A Bash script for monitoring R simulations

runSim.sh

#### Simulation running/monitoring script
####
#### Run this as: ./runSim.sh YOUR_R_SOURCE_FILE.R ANY_TEXT_FILE.txt
####
#### Lines to edit before running are indicated by '##### **'

RFILE="$1"
OUTFILE="$2"

nohup nice -10 R --vanilla --slave < $RFILE > $OUTFILE & ## Defaults to running at medium-low priority (-10). Can increase this to improve performance (maybe).

##### ** CHANGE THIS to your username on the server ####
USERNAME=myname 
##########################################

##### ** CHANGE THIS to your email address ####
EMAIL="[email protected]" 
##############################################

REPORTFILE="$OUTFILE" 

PROCSOUT="/tmp/procs.txt" 
GREPPROCS="/tmp/grepprocs.txt" 

ps -u $USERNAME > $PROCSOUT ## Capture the list of running processes
grep "$RFILE" $PROCSOUT > $GREPPROCS ## Look for a process which contains the name of your source file. If this search comes up empty, your R session isn't running anymore and your simulation is done

while [ -s $GREPPROCS ] ## While your simulation is still running...
    do 
        #echo "Still running" 
        sleep 100 ## Check again in 100 seconds
        ps -u $USERNAME > $PROCSOUT 
        grep "$RFILE" $PROCSOUT > $GREPPROCS 
    done 

SUBJECT="Auto-generated simulation message" 
# Email text/message 
EMAILMESSAGE="/tmp/emailmessage.txt" 
echo "$RFILE" > $EMAILMESSAGE 
echo "This simulation has terminated. Tail of reporting file follows:" >> $EMAILMESSAGE 
tail -n 20 $REPORTFILE  >>$EMAILMESSAGE 
# send an email using /bin/mail 

##### ** May have to CHANGE the path to /bin/mail here depending on your server configuration ########
/bin/mail -s "$SUBJECT" "$EMAIL" < $EMAILMESSAGE 
#################################################################################################

cat $EMAILMESSAGE 
echo "Script complete. Mail sent."