Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh
===================================================================
--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh	(revision 11571)
+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh	(revision 11572)
@@ -46,6 +46,7 @@
 done
 }
 #}}}
+
 #Get configuration
 #Source config file{{{1
 if [ $# -ne 1 ];
@@ -109,13 +110,13 @@
 #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"
+	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"
+	cat << END > $HOST_NAME"_settings.m"
 cluster.login='$USER';
 cluster.codepath='$ISSM_TIER/bin';
 cluster.executionpath='$EXECUTION_PATH';
@@ -138,14 +139,12 @@
 	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
+		$package_config
 		cd ..
 	done
 
-
 elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ]
 then
 
@@ -177,10 +176,8 @@
 	make distclean
 	./scripts/automakererun.sh
 	source ./configs/$COMPILE_CONFIG_FILE
+	make install
 
-	make -j $NUMCPUS_INSTALL
-	make -j $NUMCPUS_INSTALL install
-
 elif [ "$ISSM_COMPILATION" == "no" ]
 then
 	echo "Skipping ISSM compilation"
@@ -193,11 +190,8 @@
 #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
+rm startup.m #in case it alreade exists
+cp $ISSM_TIER/startup.m .
 #}}}
 #Create nightlylog directory and info.log {{{1
 #put installation elapsed time in info.log
@@ -230,7 +224,6 @@
 else 
 	MATLAB_TIER=$ISSM_TIER
 fi
-
 #}}}
 #Launch all tests on different cpus {{{1
 for (( i=1;i<=$NUMCPUS_RUN;i++ ))
@@ -280,7 +273,7 @@
 #}}}
 #concatenate all reports {{{1
 cd $ISSM_TIER/nightlylog/
-mv matlab_log1.log  matlab_log.log
+cp matlab_log1.log  matlab_log.log
 for (( i=2;i<=$NUMCPUS_RUN;i++ ))
 do
 	cat matlab_log.log matlab_log$i.log > matlab_log.log.bak