Index: /issm/trunk-jpl/scripts/jenkins.sh
===================================================================
--- /issm/trunk-jpl/scripts/jenkins.sh	(revision 16594)
+++ /issm/trunk-jpl/scripts/jenkins.sh	(revision 16594)
@@ -0,0 +1,348 @@
+#!/bin/bash
+#This bash script calls the nightlyrun.m matlab file to run our nightly test decks. 
+#It then processes the results and sends an email to the Ice developpers.
+
+#some functions
+function timer() #{{{
+{
+	if [[ $# -eq 0 ]]; then
+		echo $(date '+%s')
+	else
+		local  stime=$1
+		etime=$(date '+%s')
+
+		if [[ -z "$stime" ]]; then stime=$etime; fi
+
+		dt=$((etime - stime))
+		ds=$((dt % 60))
+		dm=$(((dt / 60) % 60))
+		dh=$((dt / 3600))
+		printf '%d:%02d:%02d' $dh $dm $ds
+	fi
+} #}}}
+function todaydate() #{{{
+{
+	suffix=`date | awk '{printf("%s-%s-%s  %s",$2,$3,$6,$4);}'`			 
+	echo $suffix;			 
+} #}}}
+function host_name() #{{{
+{
+	#return host name depending on the OS
+	if [ "$1" = "win7" ] 
+	then
+		HOST_NAME=`hostname | sed 's/-//g'`;
+	else
+		HOST_NAME=`hostname -s | sed 's/-//g'`;
+	fi
+	echo $HOST_NAME;
+} #}}}
+function pause() #{{{
+{
+pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'`
+
+while [ -n "$pid" ]
+do
+	pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'`
+done
+}
+#}}}
+
+#Get configuration
+#Source config file{{{
+if [ $# -ne 1 ];
+then
+	#no config file specified: exit
+	echo "no config file specified. Exiting..." >&2 # Error message to stderr.
+	rm NIGHTLYLOCK
+	exit 1
+fi
+if [ ! -f "$1" ]
+then
+	echo "File $1 not found!" >&2   # Error message to stderr.
+	rm NIGHTLYLOCK
+	exit 1
+fi 
+source $1;
+#}}}
+#Export ISSM_* variables{{{
+export ISSM_DIR
+export ISSM_ARCH
+#}}}
+#Initialize variables {{{
+TODAY=$(todaydate);
+HOST_NAME=$(host_name $OS);
+OS=$(uname -s)
+START_TIME=$(timer);
+ISSM_RELEASE=$(basename $(echo $REPOSITORY));
+USER=$(whoami);
+INIT_PATH=$(pwd);
+#}}}
+
+#Installation ISSM
+#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{
+if [ "$ISSM_INSTALLATION" == "checkout" ]
+then
+	rm -rf $ISSM_RELEASE
+	svn checkout "$REPOSITORY"
+elif [ "$ISSM_INSTALLATION" == "update" ]
+then
+	cd $ISSM_DIR
+	svn update
+elif [ "$ISSM_INSTALLATION" == "none" ]
+then
+	echo "Skipping ISSM installation"
+else
+	echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr.
+	exit 1
+fi
+source $ISSM_DIR/etc/environment.sh
+#}}}
+#create matlab's installation sript {{{
+cat << END > $ISSM_DIR/externalpackages/matlab/install.sh
+#!/bin/bash
+rm -rf install
+ln -s $MATLAB_PATH install
+END
+#}}}
+#install/copy/none external packages    (ISSM_EXTERNALPACKAGES){{{
+if [ "$ISSM_EXTERNALPACKAGES" == "install" ]
+then
+	
+	cd $ISSM_DIR/externalpackages
+
+	#number of packages: 
+	NUMPACKAGES=$(($(echo $EXTERNALPACKAGES | wc -w )/2))
+
+	for ((i=1;i<=$NUMPACKAGES;i++))
+	do
+		NUM1=$((2*$i-1))
+		NUM2=$((2*$i))
+		PACKAGENAME=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM1-$NUM1)
+		PACKAGEINST=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM2-$NUM2)
+
+		cd $PACKAGENAME
+		echo "======================================================";
+		echo "       Installing $PACKAGENAME (see compil.log)       ";
+		echo "======================================================";
+		./$PACKAGEINST > compil.log
+		if [ $? -ne 0 ]; then
+			echo "======================================================";
+			echo "    ERROR: installation of $PACKAGENAME failed        ";
+			echo "======================================================";
+		fi
+		source $ISSM_DIR/etc/environment.sh
+		cd ..
+	done
+
+elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ]
+then
+	cd $ISSM_DIR
+	rm -rf externalpackages
+	cp -Rf $EXTERNALPACKAGESDIR ./
+elif [ "$ISSM_EXTERNALPACKAGES" == "link" ]
+then
+	cd $ISSM_DIR
+	rm -rf externalpackages
+	ln -s  $EXTERNALPACKAGESDIR  .
+elif [ "$ISSM_EXTERNALPACKAGES" == "none" ]
+then
+	echo "Skipping external packages installation"
+else
+	echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr.
+	exit 1
+fi
+source $ISSM_DIR/etc/environment.sh
+#}}}
+#ISSM compilation yes/no                (ISSM_COMPILATION) {{{
+if [ "$ISSM_COMPILATION" == "yes" ]
+then
+	cd $ISSM_DIR
+	make uninstall
+	make clean
+	make distclean
+	./scripts/automakererun.sh
+	cat > configure.sh << EOF
+./configure $ISSM_CONFIG
+EOF
+	chmod 700 configure.sh
+	./configure.sh
+
+	#4: compile and install ISSM
+	if [ $NUMCPUS_INSTALL -gt 1 ]
+	then
+		echo "Making with " $NUMCPUS_INSTALL " cpus"
+		make -j $NUMCPUS_INSTALL install
+	else
+		make install
+	fi
+elif [ "$ISSM_COMPILATION" == "no" ]
+then
+	echo "Skipping ISSM compilation"
+else
+	echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr.
+	exit 1
+fi
+#}}}
+
+#Prepare info.log
+#{{{
+rm -rf $ISSM_DIR/nightlylog
+mkdir  $ISSM_DIR/nightlylog
+INSTALL_TIME=$(timer)
+ELAPSED=$(timer $START_TIME)
+VERSION=$(svnversion $ISSM_DIR)
+cat << END > $ISSM_DIR/nightlylog/info.log
+name:      $(echo $NAME)
+today:     $(echo $TODAY)
+user:      $(echo $USER)
+host:      $(echo $HOST_NAME)
+OS:        $(echo $OS)
+release:   $(echo $ISSM_RELEASE)
+init_path: $(echo $INIT_PATH)
+is_matlab: $(echo $MATLAB_TEST)
+is_python: $(echo $PYTHON_TEST)
+elapsed_install: $(echo $ELAPSED)
+version: $(echo $VERSION)
+END
+#}}}
+
+#matlab tests
+if [ $MATLAB_TEST -eq 1 ]; then
+#Launch all tests on different cpus {{{
+MATLAB_START_TIME=$(timer);
+for (( i=1;i<=$NUMCPUS_RUN;i++ ))
+do
+	#Launch matlab and the nightly run script
+	cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF
+	warning off %necessary to avoid a info.log of several Go for parallel runs
+	try,
+	$(if [ "$MATLAB_NROPTIONS" = ""  ]
+	then
+		echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
+	else
+		echo "runme($MATLAB_NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
+	fi
+	)
+	catch me,
+		%An error occured, get report and exit
+		message=getReport(me)
+		directory=strsplit(pwd,'/');
+		fid=fopen([issmdir '/nightlylog/matlaberror.log'], 'at');
+		fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
+		fprintf(fid,'%s',message);
+		fclose(fid);
+	end
+	disp('MATLABEXITEDCORRECTLY');
+	exit
+EOF
+	cd $ISSM_DIR/test/NightlyRun
+	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 &
+done
+
+#wait until matlab closes
+if [ "$OS" = "win7" ]; then
+	pause MATLAB
+else
+	wait
+fi
+
+#concatenate reports
+cd $ISSM_DIR/nightlylog/
+rm matlab_log.log
+for (( i=1;i<=$NUMCPUS_RUN;i++ ))
+do
+	cat matlab_log$i.log >> matlab_log.log
+done
+#}}}
+#Complete info.log {{{
+if [ $(cat matlab_log.log | grep "MATLABEXITEDCORRECTLY" | wc -l) -eq $NUMCPUS_RUN ]
+then
+	MATLABCRASH=0
+else
+	MATLABCRASH=1
+fi
+ELAPSED=$(timer $MATLAB_START_TIME)
+cat << END >>  $ISSM_DIR/nightlylog/info.log
+elapsed_matlab: $(echo $ELAPSED)
+matlab_crash:   $(echo $MATLABCRASH)
+END
+#}}}
+fi
+
+#python tests
+if [ $PYTHON_TEST -eq 1 ]; then
+#Launch all tests on different cpus {{{
+PYTHON_START_TIME=$(timer);
+export PYTHONSTARTUP=$ISSM_DIR/src/m/dev/devpath.py
+for (( i=1;i<=$NUMCPUS_RUN;i++ ))
+do
+	cd $ISSM_DIR/test/NightlyRun
+	./runme.py --output=nightly --rank=$i --numprocs=$NUMCPUS_RUN $PYTHON_NROPTIONS 2>&1 > $ISSM_DIR/nightlylog/python_log$i.log &
+done
+
+#wait until python closes
+if [ "$OS" = "win7" ]; then
+	pause MATLAB
+else
+	wait
+fi
+
+#concatenate reports
+cd $ISSM_DIR/nightlylog/
+rm python_log.log
+for (( i=1;i<=$NUMCPUS_RUN;i++ ))
+do
+	cat python_log$i.log >> python_log.log
+done
+#}}}
+#Complete info.log {{{
+if [ $(cat python_log.log | grep "PYTHONEXITEDCORRECTLY" | wc -l) -eq $NUMCPUS_RUN ]
+then
+	PYTHONCRASH=0
+else
+	PYTHONCRASH=1
+fi
+ELAPSED=$(timer $PYTHON_START_TIME)
+cat << END >>  $ISSM_DIR/nightlylog/info.log
+elapsed_python: $(echo $ELAPSED)
+python_crash:   $(echo $PYTHONCRASH)
+END
+#}}}
+fi
+
+#complete info.log
+#{{{
+ELAPSED=$(timer $START_TIME)
+cat << END >>  $ISSM_DIR/nightlylog/info.log
+elapsed_total:  $(echo $ELAPSED)
+END
+#}}}
+
+#Send Report
+#Build html report {{{
+cd $ISSM_DIR/nightlylog/
+sh ../scripts/report.sh
+echo "html report located in $ISSM_DIR/nightlylog/report.html"
+#}}}
+#send mail if requested                  (SKIPMAIL) {{{
+if [ "$SKIPMAIL" != "yes" ]
+then
+	echo "sending report..."
+	for i in `echo $MAILINGLIST`; do
+
+cat - $ISSM_DIR/nightlylog/report.html <<HERE | /usr/lib/sendmail  -oi -t
+From: "ISSM Nightly run" <$EMAIL_ADRESS>
+To: $i
+Subject: ISSM nightly runs report: $NAME
+Mime-Version: 1.0
+Content-Type: text/html
+HERE
+	done
+fi
+#}}}
+
+#remove lock file
+#{{{
+cd $ISSM_DIR/../
+rm NIGHTLYLOCK
+#}}}