ELOG GENETIS

Currently XF doesn't output all the information we need to create all these files. The only files able to be made from current XF outputs are vv_0, vv_el, and vv_az. Once we have the correct XF Outputs, it shouldn't be too much of a hassle to fix the current translation code.

Format for each of the files are the same. One column is Frequency (Hz) and the other is Gain. Attached are example files vv_0 and vv_el to visually see the format, though the frequency range is the current ARA range and not the final PUEO range as I am using ARA data to make these files. The files are named vv_0 (no .txt or .csv or any extension) and vv_el

Link to Google Doc with this information: https://docs.google.com/document/d/1iRUF6hIEyQfMK0LL21caRuHPgXYP30ZdkSkFv_-Y8R0/edit

Attachment 1: vv_0_1

8.33e+07 2.11822 
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Attachment 2: vv_el_1

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... 61 more lines ...

220

Thu May 25 15:36:54 2023

Ryan Debolt, Byran Reynolds

preliminary error tests (PUEO)

Here are some preliminary results from testing the effect of error on growth in the GA. For this test, we start with a simulated error of 0.5 because our true fitness score is bounded between 0.0 and 1.0. From here, we simulate doubling the number of neutrinos by reducing the error by root(2), then root(4), and observed the growth on the fitness scores plots. We did these three tests with both 50 and 100 individuals (plots starting with 30 use 50 and starting with 60 use 100). Looking at the plots, we can see that the only plot that shows growth is 100 individuals with halved error (corresponding to 4 times the number of neutrinos). In fact, it took going to root(25) (corresponding to 25 times the number of neutrinos) to observe comparable growth with 50 individuals. This leads us to believe we likely need to increase both neutrinos and individuals to see meaningful growth in our GA. Further tests are required to see how consistent these results are. Another test, though unrealistic, we ran 1000 individuals with the root(25), this test was optimized in around 10 generations, this could be seen as a maximum performance standard.

Attachment 1: 30_10_10_0_48_25_6_2_half_error_fitness.png

Attachment 2: 30_10_10_0_48_25_6_2_high_error_fitness.png

Attachment 3: 30_10_10_0_48_25_6_2_root2_error_fitness.png

Attachment 4: 30_10_10_0_48_25_6_2_root8_error_fitness.png

Attachment 5: 30_10_10_0_48_25_6_2_root25_error_fitness.png

Attachment 6: 60_20_20_0_96_25_6_1_half_error_fitness.png

Attachment 7: 60_20_20_0_96_25_6_1_high_error_fitness.png

Attachment 8: 60_20_20_0_96_25_6_1_root2_error_fitness.png

203

Mon Mar 20 13:35:25 2023

Amy

info on format for PUEO antenna files

William Luszczak 1:30 PM

This is the directory with the current PUEO antenna data files: https://github.com/PUEOCollaboration/pueoSim/tree/main/data/antennas. Each type of antenna will need several files:

vv_0 and hh_0 describe the on axis v and h pol gain as a function of frequency. Gain is listed as a multiplicative factor (not in dB, if I'm remembering correctly)
hv_0 and vh_0 describe the on axis cross polarization gain
vv_az and hh_az describe the off-axis gain via multiplicative factors of the boresight gain. These are currently listed as a function of frequency for reference angles of 0,10,20,30,40,50,60,70,80, and 90 degrees, though we can always adjust the reference angles if needed.
vv_el and hh_el are similar to above, but for gain as a function of elevation angle instead of azimuthal angle.

So for example, the total vpol gain in a particular frequency bin for a signal incident at azimuthal angle az and elevation angle el would be vv_0(f)*vv_az(f, az)*vv_el(f, el)

New

1:31

We can also potentially adjust this if it would be more convenient for the GENETIS people to output antenna information in a different format (or at different reference angles or whatever). The important thing is that the boresight h, v, and cross pol gains are all defined, as well as the off-axis response (as a function of azimuth and elevation)

231

Wed Jul 12 21:30:56 2023

Alex Machtay

Zoom training on XF 07/12/23

Recording of training on XFdtd by Alex Machtay on July 12, 2023.

https://osu.zoom.us/rec/share/FVKiTcQrRh8NLNYJADwugy0H2VjDo8ZlBsH16sJAGv2JINNwxxzyNfo5ueqVgOTO._XErF57Kz8KOM3a5

This link will expire in 120 days so note that we need to post a permanent recording.

Here's the GitHub repository with examples of Xmacros: https://github.com/Machtay/XFdtd_Scripts

149

Fri Mar 25 17:32:25 2022

Alex M

XFdtd Step Size Investigation

The reviewer for the paper we recently submitted mentioned that our step sizes at which we are measuring the gain in XFdtd may be too large. They pointed out that there appear to be "lobes" at 400 MHz. I ran the antenna we presented in the paper through XFdtd using a step size of 5 degrees (what we've been doing) and a step size of 1 degree (the reveiwer's recommendation). Attached are antenna responses for these two different step sizes at 200 MHz and 400 MHz. Qualitatively, there are noticeable differences in the "jaggedness" of the 400 MHz plot and how extreme the minima and maxima appear, but the basic shape is preserved. We can try to do a more quantitative analysis (ex: run these through AraSim), but doing so may be more time intensive than necessary considering that AraSim may require 5 degree steps and that adding these images to an appendix may be sufficient anyway.

Attachment 1: polar_plot_400.06_step_5.png

Attachment 2: polar_plot_400.06_step_1.png

Attachment 3: polar_plot_200.02_step_5.png

Attachment 4: polar_plot_200.02_step_1.png

Fri May 17 15:13:50 2019

Julie Rolla

XF key flash drive holders

We have 2 physical XF flash drive keys in existence. These are non-replaceable and cannot be lost! Until further notice, the keys are held by:

(1) Cade Sbrocco (sbrocco.6@buckeyemail.osu.edu )

and

(2) Abasi Brown (brown.7146@buckeyemail.osu.edu)

162

Wed Jun 8 14:45:52 2022

Alan S

XF Simulations | ARA bicone in ice | PowerPoint Slides

Beam patterns with ARA bicone contained in a cylinder of air surrounded by a shell of ice.

Attachment 1: XF_ARA_bicone_in_ice_and_air_column.pptx

235

Wed Aug 2 00:17:32 2023

Jacob Weiler

XF Antenna Drawing Progress 08/02/2023

I've been building in XF and have ran into some issues but currently have the following completed:

- Struts are placed, though they are not evenly spaced and the same. I have contacted XF to try and figure out how to get rotation/patterns to do what we need

- Circuit components and circuit board are in the xf file, though the components are not on the circuit board (I'm not totally sure how to put them on, that's the next step). The circuit components should be of spec, I looked up the part numbers from the previous ELOG post and grabbed the values from the manufacturer.

Here are the things that have not been completed/need answered:

- How to evenly space the struts connecting the shape (as stated previously, I've contacted XF to figure out how to do this easily. Im just bad at modeling in XF)

- Add circuit components to circuit board

- Add voltage and ground connections to the circuit board

- On the circuit diagram, figure out J1 and J2 connections. Meaning, which one connects to the signal from the cable and which connects to the other cone that is used as ground?

To see current antenna build go to: " /users/PAS1977/jacobweiler/GENETIS/XFzone/straightened_antenna_for_Jack.xf "

Attached are pictures in case there are issues pulling up model in XF. :)

Attachment 1: sidepic.PNG

Attachment 2: circuitboardplacement.PNG

Attachment 3: fullpic.PNG

Attachment 4: struts.PNG

Draft

Tue Mar 24 15:38:50 2020

Julie Rolla

X11 Forwarding Issue for Windows

Most of our students

(1)Ubuntu doesn't come with X11 forwarding on its own. So you can install Xlaunch

xeyes -display :0

Tue Dec 3 15:26:42 2019

Julie Rolla

Working session 12/3/19

Attendance: Julie, Alex M., Alex P., Cade, Scott.

What we have done today:
(1) Fixed Concerns regarding copying the output .uan files properly so they are not overwritten. (see #8 in this elog entry: http://radiorm.physics.ohio-state.edu/elog/GENETIS/22 for details on the error). This was corrected in part E as:

for i in `seq 1 $NPOP`

do

for freq in `seq 1 60`

do

#Remove if plotting software doesnt need

#cp data/$i.uan ${i}uan.csv

cp Antenna_Performance_Metric/${i}_${freq}.uan "$WorkingDir"/Run_Outputs/$RunName/0_${i}_${freq).uan

done

done

And in the "looping part" -- ie part G we have corrected it to say the following. Note that every time we run an iteration/generation in the loop, it writes the name of the output files the exact same (individual_frequencystep.uan). It will overwrite these files in the next generation unless we move them and rename them like so. We don't want this, because we will likely want to plot the gain patterns of the individuals we like (gain pattern data is in the .uan files).

for i in `seq 1 $NPOP`

do

for freq in `seq 1 60`

do

# Gens data used to create a .csv file for the uan file for gain plotting

# cp Antenna_Performance_Metric/$i.uan ${i}uan.csv

cp Antenna_Performance_Metric/${i}_${freq}.uan "$WorkingDir"/Run_Outputs/$RunName/${gen}_${i}_${freq}.uan

done

done

(2) Added scale factor "A" (actually called "Scale Factor" in our bash script and fitnessFunction_ARA.cpp), and the generationDNA.csv as an input file (this file is where the radii of all individuals in the current generation live).

We have added this as a variable in the fitnessFunction_ARA.cpp. It now runs as a flag pass in when it runs in the bash script. In section E:

./fitnessFunction.exe $NPOP $ScaleFactor $AntennaRadii/generationDNA.csv $InputFiles #Here's where we add the flags for the generation

and in the looping part (part G):

./fitnessFunction.exe $NPOP $ScaleFactor $AntennaRadii/generationDNA.csv $InputFiles #Here's where we add the flags for the generation

and at the top where variables are declared:

RunName='Julie_12_2_2' ## Replace when needed

TotalGens=6 ## number of generations (after initial) to run through

NPOP=4 ## number of individuals per generation; please keep this value below 99

FREQ=60 ## frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)

NNT=10000 ##Number of Neutrinos Thrown in AraSim

ScaleFactor=1.0 ##ScaleFactor used when punishing fitness scores of antennae larger than holes used in fitnessFunctoin_ARA.cpp

Note that every time the roulette algorithm runs, it's written into generationDNA.csv. We copy those right before rerunning the roulette alg in the next generation -- ie cp generationDNA.csv Run_Outputs/$RunName/${gen}_generationDNA.csv -- so that each generations parameters don't get overwritten. However, the current generation's parameters live in generationDNA.csv until the roulette alg runs in the next generation, so we can read in that file to the fitnessFunction_ARA.cpp file to determine the constraint (ie R_antenna)

(4) Implemented Alex P.'s version of his optimized AraSim. This is now fully functional in the loop.

NOTE: WE HAVE MADE A MISTAKE! WE MADE THE CONSTRAINT THE R-VALUE WE READ IN FROM THE GENERATIONDNA.CSV FILE. THIS IS NOT THE RADIUS WE THINK IT IS! WE NEED TO DO SOME TRIG ON IT TO FIX IT!!

Tue Dec 3 01:26:52 2019

Julie Rolla

Working session 12/2/19

Attendance: Julie, Alex P., Cade, Alex M., Mitchell, Evelyn (Go team!)

I. Adding Constraints on the in-ice hole size.

Today we worked on adding constraints on the drilled hole size. Our plan is to do so by penalizing the fitness scores of indiviuals with a radius larger than that of the hole in the ice. Ie in fitnessFunction_ara.cpp we would have:

if R_antenna>=R _hole

fitnessScore =fitnessScore x (e^{-[A(R_antenna-R_hole)/R_hole)]^2})

else

fitnessScore= veff (or whatever way we decide to calculate the fitness score in the future, if this ever changed)

Where "A" is a constant we can adjust to tweak how heavy the penalty is. Other things to do in order to make this work:

(1) Make constant "A" a variable in the bash script.

Do this the same way $NPOP is used in the roulette algorithm cpp program! :)

(2)Read in the roulette algorithm output file for your radius of the antenna.

Note that this isn't a super obvious thing. Right now our roulette alg outputs are saved as $(generation)_filename.csv. So, for the first gen -- ie gen 0-- it will be 0_filename.csv. For the second gen -- ie gen 1-- it will be 1_filename.csv...etc. This means we need to make sure the fitness score calculator has a way of knowing what generation we are on, in order to be sure it is grabbing the correct radius for each individual (not that of an old generation).

We will be working on this more in our meeting tomorrow. As for now, the game plan has been to make comments on what we should be adding in the correct sections of fitnessFunction_ara.cpp (and will be doing the same in the bash script shortly, too --ie XF_Loop.sh).

II. Adding Ara Values to Plot.

We haven't started this yet, but it is something we need to do. When we plot Veff vs Generation, Theta vs Generation, and R vs Generation we need to add in the value of these for the current ARA bicone as a baseline for our evolutions.

Note: All of the contents over the last month need to be added to the manual! DO NOT FORGET!

Draft

Tue Feb 25 17:10:36 2020

Alex Machtay & Alex Patton

Working Meeting 2/25/20

Today's Tasks

Mitchell, Evelyn, Eliot, Ryan: Work through the bash project; Mitchell is done, Ryan and Evelyn are close to being finished.

Leo: Worked on next presentation (not sure when he'll present--either Friday or next Tuesday).

Alex M: Continued commenting code and helped Alex P. with changes in Part_B and Roulette_algorithm .

Alex P: Fixed errors in loop, tested with an interactive job (using CPU). Errors look to be fixed up through part B. Arasim should be launching and using the $tmpdir, though we need to get further in the testing to see for sure.

Made a copy of the loop that functions without GPUs so that if GPU is unavailable some progress can be made even if it is slow.

While waiting for a GPU Alex P ran on CPUs, at half scale factor one indiviudal in XF took 32 minutes (although it was predicted to be over 2 hours).

To Do List:

We want to keep testing the loop. Right now, we are using a cpu running at half scale. This gives estimated times for each antenna of up to 2 hours. GPUs are suddenly hard to come by, so if we are relegated to using CPUs we'll probably need to scale down considerably.

Evelyn, Ryan, and Mitchell are probably going to be ready for the python project soon. If someone is around on Friday to help them they should be able to finish the bash project.

One idea is to run all the inital xmacros in the interactive job and then submit a GPU job that runs all the xfsolver command. With the hope that not having the GPU in the interactive job will make it easier to get the interactive job and to get the GPU for a shorter time because it would only be needed for a smaller segment. This would especially help with running larger amounts of individuals.

119

Fri Nov 20 17:50:05 2020

Alex M

Working Meeting 11/20/20

Alex M	We worked with Amy to track down the error we were getting with the AraSim fix. Alex P and I had gotten AraSim to compile, but running gave the error (at the bottom). We did a binary search for the source of the error and determined it comes from the if statement around line 640 in Report.cc: if ( event->Nu_Interaction[0].LQ > 0 && (fabs(viewangle-signal->CHANGLE_ICE)<=settings1->OFFCONE_LIMIT*RADDEG) ) {
Ryan	Kept testing different rations of tournament and roulette. A trend seems to appear that while full roulette was the worst run overall, it rises until a ratio of about 8R:2T with a max score of 99.22% match and then it slowly falls from that point. Need to do more testing to verify averages and to fix strange segmentation faults in crossover when running 6T and 8T ratio.

AraSim EField project Error:

*** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0 0x00002b845aeb445c in waitpid () from /lib64/libc.so.6
#1 0x00002b845ae31f52 in do_system () from /lib64/libc.so.6
#2 0x00002b84562bebf4 in TUnixSystem::StackTrace() () from /cvmfs/ara.opensciencegrid.org/trunk/centos7/root_build/lib/libCore.so
#3 0x00002b84562c13ea in TUnixSystem::DispatchSignals(ESignals) () from /cvmfs/ara.opensciencegrid.org/trunk/centos7/root_build/lib/libCore.so
#4 <signal handler called>
#5 0x000000000044fd70 in void std::vector<double, std::allocator<double> >::emplace_back<double>(double&&) ()
#6 0x00000000004c3c0e in Report::Connect_Interaction_Detector(Event*, Detector*, RaySolver*, Signal*, IceModel*, Settings*, Trigger*, int) ()
#7 0x0000000000436eb3 in main ()
===========================================================

The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum http://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at http://root.cern.ch/bugs Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5 0x000000000044fd70 in void std::vector<double, std::allocator<double> >::emplace_back<double>(double&&) ()
#6 0x00000000004c3c0e in Report::Connect_Interaction_Detector(Event*, Detector*, RaySolver*, Signal*, IceModel*, Settings*, Trigger*, int) ()
#7 0x0000000000436eb3 in main ()
===========================================================

Thu Jan 9 14:24:25 2020

Julie Rolla

Winter Break Updates and new to-do list (with deadlines)

The following items from our to-do list have been successfully completed. Below this list, you can find the remaining urgent items for our proposal due date of 1/28 (items must be completed with plenty of time to spare).

Completed items:

*Note* please check the highlighted item. This one still must be verified.

Made software plot Theta VS Gen
Fixed current L and R plots
1. These now have correct axis labels, a legend, and connect data for each individual between generations.
Produced Veff for ARA's actual bicone parameters.
1. Made XF_Loop.sh submit a job for the ARA gain AraSim input file in BiconeEvolutionOSC/AraSim/Ara_Bicone6in_outputs.txt
2. STILL MUST: Make sure that the "wait function" has been properly edited to consider the submission of this extra job in the first iteration of the loop. (Not sure if $NPOP+1 instead of $NPOP fixed it correctly) ----> CADE SHOULD LOOK AT THIS :)
Added plotting software for V_eff VS Generation (includes ARA's actual bicone V_eff as generated in #3).
Fixed the ARA hole constraint in fitnessFunction_ARA.cpp -- ie fixed the calculation to consider the correct radius "r". See http://radiorm.physics.ohio-state.edu/elog/GENETIS/28 for details.
Successfully made energy a variable in setup.txt.
1. used the same "sed" format as before in the bash script (XF_Loop.sh).
Pushed to Github.

Items to still do:

Save CAD models in XF: Due 1/15 ------>(Cade-- second most urgent one)
Stop plots from popping up during run: Due 1/15 ------>(Alex P.)
Add "save state" idea to loop: Due 1/15 ------> (Cade and maybe Alex P can help -- This is the most urgent one)
Figure out why fitnessFunction_ARA.cpp isn't plotting: Due 1/15 ------> (Julie, and Alex M)
Run the loop and evolve for results: Due 1/24 ------>(Alex M, Mitchell, Cade)
Write proposal: Final Due 1/28 ------> (Amy, Kai, Julie)

Note that the people running the loop (Alex M, Mitchell, Cade) should be producing plots and saving them. Please save all plots in this dropbox folder: https://www.dropbox.com/home/GP_Antennas/NSF%20Proposal%20Plots%20(1_28_2020)

When submitting plots, please make a new folder in there and label it "Date_of_run, Energy, Generations, Individuals". For example, my folder within this dropbox link would be: "1_10, 10^19, 10, 5". I have made sample folders in this dropbox link if needed.

You can export the plots from OSC to your machine (using CP command) or can type "display NameOfPlot.png" then screenshot and crop your plot to upload to dropbox.

Wed Nov 20 00:40:49 2019

Julie Rolla

Week 11/19/19 Update

Attendance for today's session: Cade, Julie, Alex M, Mitchell, Scott.

Tasks/to-do list:

Get loop to run up to the fitness function.
- Right now we have the bash script setup to run AraSim by submitting them as parallel jobs. Today Cade added the "wait" function within the job in order to make sure the loop doesn't continue to the next step before the Arasim data is ready. Cade will give us an update on Thursday letting us know whether or not this completed or gave an error.
Fix error at fitness function.
- Currently, the loop stops at the fitness function calculation, and aborts (program fitnessFunction_ARA.cpp). We are unsure of why at the moment. Here are the things we are looking into.
  - Run this outside of the loop-- ie compile the fitnessFunction_ARA.cpp (g++ -std=c++11 fitnessFunction_ARA.cpp -o fitnessFunction.exe), and run the executable(./fitnessFunction.exe). What happens?
    - Julie and Alex did this. It gave a segmentation fault. We need to look into this further.
    - We double-checked that this .exe was properly created from compiling, and it was.
  - Double-check our AraSim output by checking:
    - Format
    - File type
  - Is there an error past the fitness function, and it's killing the loop after this runs?
    - Is his output not properly going into the gen alg?
    - Are the output files properly:
      - Filled
      - Formatted
      - Put in the right place
  - Look at how it's calculating the fitness score.

Since it seems like Alex and I may have found a problem at our first "test", this could be the issue. We will investigate it further. If (1) Cade's "wait" function works, and (2) we can fix this issue with the loop stopping at the fitness score calculation, ideally this means that the loop is then running.

Today we also found that it is better to run on the terminal through an interactive job than a virtual desktop. This is MUCH faster -- ie we don't have to wait nearly as long as we do to get a node via a virtual desktop. This means that everyone with a PC needs to either (1) work out their issues with X11 forwarding crashing (Mitchell succeeded at this today by making sure Xquartz was set up to work via ssh to Pitzer in the settings), or (2) dual boot Linux. It seems that Mac users are not having issues, but that some of the Windows users are having their OS completely crash when XF GUI tries to forward. Users can test whether or not their X11 forwarding is working by doing the following:

Logging onto Pitzer
Typing "module load xfdtd"
Then typing "xfdtd"

This should successfully open the GUI for XF. If it crashes, users may have to do one of the things I mentioned above. Once we do succeed at having this setup, you can start an interactive job via the command:

qsub -I -X -l walltime=1:00:00 -l nodes=1:ppn=10

You then have to wait until the node is free. This has taken about 1/3 of the time to get than when requesting a virtual desktop. Note that, however, we may need a higher ppn (maybe something like 40). This is not totally clear yet.

Fri Nov 15 09:59:27 2019

Julie Rolla

Week 11/15/19 Update

Attendance for today's session: Cade, Julie, Alex M, Mitchell, Scott.

Tasks worked on:

Continue to fix continuity of loop: Cade and Julie worked on fixing the following errors:
1. In section D of the loop, it currently
  - Moves the output from the python conversion to $AraSimExec directory.
  - Renames it as a .txt file (note the $i is renaming each in line with $NPOP).

for i in `seq 1 $NPOP`

do

mv evol_antenna_model_$i.dat $AraSimExec

done

for i in `seq 1 $NPOP`

do

cp evol_antenna_model_$i.dat a_$i.txt

done

However, this wasn't working and it was only properly renaming individual 1. To check this,

We confirmed it is properly iterating the first loop by using the "echo" command. The second loop was not properly iterating, however.
We were able to fix it by combining these steps. This was confirmed to have worked.

for i in `seq 1 $NPOP`

do

mv evol_antenna_model_$i.dat $AraSimExec/a_$i.txt

done

2. We got this iteration $i to work in the job script -- ie as an input file variable. The loop now successfully submits AraSim as a job with the proper input files.

Clean bash script
- Mitchell and Alex M worked again today on turning every function possible into functions (and putting them in their own .sh scripts that are being called by XF_Loop.sh).
  - The loop runs the first generation "manually" -- ie each step was spelled out, and nothing is put into a loop. The second+ generations then run as a loop. This is because we need to initialize the first XF run -- which then has no problems in the later iterations.
    - Alex M. and Mitchell are now turning each section A-F into individual functions and put into their own .sh scripts. Thus section A would just be calling another .sh script. In gen 2+ we then loop over these SectionA.sh through SectionF.sh functions. All of these just got completed. He just needs to add the change Julie and Cade made today, and clean some things up.
      - For example, he has an "if else" statement that tells it whether or not it's the first (XF initializes) generation, or in generation 2+. Cade has a few changes he would like Alex to make to clean up this part of the run.
  - Idea: The loop used to run the first generation "manually" -- ie each step was spelled out, and nothing was put into a loop. The second+ generations then ran as a loop. Since we were able to get XF to import the xmacro scripts automatically -- as well as save the project with the correct name (matching the expected name initialize in the bash script)-- they've gotten rid of that first "manual" iteration, and are now fully running all generations as a loop. We haven't tested whether or not we can make this change yet, but it is worth looking into now that some changes have been successfully made with XF.

Quick note from Julie:

I tried to run from the terminal once Cade left. I get the following output/error that we should make sure isn't happening for other users (since most of this is a permissions issue that I thought we fixed. I can look into the other errors and see if anyone else gets them). For whatever reason, Cade is not having the same output errors; he is able to run the same copy just fine.

Roulette algorithm initialized.

./XF_Loop.sh: line 136: output.xmacro: Permission denied

./XF_Loop.sh: line 137: output.xmacro: Permission denied

./XF_Loop.sh: line 138: output.xmacro: Permission denied

./XF_Loop.sh: line 139: output.xmacro: Permission denied

./XF_Loop.sh: line 140: output.xmacro: Permission denied

./XF_Loop.sh: line 146: simulation_PEC.xmacro: Permission denied

./XF_Loop.sh: line 147: simulation_PEC.xmacro: Permission denied

./XF_Loop.sh: line 149: simulation_PEC.xmacro: Permission denied

./XF_Loop.sh: line 158: simulation_PEC.xmacro: Permission denied

Opening XF user interface...

*** Please remember to save the project with the same name as RunName! ***

1. Import and run simulation_PEC.xmacro

2. Import and run output.xmacro

3. Close XF

Lmod has detected the following error: The following module(s) are unknown: "xfdtd"

Please check the spelling or version number. Also try "module spider ..."

It is also possible your cache file is out-of-date; it may help to try:

$ module --ignore-cache load "xfdtd"

Also make sure that all modulefiles written in TCL start with the string #%Module

./XF_Loop.sh: line 172: xfdtd: command not found

./XF_Loop.sh: line 177: cd: /fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Run_Outputs/Julie/Julie.xf/Simulations/000001/Run0001/: No such file or directory

./XF_Loop.sh: line 178: xfsolver: command not found

./XF_Loop.sh: line 177: cd: /fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Run_Outputs/Julie/Julie.xf/Simulations/000002/Run0001/: No such file or directory

./XF_Loop.sh: line 178: xfsolver: command not found

./XF_Loop.sh: line 183: xfdtd: command not found

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Resuming...

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Resuming...

NOTE: You may want to change the following in your job for Owens

   nodes=1:ppn=1 defaulting to mem=4571MB

Please review the Owens documentation:

   https://www.osc.edu/supercomputing/computing/owens

Feel free to contact oschelp@osc.edu if you have any questions.

8485416.owens-batch.ten.osc.edu

rm: cannot remove ‘outputs/*.root’: No such file or directory

NOTE: You may want to change the following in your job for Owens

   nodes=1:ppn=1 defaulting to mem=4571MB

Please review the Owens documentation:

   https://www.osc.edu/supercomputing/computing/owens

Feel free to contact oschelp@osc.edu if you have any questions.

8485417.owens-batch.ten.osc.edu

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mv: cannot stat ‘*.root’: No such file or directory

Fitness function initialized.

0

Data successfully read. Data successfully written.

Tue Nov 12 15:45:33 2019

Julie Rolla

Week 11/12/19 Update

Attendance for today's session: Cade, Julie, Alex M, Alex P, Mitchell, Scott.

Monday was a holiday, and we will be replaceing that meeting later this week. Today we worked on the following tasks:

Tasks:

Check continuity of loop
- Alex M will try another run tonight, and has already requested a virtual desktop.
Install Arasim to /fs/projects/PAS0654/BiconeEvolutionOCS to be edited and messed with
- Cade is testing whether or not this is running within the loop. He had gotten a few errors, and it is not completing. It's submitting the job with the new bash script, but it is not actually running.
  - Found an error. The bash script was not grabbing the correct AraSim directory. More updates to come.
Clean bash script
- Mitchell and Alex M are putting all current functions hard-coded in into their own .sh scrips that are now being called in the main bash script.
Update Manual
- Cade and I are updating the manual with new changes. We have officially retired the old version of the manual that was used for runs with Nutau. We have saved that version and uploaded it to the elog here: http://radiorm.physics.ohio-state.edu/elog/GENETIS/17

Right now Elliot and Leo have decided to focus on working with Keith. They will not be contributing to this project for the remainder of the semester. Students have been posting individual updates here: https://www.dropbox.com/home/GP_Antennas/Updates

I've also attached the meeting minutes from the call last week, in order to keep track of updates.

Attachment 1: GENETIS_meeting_minutes_11_|_7.pdf

134

Wed Jul 14 15:45:30 2021

Ethan Fahimi

Wednesday Updates (7/14/2021)

Ethan	Worked with Alex on fixing a few bugs with AREA. We are trying to solve an issue where the individuals are not finishing runs (around one in every four gens with 100 individuals). We believe some individuals may be too good and are then taking more than the wall time we have given them. Alex is testing this while I am working on a script that will add all the weights in the temp_{ind}.txt files. (See weightAdder.py for more)

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