Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/BuildDakotaCustom.cmake.mac.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/BuildDakotaCustom.cmake.mac.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/BuildDakotaCustom.cmake.mac.patch	(revision 19544)
@@ -0,0 +1,14 @@
+64,65c64,65
+< #set( DAKOTA_HAVE_MPI ON
+< #     CACHE BOOL "Build with MPI enabled" FORCE)
+---
+> set( DAKOTA_HAVE_MPI OFF
+>      CACHE BOOL "Build with MPI disabled" FORCE)
+91,93c91,93
+< #set( CMAKE_INSTALL_PREFIX
+< #     "/path/to/Dakota/installation"
+< #     CACHE PATH "Path to Dakota installation" )
+---
+> set( CMAKE_INSTALL_PREFIX
+>      "$ENV{ISSM_DIR}/externalpackages/dakota/install"
+>      CACHE PATH "Path to Dakota installation" )
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/BuildDakotaCustom.cmake.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/BuildDakotaCustom.cmake.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/BuildDakotaCustom.cmake.patch	(revision 19544)
@@ -0,0 +1,20 @@
+73,77c73,77
+< #set(BOOST_ROOT
+< #    "path/to/custom/Boost/install/directory"
+< #    CACHE PATH "Use non-standard Boost install" FORCE)
+< #set( Boost_NO_SYSTEM_PATHS TRUE
+< #     CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE)
+---
+> set(BOOST_ROOT
+>     "$ENV{ISSM_DIR}/externalpackages/boost/install"
+>     CACHE PATH "Use non-standard Boost install" FORCE)
+> set( Boost_NO_SYSTEM_PATHS TRUE
+>      CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE)
+91,93c91,93
+< #set( CMAKE_INSTALL_PREFIX
+< #     "/path/to/Dakota/installation"
+< #     CACHE PATH "Path to Dakota installation" )
+---
+> set( CMAKE_INSTALL_PREFIX
+>      "$ENV{ISSM_DIR}/externalpackages/dakota/install"
+>      CACHE PATH "Path to Dakota installation" )
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/CMakeLists.txt.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/CMakeLists.txt.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/CMakeLists.txt.patch	(revision 19544)
@@ -0,0 +1,4 @@
+47a48,50
+> set(BUILD_STATIC_LIBS ON CACHE BOOL "Set to ON to build static libraries" FORCE)
+> set(BUILD_SHARED_LIBS OFF CACHE BOOL "Set to ON to build DSO libraries" FORCE)
+> 
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/CMakeLists.txt.pfe.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/CMakeLists.txt.pfe.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/CMakeLists.txt.pfe.patch	(revision 19544)
@@ -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/configs/6.1-mpi/DakotaDev.cmake.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/DakotaDev.cmake.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/DakotaDev.cmake.patch	(revision 19544)
@@ -0,0 +1,14 @@
+5,8c5,8
+< set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build")
+< set(ENABLE_SPEC_MAINT TRUE CACHE BOOL 
+<   "Enable DAKOTA specification maintenance mode?")
+< set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?")
+---
+> #set(ENABLE_DAKOTA_DOCS TRUE CACHE BOOL "Enable DAKOTA documentation build")
+> #set(ENABLE_SPEC_MAINT TRUE CACHE BOOL 
+> #  "Enable DAKOTA specification maintenance mode?")
+> #set(PECOS_ENABLE_TESTS TRUE CACHE BOOL "Enable Pecos-specific tests?")
+14c14
+< #set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE)
+---
+> set(HAVE_X_GRAPHICS OFF CACHE BOOL "Disable dependency on X libraries" FORCE)
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/NonDLocalReliability.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/NonDLocalReliability.cpp.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/NonDLocalReliability.cpp.patch	(revision 19544)
@@ -0,0 +1,9 @@
+2645a2646
+> 		 // add sensitivity output to importance factors (jes, 8/06/10)
+2651c2652,2655
+< 	    << std::setw(width) << impFactor(j,i) << '\n';
+---
+> 	    << std::setw(width) << impFactor(j,i) 
+> 		 << "  Sensitivity = "
+> 		 << std::resetiosflags(std::ios::adjustfield)
+> 		 << std::setw(width) << fnGradsMeanX(j,i) << '\n';
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/NonDSampling.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/NonDSampling.cpp.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/NonDSampling.cpp.patch	(revision 19544)
@@ -0,0 +1,25 @@
+780,786c780,787
+<   if (!subIteratorFlag) {
+<     nonDSampCorr.compute_correlations(vars_samples, resp_samples);
+<     // archive the correlations to the results DB
+<     nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels,
+< 				      div_labels, dsv_labels, drv_labels,
+< 				      iteratedModel.response_labels());
+<   }
+---
+> //don't compute for now, too expensive.
+> //  if (!subIteratorFlag) {
+> //   nonDSampCorr.compute_correlations(vars_samples, resp_samples);
+> //    // archive the correlations to the results DB
+> //    nonDSampCorr.archive_correlations(run_identifier(), resultsDB, cv_labels,
+> //				      div_labels, dsv_labels, drv_labels,
+> //				      iteratedModel.response_labels());
+> //  }
+1277,1278c1278,1281
+<     nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels,
+< 				    drv_labels,iteratedModel.response_labels());
+---
+> 
+> //don't output for now.
+> //    nonDSampCorr.print_correlations(s, cv_labels, div_labels, dsv_labels,
+> //				    drv_labels,iteratedModel.response_labels());
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/ParallelLibrary.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/ParallelLibrary.cpp.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/ParallelLibrary.cpp.patch	(revision 19544)
@@ -0,0 +1,24 @@
+51a54,76
+> /** This constructor is provided for the ISSM software, to run serial
+>  * Dakota in a parallel MPI ring: */
+> ParallelLibrary::ParallelLibrary(char* serial_mode):
+>	  mpiManager(dummy_mpi_mgr), programOptions(dummy_prg_opt),
+>	    outputManager(dummy_out_mgr), dummyFlag(true), outputTimings(false)
+> {
+>   initialize_timers();
+> 
+>   // do not initialize MPI.  Get worldRank/worldSize if available
+>   ParallelLevel pl;
+> #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota!
+>   pl.serverIntraComm = MPI_COMM_NULL;
+>   Cout << "Running Dakota 6.1 MPI executable in serial mode on CPU 0 for ISSM." << std::endl;
+> #else // mpi not available
+>   pl.serverIntraComm = MPI_COMM_NULL;
+>   Cout << "Running Dakota 6.1 serial executable in serial mode for ISSM." << std::endl;
+> #endif // HAVE_MPI
+> 
+>   parallelLevels.push_back(pl);
+>   increment_parallel_configuration();
+> }
+> 
+> 
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/ParallelLibrary.hpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/ParallelLibrary.hpp.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/ParallelLibrary.hpp.patch	(revision 19544)
@@ -0,0 +1,3 @@
+475a476,477
+>   /// library mode constructor, serial mode (for the ISSM software)
+>   ParallelLibrary(char* serial_mode);
Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/pecos_global_defs.hpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/pecos_global_defs.hpp.patch	(revision 19544)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/6.1-mpi/pecos_global_defs.hpp.patch	(revision 19544)
@@ -0,0 +1,4 @@
+25a26
+> #ifndef PI
+26a28
+> #endif