Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.patch	(revision 15245)
@@ -0,0 +1,40 @@
+41,46c41,46
+< #set( BLAS_LIBS 
+< #      "/usr/lib64"
+< #      CACHE FILEPATH "Use non-standard BLAS library path" FORCE )
+< #set( LAPACK_LIBS 
+< #      "/usr/lib64"
+< #      CACHE FILEPATH "Use non-standard BLAS library path" FORCE )
+---
+> set( BLAS_LIBS 
+>       "/usr/lib64/libblas.so.3.0.3"
+>       CACHE FILEPATH "Use non-standard BLAS library path" FORCE )
+> set( LAPACK_LIBS 
+>       "/usr/lib64/liblapack.so.3.0.3"
+>       CACHE FILEPATH "Use non-standard BLAS library path" FORCE )
+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)
+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/5.3.1/DakotaDev.cmake.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/DakotaDev.cmake.patch	(revision 15245)
@@ -0,0 +1,16 @@
+4,8c4,8
+< set(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?")
+< 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(DAKOTA_HAVE_MPI TRUE CACHE BOOL "Enable MPI in DAKOTA?")
+> #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/5.3.1/NonDLocalReliability.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/NonDLocalReliability.cpp.patch	(revision 15245)
@@ -0,0 +1,9 @@
+2587a2588
+> 	  // add sensitivity output to importance factors (jes, 8/06/10)
+2592c2593,2596
+< 	    << 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/5.3.1/NonDSampling.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/NonDSampling.cpp.patch	(revision 15245)
@@ -0,0 +1,25 @@
+703,709c703,710
+<   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, 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, drv_labels,
+> //				      iteratedModel.response_labels());
+> //  }
+1196,1197c1197,1200
+<     nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels,
+< 				    iteratedModel.response_labels());
+---
+> 
+> //don't output for now.
+> //    nonDSampCorr.print_correlations(s, cv_labels, div_labels, drv_labels,
+> //				    iteratedModel.response_labels());
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/ParallelLibrary.cpp.patch	(revision 15245)
@@ -0,0 +1,40 @@
+107a108
+>   initialized=0; //we run serially all the time!
+133a135
+>   initialized=0; //we run serially all the time!
+141a144,176
+> /** This constructor is provided for the ISSM software, to run serial
+>  * Dakota in a parallel MPI ring: */
+> ParallelLibrary::ParallelLibrary(char* serial_mode):
+>   worldRank(0), worldSize(1),
+>   mpirunFlag(false), ownMPIFlag(false), dummyFlag(false),
+>   stdOutputToFile(false), stdErrorToFile(false), checkFlag(false),
+>   preRunFlag(true), runFlag(true), postRunFlag(true), userModesFlag(false),
+>   startClock(0), stopRestartEvals(0),
+>   currPLIter(parallelLevels.end()), currPCIter(parallelConfigurations.end())
+> {
+>   startClock   = clock();
+> #ifdef DAKOTA_UTILIB
+>   utilib::exception_mngr::set_mode(utilib::exception_mngr::Abort);
+>   startCPUTime = CPUSeconds();       // see utilib/src/sys/seconds.cpp
+>   startWCTime  = WallClockSeconds(); // see utilib/src/sys/seconds.cpp
+> #endif // DAKOTA_UTILIB
+> 
+>   // 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 5.3.1 MPI executable in serial mode on CPU 0 for ISSM.";
+> #else // mpi not available
+>   pl.serverIntraComm = MPI_COMM_NULL;
+>   Cout << "Running Dakota 5.3.1 serial executable in serial mode for ISSM.\n";
+> #endif // HAVE_MPI
+> 
+>   parallelLevels.push_back(pl);
+>   currPLIter = parallelLevels.begin();
+>   increment_parallel_configuration();
+> }
+> 
+> 
+1536a1572
+>   initialized=0; //we run serially all the time!
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/ParallelLibrary.hpp.patch	(revision 15245)
@@ -0,0 +1,3 @@
+358a359,360
+>   /// library mode constructor, serial mode (for the ISSM software)
+>   ParallelLibrary(char* serial_mode);
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch	(revision 15245)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/pecos_global_defs.hpp.patch	(revision 15245)
@@ -0,0 +1,4 @@
+25a26
+> #ifndef PI
+26a28
+> #endif
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch	(revision 15244)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3/ParallelLibrary.cpp.patch	(revision 15245)
@@ -4,5 +4,5 @@
 >   initialized=0; //we run serially all the time!
 137a140,172
-> /** This constructor is provided for the Issm software, to run serial
+> /** This constructor is provided for the ISSM software, to run serial
 >  * Dakota in a parallel MPI ring: */
 > ParallelLibrary::ParallelLibrary(char* serial_mode):
@@ -25,8 +25,8 @@
 > #ifdef HAVE_MPI // mpi available, we still don't want to run in parallel for Dakota!
 >   pl.serverIntraComm = MPI_COMM_NULL;
->   Cout << "Running Dakota MPI executable in serial mode on CPU 0 for ISSM.";
+>   Cout << "Running Dakota 5.3 MPI executable in serial mode on CPU 0 for ISSM.";
 > #else // mpi not available
 >   pl.serverIntraComm = MPI_COMM_NULL;
->   Cout << "Running Dakota serial executable in serial mode for ISSM.\n";
+>   Cout << "Running Dakota 5.3 serial executable in serial mode for ISSM.\n";
 > #endif // HAVE_MPI
 > 
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch	(revision 15244)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3/ParallelLibrary.hpp.patch	(revision 15245)
@@ -1,3 +1,3 @@
 358a359,360
->   /// library mode constructor, serial mode (for the Issm software)
+>   /// library mode constructor, serial mode (for the ISSM software)
 >   ParallelLibrary(char* serial_mode);