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| Important Plots, Tables, and Measurements |
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 Sun Apr 23 14:54:50 2017, Hannah Hasan, Other, Simulation, Plotting ShelfMC Parameter Space, Other 
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 Fri Oct 6 15:15:53 2017, Hannah Hasan, Other, Simulation, Plotting ShelfMC Parameter Space, Other 6x
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Message ID: 27
Entry time: Fri Oct 6 15:15:53 2017
In reply to: 16
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| Author: |
Hannah Hasan |
| Type: |
Other |
| Category: |
Simulation |
| Subject: |
Plotting ShelfMC Parameter Space |
| Project: |
Other |
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Attached are instructions and scripts for carrying out a parameter space scan with ShelfMC, the simulation package for the ARIANNA detector.
Because some of the plotted outputs looked like colored stripes and did not offer any insight into how effective volume changed with some variables, I made some changes to the simulation and plotting scripts so that different maximum, minimum, and increment values can be chosen for each variable. Now rather than having fixed, hard-coded values for all variables, the parameter space scan and plotting is more flexible for use with variable inputs.
| Quote: |
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I am trying to write a script that will plot a 2d histogram of effective volume versus two of ShelfMC's parameters.
The script prompts the user for which two parameters (out of five that we vary in our parameter space scan) to plot along the x- and y-axes, as well as what values to hold the other 3 parameters constant at. It then collects the necessary root files from simulation results, generates a plotting script, and runs the plotting script to produce a plot in pdf form.
After many struggles I have the script written to the point where it functions, but the plots don't look right. Some plots look like they could be actual data (like Veff_A_I), and others just look flat-out wrong (like Veff_R_S).
I have yet to pin down the cause of this, but hopefully will be able to sometime in the near future.
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#!/bin/bash
#PBS -l walltime=04:00:00
#PBS -l nodes=1:ppn=1,mem=4000mb
#PBS -N hannah_SetupJob
#PBS -j oe
#PBS -A PCON0003
#Jude Rajasekera 3/20/17
#Modified by Hannah Hasan on 09/17/2017
#directories
WorkDir=$TMPDIR
tmpShelfmc=$HOME/ShelfMC/git_shelfmc #set your ShelfMC directory here
AttenMin=600 # MINIMUM attenuation length for the simulation *****ALL UNITS ARE IN METERS*****
AttenMax=1000 # MAXIMUM attenuation length
AttenInc=400 # INCREMENT for attenuation length
RadiusMin=3 # MINIMUM radius
RadiusMax=31 # MAXIMUM radius
RadiusInc=7 # INCREMENT
IceMin=500 # etc...
IceMax=2900
IceInc=400
FirnMin=60
FirnMax=120
FirnInc=60
StDepthMin=0
StDepthMax=200
StDepthInc=50
#controlled variables for run
runName='e18_ParamSpaceScan' #name of run
NNU=10000000 #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=20 #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="$L #ATTEN_UP, this is the conjuction of the plot attenlength_up and attlength_down when setting REFLECT_RATE=0.5(3dB)"
input22="250 #ATTEN_DOWN, this is the average attenlength_down before Minna Bluff measurement(not used anymore except for CONST_ATTENLENGTH)"
input23="4 #NSIGMA, threshold of trigger"
input24="1 #ATTEN_FACTOR, change of the attenuation length"
input25="0.85 #REFLECT_RATE,power reflection rate at the ice bottom"
input26="0 #GZK, 1 means using GZK flux, 0 means E-2 flux"
input27="0 #FANFLUX, use fenfang's flux which only covers from 10^17 eV to 10^20 eV"
input28="0 #WIDESPECTRUM, use 10^16 eV to 10^21.5 eV as the energy spectrum, otherwise use 17-20"
input29="1 #SHADOWING"
input30="1 #DEPTH_DEPENDENT_N;0 means uniform firn, 1 means n_firn is a function of depth"
input31="0 #HEXAGONAL"
input32="1 #SIGNAL_FLUCT 1=add noise fluctuation to signal or 0=do not"
input33="4.0 #GAINV gain dependency"
input34="1 #TAUREGENERATION if 1=tau regeneration effect, if 0=original"
input35="$AR #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/cond0092/ShelfMC/git_shelfmc/GainFiles/LP_gain_manual.txt #GAINFILENAME"
input40="$SD #STATION_DEPTH"
#######################################################################################################
cd $TMPDIR
mkdir $runName
cd $runName
initSeed=$seed
counter=0
for ((L=$AttenMin;L<=$AttenMax;L+=$AttenInc)) #Attenuation length
do
mkdir Atten_Up$L
cd Atten_Up$L
for ((AR=$RadiusMin;AR<=$RadiusMax;AR+=$RadiusInc)) #Station radius (measured from center of radius to antenna
do
mkdir AntennaRadius$AR
cd AntennaRadius$AR
for ((T=$IceMin;T<=$IceMax;T+=$IceInc)) #Ice thickness
do
mkdir IceThick$T
cd IceThick$T
for ((FT=$FirnMin;FT<=$FirnMax;FT+=$FirnInc)) #Firn thickness
do
mkdir FirnThick$FT
cd FirnThick$FT
for ((SD=$StDepthMin;SD<=$StDepthMax;SD+=$StDepthInc)) #Station depth
do
mkdir StationDepth$SD
cd StationDepth$SD
#####Do file operations###########################################
counter=$((counter+1))
echo "Counter = $counter ; L = $L ; AR = $AR ; 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)"
input35="$AR #ST4_R radius in meters between center of station and antenna"
input10="$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='$ppn >> run_shelfmc_multithread.sh
echo '#PBS -l walltime=00:10:00' >> run_shelfmc_multithread.sh #change walltime as necessary
echo '#PBS -N hannah_'$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'/'AntennaRadius$AR'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD'/Setup'$i' _'$i'$runName &' >> run_shelfmc_multithread.sh
done
# echo './shelfmc_stripped.exe $runName/'Atten_Up$L'/'AntennaGap$ATGap'/'IceThick$T'/'FirnThick$FT'/'StationDepth$SD'/Setup1 _01$runName &' >> run_shelfmc_multithread.sh
echo 'wait' >> run_shelfmc_multithread.sh
echo 'cd $runName/'Atten_Up$L'/'AntennaRadius$AR'/'IceThick$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
echo 'rm -rf Setup*' >> 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 $HOME
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#!/bin/bash
#Jude Rajasekera 3/20/17
tmpShelfmc=$HOME/ShelfMC/git_shelfmc #location of Shelfmc
runName=e18_ParamSpaceScan #name of run
cd $tmpShelfmc #move to home directory
AttenMin=500 # MINIMUM attenuation length for the simulation
AttenMax=1000 # MAXIMUM attenuation length
AttenInc=100 # INCREMENT for attenuation length
RadiusMin=3 # MINIMUM radius
RadiusMax=31 # MAXIMUM radius
RadiusInc=7 # INCREMENT
IceMin=500 # etc...
IceMax=2900
IceInc=400
FirnMin=60
FirnMax=140
FirnInc=20
StDepthMin=0
StDepthMax=200
StDepthInc=50
if [ ! -f ./jobList.txt ]; then #see if there is an existing job file
echo "Creating new job List"
for ((L=$AttenMin;L<=$AttenMax;L+=$AttenInc)) #Attenuation length
do
for ((AR=$RadiusMin;AR<=$RadiusMax;AR+=$RadiusInc)) #Station radius (measured from center of radius to antenna
do
for ((T=$IceMin;T<=$IceMax;T+=$IceInc)) #Ice thickness
do
for ((FT=$FirnMin;FT<=$FirnMax;FT+=$FirnInc)) #Firn thickness
do
for ((SD=$StDepthMin;SD<=$StDepthMax;SD+=$StDepthInc)) #Station depth
do
echo "cd $runName/Atten_Up$L/AntennaRadius$AR/IceThick$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 "cond0092") #change username here
echo '__________Current Running Jobs__________'
echo "$jobs"
echo ''
runningJobs=$(showq | grep "cond0092" | wc -l) #change username here
echo Number of Running Jobs = $runningJobs
echo Number of jobs left = $numbLeft
if [ $runningJobs -le 20 ];then
line=$(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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------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
***Summary/Instructions for colorplot.sh (followed by same for colorplot_loop.sh)
------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
colorplot
------------------------------------------------------------------------------------------------------------
______ __ __ __
/ ___/ _____ | | _____ __ ___ __ ___ | | _____ | |__
| / / _ \| |/ _ \| `__/| `_ \| |/ _ \| _/
| \____| (_) | | (_) | | | |_) | | (_) | |__
\______|\_____/|__|\_____/|__| | .___/|__|\_____/ \____\
|__|
------------------------------------------------------------------------------------------------------------
Interactive script - to be run after parameter space scan has been performed. Produces a single plot.
Will plot, for a user-selected ShelfMC scan, the effective volume versus any two variables of the user's
choice out of the 5 parameters we vary:
attenuation length, antenna radius, ice thickness, firn depth, and station depth
Also will allow user to choose what values to hold the other 3 variables constant at
Will add together necessary files, create root script for plotting, and execute root script
------------------------------------------------------------------------------------------------------------
***To use colorplot.sh:
- On line 6 of colorplot.sh, set $shelfmc to your ShelfMC directory. This directory should hold the
parameter space scan directory, and a directory called "outputs". The "outputs" directory may be empty.
- In the variable lines, on line23, line27, and line30, change 20 to the number of processors your ShelfMC runs were
split across ($ppn in setup.sh)
- Ensure that the parameter values on lines 8-26 match those for the run you wish to plot
Make sure colorplot.sh has execute permission - if not, type 'chmod u+x colorplot.sh'
Run the script by typing './colorplot.sh'
The following instructions will also be provided in the execution of the script.
- Enter the name of the run as prompted
- Make your selections for the two variables to plot along the X- and Y- axes. Your options are:
A - Attenuation Length
R - Antenna Radius
I - Ice Thickness
F - Firn Thickness
S - Station Depth
*****Please only use capital letters in your selection
- Select values at which to hold the remaining parameters constant. Please select only the numbers allowed
as prompted.
- Your plot will be in the $shelfmc/outputs/[name of scan]_[x variable]_[y variable] directory
If you wish to keep the root file and/or the plotting script, comment out line 488 and/or line 489
accordingly in colorplot.sh
------------------------------------------------------------------------------------------------------------
colorplot_loop
------------------------------------------------------------------------------------------------------------
______ __ __ __ __
/ ___/ _____ | | _____ __ ___ __ ___ | | _____ | |__ | | _____ _____ __ ___
| / / _ \| |/ _ \| `__/| `_ \| |/ _ \| _/ | |/ _ \ / _ \| `_ \
| \____| (_) | | (_) | | | |_) | | (_) | |__ | | (_) | (_) | |_) |
\______|\_____/|__|\_____/|__| | .___/|__|\_____/ \____\ ______ |__|\_____/ \_____/| .___/
|__| |__|
------------------------------------------------------------------------------------------------------------
A more flexible extension of colorplot!
Interactive script to be run after the parameter space scan has been performed. Produces multiple plots.
Like colorplot.sh, colorplot_loop.sh will prompt the user for two variables against which to plot the
effective volume, from the options:
attenuation length, antenna radius, ice thickness, firn depth, and station depth
Unlike colorplot.sh, colorplot_loop.sh does not prompt for constant values of the remaining three variables,
but instead loops over all combinations of constants to produce many plots with the selected X- and Y- axes
Before using this script, please ensure that you have space for hundreds of thousands of files (some
clusters may have a file limit for each user - for instance, Ruby has a 1 million file limit per user).
The script will delete all files except the .pdf plots, but prior to this deletion there could be a few
hundred thousand new files in your system.
------------------------------------------------------------------------------------------------------------
***To use colorplot_loop.sh:
- On line 6 of colorplot.sh, set $shelfmc to your ShelfMC directory. This directory should hold the
parameter space scan directory, and a directory called "outputs". The "outputs" directory may be empty.
- Ensure that lines 8-26 match lines 15-33 of setup.sh and scheduler.sh for the desired parameter space scan
- On lines 50, 54, and 57, change 20 to the number of processors your ShelfMC runs were
split across ($ppn in setup.sh)
Make sure colorplot_loop.sh has execute permission - if not, type 'chmod u+x colorplot_loop.sh'
OPTIONAL: Since colorplot_loop can take several minutes to run, it may be desirable to do $screen prior to
executing the script, in case the connection to the host is interrupted.
Run the script by typing ./colorplot_loop.sh
The following instructions will also be provided in the execution of the script.
- Enter the name of the run as prompted
- Make your selections for the two variables to plot along the X- and Y- axes. Your options are:
A - Attenuation Length
R - Antenna Radius
I - Ice Thickness
F - Firn Thickness
S - Station Depth
*****Please only use capital letters in your selection
- Your plots will be in the $shelfmc/outputs/[name of scan]_[x variable]_[y variable] directory
If you wish to keep the collected root files and/or plotting scripts, comment out line 1034
and/or line 1035 accordingly in colorplot_loop.sh
------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
__ -- __
_-` --_
/ ___\
/ -```-`` \
/ / /..\ -_
| | \``/ --__
| \ - ____
| |_-``--___ o | --_
| ``--____``--__ | \
\ -`` ``--__`-- \ |
\ ``-_ \ \ |
\ `_ --___ \ /
| \. |/
-_ | \
-_/ \
\
)
)
)
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/
/
/
/
-`
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