Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/index.html
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/index.html	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/index.html	(revision 22892)
@@ -7,14 +7,11 @@
         <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js"></script>
         <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css"></link>
-        <script type="text/javascript" src="lib/bin/issm-binaries.js"> </script>
-        <script type="text/javascript" src="lib/bin/issm-extlibraries.js"> </script>
-        <script type="text/javascript" src="lib/Exp/Square.js"></script>
-        <script type="text/javascript" src="lib/Par/SquareShelfConstrained.js"></script>
-        <script type="text/javascript" src="lib/Data/SquareShelfConstrained.data.js"></script>
-        <script type="text/javascript" src="lib/mesh2d.js"></script>
-        <script type="text/javascript" src="lib/mesh3dprisms.js"></script>
-        <script type="text/javascript" src="lib/bin/model.js"></script>
-        <!--<script src="scripts/runscript.js"></script>-->
-        <script src="scripts/runscript.js"></script>
+        <script type="text/javascript" src="../../../bin/issm-bin.js"> </script>
+        <script type="text/javascript" src="../../../bin/IssmModule.js"> </script>
+        <script type="text/javascript" src="../../../bin/issm-prebin.js"> </script>
+        <script type="text/javascript" src="../../../test/Exp/Square.js"></script>
+        <script type="text/javascript" src="../../../test/Par/SquareShelfConstrained.js"></script>
+        <script type="text/javascript" src="../../../test/Data/SquareShelfConstrained.data.js"></script>
+        <script src="./scripts/runscript.js"></script>
 
         <style>
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/karma.conf.js
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/karma.conf.js	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/karma.conf.js	(revision 22892)
@@ -12,6 +12,6 @@
     // list of files / patterns to load in the browser
     files: [
-      'node_modules/jquery/dist/jquery.min.js',
-      'node_modules/mathjs/dist/math.min.js',
+      './../../../externalpackages/emscripten/src/node/4.1.1_64bit/lib/node_modules/jquery/dist/jquery.min.js',
+      './../../../externalpackages/emscripten/src/node/4.1.1_64bit/lib/node_modules/mathjs/dist/math.min.js',
       'lib/Exp/Square.js',
       'lib/Par/SquareShelfConstrained.js',
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/scripts/runscript.js
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/scripts/runscript.js	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/javascript/karma/scripts/runscript.js	(revision 22892)
@@ -4,5 +4,5 @@
     });
 
-    var PORT=8081;
+    var PORT=80;
     var tests = []; //last test to check
 
@@ -30,5 +30,5 @@
             $('#debug').empty();
             var id = this.id.replace(/[^\d]/g, ''); 
-            $.getScript('http://localhost:'+PORT+'/test'+id+'.js', function(src, status) {
+            $.getScript('../../../test/NightlyRun/test'+id+'.js', function(src, status) {
                 console.log('='.repeat(30));
                 console.log('Status: ' + status);
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/jenkins.sh
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/jenkins.sh	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/jenkins.sh	(revision 22892)
@@ -10,4 +10,5 @@
 #Server URI
 SERVER='https://ross.ics.uci.edu:8080'
+#SERVER='http://ross.ics.uci.edu:8080'
 
 #Get configuration
@@ -29,4 +30,5 @@
 MATLAB_TEST=0
 PYTHON_TEST=0
+JAVASCRIPT_TEST=0
 
 #source configuration script
@@ -58,6 +60,7 @@
 	#Process html page and get the list of files that has changed (tricky...)
 	#cat changes | grep '="The file was modified"' | sed -e 's/.*<\/td><td><a>\(.*\)<\/a><\/td><td>.*/\1/' > $ISSM_DIR/TEMP
-	cat changes | grep 'document_edit' |sed -e 's/document_edit.png/document_edit.png\
-		/g' | sed -e 's/.*<\/a><\/td><td>\(.*\)<\/td><\/tr>.*/\1/' | grep -v 'document_edit.png' > $ISSM_DIR/TEMP
+	#cat changes | grep 'document_edit' |sed -e 's/document_edit.png/document_edit.png\
+		#/g' | sed -e 's/.*<\/a><\/td><td>\(.*\)<\/td><\/tr>.*/\1/' | grep -v 'document_edit.png' > $ISSM_DIR/TEMP
+	cat changes  | tr " " "\n" | grep trunk |  sed -e 's/.*<a>\(.*\)<\/a>.*/\1/' > $ISSM_DIR/TEMP
 
 	#Print list of files
@@ -124,7 +127,11 @@
 echo "<testsuite tests=\"$NUMPACKAGES\">" > $EXTERNAL_TEST_FILE
 
-# Need a source here for when builds start midway through installation of 
-# externalpackages.
+# Need a source here for when builds start midway through installation of externalpackages.
 source $ISSM_DIR/etc/environment.sh
+
+if [ "$OS" == "win" ]; then
+	echo " == WINDOWS ENVIRONMENT DETECTED =="
+	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
+fi
 
 EXTERNALPACKAGES_FAILED=0;
@@ -140,5 +147,5 @@
 
 	#install if requested or if previous install has not been successful
-	if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -d ./install ] || [ ! "$(ls -A ./install)" ]; then
+	if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -d ./install -a ! -d ./install-javascript ] || ([ -d ./install ] && [ ! "$(ls -A ./install)" ]) || ([ -d ./install-javascript ] && [ ! "$(ls -A ./install-javascript)" ]); then
 		echo "======================================================";
 		echo "       Installing $PACKAGENAME                        ";
@@ -146,8 +153,9 @@
 
 		./$PACKAGEINST &> compil.log
-		if [ $? -ne 0 ]; then
+		if [ $? -ne 0 ] && [ "$PACKAGENAME" != "boost" ]; then
 			echo "======================================================";
 			echo "    ERROR: installation of $PACKAGENAME failed        ";
 			echo "======================================================";
+			cat compil.log
 			echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\">" >> $EXTERNAL_TEST_FILE
 			echo '<failure message="failure">External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
@@ -180,11 +188,21 @@
 fi
 
+# Source here to include any newly installed externalpackages on the path. 
 source $ISSM_DIR/etc/environment.sh
 
-if [ "$OS" == "win" ]
-then
+if [ "$OS" == "win" ]; then
 	echo " == WINDOWS ENVIRONMENT DETECTED =="
 	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
 fi
+
+#Set CXX/CC flags for JS runs after exnteralpackages to avoid conflicts during their compilation
+CXX_PREVIOUS=$CXX
+CC_PREVIOUS=$CC
+if [ $JAVASCRIPT_TEST -eq 1 ]; then
+	export CXX=em++
+	export CC=emcc
+	source $ISSM_DIR/externalpackages/emscripten/install/emsdk_env.sh
+fi
+
 #}}}
 #ISSM compilation yes/no                (ISSM_COMPILATION) {{{
@@ -200,5 +218,15 @@
 		make distclean
 		./scripts/automakererun.sh
+		if [ $? -ne 0 ]; then 
+			echo "autoreconf failed!"
+			exit 1
+		fi
 		eval "./configure $ISSM_CONFIG"
+		if [ $? -ne 0 ]; then 
+			echo "ISSM configuration failed (see options below)"
+			echo $ISSM_CONFIG
+			echo "ISSM configuration failed!"
+			exit 1
+		fi
 	fi
 
@@ -213,4 +241,10 @@
 		make
 	fi
+	if [ $? -ne 0 ] && [ $NUMCPUS_INSTALL -gt 1 ]; then 
+		echo " "
+		echo "Compilation failed, trying to compile with only one threatd"
+		echo " "
+		make
+	fi
 	if [ $? -ne 0 ]; then 
 		echo "ISSM_COMPILATION failed!"
@@ -226,4 +260,8 @@
 fi
 #}}}
+
+#Restore CXX/CC to their previous values 
+export CXX=$CXX_PREVIOUS
+export CC=$CC_PREVIOUS
 
 #matlab tests
@@ -258,7 +296,7 @@
 	cd $ISSM_DIR/test/NightlyRun
 	if [ "$OS" = "win" ]; then
-		$MATLAB_PATH/bin/matlab -nojvm -nosplash -r "addpath $ISSM_DIR_WIN/src/m/dev; devpath; addpath $ISSM_DIR_WIN/nightlylog/; matlab_run$i" -logfile $ISSM_DIR_WIN/nightlylog/matlab_log$i.log &
-	else
-		$MATLAB_PATH/bin/matlab -nojvm -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; matlab_run$i" -logfile $ISSM_DIR/nightlylog/matlab_log$i.log &
+		$MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR_WIN/src/m/dev; devpath; addpath $ISSM_DIR_WIN/nightlylog/; matlab_run$i" -logfile $ISSM_DIR_WIN/nightlylog/matlab_log$i.log &
+	else
+		$MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; matlab_run$i" -logfile $ISSM_DIR/nightlylog/matlab_log$i.log &
 	fi
 done
@@ -289,5 +327,7 @@
 echo '-----------------------------'
 
-rm matlab_log.log
+if [ -f matlab_log.log ]; then
+	rm matlab_log.log
+fi
 
 for job in `jobs -p`
@@ -311,5 +351,4 @@
 if [ $PYTHON_TEST -eq 1 ]; then
 #Launch all tests on different cpus
-PYTHON_START_TIME=$(timer);
 export PYTHONSTARTUP=$ISSM_DIR/src/m/dev/devpath.py
 export PYTHONUNBUFFERED=1 #we don't want python to buffer otherwise issm.exe output is not captured
@@ -324,5 +363,7 @@
 # concatenate reports
 cd $ISSM_DIR/nightlylog/
-rm python_log.log
+if [ -f python_log.log ]; then
+	rm python_log.log
+fi
 
 for job in `jobs -p`
@@ -429,5 +470,5 @@
 				echo 'end' >> $FILE
 
-				$MATLAB_PATH/bin/matlab -nosplash -nodisplay -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; runme" -logfile $ISSM_DIR/nightlylog/$LOG_FILE
+				$MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; runme" -logfile $ISSM_DIR/nightlylog/$LOG_FILE
 				echo "starting: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
 				cat $ISSM_DIR/nightlylog/$LOG_FILE >> $ISSM_DIR/nightlylog/matlab_log_examples.log
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan	(revision 22892)
@@ -7,5 +7,5 @@
 MATLAB_PATH="/usr/local/MATLAB/R2015a"
 
-#ISSM CONFIGURATION 
+#ISSM CONFIGURATION
 ISSM_CONFIG='--prefix=$ISSM_DIR\
 	--disable-static \
@@ -39,12 +39,13 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools     install.sh                
-						mpich         install-3.2-linux64.sh    
-						petsc         install-3.7-linux64.sh    
-						triangle      install-linux64.sh        
-						boost         install.sh                
-						dakota        install-6.2-linux64.sh  
-						chaco         install.sh 
-						m1qn3         install.sh          
+EXTERNALPACKAGES="autotools     install.sh
+						cmake        install.sh
+						mpich         install-3.2-linux64.sh
+						petsc         install-3.7-linux64.sh
+						triangle      install-linux64.sh
+						boost         install-1.55-linux.sh
+						dakota        install-6.2-linux64.sh
+						chaco         install.sh
+						m1qn3         install.sh
 						shell2junit   install.sh"
 
@@ -64,4 +65,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-PYTHON_NROPTIONS="--exclude 119 514 701 702 435"
-MATLAB_NROPTIONS="'exclude',[119,514,701,702,435]"
+PYTHON_NROPTIONS="--exclude 701 702 435"
+MATLAB_NROPTIONS="'exclude',[701,702,435]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan_ad
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan_ad	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan_ad	(revision 22892)
@@ -28,5 +28,6 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh                
+EXTERNALPACKAGES="autotools install.sh
+					cmake install.sh                
 					 mpich install-3.2-linux64.sh
 					 petsc install-3.7-linux64.sh
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan_ampi
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan_ampi	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_caladan_ampi	(revision 22892)
@@ -37,5 +37,6 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh 
+EXTERNALPACKAGES="autotools install.sh
+					 cmake install.sh 
 					 mpich install-3.2-linux64.sh
 					 petsc install-3.7-linux64.sh
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross	(revision 22892)
@@ -7,5 +7,5 @@
 MATLAB_PATH="/usr/local/MATLAB/R2015a"
 
-#ISSM CONFIGURATION 
+#ISSM CONFIGURATION
 ISSM_CONFIG='--prefix=$ISSM_DIR\
 	--disable-static \
@@ -37,10 +37,11 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools     install.sh                
-						mpich         install-3.2-linux64.sh    
-						petsc         install-3.7-linux64.sh    
-						triangle      install-linux64.sh        
-						chaco         install.sh 
-						m1qn3         install.sh          
+EXTERNALPACKAGES="autotools     install.sh
+						cmake        install.sh
+						mpich         install-3.2-linux64.sh
+						petsc         install-3.7-linux64.sh
+						triangle      install-linux64.sh
+						chaco         install.sh
+						m1qn3         install.sh
 						python        install-2.7.3-linux64.sh
                   nose          install-linux64-python2.sh
@@ -67,5 +68,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435"
+PYTHON_NROPTIONS=""
 MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]"
-#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435,IdFromString('Dakota')]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_ad
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_ad	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_ad	(revision 22892)
@@ -14,4 +14,5 @@
 				--without-kml \
 				--without-GiaIvins \
+				--without-Love \
 				--with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \
 				--with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \
@@ -20,4 +21,5 @@
 				--with-python-numpy-dir=/usr/lib/python2.7/dist-packages/numpy\
 				--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+				--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
 				--enable-development \
 				--enable-debugging '
@@ -32,5 +34,6 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh                
+EXTERNALPACKAGES="autotools install.sh
+					 cmake install.sh                
 					 mpich install-3.2-linux64.sh
 					 petsc install-3.7-linux64.sh
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_ampi
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_ampi	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_ampi	(revision 22892)
@@ -21,5 +21,5 @@
 				--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
 				--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-				--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
+				--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpifort -lmpi" \
 				--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 				--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
@@ -40,5 +40,6 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh 
+EXTERNALPACKAGES="autotools install.sh
+					 cmake install.sh 
 					 mpich install-3.2-linux64.sh
 					 petsc install-3.7-linux64.sh
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_dakota
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_dakota	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_dakota	(revision 22892)
@@ -7,5 +7,5 @@
 MATLAB_PATH="/usr/local/MATLAB/R2015a"
 
-#ISSM CONFIGURATION 
+#ISSM CONFIGURATION
 ISSM_CONFIG='--prefix=$ISSM_DIR\
 	--disable-static \
@@ -13,18 +13,18 @@
 	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
 	--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
+	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
 	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
-	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
-	--with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
+	--with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
 	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
-	--with-boost-dir=$ISSM_DIR/externalpackages/boost/install/ \
-	--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
+	--with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
+	--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
 	--with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
 	--with-numthreads=4 \
 	--enable-development \
-	--enable-debugging '
+	--enable-debugging'
 
 #PYTHON and MATLAB testing
@@ -37,12 +37,13 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools     install.sh                
-						mpich         install-3.2-linux64.sh    
-						petsc         install-3.7-linux64.sh    
-						triangle      install-linux64.sh        
-						boost         install-1.55-linux.sh                
-						dakota        install-6.2-linux64.sh  
-						chaco         install.sh 
-						m1qn3         install.sh          
+EXTERNALPACKAGES="autotools     install.sh
+						cmake        install.sh
+						mpich         install-3.2-linux64.sh
+						petsc         install-3.7-linux64.sh
+						triangle      install-linux64.sh
+						boost         install-1.55-linux.sh
+						dakota        install-6.2-linux64.sh
+						chaco         install.sh
+						m1qn3         install.sh
 						shell2junit   install.sh"
 
@@ -62,4 +63,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-PYTHON_NROPTIONS=""
-MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435]"
+PYTHON_NROPTIONS="--exclude 243 701 702 435"
+MATLAB_NROPTIONS="'exclude',[243,701,702,435]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_gia
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_gia	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_gia	(revision 22892)
@@ -38,4 +38,5 @@
 #List of external pakages to be installed and their installation scripts
 EXTERNALPACKAGES="autotools     install.sh
+					 	cmake 		  install.sh
 						mpich         install-3.2-linux64.sh    
 						petsc         install-3.7-linux64.sh    
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_iceocean
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_iceocean	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_iceocean	(revision 22892)
@@ -20,4 +20,5 @@
 	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
 	--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
+	--with-ocean=yes \
 	--with-numthreads=4 \
 	--enable-development \
@@ -33,7 +34,7 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools     install.sh                
-						mpich         install-3.2-linux64.sh    
+EXTERNALPACKAGES="autotools     install.sh    
 						cmake         install.sh                
+						mpich      	  install-3.2-linux64.sh                
 						petsc         install-3.7-linux64.sh    
 						triangle      install-linux64.sh        
@@ -55,4 +56,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-MATLAB_NROPTIONS="'benchmark','all','id',4001"
+MATLAB_NROPTIONS="'benchmark','all','id',[4001 4002]"
 PYTHON_NROPTIONS=""
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_javascript
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_javascript	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_javascript	(revision 22892)
@@ -10,7 +10,10 @@
     --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install-javascript" \
     --with-gsl-dir="$ISSM_DIR/externalpackages/gsl/install-javascript" \
-    --without-kml\
-    --without-kriging\
-    --with-cxxoptflags="-O2"'
+	--without-Love \
+    --without-kml \
+    --without-kriging \
+    --with-cxxoptflags="-O2" \
+    CXXFLAGS="-O2" \
+    CFLAGS="-O2"'
 
 #PYTHON and MATLAB testing
@@ -24,6 +27,8 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="emscripten	  install.sh        
-						gsl			  install-javascript.sh    
+EXTERNALPACKAGES="autotools     install.sh
+						cmake         install.sh
+						emscripten    install.sh        
+						gsl           install-javascript.sh    
 						triangle      install-javascript.sh        
 						shell2junit   install.sh"
@@ -44,4 +49,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-#PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435"
+#PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 435"
 #MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435,IdFromString('Dakota')]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_python
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_python	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_python	(revision 22892)
@@ -7,5 +7,5 @@
 MATLAB_PATH="/usr/local/MATLAB/R2015a"
 
-#ISSM CONFIGURATION 
+#ISSM CONFIGURATION
 ISSM_CONFIG='--prefix=$ISSM_DIR\
 	--disable-static \
@@ -36,9 +36,10 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="mpich         install-3.2-linux64.sh    
-						petsc         install-3.7-linux64.sh    
-						triangle      install-linux64.sh        
-						chaco         install.sh 
-						m1qn3         install.sh          
+EXTERNALPACKAGES="mpich         install-3.2-linux64.sh
+						cmake         install.sh
+						petsc         install-3.7-linux64.sh
+						triangle      install-linux64.sh
+						chaco         install.sh
+						m1qn3         install.sh
 						shell2junit   install.sh"
 
@@ -58,4 +59,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435"
+PYTHON_NROPTIONS=""
 MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_se
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_se	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_se	(revision 22892)
@@ -15,5 +15,5 @@
 	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
 	--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
+	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
 	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
@@ -36,10 +36,10 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools     install.sh                
-						mpich         install-3.2-linux64.sh    
-						cmake         install.sh
+EXTERNALPACKAGES="autotools     install.sh    
+						cmake         install.sh                
+						mpich         install-3.2-linux64.sh
 						petsc         install-3.7-linux64.sh    
 						triangle      install-linux64.sh        
-						boost         install.sh                
+						boost         install-1.55-linux.sh
 						python        install-2.7.3-linux64.sh
                   nose          install-linux64-python2.sh
@@ -63,6 +63,6 @@
 NUMCPUS_INSTALL=5
 
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=4
+#number of cpus used in the nightly runs. (pb of access to all_vertices.txt if more than 1)
+NUMCPUS_RUN=1
 
 #Nightly run options. The matlab routine runme.m will be called
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_static
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_static	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_static	(revision 22892)
@@ -16,5 +16,5 @@
 	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
 	--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
+	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpifort" \
 	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
 	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
@@ -23,4 +23,5 @@
 	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
+	--with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
 	--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
 	--with-numthreads=4'
@@ -41,4 +42,6 @@
 						petsc        install-3.7-linux64-static.sh
 						triangle     install-linux64.sh
+						math77        install.sh
+						gmsh          install-static.sh
 						shell2junit  install.sh"
 
@@ -58,5 +61,5 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-##                           bamg mesh   FS                     
+##                           FS                     
 #PYTHON_NROPTIONS=""
-#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,435,IdFromString('Dakota')]"
+#MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_test
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_test	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/linux64_ross_test	(revision 22892)
@@ -7,5 +7,5 @@
 MATLAB_PATH="/usr/local/MATLAB/R2015a"
 
-#ISSM CONFIGURATION 
+#ISSM CONFIGURATION
 ISSM_CONFIG='--prefix=$ISSM_DIR\
 	--disable-static \
@@ -39,12 +39,12 @@
 
 #List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools     install.sh                
-						mpich         install-3.2-linux64.sh    
-						petsc         install-3.7-linux64.sh    
-						triangle      install-linux64.sh        
-						boost         install.sh                
-						dakota        install-6.2-linux64.sh  
-						chaco         install.sh 
-						m1qn3         install.sh          
+EXTERNALPACKAGES="autotools     install.sh
+						mpich         install-3.2-linux64.sh
+						petsc         install-3.7-linux64.sh
+						triangle      install-linux64.sh
+						boost         install-1.55-linux.sh
+						dakota        install-6.2-linux64.sh
+						chaco         install.sh
+						m1qn3         install.sh
 						shell2junit   install.sh"
 
@@ -64,4 +64,4 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 435"
-MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,435]"
+PYTHON_NROPTIONS="--exclude 243 701 702 435"
+MATLAB_NROPTIONS="'exclude',[243,701,702,435]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island	(revision 22892)
@@ -54,5 +54,5 @@
 #by Matlab and runme.m
 #ex: "'id',[101 102 103]"
-##                           bamg mesh   FS                     
+##                           FS                     
 PYTHON_NROPTIONS=""
-MATLAB_NROPTIONS="'exclude',[119,514,701,702,703,435,IdFromString('Dakota')]"
+MATLAB_NROPTIONS="'exclude',[701,702,703,435,IdFromString('Dakota')]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island_dakota_static
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island_dakota_static	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island_dakota_static	(revision 22892)
@@ -14,8 +14,8 @@
 	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
 	--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi " \
+	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpl -lpmpich" \
 	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
-	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
-	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
@@ -23,5 +23,5 @@
 	--with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
 	--with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
-	--with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
+	--with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
 	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a /usr/local/gfortran/lib/libquadmath.a /usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0/libgcc.a" \
 	--with-numthreads=4'
@@ -39,7 +39,7 @@
 						cmake        install.sh
 						chaco        install-macosx64.sh
-						mpich        install-3.2-macosx64-static.sh
+						mpich        install-3.0-macosx64-static.sh
 						m1qn3        install.sh
-						petsc        install-3.7-macosx64-static.sh
+						petsc        install-3.6-macosx64-static.sh
 						triangle     install-macosx64.sh
 						boost        install-1.55-macosx-el_capitan.sh
@@ -64,3 +64,3 @@
 ##                           bamg mesh   FS                     
 #PYTHON_NROPTIONS=""
-#MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,435,IdFromString('Dakota')]"
+#MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]"
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island_static
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island_static	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/macosx_pine-island_static	(revision 22892)
@@ -15,11 +15,12 @@
 	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
 	--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
-	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
-	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
-	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
-	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
+	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpl -lpmpich" \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
 	--with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
+	--with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
 	--with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a /usr/local/gfortran/lib/libquadmath.a /usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0/libgcc.a" \
 	--with-numthreads=4'
@@ -36,10 +37,13 @@
 EXTERNALPACKAGES="autotools    install.sh
 						cmake        install.sh
-						mpich        install-3.2-macosx64-static.sh
+						mpich        install-3.0-macosx64-static.sh
 						m1qn3        install.sh
-						petsc        install-3.7-macosx64-static.sh
+						petsc        install-3.6-macosx64-static.sh
 						triangle     install-macosx64.sh
+						math77        install.sh
+						gmsh          install-static.sh
 						shell2junit  install.sh"
 
+#for SLR we need gmsh to mesh, math77, and gmt (which itself needs gdal and netcdf...)
 #-----------------#
 # 4: test options #
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/windows
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/windows	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/windows	(revision 22892)
@@ -11,8 +11,9 @@
 	--with-vendor=MSVC-Win64  \
 	--with-cxxoptflags='-fp:strict' \
-   --disable-static \
+	--disable-static \
 	--enable-standalone-libraries \
 	--with-fortran=no  \
 	--without-GiaIvins \
+	--without-Love \
 	--without-kriging \
 	--without-kml \
@@ -60,4 +61,4 @@
 
 #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version
-MATLAB_NROPTIONS="'exclude',[104, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341,460,243]"
+MATLAB_NROPTIONS="'exclude',[104,119, 124,125,126, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 250, 251, 412, 413, 414, 417, 418, 420, 440,444, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280, 801, 802, 803, 804, 805, 291, 340, 341, 460, 243, 430, 441, 442, 463, 464, 465, 244]"
 PYTHON_NROPTIONS=""
Index: /issm/branches/trunk-larour-NatGeoScience2016/jenkins/windows_test
===================================================================
--- /issm/branches/trunk-larour-NatGeoScience2016/jenkins/windows_test	(revision 22891)
+++ /issm/branches/trunk-larour-NatGeoScience2016/jenkins/windows_test	(revision 22892)
@@ -31,4 +31,4 @@
 
 #In Windows, we don't yet have MUMPS, can't do full stokes, so exclude all FS runs. Also exclude all runs with Dakota. And exclude higher order runs that have penalties. And 800+ tests because we don't want to have --with-development since we do the binaries with this version
-MATLAB_NROPTIONS="'exclude',[104, 124, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 412, 413, 414, 417, 418, 420, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280,801,802,803,804,805,291,340,341]"
+MATLAB_NROPTIONS="'exclude',[104, 124, 204, 211, 215, 220, 221, 285, 290, 308, 322, 404, 421, 422, 503, 507, 510, 511, 513, 701, 702, 703, 218, 234, 235, 412, 413, 414, 417, 418, 420, 205, 274, 331, 405, 409, 455, 612, 514, 435, 280, 801, 802, 803, 804, 805, 291, 340, 341]"
 PYTHON_NROPTIONS=""