Files as semaphores

#!/bin/sh -login
#PBS -l nodes=1:ppn=1,walltime=00:30:00,feature=gbe,mem=1gb
#PBS -j oe
#PBS -m a

#Files as semifors  
# Script written by Dirk Colbry

#CHANGE the following to filter files that need to be processed
filefilter="*.do"

#Create a flags directory if one is not already created
cd ${PBS_O_WORKDIR}
mkdir -p flags

#Check to see if job being run from an array. Space jobs so they do not run on
#top of each other. This is probably unessary
if [ ! "${PBS_ARRAYID}" = "" ]
then
    sleep ${PBS_ARRAYID}
fi

# Find the most recent file not in the flags directory
# This indicates that the file has not been proceesed
for file in `echo $filefilter`  
do
    if [ ! -f ./flags/${file}.flag ]
    then
        #Create the file so other jobs will not run the same program
        touch ./flags/${file}.flag
        dofile=$file
        break
    fi
done

#Check to see if dofile is empty
#This indicates all files have been processed
if [ "$dofile" == "" ]
then
    echo "All jobs completed!"
    exit 0
fi

#CHANGE the following to run the program of interest using the dofile as an input
module load stata
stata-se -b ${dofile}

#Save the return value of the last command
RET=$?

#Put the job statistics on the flag file as a record and to indicate
# the program execited successfully.
if [ "$RET" = "0" ]
then
    qstat -f ${PBS_JOBID} > ./flags/${dofile}.flag
else
    qstat -f ${PBS_JOBID}
    echo "job with dofile=${dofile} completed with error ${RET}"
    exit $RET
fi

#Check to see if anything is left that needs to be done
for file in `echo $filefilter`  
do
    if [ ! -f ./flags/${file}.flag ]
    then
        #flag missing...start another job
        qsub mainrun.qsub
        exit $RET  
    fi
done

#Nothing is left to be done... Exit
#Note, return value (RET) should be zero
echo "ALL JOBS COMPLETED!"
exit $RET