Index: /issm/trunk-jpl/externalpackages/dakota/install-linux64-cloud.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-linux64-cloud.sh	(revision 13706)
+++ /issm/trunk-jpl/externalpackages/dakota/install-linux64-cloud.sh	(revision 13706)
@@ -0,0 +1,97 @@
+#!/bin/bash
+set -eu
+
+#Some cleanup
+rm -rf Dakota
+rm -rf src 
+rm -rf install 
+mkdir src install 
+
+#Download from ISSM server
+$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/Dakota_4_3.src.tar.gz' 'Dakota_4_3.src.tar.gz'
+
+#Untar 
+tar -zxvf  Dakota_4_3.src.tar.gz
+
+#Move Dakota to src directory
+mv Dakota/* src
+rm -rf Dakota
+
+#Apply patches
+patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch
+patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch
+patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch
+patch src/src/NonDSampling.C ./NonDSampling.C.patch
+patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch
+patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch    #  source not even used?
+#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch
+
+#Configure dakota
+cd src
+./configure \
+	--prefix="$ISSM_DIR/externalpackages/dakota/install" \
+	--without-graphics  \
+	--with-pic \
+	--disable-mpi \
+	--with-blas=/usr/lib/libblas.so \
+	--with-lapack=/usr/lib/liblapack.so
+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: /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh	(revision 13705)
+++ /issm/trunk-jpl/externalpackages/petsc/install-dev-linux64.sh	(revision 13706)
@@ -1,6 +1,5 @@
 #!/bin/bash
-set -eu
 
-STEP=1
+STEP=2
 
 if [ $STEP -eq 1 ]; then
@@ -52,5 +51,6 @@
 	--download-spai=yes \
 	--download-superlu=http://crd.lbl.gov/~xiaoye/SuperLU/superlu_4.3.tar.gz \
-	--download-hypre=yes 
+	--download-hypre=yes \
+	--download-c2html=yes
 #	--with-pic=1