Index: /issm/trunk-jpl/cron/nightlyrun.sh.new
===================================================================
--- /issm/trunk-jpl/cron/nightlyrun.sh.new	(revision 11548)
+++ /issm/trunk-jpl/cron/nightlyrun.sh.new	(revision 11548)
@@ -0,0 +1,345 @@
+#!/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() #{{{1
+{
+	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() #{{{1
+{
+	suffix=`date | awk '{printf("%s-%s-%s  %s",$2,$3,$6,$4);}'`			 
+	echo $suffix;			 
+} #}}}
+function host_name() #{{{1
+{
+	#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() #{{{1
+{
+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{{{1
+if [ $# -ne 1 ];
+then
+	#no config file specified: exit
+	echo "no config file specified. Exiting..." >&2 # Error message to stderr.
+	exit 1
+fi
+if [ ! -f "$1" ]
+then
+	echo "File $1 not found!" >&2   # Error message to stderr.
+	exit 1
+fi 
+source $1;
+#}}}
+#Export ISSM_* variables{{{1
+export ISSM_DIR
+export ISSM_TIER
+export ISSM_ARCH
+#}}}
+#Initialize variables {{{1
+TODAY=$(todaydate);
+HOST_NAME=$(host_name $MACHINE);
+START_TIME=$(timer);
+ISSM_RELEASE=$(basename $(echo $REPOSITORY));
+USER=$(whoami);
+INIT_PATH=$(pwd);
+#}}}
+
+#Lauch installation
+#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{1
+if [ "$ISSM_INSTALLATION" == "checkout" ]
+then
+
+	#Erase previous code and Fetch the new one
+	rm -rf $ISSM_RELEASE
+	svn checkout "$REPOSITORY"
+
+elif [ "$ISSM_INSTALLATION" == "update" ]
+then
+
+	#only update ISSM
+	cd $ISSM_TIER
+	svn update
+
+elif [ "$ISSM_INSTALLATION" == "none" ]
+then
+
+	#do nothing
+	echo "Skipping ISSM installation"
+
+else
+
+	#Error message
+	echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr.
+	exit 1
+
+fi
+#}}}
+#Create cluster's settings{{{1
+#create simpler  cluster.rc file, with only the cluster we are interested in.
+cd $ISSM_TIER/test/NightlyRun/
+if [ "$MACHINE" = "win7" ]; then
+cat << END > $HOST_NAME"_settings.m"
+cluster.login='$USER';
+cluster.codepath='`cygpath -m $ISSM_TIER/bin`';
+cluster.executionpath='`cygpath -m $EXECUTION_PATH`';
+END
+else
+cat << END > $HOST_NAME"_settings.m"
+cluster.login='$USER';
+cluster.codepath='$ISSM_TIER/bin';
+cluster.executionpath='$EXECUTION_PATH';
+END
+fi
+#}}}
+#Source environment variables with new matlab path {{{1
+cd $ISSM_TIER/etc
+source environment.sh MATLAB_DIR=$MATLAB_PATH
+#}}}
+#install/copy/none external packages    (ISSM_EXTERNALPACKAGES){{{1
+if [ "$ISSM_EXTERNALPACKAGES" == "install" ]
+then
+	
+	cd $ISSM_TIER/externalpackages
+	#number of packages: 
+	numpackages=`echo $EXTERNALPACKAGES | wc -w`
+
+	for (( i=1; i<=$numpackages; i++ ))
+	do
+		package=`echo $EXTERNALPACKAGES | cut -d " " -f $i-$i`
+		package_config=`echo $EXTERNALPACKAGES_CONFIGS | cut -d " " -f $i-$i`
+		package_numcpus=`echo $EXTERNALPACKAGES_NUMCPUS | cut -d " " -f $i-$i`
+
+		cd $package
+		$package_config $package_numcpus
+		cd ..
+	done
+
+
+elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ]
+then
+
+	#erase externapackages, and link with externalpackages_dir
+	cd $ISSM_TIER
+	rm -rf externalpackages
+	cp -Rf $EXTERNALPACKAGESDIR ./
+
+elif [ "$ISSM_EXTERNALPACKAGES" == "none" ]
+then
+
+	#Do nothing
+	echo "Skipping external packages installation"
+
+else
+
+	#Error message
+	echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr.
+	exit 1
+
+fi
+#}}}
+#ISSM compilation yes/no                (ISSM_COMPILATION) {{{1
+if [ "$ISSM_COMPILATION" == "yes" ]
+then
+
+	cd $ISSM_TIER
+	make clean
+	make distclean
+	./scripts/automakererun.sh
+	source ./configs/$COMPILE_CONFIG_FILE
+
+	make -j $NUMCPUS_INSTALL
+	make -j $NUMCPUS_INSTALL install
+
+elif [ "$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 run
+#create softlink to startup {{{1
+cd $ISSM_TIER/test/NightlyRun/
+if [ "$MACHINE" = "win7" ]; then
+	cp $ISSM_TIER/startup.m .
+else
+	ln -s $ISSM_TIER/startup.m .
+fi
+#}}}
+#Create nightlylog directory and info.log {{{1
+#put installation elapsed time in info.log
+INSTALL_TIME=$(timer)
+ELAPSED_INSTALL=$(timer $START_TIME)
+rm -rf $ISSM_TIER/nightlylog
+mkdir  $ISSM_TIER/nightlylog
+cat << END > $ISSM_TIER/nightlylog/info.log
+today:     $(echo $TODAY)
+user:      $(echo $USER)
+host:      $(echo $HOST_NAME)
+OS:        $(echo $MACHINE)
+release:   $(echo $ISSM_RELEASE)
+init_path: $(echo $INIT_PATH)
+elapsed_install: $(echo $ELAPSED_INSTALL)
+END
+#}}}
+#check NUMCPUS_RUN options {{{1
+if [ "$NUMCPUS_RUN" = "" ]
+then
+	echo "NUMCPUS_RUN option not found, defaulting to NUMCPUS_RUN = 1"
+	NUMCPUS_RUN=1
+fi
+#}}}
+
+#Run tests
+#on Matlab and windows machines, we'll need a windows style path:  {{{
+if [ "$MACHINE" = "win7" ]; then
+	MATLAB_TIER=`cygpath -m $ISSM_TIER`
+else 
+	MATLAB_TIER=$ISSM_TIER
+fi
+
+#}}}
+#Launch all tests on different cpus {{{1
+for (( i=1;i<=$NUMCPUS_RUN;i++ ))
+do
+	#Launch matlab and the nightly run script
+	cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF
+	warning off %necessary to avoid a info.log of several Go for parallel runs
+	try,
+	cd $MATLAB_TIER/test/NightlyRun
+	startup;
+	$(if [ "$NROPTIONS" = ""  ]
+	then
+		echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
+	else
+		#echo "runme('id',[101 102]);" 
+		echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
+	fi
+	)
+	catch me,
+		%An error occured, get report and exit
+		message=getReport(me)
+		directory=strsplit(pwd,'/');
+		fid=fopen([ISSM_TIER '/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
+
+	#Start run from nightlylog directory
+	cd $ISSM_TIER/nightlylog/
+
+	#Start test
+	$MATLABBIN  -nojvm -nosplash  -r matlab_run$i -logfile matlab_log$i.log &
+
+done
+
+#wait until matlab closes
+if [ "$MACHINE" = "win7" ]; then
+	pause MATLAB
+else
+	wait
+fi
+
+#}}}
+#concatenate all reports {{{1
+cd $ISSM_TIER/nightlylog/
+mv matlab_log1.log  matlab_log.log
+for (( i=2;i<=$NUMCPUS_RUN;i++ ))
+do
+	cat matlab_log.log matlab_log$i.log > matlab_log.log.bak
+	mv matlab_log.log.bak matlab_log.log
+done
+#}}}
+#Complete info.log {{{1
+if [ $(cat matlab_log.log | grep "MATLABEXITEDCORRECTLY" | wc -l) -eq $NUMCPUS_RUN ]
+then
+	MATLABCRASH=0
+else
+	MATLABCRASH=1
+fi
+ELAPSED_RUN=$(timer $INSTALL_TIME)
+ELAPSED_TOTAL=$(timer $START_TIME)
+cat << END >>  $ISSM_TIER/nightlylog/info.log
+elapsed_run:   $(echo $ELAPSED_RUN)
+elapsed_total: $(echo $ELAPSED_TOTAL)
+matlab_crash:  $(echo $MATLABCRASH)
+END
+#}}}
+
+#Send Report
+#Build html report {{{1
+cd $ISSM_TIER/nightlylog/
+sh ../scripts/report.sh
+echo "html report located in $ISSM_TIER/nightlylog/report.html"
+#}}}
+#send mail if requested                  (SKIPMAIL) {{{1
+if [ "$SKIPMAIL" != "yes" ]
+then
+	echo "sending report..."
+	source $ISSM_TIER/cron/mailinglist
+	for i in `echo $MAILINGLIST`; do
+
+		if [ "$MACHINE" = "win7" ]
+		then
+			echo $i
+			email -html -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/nightlylog/report.html
+		else 
+			if [ "$MACHINE" = "astrid" ]
+			then
+cat - $ISSM_TIER/nightlylog/report.html <<HERE | /usr/lib/sendmail  -oi -t
+From: "ISSM Nightly run" <$EMAIL_ADRESS>
+To: $i
+Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER.
+Mime-Version: 1.0
+Content-Type: text/html
+HERE
+		else
+cat - $ISSM_TIER/nightlylog/report.html <<HERE | /usr/sbin/sendmail  -oi -t
+From: "ISSM Nightly run" <$EMAIL_ADRESS>
+To: $i
+Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER.
+Mime-Version: 1.0
+Content-Type: text/html
+HERE
+			fi
+		fi
+	done
+fi
+#}}}