Index: /issm/trunk-jpl/configure.ac
===================================================================
--- /issm/trunk-jpl/configure.ac	(revision 26342)
+++ /issm/trunk-jpl/configure.ac	(revision 26343)
@@ -26,5 +26,5 @@
 AM_INIT_AUTOMAKE([foreign])
 AC_CONFIG_HEADERS([./config.h])		# Config file must be config.h
-AM_SILENT_RULES([yes])				# Do not show compilation command by default
+AM_SILENT_RULES([yes])				# Reduce compilation and linking output (comment this line out or set value to "no" for verbose output)
 AM_PROG_AR
 
Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 26342)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 26343)
@@ -446,8 +446,8 @@
 	export BOOST_DIR=${BOOST_ROOT}
 	export BOOSTROOT=${BOOST_ROOT}
-	library_path_prepend "${BOOST_ROOT}/lib"
-	ld_library_path_prepend "${BOOST_ROOT}/lib"
-	dyld_library_path_prepend "${BOOST_ROOT}/lib"
-	path_prepend "${BOOST_ROOT}/bin"
+	library_path_append "${BOOST_ROOT}/lib"
+	ld_library_path_append "${BOOST_ROOT}/lib"
+	dyld_library_path_append "${BOOST_ROOT}/lib"
+	path_append "${BOOST_ROOT}/bin"
 fi
 
Index: /issm/trunk-jpl/externalpackages/petsc/install-3.13-pleiades.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/petsc/install-3.13-pleiades.sh	(revision 26342)
+++ /issm/trunk-jpl/externalpackages/petsc/install-3.13-pleiades.sh	(revision 26343)
@@ -6,4 +6,7 @@
 #
 VER="3.13.6"
+
+PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
+PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
 
 # Download source
@@ -30,18 +33,27 @@
 	--prefix="${PREFIX}" \
 	--PETSC_DIR="${PETSC_DIR}" \
-	--with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort\
-	-COPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -CXXOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" -FOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
+	--with-cc=icc \
+	--with-cpp=/usr/bin/cpp \
+	--with-cxx=icpc \
+	--with-fc=ifort \
+	-COPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
+	-CXXOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
+	-FOPTFLAGS="-g -O3 -axCORE-AVX2,AVX -xSSE4.2" \
 	--with-blas-lapack-dir="/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/" \
+	--with-scalapack-include=/nasa/intel/Compiler/2016.2.181/mkl/include \
+	--with-scalapack-lib="/nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/libmkl_blacs_sgimpt_lp64.so" \
 	--known-mpi-shared-libraries=1 \
+	--with-gnu-compilers=0 \
+	--with-vendor-compilers=intel \
 	--with-debugging=0 \
 	--with-valgrind=0 \
 	--with-x=0 \
 	--with-ssl=0 \
-	--with-batch=1  \
+	--with-batch=1 \
 	--with-shared-libraries=1 \
 	--download-metis=1 \
 	--download-parmetis=1 \
 	--download-mumps=1 \
-	--download-scalapack=1
+	--download-zlib=1
 
 # Compile and install
Index: /issm/trunk-jpl/jenkins/pleiades-basic
===================================================================
--- /issm/trunk-jpl/jenkins/pleiades-basic	(revision 26343)
+++ /issm/trunk-jpl/jenkins/pleiades-basic	(revision 26343)
@@ -0,0 +1,56 @@
+#--------------------#
+# ISSM Configuration #
+#--------------------#
+
+ISSM_CONFIG='\
+	--prefix=${ISSM_DIR} \
+	--with-wrappers=no \
+	--with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+	--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
+	--with-mpi-include=" " \
+	--with-mpi-libflags=" -lmpi" \
+	--with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/mkl/lib/intel64/ -mkl=cluster " \
+	--with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+	--with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+	--with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
+	--with-cxxoptflags="-g -O3 -axCORE-AVX2,AVX -xSSE4.2 -ipo -no-inline-min-size -inline-max-size=345 -no-inline-max-total-size -no-inline-max-per-routine -no-inline-max-per-compile " \
+	--with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
+	--with-vendor="intel-pleiades" \
+	--enable-development
+'
+
+#-------------------#
+# External Packages #
+#-------------------#
+
+EXTERNALPACKAGES="
+	petsc	install-3.13-pleiades.sh
+	m1qn3	install.sh
+"
+
+#---------#
+# Testing #
+#---------#
+
+# Test suites
+MATLAB_TEST=0
+PYTHON_TEST=0
+JAVASCRIPT_TEST=0
+EXAMPLES_TEST=0
+
+# Number of CPUs used in ISSM compilation
+#
+# NOTE: One is usually safer as some packages are very sensitive to parallel
+# 		compilation.
+#
+NUMCPUS_INSTALL=8
+
+# Number of CPUs used in the nightly runs
+NUMCPUS_RUN=1
+
+# Nightly run options
+#
+# See documentation in test/NightlyRun/runme.* for more information.
+#
+MATLAB_NROPTIONS=""
+PYTHON_NROPTIONS=""
Index: /issm/trunk-jpl/m4/issm_options.m4
===================================================================
--- /issm/trunk-jpl/m4/issm_options.m4	(revision 26342)
+++ /issm/trunk-jpl/m4/issm_options.m4	(revision 26343)
@@ -612,15 +612,17 @@
 		dnl   	AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_], ${DAKOTA_VERSION}, [Dakota version number])
 		dnl
-		DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
-		if test -n "${DAKOTA_VERSION_OUTPUT}"; then
-			DAKOTA_VERSION=`echo ${DAKOTA_VERSION_OUTPUT} grep "Dakota version" | sed 's/Dakota version //' | sed 's/ .*//'`
-		elif test -f "${DAKOTA_ROOT}/VERSION"; then
+		if test -f "${DAKOTA_ROOT}/VERSION"; then
 			DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/VERSION | grep 'DAKOTA Version' | sed 's/.*DAKOTA Version //' | sed 's/ .*//'`
-		elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.C"; then
-			DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
-		elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp"; then
-			DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
 		else
-			AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
+			DAKOTA_VERSION_OUTPUT=`${DAKOTA_ROOT}/bin/dakota -v`
+			if test -n "${DAKOTA_VERSION_OUTPUT}"; then
+				DAKOTA_VERSION=`echo ${DAKOTA_VERSION_OUTPUT} grep "Dakota version" | sed 's/Dakota version //' | sed 's/ .*//'`
+			elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.C"; then
+				DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+			elif test -f "${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp"; then
+				DAKOTA_VERSION=`cat ${DAKOTA_ROOT}/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
+			else
+				AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
+			fi
 		fi
 		AC_MSG_RESULT([${DAKOTA_VERSION}])
Index: /issm/trunk-jpl/src/c/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/c/Makefile.am	(revision 26342)
+++ /issm/trunk-jpl/src/c/Makefile.am	(revision 26343)
@@ -1,3 +1,3 @@
-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@
+AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @MPIINCL@ @PARMETISINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJINCL@ @ESMFINCL@
 AM_FCFLAGS = @SEMICINCL@
 
@@ -6,5 +6,5 @@
 EXEEXT=$(ISSMEXT)
 
-#Library declaration {{{
+# Library declaration {{{
 if !WINDOWS
 lib_LTLIBRARIES = libISSMCore.la
@@ -23,8 +23,8 @@
 #}}}
 
-#Core sources
+# Core sources
 issm_sources =
 
-#BAMG sources  {{{
+# BAMG sources {{{
 if BAMG
 issm_sources += \
@@ -57,5 +57,5 @@
 	./modules/BamgTriangulatex/BamgTriangulatex.cpp
 
-#do not include AmrBamg with AD
+# Do not include AmrBamg with AD
 if ADOLC
 issm_sources += \
@@ -71,5 +71,5 @@
 endif
 #}}}
-#Core sources{{{
+# Core sources {{{
 issm_sources += \
 	./datastructures/DataSet.cpp \
@@ -344,5 +344,5 @@
 	./classes/Inputs/ArrayInput.cpp
 #}}}
-#ADJOINTMPI/MeDiPack sources {{{
+# ADJOINTMPI/MeDiPack sources {{{
 if ADJOINTMPI
 issm_sources += ./toolkits/codipack/ampi_interface.cpp
@@ -351,6 +351,6 @@
 issm_sources += ./toolkits/codipack/ampi_interface.cpp
 endif
-# }}}
-#DAKOTA sources  {{{
+#}}}
+# DAKOTA sources {{{
 if DAKOTA
 issm_sources += \
@@ -369,5 +369,5 @@
 endif
 #}}}
-#Petsc sources  {{{
+# PETSc sources {{{
 if PETSC
 issm_sources += \
@@ -391,20 +391,20 @@
 endif
 #}}}
-#Mumps sources  {{{
+# MUMPS sources {{{
 if MUMPS
 issm_sources += ./toolkits/mumps/MumpsSolve.cpp
 endif
 #}}}
-#Gsl sources  {{{
+#GSL sources {{{
 if GSL
 issm_sources += ./toolkits/gsl/DenseGslSolve.cpp
 endif
 #}}}
-#proj sources  {{{
+# PROJ sources {{{
 if PROJ
 issm_sources += ./modules/CoordinateSystemTransformx/CoordinateSystemTransformx.cpp
 endif
 #}}}
-#Analyses{{{
+# Analyses {{{
 if ADJOINTBALANCETHICKNESS
 issm_sources += ./analyses/AdjointBalancethicknessAnalysis.cpp
@@ -521,5 +521,5 @@
 endif
 #}}}
-#Love sources (only if have fortran){{{
+# Love sources (only if have Fortran) {{{
 if LOVE
 if FORTRAN
@@ -536,5 +536,5 @@
 endif
 #}}}
-#Esa sources  {{{
+# Esa sources {{{
 if ESA
 issm_sources += \
@@ -543,10 +543,10 @@
 endif
 #}}}
-#Oceansources  {{{
+# Ocean sources {{{
 if OCEAN
 issm_sources += ./modules/OceanExchangeDatax/OceanExchangeDatax.cpp
 endif
 #}}}
-#Sampling sources  {{{
+# Sampling sources {{{
 if SAMPLING
 issm_sources += \
@@ -554,6 +554,6 @@
 	./analyses/SamplingAnalysis.cpp
 endif
-# }}}
-#Slc sources  {{{
+#}}}
+# SLC sources {{{
 if SEALEVELCHANGE
 issm_sources += \
@@ -563,5 +563,5 @@
 	./classes/SealevelGeometry.cpp
 
-#gia ivins physics (only if have fortran)
+# GIA Ivins physics (only if have Fortran)
 if FORTRAN
 issm_sources += \
@@ -578,15 +578,15 @@
 endif
 #}}}
-#Metis sources  {{{
+# METIS sources {{{
 if METIS
 issm_sources += ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp
 endif
 #}}}
-#Esmf sources  {{{
+# Esmf sources {{{
 if ESMF
 issm_sources += ./main/esmfbinders.cpp
 endif
 #}}}
-#SEMIC sources  {{{
+# SEMIC sources {{{
 if SEMIC
 if FORTRAN
@@ -595,6 +595,6 @@
 endif
 #}}}
-#Wrapper sources
-#Kml sources  {{{
+# Wrapper sources
+# Kml sources {{{
 kml_sources = \
 	./modules/Exp2Kmlx/Exp2Kmlx.cpp \
@@ -632,8 +632,8 @@
 	./kml/KMLFileReadUtils.cpp
 #}}}
-#NEOPZ sources  {{{
+# NEOPZ sources {{{
 neopz_sources = ./classes/AmrNeopz.cpp
 #}}}
-#Modules sources{{{
+# Modules sources {{{
 modules_sources = \
 	./shared/Threads/LaunchThread.cpp \
@@ -678,6 +678,6 @@
 #}}}
 
-#kriging (WRAPPER and executable)
-#Kriging sources  {{{
+# Kriging (wrapper and executable)
+# Kriging sources {{{
 if KRIGING
 issm_sources += \
@@ -697,5 +697,5 @@
 endif
 #}}}
-#Library flags and sources {{{
+# Library flags and sources {{{
 ALL_CXXFLAGS = $(CXXFLAGS) $(CXXOPTFLAGS)
 
@@ -711,5 +711,5 @@
 if !WINDOWS
 if !STANDALONE_LIBRARIES
-libISSMCore_la_LIBADD = $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
+libISSMCore_la_LIBADD = $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(OSLIBS)
 if FORTRAN
 libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB)
@@ -785,5 +785,5 @@
 
 if !MSYS2
-#Overload library, to overload any non-standard symbols. {{{
+# Overload library, to overload any non-standard symbols {{{
 libISSMOverload_la_SOURCES = ./shared/String/ApiPrintf.cpp
 libISSMOverload_la_CFLAGS  = -D_C_ -fPIC $(COPTFLAGS) $(CFLAGS)
@@ -800,5 +800,5 @@
 endif
 #}}}
-#Executable {{{
+# Executable {{{
 if ANDROID
 if ANDROIDEXE
@@ -815,5 +815,5 @@
 endif
 
-#Standard libraries
+# Standard libraries
 LDADD = ./libISSMCore.la 
 
@@ -826,5 +826,5 @@
 endif
 
-#External packages
+# External packages
 LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
 
Index: /issm/trunk-jpl/src/wrappers/javascript/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/javascript/Makefile.am	(revision 26342)
+++ /issm/trunk-jpl/src/wrappers/javascript/Makefile.am	(revision 26343)
@@ -1,3 +1,3 @@
-AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@
+AM_CPPFLAGS = @DAKOTAINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @CODIPACKINCL@
 AUTOMAKE_OPTIONS = subdir-objects
 
Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am
===================================================================
--- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 26342)
+++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am	(revision 26343)
@@ -1,3 +1,3 @@
-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
+AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @MATLABINCL@ @PETSCINCL@ @MPIINCL@ @SPOOLESINCL@ @PARMETISINCL@ @METISINCL@ @TRIANGLEINCL@ @CHACOINCL@ @SCOTCHINCL@ @SHAPELIBINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MEDIPACKINCL@ @CODIPACKINCL@ @PROJINCL@
 AUTOMAKE_OPTIONS = subdir-objects