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| Entry time: | Tue Apr 25 10:35:43 2017
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| Attachment 1: |
ParameterSpaceScan_instructions.txt
This document will explain how to dowload, configure, and run a parameter space search for ShelfMC on a computing cluster.
These scripts explore the ShelfMC parameter space by varying ATTEN_UP, REFLECT_RATE, ICETHICK, FIRNDEPTH, and STATION_DEPTH for certain rages.
The ranges and increments can be found in setup.sh.
In order to vary STATION_DEPTH, some changes were made to the ShelfMC code. Follow these steps to allow STATION_DEPTH to be an input parameter.
1.cd to ShelfMC directory
2.Do $sed -i -e 's/ATDepth/STATION_DEPTH/g' *.cc
3.Open declaration.hh. Replace line 87 "const double ATDepth = 0.;" with "double STATION_DEPTH;"
4.In functions.cc go to line 1829. This is the ReadInput() method. Add the lines below to the end of this method.
GetNextNumber(inputfile, number); // new line for station Depth
STATION_DEPTH = (double) atof(number.c_str()); //new line
5.Do $make clean all
#######Script Descriptions########
setup.sh -> This script sets up the necessary directories and setup files for all the runs
scheduler.sh -> This script submits and monitors all jobs.
#######DOWNLOAD########
1.Download setup.sh and scheduler.sh
2.Move both files into your ShelfMC directory
3.Do $chmod u+x setup.sh and $chmod u+x scheduler.sh
######CONFIGURE#######
1.Open setup.sh
2.On line 4, modify the job name
3.On line 6, modify group name
4.On line 10, specify your ShelfMC directory
5.On line 13, modify your run name
6.On line 14, specify the NNU per run
7.On line 15, specify the starting seed
8.On line 17, specify the number of processors per node on your cluster
9.On lines 19-56, edit the input.txt parameters that you want to keep constant for every run
10.On line 57, specify the location of the LP_gain_manual.txt
11.On line 126, change walltime depending on total NNU. Remember this wall time will be 20x shorter than a single processor run.
12.On line 127, change job prefix
13.On line 129, change the group name if needed
14.Save file
15.Open scheduler.sh
16.On line 4, specify your ShelfMC directory
17.On line 5, modify run name. Make sure it is the same runName as you have in setup.sh
18.On lines 35 and 39, replace cond0091 with your username for the cluster
19.On line 42, you can pick how many nodes you want to use at any given time. It is set to 6 intially.
20.Save file
#######RUN#######
1.Do $qsub setup.sh
2.Wait for setup.sh to finish. This script is creating the setup files for all runs. This may take about an hour.
3.When setup.sh is done, there should be a new directory in your home directory. Move this directory to your ShelfMC directory.
4.Do $screen to start a new screen that the scheduler can run on. This is incase you lose connection to the cluster mid run.
5.Do $./scheduler.sh to start script. This script automatically submits jobs and lets you see the status of the runs. This will run for several hours.
5.The scheduler makes a text file of all jobs called jobList.txt in the ShelfMC dir. Make sure to delete jobList.txt before starting a whole new run.
######RESULT#######
1.When Completed, there will be a great amount of data in the run files, about 460GB.
2.The run directory is organized in tree, results for particular runs can be found by cd'ing deeper into the tree.
3.In each run directory, there will be a resulting root file, all the setup files, and a log file for the run.
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| Attachment 2: |
setup.sh
#!/bin/bash
#PBS -l walltime=04:00:00
#PBS -l nodes=1:ppn=1,mem=4000mb
#PBS -N jude_SetupJob
#PBS -j oe
#PBS -A PCON0003
#Jude Rajasekera 3/20/17
#directories
WorkDir=$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 $HOME
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| Attachment 3: |
scheduler.sh
#!/bin/bash
#Jude Rajasekera 3/20/17
tmpShelfmc=$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
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