Index: /issm/trunk-jpl/cron/nightlyrun.sh
===================================================================
--- /issm/trunk-jpl/cron/nightlyrun.sh	(revision 11551)
+++ /issm/trunk-jpl/cron/nightlyrun.sh	(revision 11552)
@@ -29,13 +29,22 @@
 {
 	#return host name depending on the OS
-	if [ "$1" = "wineric" ] 
+	if [ "$1" = "win7" ] 
 	then
-		HOST_NAME=`hostname`;
+		HOST_NAME=`hostname | sed 's/-//g'`;
 	else
-		HOST_NAME=`hostname -s`;
+		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
@@ -74,5 +83,5 @@
 	#Erase previous code and Fetch the new one
 	rm -rf $ISSM_RELEASE
-	svn checkout $REPOSITORY
+	svn checkout "$REPOSITORY"
 
 elif [ "$ISSM_INSTALLATION" == "update" ]
@@ -100,4 +109,11 @@
 #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';
@@ -105,4 +121,5 @@
 cluster.executionpath='$EXECUTION_PATH';
 END
+fi
 #}}}
 #Source environment variables with new matlab path {{{1
@@ -113,18 +130,20 @@
 if [ "$ISSM_EXTERNALPACKAGES" == "install" ]
 then
+	
 	cd $ISSM_TIER/externalpackages
-	for ep in $EXTERNALPACKAGES
-	do 
-		cd $ep
-		case $ep in
-			"mpich2" )   ./install-1.0.2-linux64.sh ;;
-			"petsc" )    ./install-3.2-linux64.sh   ;;
-			"metis" )    ./install-4.0-linux64.sh ;;
-			"triangle" ) ./install-linux64.sh ;;
-			"dakota" )   ./install-linux64-astrid.sh ;;
-			*)           ./install.sh $NUMCPUS_INSTALL
-		esac
+	#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 [ "$ISSM_EXTERNALPACKAGES" == "copy" ]
@@ -158,18 +177,8 @@
 	make distclean
 	./scripts/automakererun.sh
-	./configs/config-linux64-astrid.sh
-
-	#4: compile and install ISSM
-	if [ "$MACHINE" = "wineric" ] 
-	then
-		cd $ISSM_TIER/src/c
-		./intel-compile.sh
-		cd $ISSM_TIER/src/mex
-		make install
-		cd $ISSM_TIER
-	else
-		make -j $NUMCPUS_INSTALL
-		make -j $NUMCPUS_INSTALL install
-	fi
+	source ./configs/$COMPILE_CONFIG_FILE
+
+	make -j $NUMCPUS_INSTALL
+	make -j $NUMCPUS_INSTALL install
 
 elif [ "$ISSM_COMPILATION" == "no" ]
@@ -185,5 +194,9 @@
 #create softlink to startup {{{1
 cd $ISSM_TIER/test/NightlyRun/
-ln -s $ISSM_TIER/startup.m .
+if [ "$MACHINE" = "win7" ]; then
+	cp $ISSM_TIER/startup.m .
+else
+	ln -s $ISSM_TIER/startup.m .
+fi
 #}}}
 #Create nightlylog directory and info.log {{{1
@@ -212,4 +225,12 @@
 
 #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++ ))
@@ -219,5 +240,5 @@
 	warning off %necessary to avoid a info.log of several Go for parallel runs
 	try,
-	cd $ISSM_TIER/test/NightlyRun
+	cd $MATLAB_TIER/test/NightlyRun
 	startup;
 	$(if [ "$NROPTIONS" = ""  ]
@@ -225,4 +246,5 @@
 		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
@@ -245,10 +267,15 @@
 
 	#Start test
-	MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8
-	/usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab  -nojvm -nosplash  -r matlab_run$i -logfile matlab_log$i.log &
+	$MATLABBIN  -nojvm -nosplash  -r matlab_run$i -logfile matlab_log$i.log &
+
 done
 
 #wait until matlab closes
-wait
+if [ "$MACHINE" = "win7" ]; then
+	pause MATLAB
+else
+	wait
+fi
+
 #}}}
 #concatenate all reports {{{1
@@ -290,7 +317,8 @@
 	for i in `echo $MAILINGLIST`; do
 
-		if [ "$MACHINE" = "wineric" ]
+		if [ "$MACHINE" = "win7" ]
 		then
-			email -html -f "ISSM Nightly run $EMAIL_ADRESS" -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/test/Verification/NightlyRun/report.html
+			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" ]
Index: sm/trunk-jpl/cron/nightlyrun.sh.new
===================================================================
--- /issm/trunk-jpl/cron/nightlyrun.sh.new	(revision 11551)
+++ 	(revision )
@@ -1,345 +1,0 @@
-#!/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
-#}}}