## annotated sample PBS batch job specification for OSC
## Sam Stafford 05/11/2017

#PBS -N j_ai06_${RUN_NUMBER}

##PBS -m abe       ##  request an email on job completion
#PBS -l mem=16GB   ##  request 16GB memory
##PBS -l walltime=06:00:00  ## set this in qsub
#PBS -j oe         ## merge stdout and stderr into a single output log file
#PBS -A PAS0174

echo "run number " $RUN_NUMBER
echo "cal pulser " $CAL_PULSER
echo "baseline file " $BASELINE_FILE
echo "temp dir is " $TMPDIR
echo "ANITA_DATA_REMOTE_DIR="$ANITA_DATA_REMOTE_DIR
set -x


## copy the files from kingbee to the temporary workspace  
##    (if you set up public key authentication between kingbee and OSC, you won't need a password; just google "public key authentication")
mkdir $TMPDIR/run${RUN_NUMBER}   ## make a directory for this run number
scp stafford.16@kingbee.mps.ohio-state.edu:/data/anita/anita3/flightData/copiedBySam/run${RUN_NUMBER}/calEventFile${RUN_NUMBER}.root $TMPDIR/run${RUN_NUMBER}/calEventFile${RUN_NUMBER}.root
scp stafford.16@kingbee.mps.ohio-state.edu:/data/anita/anita3/flightData/copiedBySam/newerData/run${RUN_NUMBER}/gpsEvent${RUN_NUMBER}.root $TMPDIR/run${RUN_NUMBER}/gpsEvent${RUN_NUMBER}.root
scp stafford.16@kingbee.mps.ohio-state.edu:/data/anita/anita3/flightData/copiedBySam/newerData/run${RUN_NUMBER}/timedHeadFile${RUN_NUMBER}.root $TMPDIR/run${RUN_NUMBER}/timedHeadFile${RUN_NUMBER}.root
scp stafford.16@kingbee.mps.ohio-state.edu:/data/anita/anita3/flightData/copiedBySam/newerData/run${RUN_NUMBER}/decBlindHeadFileV1_${RUN_NUMBER}.root $TMPDIR/run${RUN_NUMBER}/decBlindHeadFileV1_${RUN_NUMBER}.root

## set up the environment variables to point to the temporary work space
export ANITA_DATA_REMOTE_DIR=$TMPDIR
export ANITA_DATA_LOCAL_DIR=$TMPDIR
echo "ANITA_DATA_REMOTE_DIR="$ANITA_DATA_REMOTE_DIR

## run the analysis program
cd analysisSoftware
./analyzerIterator06 ${CAL_PULSER} -S1 -Noverlap --FILTER_OPTION=4 ${BASELINE_FILE} ${RUN_NUMBER} -O
echo "batch job ending"