Index: sm/trunk-jpl/externalpackages/dakota/LHSDriver.cpp.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/LHSDriver.cpp.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,8 +1,0 @@
-766c766
-<   /*char output_string[32], message_string[32], title_string[32],
----
->   char output_string[32], message_string[32], title_string[32],
-802c802
-<   check_error(err_code, "lhs_files");*/
----
->   check_error(err_code, "lhs_files");
Index: sm/trunk-jpl/externalpackages/dakota/NIDRProblemDescDB.C.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NIDRProblemDescDB.C.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,4 +1,0 @@
-95a96,98
->   
->   //close the input file
->   fclose(nidrin);
Index: sm/trunk-jpl/externalpackages/dakota/NIDRProblemDescDB.C.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NIDRProblemDescDB.C.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,5 +1,0 @@
-109a110,113
-> 
->   //close the input file
->   fclose(nidrin);
-> 
Index: sm/trunk-jpl/externalpackages/dakota/NonDLocalReliability.C.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NonDLocalReliability.C.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,7 +1,0 @@
-2276a2277
-> 	  // add sensitivity output to importance factors (jes, 8/06/10)
-2280c2281,2282
-< 	    << impFactor[i][j] << '\n';
----
-> 	    << impFactor[i][j] << "  Sensitivity = " << setw(write_precision+7)
-> 	    << fnGradsMeanX(i, j) << '\n';
Index: sm/trunk-jpl/externalpackages/dakota/NonDLocalReliability.C.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NonDLocalReliability.C.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,9 +1,0 @@
-2218a2219
-> 	  // add sensitivity output to importance factors (jes, 8/06/10)
-2223c2224,2227
-< 	    << 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: sm/trunk-jpl/externalpackages/dakota/NonDSampling.C.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NonDSampling.C.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,15 +1,0 @@
-656a657,658
-> 
-> 
-659a662,663
->    
-> 	return; //don't compute for now, too expensive.
-705c709
-<   //calculate simple rank correlation coeff
----
->   //calculate simple correlation coeff
-710a715
-> 
-1071a1077,1078
-> 
-> 	return; //don't output for now.
Index: sm/trunk-jpl/externalpackages/dakota/NonDSampling.C.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NonDSampling.C.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,14 +1,0 @@
-438,439c438,440
-<   if (!subIteratorFlag)
-<     nonDSampCorr.compute_correlations(vars_samples, resp_samples);
----
-> //don't compute for now, too expensive.
-> //  if (!subIteratorFlag)
-> //    nonDSampCorr.compute_correlations(vars_samples, resp_samples);
-894,895c895,897
-<     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: sm/trunk-jpl/externalpackages/dakota/NonDUnilevelRBDO.C.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NonDUnilevelRBDO.C.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,10 +1,0 @@
-1052,1053c1052,1057
-< 	  s << "  Importance Factor for variable " << setw(11)
-< 	    << uv_labels[j].data() << " = " << impFactor[i][j] << '\n';
----
-> 	  // add sensitivity output to importance factors (jes, 8/06/10)
-> 	  s << "  Importance Factor for variable " << setiosflags(ios::left)
-> 	    << setw(11) << uv_labels[j].data() << " = "
-> 	    << resetiosflags(ios::adjustfield) << setw(write_precision+7)
-> 	    << impFactor[i][j] << "  Sensitivity = " << setw(write_precision+7)
-> 	    << fnGradsMeanX(i, j) << '\n';
Index: sm/trunk-jpl/externalpackages/dakota/NonDUnilevelRBDO.C.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/NonDUnilevelRBDO.C.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,7 +1,0 @@
-1046a1047
-> 	  // add sensitivity output to importance factors (jes, 8/06/10)
-1048c1049,1050
-< 	    << uv_labels[j].data() << " = " << impFactor[i][j] << '\n';
----
-> 	    << uv_labels[j].data() << " = " << impFactor[i][j]
-> 	    << "  Sensitivity = " << fnGradsMeanX(i,j) << '\n';
Index: sm/trunk-jpl/externalpackages/dakota/ParallelLibrary.C.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/ParallelLibrary.C.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,34 +1,0 @@
-134a135
->   initialized=0; //we run serially all the time!
-165a167,197
-> /** 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), dryRunFlag(false), dummyFlag(false),
->   stdOutputFlag(false), stdErrorFlag(false), startClock(0),
->   stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL),
->   writeRestartFilename(NULL), 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 in serial mode on CPU 0, inside an MPI ring.";
-> #else // mpi not available
->   pl.serverIntraComm = MPI_COMM_NULL;
->   Cout << "Running Dakota in serial mode.\n";
-> #endif // HAVE_MPI
-> 
->   parallelLevels.insert(pl);
->   currPLIter = parallelLevels.begin();
->   increment_parallel_configuration();
-> }
-> 
Index: sm/trunk-jpl/externalpackages/dakota/ParallelLibrary.C.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/ParallelLibrary.C.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,36 +1,0 @@
-178a179
->   initialized=0; //we run serially all the time!
-214a216,248
-> /** 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 5.2 MPI executable in serial mode on CPU 0 for ISSM.";
-> #else // mpi not available
->   pl.serverIntraComm = MPI_COMM_NULL;
->   Cout << "Running Dakota 5.2 serial executable in serial mode for ISSM.\n";
-> #endif // HAVE_MPI
-> 
->   parallelLevels.push_back(pl);
->   currPLIter = parallelLevels.begin();
->   increment_parallel_configuration();
-> }
-> 
-> 
Index: sm/trunk-jpl/externalpackages/dakota/ParallelLibrary.H.4.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/ParallelLibrary.H.4.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,3 +1,0 @@
-346a347,348
->   /// library mode constructor, serial mode
->   ParallelLibrary(char*  serial_mode);
Index: sm/trunk-jpl/externalpackages/dakota/ParallelLibrary.H.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/ParallelLibrary.H.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,3 +1,0 @@
-358a359,360
->   /// library mode constructor, serial mode (for the Issm software)
->   ParallelLibrary(char*  serial_mode);
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/LHSDriver.cpp.patch	(revision 14273)
@@ -0,0 +1,8 @@
+766c766
+<   /*char output_string[32], message_string[32], title_string[32],
+---
+>   char output_string[32], message_string[32], title_string[32],
+802c802
+<   check_error(err_code, "lhs_files");*/
+---
+>   check_error(err_code, "lhs_files");
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NIDRProblemDescDB.C.patch	(revision 14273)
@@ -0,0 +1,4 @@
+95a96,98
+>   
+>   //close the input file
+>   fclose(nidrin);
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDLocalReliability.C.patch	(revision 14273)
@@ -0,0 +1,7 @@
+2276a2277
+> 	  // add sensitivity output to importance factors (jes, 8/06/10)
+2280c2281,2282
+< 	    << impFactor[i][j] << '\n';
+---
+> 	    << impFactor[i][j] << "  Sensitivity = " << setw(write_precision+7)
+> 	    << fnGradsMeanX(i, j) << '\n';
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDSampling.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDSampling.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDSampling.C.patch	(revision 14273)
@@ -0,0 +1,15 @@
+656a657,658
+> 
+> 
+659a662,663
+>    
+> 	return; //don't compute for now, too expensive.
+705c709
+<   //calculate simple rank correlation coeff
+---
+>   //calculate simple correlation coeff
+710a715
+> 
+1071a1077,1078
+> 
+> 	return; //don't output for now.
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/NonDUnilevelRBDO.C.patch	(revision 14273)
@@ -0,0 +1,10 @@
+1052,1053c1052,1057
+< 	  s << "  Importance Factor for variable " << setw(11)
+< 	    << uv_labels[j].data() << " = " << impFactor[i][j] << '\n';
+---
+> 	  // add sensitivity output to importance factors (jes, 8/06/10)
+> 	  s << "  Importance Factor for variable " << setiosflags(ios::left)
+> 	    << setw(11) << uv_labels[j].data() << " = "
+> 	    << resetiosflags(ios::adjustfield) << setw(write_precision+7)
+> 	    << impFactor[i][j] << "  Sensitivity = " << setw(write_precision+7)
+> 	    << fnGradsMeanX(i, j) << '\n';
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/ParallelLibrary.C.patch	(revision 14273)
@@ -0,0 +1,34 @@
+134a135
+>   initialized=0; //we run serially all the time!
+165a167,197
+> /** 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), dryRunFlag(false), dummyFlag(false),
+>   stdOutputFlag(false), stdErrorFlag(false), startClock(0),
+>   stdOutputFilename(NULL), stdErrorFilename(NULL), readRestartFilename(NULL),
+>   writeRestartFilename(NULL), 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 in serial mode on CPU 0, inside an MPI ring.";
+> #else // mpi not available
+>   pl.serverIntraComm = MPI_COMM_NULL;
+>   Cout << "Running Dakota in serial mode.\n";
+> #endif // HAVE_MPI
+> 
+>   parallelLevels.insert(pl);
+>   currPLIter = parallelLevels.begin();
+>   increment_parallel_configuration();
+> }
+> 
Index: /issm/trunk-jpl/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/4.2/ParallelLibrary.H.patch	(revision 14273)
@@ -0,0 +1,3 @@
+346a347,348
+>   /// library mode constructor, serial mode
+>   ParallelLibrary(char*  serial_mode);
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NIDRProblemDescDB.C.patch	(revision 14273)
@@ -0,0 +1,5 @@
+109a110,113
+> 
+>   //close the input file
+>   fclose(nidrin);
+> 
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDLocalReliability.C.patch	(revision 14273)
@@ -0,0 +1,9 @@
+2218a2219
+> 	  // add sensitivity output to importance factors (jes, 8/06/10)
+2223c2224,2227
+< 	    << 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/5.2/NonDSampling.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDSampling.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDSampling.C.patch	(revision 14273)
@@ -0,0 +1,14 @@
+438,439c438,440
+<   if (!subIteratorFlag)
+<     nonDSampCorr.compute_correlations(vars_samples, resp_samples);
+---
+> //don't compute for now, too expensive.
+> //  if (!subIteratorFlag)
+> //    nonDSampCorr.compute_correlations(vars_samples, resp_samples);
+894,895c895,897
+<     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/5.2/NonDUnilevelRBDO.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/NonDUnilevelRBDO.C.patch	(revision 14273)
@@ -0,0 +1,7 @@
+1046a1047
+> 	  // add sensitivity output to importance factors (jes, 8/06/10)
+1048c1049,1050
+< 	    << uv_labels[j].data() << " = " << impFactor[i][j] << '\n';
+---
+> 	    << uv_labels[j].data() << " = " << impFactor[i][j]
+> 	    << "  Sensitivity = " << fnGradsMeanX(i,j) << '\n';
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/ParallelLibrary.C.patch	(revision 14273)
@@ -0,0 +1,36 @@
+178a179
+>   initialized=0; //we run serially all the time!
+214a216,248
+> /** 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 5.2 MPI executable in serial mode on CPU 0 for ISSM.";
+> #else // mpi not available
+>   pl.serverIntraComm = MPI_COMM_NULL;
+>   Cout << "Running Dakota 5.2 serial executable in serial mode for ISSM.\n";
+> #endif // HAVE_MPI
+> 
+>   parallelLevels.push_back(pl);
+>   currPLIter = parallelLevels.begin();
+>   increment_parallel_configuration();
+> }
+> 
+> 
Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/ParallelLibrary.H.patch	(revision 14273)
@@ -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/5.2/pecos_global_defs.hpp.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch	(revision 14273)
+++ /issm/trunk-jpl/externalpackages/dakota/configs/5.2/pecos_global_defs.hpp.patch	(revision 14273)
@@ -0,0 +1,4 @@
+24a25
+> #ifndef PI
+25a27
+> #endif
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-altix64-cosmos.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-altix64-cosmos.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-altix64-cosmos.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-discover.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-discover.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-discover.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-astrid.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-astrid.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-astrid.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-cloud.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-cloud.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-cloud.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-murdo.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-murdo.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-linux64-murdo.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-macosx64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-macosx64.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-macosx64.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades-petsc3.3.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-4.2-pleiades.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.4.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.4.2.patch
-patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.4.2.patch
-patch src/src/NonDSampling.C ./NonDSampling.C.4.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.4.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.4.2.patch    #  source not even used?
-#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.4.2.patch
+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
Index: /issm/trunk-jpl/externalpackages/dakota/install-5.2-linux64-astrid.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/install-5.2-linux64-astrid.sh	(revision 14272)
+++ /issm/trunk-jpl/externalpackages/dakota/install-5.2-linux64-astrid.sh	(revision 14273)
@@ -19,11 +19,11 @@
 
 #Apply patches
-patch src/src/ParallelLibrary.C ./ParallelLibrary.C.5.2.patch
-patch src/src/ParallelLibrary.H ./ParallelLibrary.H.5.2.patch
-#patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.5.2.patch    #  causes segfault in 5.2
-patch src/src/NonDSampling.C ./NonDSampling.C.5.2.patch
-patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.5.2.patch
-patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.5.2.patch    #  source not even used?
-patch src/packages/pecos/src/pecos_global_defs.hpp ./pecos_global_defs.hpp.5.2.patch
+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
Index: sm/trunk-jpl/externalpackages/dakota/pecos_global_defs.hpp.5.2.patch
===================================================================
--- /issm/trunk-jpl/externalpackages/dakota/pecos_global_defs.hpp.5.2.patch	(revision 14272)
+++ 	(revision )
@@ -1,4 +1,0 @@
-24a25
-> #ifndef PI
-25a27
-> #endif