Doing large runs of ShelfMC can be time intensive. However, if you have access to a computing cluster like Ruby or KingBee, where you are given a node with multiple processors, ShelfMC runs can be optimized by utilizing all available processors on a node. The multithread_shelfmc.sh script automates these runs for you. The script and instructions are attached below.

#!/bin/bash
#Jude Rajasekera 3/20/2017
shelfmcDir=/users/PCON0003/cond0091/ShelfMC #put your shelfmc directory address here 
 

runName='TestRun' #name of run
NNU=500000 #total NNU per run
seed=42 #initial seed for every run,each processor will recieve a different seed (42,43,44,45...)
NNU="$(($NNU / 20))" #calculating NNU per processor, change 20 to however many processor your cluster has per node
ppn=20 #processors per node
########################### make changes for input.txt file here #####################################################
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="575     #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="$122    #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="1000   #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="1      #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="/users/PCON0003/cond0091/ShelfMC/temp/LP_gain_manual.txt     #GAINFILENAME"
###########################################################################################

cd $shelfmcDir #cd to dir containing shelfmc
mkdir $runName #make a folder for run
cd $runName    #cd into run folder
initSeed=$seed 

for (( i=1; i<=$ppn;i++)) #make 20 setup files for 20 processors
do
    mkdir Setup$i #make setup folder i
    cd Setup$i #go into setup folder i
    
    seed="$(($initSeed+$i-1))" #calculate seed for this iteration
    input3="$seed      #seed Seed for Rand3" #save new input line    
    for j in {1..40} #print all input.txt lines 
    do
	lineName=input$j
        echo "${!lineName}" >> input.txt #print line to input.txt file
    done
    cd ..
done



pwd=`pwd`

#create job file
echo '#!/bin/bash' >> run_shelfmc_multithread.sh
echo '#PBS -l nodes=1:ppn='$ppn >> run_shelfmc_multithread.sh #change depending on processors per node
echo '#PBS -l walltime=00:05:00' >> run_shelfmc_multithread.sh #change walltime depending on run size, will be 20x shorter than single processor run time
echo '#PBS -N shelfmc_'$runName'_job' >> run_shelfmc_multithread.sh
echo '#PBS -j oe'  >> run_shelfmc_multithread.sh
echo '#PBS -A PCON0003' >> run_shelfmc_multithread.sh #change to specify group
echo 'cd ' $shelfmcDir >> run_shelfmc_multithread.sh 
echo 'runName='$runName  >> run_shelfmc_multithread.sh
for (( k=1; k<=$ppn;k++))
do
    echo './shelfmc_stripped.exe $runName/Setup'$k' _'$k'$runName &' >> run_shelfmc_multithread.sh #execute commands for 20 setup files
done
echo 'wait' >> run_shelfmc_multithread.sh #wait until all runs are finished
echo 'cd $runName' >> run_shelfmc_multithread.sh #go into run folder 
echo 'for (( i=1; i<='$ppn';i++)) #20 iterations' >> run_shelfmc_multithread.sh 
echo 'do' >> run_shelfmc_multithread.sh
echo '  cd Setup$i #cd into setup dir' >> run_shelfmc_multithread.sh
echo '  mv *.root ..' >> run_shelfmc_multithread.sh #move root files to runDir
echo '  cd ..' >> run_shelfmc_multithread.sh
echo 'done' >> run_shelfmc_multithread.sh
echo 'hadd Result_'$runName'.root *.root' >> run_shelfmc_multithread.sh #add all root files
echo 'rm *ShelfMCTrees*' >> run_shelfmc_multithread.sh #delete all partial root files

chmod u+x run_shelfmc_multithread.sh

echo "Run files created"
echo "cd into run folder and do $ qsub run_shelfmc_multithread.sh"