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GENETIS
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Tue Feb 3 18:01:40 2026
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<p> <table width="98%" align="center" cellspacing="1" style="border:1px solid #486090;"> <tbody> <tr> <td cellpadding="3px" style="background-color:#486090; font-weidht:bold; color:white;">Quote:</td></tr> <tr> <td cellpadding="10px" style="background-color:#FFFFB0;"><p><em>Attendance for today's session: Cade, Julie, Alex M, Mitchell, Scott. </em></p> <p> </p> <p><span style="font-size:16px"><u><strong>Tasks worked on:</strong></u></span></p> <ul> <li><strong>Continue to fix continuity of loop: Cade and Julie worked on fixing the following errors:</strong> <ol> <li>In section D of the loop, it currently <ul> <li>Moves the output from the python conversion to $AraSimExec directory. </li> <li>Renames it as a .txt file (note the $i is renaming each in line with $NPOP). </li> </ul> </li> </ol> </li> </ul> <blockquote> <p>for i in `seq 1 $NPOP`</p> <p>do</p> <p> mv evol_antenna_model_$i.dat $AraSimExec</p> <p>done</p> <p>for i in `seq 1 $NPOP`</p> <p>do</p> <p> cp evol_antenna_model_$i.dat a_$i.txt</p> <p>done</p> </blockquote> <p>However, this wasn't working and it was only properly renaming individual 1. To check this,</p> <ul> <li>We confirmed it is properly iterating the first loop by using the "echo" command. The second loop was not properly iterating, however.</li> <li>We were able to fix it by combining these steps. This was confirmed to have worked. </li> </ul> <blockquote> <p>for i in `seq 1 $NPOP`</p> <p>do</p> <p> mv evol_antenna_model_$i.dat $AraSimExec/a_$i.txt</p> <p>done</p> </blockquote> <p> 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. </p> <p> </p> <ul> <li><strong>Clean bash script</strong> <ul> <li>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). <ul> <li>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. <ul> <li>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. <ul> <li>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. </li> </ul> </li> </ul> </li> <li>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. </li> </ul> </li> </ul> </li> </ul> <p> </p> <p>Quick note from Julie:</p> <p>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. </p> <p> </p> <blockquote> <p><span style="font-size:11px">Roulette algorithm initialized.</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 136: output.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 137: output.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 138: output.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 139: output.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 140: output.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 146: simulation_PEC.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 147: simulation_PEC.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 149: simulation_PEC.xmacro: Permission denied</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 158: simulation_PEC.xmacro: Permission denied</span></p> <p> </p> <p><span style="font-size:11px">Opening XF user interface...</span></p> <p><span style="font-size:11px">*** Please remember to save the project with the same name as RunName! ***</span></p> <p> </p> <p><span style="font-size:11px">1. Import and run simulation_PEC.xmacro</span></p> <p><span style="font-size:11px">2. Import and run output.xmacro</span></p> <p><span style="font-size:11px">3. Close XF</span></p> <p><span style="font-size:11px"><strong>Lmod has detected the following error: </strong> The following module(s) are unknown: "xfdtd"</span></p> <p> </p> <p><span style="font-size:11px">Please check the spelling or version number. Also try "module spider ..."</span></p> <p><span style="font-size:11px">It is also possible your cache file is out-of-date; it may help to try:</span></p> <p><span style="font-size:11px"> $ module --ignore-cache load "xfdtd"</span></p> <p><span style="font-size:11px">Also make sure that all modulefiles written in TCL start with the string #%Module</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 172: xfdtd: command not found</span></p> <p><span style="font-size:11px">./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</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 178: xfsolver: command not found</span></p> <p><span style="font-size:11px">./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</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 178: xfsolver: command not found</span></p> <p><span style="font-size:11px">./XF_Loop.sh: line 183: xfdtd: command not found</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/AraSimTestJob.sh’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Antenna_Performance_Metric/AraOut_%num%.txt’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of 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style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Antenna_Performance_Metric/AraOut_%num%.txt’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Loop_Functions/XF_Loop3.sh’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Loop_Functions/#Part_C.sh#’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Loop_Functions/#Part_A.sh#’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing 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‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957217’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957222’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957226’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957221’: Operation not permitted</span></p> <p><span style="font-size:11px">Resuming...</span></p> <p><span style="font-size:11px">NOTE: You may want to change the following in your job for Owens</span></p> <p> </p> <p><span style="font-size:11px"> nodes=1:ppn=1 defaulting to mem=4571MB</span></p> <p> </p> <p><span style="font-size:11px">Please review the Owens documentation:</span></p> <p><span style="font-size:11px"> https://www.osc.edu/supercomputing/computing/owens</span></p> <p> </p> <p><span style="font-size:11px">Feel free to contact oschelp@osc.edu if you have any questions.</span></p> <p> </p> <p><span style="font-size:11px">8485416.owens-batch.ten.osc.edu</span></p> <p><span style="font-size:11px">rm: cannot remove ‘outputs/*.root’: No such file or directory</span></p> <p><span style="font-size:11px">NOTE: You may want to change the following in your job for Owens</span></p> <p> </p> <p><span style="font-size:11px"> nodes=1:ppn=1 defaulting to mem=4571MB</span></p> <p> </p> <p><span style="font-size:11px">Please review the Owens documentation:</span></p> <p><span style="font-size:11px"> https://www.osc.edu/supercomputing/computing/owens</span></p> <p> </p> <p><span style="font-size:11px">Feel free to contact oschelp@osc.edu if you have any questions.</span></p> <p> </p> <p><span style="font-size:11px">8485417.owens-batch.ten.osc.edu</span></p> <p><span style="font-size:11px">rm: cannot remove ‘outputs/*.root’: No such file or directory</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/AraSimTestJob.sh’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Antenna_Performance_Metric/AraOut_%num%.txt’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Loop_Functions/XF_Loop3.sh’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Loop_Functions/#Part_C.sh#’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Loop_Functions/#Part_A.sh#’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957233’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957230’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957234’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957224’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957220’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957220’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957234’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957227’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957233’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957218’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957224’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957231’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957226’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957221’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957223’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957217’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957227’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957218’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957223’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957225’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957230’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957225’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957222’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957231’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957217’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957222’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.o957226’: Operation not permitted</span></p> <p><span style="font-size:11px">chmod: changing permissions of ‘/fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/scriptEOFiles/AraSimCall.sh.e957221’: Operation not permitted</span></p> <p><span style="font-size:11px">mv: cannot stat ‘*.root’: No such file or directory</span></p> <p><span style="font-size:11px">Fitness function initialized.</span></p> <p><span style="font-size:11px">0 </span></p> <p><span style="font-size:11px">Data successfully read. Data successfully written.</span></p> </blockquote></td> </tr> </tbody> </table> </p><p> </p>
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