-#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \
-#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack"
-
-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 [ $# -eq 0 ];
-then
-	make
-	make install
-else
-	make -j $1
-	make -j $1 install
-fi
-cd ..
-
-#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing!
-cd install/lib
-mv libamplsolver.a libamplsolver.a.bak
-ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a
Index: sm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades.sh	(revision 21688)
+++ 	(revision )
@@ -1,97 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf Dakota
-rm -rf src
-rm -rf install
-mkdir src install
-
-#Download from ISSM server
-$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 configs/4.2/ParallelLibrary.C.patch
-patch src/src/ParallelLibrary.H configs/4.2/ParallelLibrary.H.patch
-patch src/src/NIDRProblemDescDB.C configs/4.2/NIDRProblemDescDB.C.patch
-patch src/src/NonDSampling.C configs/4.2/NonDSampling.C.patch
-patch src/src/NonDLocalReliability.C configs/4.2/NonDLocalReliability.C.patch
-patch src/src/NonDUnilevelRBDO.C configs/4.2/NonDUnilevelRBDO.C.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp configs/4.2/LHSDriver.cpp.patch
-
-#Configure dakota
-cd src
-./configure \
---prefix="$ISSM_DIR/externalpackages/dakota/install/" \
---without-graphics  \
---with-pic \
---disable-mpi \
---with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \
---with-lapack="-L/nasa/intel/mkl/10.0.011/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 [ $# -eq 0 ];
-then
-	make
-	make install
-else
-	make -j $1
-	make -j $1 install
-fi
-cd ..
-
-#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing!
-cd install/lib
-mv libamplsolver.a libamplsolver.a.bak
-ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a
Index: sm/trunk-jpl/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-5.2-pleiades-petsc3.3.sh	(revision 21688)
+++ 	(revision )
@@ -1,59 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf Dakota
-rm -rf src
-rm -rf install
-mkdir src install
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_5_2.src.tar.gz' 'Dakota_5_2.src.tar.gz'
-
-#Untar 
-tar -zxvf Dakota_5_2.src.tar.gz
-
-#Move Dakota to src directory
-mv Dakota/* src
-rm -rf Dakota
-
-#Apply patches
-patch src/src/ParallelLibrary.C configs/5.2/ParallelLibrary.C.patch
-patch src/src/ParallelLibrary.H configs/5.2/ParallelLibrary.H.patch
-#patch src/src/NIDRProblemDescDB.C configs/5.2/NIDRProblemDescDB.C.patch    #  causes segfault in 5.2
-patch src/src/NonDSampling.C configs/5.2/NonDSampling.C.patch
-patch src/src/NonDLocalReliability.C configs/5.2/NonDLocalReliability.C.patch
-patch src/src/NonDUnilevelRBDO.C configs/5.2/NonDUnilevelRBDO.C.patch    #  source not even used?
-patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.2/pecos_global_defs.hpp.patch
-
-#Configure dakota
-cd src
-./configure \
---prefix="$ISSM_DIR/externalpackages/dakota/install/" \
---without-graphics  \
---with-pic \
---disable-mpi \
---with-plugin \
---with-blas="-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread" \
---with-lapack="-L/nasa/intel/mkl/10.0.011/lib/em64t/ -lmkl -lmkl_lapack -liomp5 -lpthread"
-
-#--with-blas=/nasa/intel/Compiler/2012.0.032/mkl/lib/intel64/libmkl_intel_lp64.a \
-#--with-lapack=/nasa/intel/Compiler/2012.0.032/mkl/lib/intel64/libmkl_intel_lp64.a 
-#--with-blas="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread" \
-#--with-lapack="-L/nasa/intel/mkl/10.0.011/lib/64/ -lmkl -lmkl_lapack -liomp5 -lpthread"
-#--with-blas="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack" \
-#--with-lapack="-L/nasa/intel/Compiler/11.1/046/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_lapack"
-
-cd ..
-
-#Compile and install dakota
-cd src
-if [ $# -eq 0 ];
-then
-	make
-	make install
-else
-	make -j $1
-	make -j $1 install
-fi
-cd ..
Index: sm/trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-pleiades.sh	(revision 21688)
+++ 	(revision )
@@ -1,51 +1,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf Dakota
-rm -rf src 
-rm -rf build 
-rm -rf install 
-mkdir src build install 
-
-#Download from ISSM server
-$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.pfe.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 ..