Index: /issm/trunk-jpl/jenkins/jenkins.sh
===================================================================
--- /issm/trunk-jpl/jenkins/jenkins.sh	(revision 26044)
+++ /issm/trunk-jpl/jenkins/jenkins.sh	(revision 26045)
@@ -7,4 +7,8 @@
 # members of the ISSM development team.
 #
+# NOTE:
+# - Variable OS is set in environment by running 
+#	`source $ISSM_DIR/etc/environment.sh`.
+#
 # TODO:
 # - Rename TEMP to something more descriptive (ensure first that other parts of
@@ -17,7 +21,7 @@
 
 echo "Cleaning up execution directory"
-rm -rf $ISSM_DIR/execution/*
-rm -rf $ISSM_DIR/nightlylog
-mkdir $ISSM_DIR/nightlylog
+rm -rf ${ISSM_DIR}/execution/*
+rm -rf ${ISSM_DIR}/nightlylog
+mkdir ${ISSM_DIR}/nightlylog
 
 #Server URI
@@ -56,11 +60,4 @@
 fi
 
-#Get Operating system (OS) name{{{
-OS=$(uname -s)
-if [[ $OS == CYGWIN* ]]; then
-	OS="win";
-fi
-#}}}
-
 #Install ISSM
 #Determining installation type depending on svn changes{{{
@@ -68,6 +65,6 @@
 echo "             Determining Installation type            "
 echo "======================================================";
-if [ -a $ISSM_DIR/svn_revision_old ]; then
-	SVN_PREVIOUS=$(cat $ISSM_DIR/svn_revision_old)
+if [ -a ${ISSM_DIR}/svn_revision_old ]; then
+	SVN_PREVIOUS=$(cat ${ISSM_DIR}/svn_revision_old)
 	SVN_CURRENT=$SVN_REVISION_1
 	echo "Previous revision number: $SVN_PREVIOUS"
@@ -77,5 +74,5 @@
 	#
 
-	#svn --non-interactive --no-auth-cache --trust-server-cert diff -r $SVN_PREVIOUS:$SVN_CURRENT --summarize $ISSM_DIR | awk '{print $NF}' > $ISSM_DIR/TEMP
+	#svn --non-interactive --no-auth-cache --trust-server-cert diff -r $SVN_PREVIOUS:$SVN_CURRENT --summarize ${ISSM_DIR} | awk '{print $NF}' > ${ISSM_DIR}/TEMP
 
 	# Get list of changes from Jenkins itself as svn requires credentials
@@ -84,13 +81,13 @@
 
 	# 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 '="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 | tr " " "\n" | grep trunk | sed -e 's/.*<a>\(.*\)<\/a>.*/\1/' > $ISSM_DIR/TEMP
+		#/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 changed files
 	echo "   "
 	echo "List of updated files"
-	cat $ISSM_DIR/TEMP
+	cat ${ISSM_DIR}/TEMP
 	echo "   "
 
@@ -102,5 +99,5 @@
 	# If the contents of the externalpackages directory were modified in any
 	# way, check for changed external packages
-	if [ ! -z "$(cat $ISSM_DIR/TEMP | grep externalpackages)" ]; then
+	if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep externalpackages)" ]; then
 		echo "  -- checking for changed externalpackages... yes"
 		ISSM_EXTERNALPACKAGES="yes"
@@ -112,6 +109,6 @@
 	# If the Makefile or m4 diirectory were changed in any way or if certain
 	# binary files from a previous compilation do not exist, reconfigure
-	if [ ! -z "$(cat $ISSM_DIR/TEMP | grep -e "Makefile.am" -e "m4" )" ] ||
-		[ ! -f "$ISSM_DIR/bin/issm.exe" ] && [ ! -f "$ISSM_DIR/bin/issm-bin.js" ] ||
+	if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep -e "Makefile.am" -e "m4" )" ] ||
+		[ ! -f "${ISSM_DIR}/bin/issm.exe" ] && [ ! -f "${ISSM_DIR}/bin/issm-bin.js" ] ||
 		[ "$ISSM_EXTERNALPACKAGES" == "yes" ]; then
 		echo "  -- checking for reconfiguration... yes"
@@ -123,5 +120,5 @@
 
 	# If source files were changed in any way, recompile
-	if [ ! -z "$(cat $ISSM_DIR/TEMP | grep -e "\.cpp" -e "\.h" )" ] ||
+	if [ ! -z "$(cat ${ISSM_DIR}/TEMP | grep -e "\.cpp" -e "\.h" )" ] ||
 		[ "$ISSM_RECONFIGURE" == "yes" ]; then
 		echo "  -- checking for recompilation... yes"
@@ -134,5 +131,5 @@
 	# Cleanup
 	rm changes
-	rm $ISSM_DIR/TEMP
+	rm ${ISSM_DIR}/TEMP
 else
 	echo "Previous revision not found, this must be a fresh install"
@@ -147,5 +144,5 @@
 echo " "
 echo "Recording current svn version: $SVN_REVISION_1"
-echo $SVN_REVISION_1 > $ISSM_DIR/svn_revision_old
+echo $SVN_REVISION_1 > ${ISSM_DIR}/svn_revision_old
 #}}}
 
@@ -157,14 +154,14 @@
 
 #Jenkins XML files for individual packages
-EXTERNAL_TEST_FILE="$ISSM_DIR/nightlylog/results/external.xml"
-mkdir -p $ISSM_DIR/nightlylog/results
+EXTERNAL_TEST_FILE="${ISSM_DIR}/nightlylog/results/external.xml"
+mkdir -p ${ISSM_DIR}/nightlylog/results
 echo "<testsuite tests=\"$NUMPACKAGES\">" > $EXTERNAL_TEST_FILE
 
 # Need a source here for when builds start midway through installation of externalpackages.
-source $ISSM_DIR/etc/environment.sh
-
-if [ "$OS" == "win" ]; then
+source ${ISSM_DIR}/etc/environment.sh
+
+if [ "${OS}" == CYGWIN* ]; then
 	echo " == WINDOWS ENVIRONMENT DETECTED =="
-	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
+	source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh
 fi
 
@@ -178,6 +175,6 @@
 
 	#install if requested or if previous install has not been successful
-	if [ "$ISSM_EXTERNALPACKAGES" == "yes" ]; then # NOTE: Removed check on if 'install' directory exist
-		cd $ISSM_DIR/externalpackages/$PACKAGENAME
+	if [ "${ISSM_EXTERNALPACKAGES}" == "yes" ]; then # NOTE: Removed check on if 'install' directory exist
+		cd ${ISSM_DIR}/externalpackages/$PACKAGENAME
 
 		echo "======================================================";
@@ -186,5 +183,5 @@
 
 		./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log
-		if [ $? -ne 0 ] && [ "$PACKAGENAME" != "boost" ]; then
+		if [ $? -ne 0 ] && [ "${PACKAGENAME}" != "boost" ]; then
 			cat compil.log
 			echo "======================================================";
@@ -200,5 +197,5 @@
 			echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\"/>" >> $EXTERNAL_TEST_FILE
 		fi
-		source $ISSM_DIR/etc/environment.sh
+		source ${ISSM_DIR}/etc/environment.sh
 
 		#If external package is rebuilt, we also need to recompile
@@ -223,9 +220,9 @@
 
 # Source here to include any newly installed externalpackages on the path.
-source $ISSM_DIR/etc/environment.sh
-
-if [ "$OS" == "win" ]; then
+source ${ISSM_DIR}/etc/environment.sh
+
+if [ "${OS}" == CYGWIN* ]; then
 	echo " == WINDOWS ENVIRONMENT DETECTED =="
-	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
+	source ${ISSM_DIR}/externalpackages/windows/windows_environment.sh
 fi
 
@@ -247,12 +244,12 @@
 	#export EMCC_DEBUG=1 # Uncomment to enable debugging
 	export EMCC_CFLAGS="-s ERROR_ON_UNDEFINED_SYMBOLS=0" # Required after v1.38.14 to avoid undefined symbol warnings from our Fortran object files being treated as errors
-	source $ISSM_DIR/externalpackages/emscripten/install/emsdk_env.sh
+	source ${ISSM_DIR}/externalpackages/emscripten/install/emsdk_env.sh
 fi
 
 #}}}
 #ISSM compilation yes/no                (ISSM_COMPILATION) {{{
-if [ "$ISSM_COMPILATION" == "yes" ]; then
+if [ "${ISSM_COMPILATION}" == "yes" ]; then
 	cd $ISSM_DIR
-	if [ "$ISSM_RECONFIGURE" == "yes" ]; then
+	if [ "${ISSM_RECONFIGURE}" == "yes" ]; then
 		echo "======================================================";
 		echo "             Cleaning up and reconfiguring            "
@@ -265,5 +262,5 @@
 			exit 1
 		fi
-		eval "./configure $ISSM_CONFIG"
+		eval "./configure ${ISSM_CONFIG}"
 		if [ $? -ne 0 ]; then
 			echo "ISSM configuration failed (see options below)"
@@ -279,7 +276,11 @@
 	echo "======================================================"
 	if [ $NUMCPUS_INSTALL -gt 1 ]; then
-		echo "Making with " $NUMCPUS_INSTALL " cpus"
+		echo "Making with ${NUMCPUS_INSTALL} cpus"
+
+		# To debug compilation/linking, add 'V=1' option to the call to make
+		#make -j $NUMCPUS_INSTALL V=1
 		make -j $NUMCPUS_INSTALL
 	else
+		#make V=1
 		make
 	fi
@@ -295,6 +296,5 @@
 	fi
 	make install
-elif [ "$ISSM_COMPILATION" == "no" ]
-then
+elif [ "${ISSM_COMPILATION}" == "no" ]; then
 	echo "Skipping ISSM compilation"
 else
@@ -314,11 +314,11 @@
 	for (( i=1;i<=$NUMCPUS_RUN;i++ )); do
 		#Launch matlab and the nightly run script
-		cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF
+		cat > ${ISSM_DIR}/nightlylog/matlab_run$i.m << EOF
 		warning off %necessary to avoid a log of several Go for parallel runs
 		try,
-			$(if [ "$MATLAB_NROPTIONS" = "" ]; then
-				echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
+			$(if [ "${MATLAB_NROPTIONS}" = "" ]; then
+				echo "runme('output','nightly','rank',${i},'numprocs',${NUMCPUS_RUN});"
 			else
-				echo "runme($MATLAB_NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
+				echo "runme(${MATLAB_NROPTIONS},'output','nightly','rank',${i},'numprocs',${NUMCPUS_RUN});"
 			fi)
 		catch me,
@@ -335,34 +335,42 @@
 EOF
 		cd $ISSM_DIR/test/NightlyRun
-		if [ "$OS" = "win" ]; then
-			$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 &
+		if [[ "${OS}" == CYGWIN* || "${OS}" == MINGW* ]]; then
+			$MATLAB_PATH/bin/matlab -nodesktop -nosplash -nojvm -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 &
+			$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
 
-	#wait until matlab closes
-	if [ "$OS" = "win" ]; then
+	# Wait for MATLAB to exit
+	if [[ "${OS}" == CYGWIN* ]]; then
 		sleep 5;
-		echo "Waiting for matlab on windows"
+		echo "Waiting for MATLAB to exit"
 		pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}')
 		echo '-----------------------------'
-		echo "pid: $pid"
+		echo "pid: ${pid}"
 		echo '-----------------------------'
-		while [ -n "$pid" ]; do
+		while [ -n "${pid}" ]; do
 			pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}')
 			sleep 1;
 		done
 		echo "DONE!"
+	elif [[ "${OS}" == MINGW* ]]; then
+		# NOTE: The PID query used here may work as well on Cygwin. If so, combine the two conditional blocks.
+		sleep 5;
+		echo "Waiting for MATLAB to exit"
+		pid=$(ps -W | grep MATLAB | awk '{print $1}')
+		echo '-----------------------------'
+		echo "pid: ${pid}"
+		echo '-----------------------------'
+		while [ -n "${pid}" ]; do
+			pid=$(ps -W | grep MATLAB | awk '{print $1}')
+			sleep 1;
+		done
 	else
 		wait
 	fi
 
-	#concatenate reports
-	cd $ISSM_DIR/nightlylog/
-	#echo 'CHECKING NIGHTLYLOG DIRECTORY'
-	#echo '-----------------------------'
-	#ls -la
-	#echo '-----------------------------'
+	# Concatenate logs
+	cd $ISSM_DIR/nightlylog
 
 	if [ -f matlab_log.log ]; then
@@ -371,5 +379,5 @@
 
 	for job in `jobs -p`; do
-		echo "Waiting on: $job"
+		#echo "Waiting on: ${job}" # Commented out because it really has nothing to do with MATLAB processes
 		wait $job
 	done
@@ -390,5 +398,5 @@
 if [ $PYTHON_TEST -eq 1 ]; then
 	#Launch all tests on different cpus
-	export PYTHONPATH="$ISSM_DIR/src/m/dev"
+	export PYTHONPATH="${ISSM_DIR}/src/m/dev"
 	export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
 	export PYTHONUNBUFFERED=1 #we don't want python to buffer otherwise issm.exe output is not captured
@@ -401,6 +409,6 @@
 	done
 
-	# concatenate reports
-	cd $ISSM_DIR/nightlylog/
+	# Concatenate logs
+	cd $ISSM_DIR/nightlylog
 	if [ -f python_log.log ]; then
 		rm python_log.log
@@ -409,5 +417,5 @@
 	for job in `jobs -p`
 	do
-		echo "Waiting on: $job"
+		echo "Waiting on: ${job}"
 		wait $job
 	done
@@ -432,5 +440,5 @@
 # }}}
 
-#process logs to be junit compatible
+# Process logs to be JUnit compatible
 #{{{
 cd $ISSM_DIR/nightlylog