These scripts allow you to do thousands of ShelfMC runs while varying certain parameters of your choice. As is, the attenuation length, reflection, ice thickness, firn depth, station depth is varied over certain rages; in total, the whole Parameter Space Scan does 5250 runs on a cluster like Ruby or KingBee. The scripts and instructions are attached below. 

#!/bin/bash
#PBS -l walltime=04:00:00
#PBS -l nodes=1:ppn=1,mem=4000mb
#PBS -N jude_SetupJob
#PBS -j oe
#PBS -A PCON0003
#Jude Rajasekera 3/20/17
#directories
WorkDir=$TMPDIR   
tmpShelfmc=$HOME/shelfmc/ShelfMC #set your ShelfMC directory here

#controlled variables for run
runName='ParamSpaceScanDir' #name of run
NNU=500000 #NNU per run
seed=42 #starting seed for every run, each processor will recieve a different seed (42,43,44,45...)
NNU="$(($NNU / 20))" #calculating processors per node, change 20 to however many processors your cluster has per node
ppn=5 #number of processors per node on cluster
########################### input.txt file ####################################################
input1="#inputs for ARIANNA simulation, do not change order unless you change ReadInput()"
input2="$NNU #NNU, setting to 1 for unique neutrino"
input3="$seed      #seed Seed for Rand3"
input4="18.0    #EXPONENT, !should be exclusive with SPECTRUM"
input5="1000    #ATGap, m, distance between stations"
input6="4       #ST_TYPE, !restrict to 4 now!"
input7="4 #N_Ant_perST, not to be confused with ST_TYPE above"
input8="2 #N_Ant_Trigger, this is the minimum number of AT to trigger"
input9="30      #Z for ST_TYPE=2"
input10="$T   #ICETHICK, thickness of ice including firn, 575m at Moore's Bay"
input11="1       #FIRN, KD: ensure DEPTH_DEPENDENT is off if FIRN is 0"
input12="1.30    #NFIRN 1.30"
input13="$FT      #FIRNDEPTH in meters"
input14="1 #NROWS 12 initially, set to 3 for HEXAGONAL"
input15="1 #NCOLS 12 initially, set to 5 for HEXAGONAL"
input16="0       #SCATTER"
input17="1       #SCATTER_WIDTH,how many times wider after scattering"
input18="0       #SPECTRUM, use spectrum, ! was 1 initially!"
input19="0       #DIPOLE,  add a dipole to the station, useful for st_type=0 and 2"
input20="0       #CONST_ATTENLENGTH, use constant attenuation length if ==1"
input21="$L     #ATTEN_UP, this is the conjuction of the plot attenlength_up and attlength_down when setting REFLECT_RATE=0.5(3dB)"
input22="250     #ATTEN_DOWN, this is the average attenlength_down before Minna Bluff measurement(not used anymore except for CONST_ATTENLENGTH)"
input23="4 #NSIGMA, threshold of trigger"
input24="1      #ATTEN_FACTOR, change of the attenuation length"
input25="$Rval    #REFLECT_RATE,power reflection rate at the ice bottom"
input26="0       #GZK, 1 means using GZK flux, 0 means E-2 flux"
input27="0       #FANFLUX, use fenfang's flux which only covers from 10^17 eV to 10^20 eV"
input28="0       #WIDESPECTRUM, use 10^16 eV to 10^21.5 eV as the energy spectrum, otherwise use 17-20"
input29="1       #SHADOWING"
input30="1       #DEPTH_DEPENDENT_N;0 means uniform firn, 1 means n_firn is a function of depth"
input31="0 #HEXAGONAL"
input32="1       #SIGNAL_FLUCT 1=add noise fluctuation to signal or 0=do not"
input33="4.0     #GAINV  gain dependency"
input34="1       #TAUREGENERATION if 1=tau regeneration effect, if 0=original"
input35="3.0     #ST4_R radius in meters between center of station and antenna"
input36="350     #TNOISE noise temperature in Kelvin"
input37="80      #FREQ_LOW low frequency of LPDA Response MHz #was 100"
input38="1000    #FREQ_HIGH high frequency of LPDA Response MHz"
input39="/home/rajasekera.3/shelfmc/ShelfMC/temp/LP_gain_manual.txt     #GAINFILENAME"
input40="$SD     #STATION_DEPTH"
#######################################################################################################

cd $TMPDIR   
mkdir $runName
cd $runName

initSeed=$seed
counter=0
for L in {500..1000..100} #attenuation length 500-1000
do
    mkdir Atten_Up$L
    cd Atten_Up$L

    for R in {0..100..25} #Reflection Rate 0-1
    do
        mkdir ReflectionRate$R
        cd ReflectionRate$R
        if [ "$R" = "100" ]; then #fixing reflection rate value
            Rval="1.0"
        else
            Rval="0.$R"
        fi

        for T in {500..2900..400} #Thickness of Ice 500-2900
        do
            mkdir IceThick$T
            cd IceThick$T
            for FT in {60..140..20} #Firn Thinckness 60-140
            do
                mkdir FirnThick$FT
                cd FirnThick$FT
                for SD in {0..200..50} #Station Depth
                do
                    mkdir StationDepth$SD
                    cd StationDepth$SD
                    #####Do file operations###########################################
                    counter=$((counter+1))
                    echo "Counter = $counter ; L = $L ; R = $Rval ; T = $T ; FT = $FT ; SD = $SD " #print variables

                    #define changing lines
                    input21="$L     #ATTEN_UP, this is the conjuction of the plot attenlength_up and attlength_down when setting REFLECT_RATE=0.5(3dB)"
                    input25="$Rval    #REFLECT_RATE,power reflection rate at the ice bottom"
                    input10="$T   #ICETHICK, thickness of ice including firn, 575m at Moore's Bay"
                    input13="$FT      #FIRNDEPTH in meters"
                    input40="$SD       #STATION_DEPTH"
		    
		    for (( i=1; i<=$ppn;i++)) #make 20 setup files for 20 processors
                    do

                        mkdir Setup$i #make setup folder
                        cd Setup$i #go into setup folder
                        seed="$(($initSeed + $i -1))" #calculate seed for this iteration
                        input3="$seed      #seed Seed for Rand3"

                        for j in {1..40} #print all input.txt lines
                        do
                            lineName=input$j
                            echo "${!lineName}" >> input.txt
                        done
			
                        cd ..
                    done
		    
		    pwd=`pwd`
                    #create job file
		    echo '#!/bin/bash' >> run_shelfmc_multithread.sh
		    echo '#PBS -l nodes=1:ppn='$ppn >> run_shelfmc_multithread.sh
		    echo '#PBS -l walltime=00:05:00' >> run_shelfmc_multithread.sh #change walltime as necessary
		    echo '#PBS -N jude_'$runName'_job' >> run_shelfmc_multithread.sh #change job name as necessary
		    echo '#PBS -j oe'  >> run_shelfmc_multithread.sh
		    echo '#PBS -A PCON0003' >> run_shelfmc_multithread.sh #change group if necessary
		    echo 'cd ' $tmpShelfmc >> run_shelfmc_multithread.sh
		    echo 'runName='$runName  >> run_shelfmc_multithread.sh
		    for (( i=1; i<=$ppn;i++))
		    do
			echo './shelfmc_stripped.exe $runName/'Atten_Up$L'/'ReflectionRate$R'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD'/Setup'$i' _'$i'$runName &' >> run_shelfmc_multithread.sh
		    done
		   # echo './shelfmc_stripped.exe $runName/'Atten_Up$L'/'ReflectionRate$R'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD'/Setup1 _01$runName &' >> run_shelfmc_multithread.sh
		    echo 'wait' >> run_shelfmc_multithread.sh
		    echo 'cd $runName/'Atten_Up$L'/'ReflectionRate$R'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD >> run_shelfmc_multithread.sh
		    echo 'for (( i=1; i<='$ppn';i++)) #20 iterations' >> run_shelfmc_multithread.sh
		    echo 'do' >> run_shelfmc_multithread.sh
		    echo '  cd Setup$i #cd into setup dir' >> run_shelfmc_multithread.sh
		    echo '  mv *.root ..' >> run_shelfmc_multithread.sh
		    echo '  cd ..' >> run_shelfmc_multithread.sh
		    echo 'done' >> run_shelfmc_multithread.sh
		    echo 'hadd Result_'$runName'.root *.root' >> run_shelfmc_multithread.sh
		    echo 'rm *ShelfMCTrees*' >> run_shelfmc_multithread.sh

		    chmod u+x run_shelfmc_multithread.sh # make executable

                    ##################################################################
                    cd ..
                done
                cd ..
            done
            cd ..
        done
        cd ..
    done
    cd ..
done
cd 

mv $WorkDir/$runName $HOME

#!/bin/bash
#Jude Rajasekera 3/20/17

tmpShelfmc=$HOME/shelfmc/ShelfMC #location of Shelfmc
runName=ParamSpaceScanDir #name of run

cd $tmpShelfmc #move to home directory

if [ ! -f ./jobList.txt ]; then #see if there is an existing job file
    echo "Creating new job List"
    for L in {500..1000..100} #attenuation length 500-1000
    do
	for R in {0..100..25} #Reflection Rate 0-1
	do
            for T in {500..2900..400} #Thickness of Ice 500-2900
            do
		for FT in {60..140..20} #Firn Thinckness 60-140
		do
                    for SD in {0..200..50} #Station Depth
                    do
		    echo "cd $runName/Atten_Up$L/ReflectionRate$R/IceThick$T/FirnThick$FT/StationDepth$SD" >> jobList.txt
                    done
		done
            done
	done
    done
else 
    echo "Picking up from last job"
fi


numbLeft=$(wc -l < ./jobList.txt)
while [ $numbLeft -gt 0 ];
do
    jobs=$(showq | grep "rajasekera.3") #change username here
    echo '__________Current Running Jobs__________'
    echo "$jobs"
    echo ''
    runningJobs=$(showq | grep "rajasekera.3" | wc -l) #change unsername here
    echo Number of Running Jobs = $runningJobs 
    echo Number of jobs left = $numbLeft
    if [ $runningJobs -le 6 ];then
	line=$(head -n 1 jobList.txt)
	$line
	echo Submit Job && pwd
	qsub run_shelfmc_multithread.sh
	cd $tmpShelfmc
	sed -i 1d jobList.txt
    else
	echo "Full Capacity"
    fi
    sleep 1
    numbLeft=$(wc -l < ./jobList.txt)
done