Index: /issm/trunk/externalpackages/dakota/install.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install.sh	(revision 968)
+++ /issm/trunk/externalpackages/dakota/install.sh	(revision 969)
@@ -6,9 +6,9 @@
 #Some cleanup
 rm -rf Dakota
-rm -rf src src_nomatlab
-rm -rf install install_nomatlab
+rm -rf src 
+rm -rf install 
 
 #Create src and install directories
-mkdir src src_nomatlab install install_nomatlab
+mkdir src install 
 
 #version of doxygen
@@ -21,5 +21,4 @@
 mv Dakota/* src
 rm -rf Dakota
-cp -Rf src src_nomatlab
 
 #Apply patches
@@ -27,24 +26,53 @@
 patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch
 
-patch src_nomatlab/src/ParallelLibrary.C ./ParallelLibrary.C.patch
-patch src_nomatlab/src/ParallelLibrary.H ./ParallelLibrary.H.patch
-
 #Configure dakota
 cd src
-./configure --prefix="$ISSM_DIR/externalpackages/dakota/install" --without-graphics  --with-matlab=$MATLAB_DIR
+./configure --prefix="$ISSM_DIR/externalpackages/dakota/install" --without-graphics  --with-pic
+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 
+
 
 #Compile dakota
+cd src 
 make  -j $NUMCPUS
 
 #Install dakota
-make  install
-
-#Configure dakota with no matlab
-cd ../src_nomatlab
-./configure --prefix="$ISSM_DIR/externalpackages/dakota/install_nomatlab" --without-graphics 
-
-#Compile dakota
-make  -j $NUMCPUS
-
-#Install dakota
-make  install
+make  -j $NUMCPUS install