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GENETIS
GENETIS
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Entry time:
Tue Feb 3 15:12:06 2026
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<p>Attendance: Julie, Mitchell, Ryan, Evelyn, Eliot, Alex M.</p> <h2><u>Today's Tasks</u></h2> <p><strong>Julie:</strong> Worked on C++ project, and helping others with the Python project; I also made additions, clarifications, and edits to the Bash project (also updated the solutions and pushed them to gitHub). I still need to do the following:</p> <ul> <li>Add the instructions from the google doc to the GitHub pages for both the Python and the Bash projects.</li> <li>Work on the C++ project!</li> <li>Run a test evolution this weekend to make sure AraSim stuff is fixed and that XF job submissions work. </li> <li>EVOLVE</li> </ul> <p><strong>Mitchell: </strong>Started Python Project.</p> <p><strong>Evelyn, Eliot, Ryan:</strong> Work through my bash project. </p> <p><strong>Leo:</strong> Worked on lectures. </p> <p><strong>Alex M:</strong> Helped make XF job scripts. Needs to do the following:</p> <ul> <li>Parallelize the AraActualBicone properly. </li> <li>EVOLVE!</li> </ul> <p><strong>Alex P:</strong> Needs to do the following:</p> <ul> <li>Do a test run to see if the scaling (when we also scale the grid spacing) actually affects the run time for XF.</li> </ul> <p> </p> <p> </p> <h2><strong><u>TO-DO List</u></strong></h2> <ol> <li><u>Scaling test run:</u> Do a test run to see if the scaling (when we also scale the grid spacing) actually affects the run time for XF. <span style="background-color:#FFFF00">(ALEX P)</span></li> <li><u>Evolve</u>: Right now, we are using an interactive job with only a CPU running at half scale, and have just edited our software so that we submit jobs for the XF simulations requesting 1GPU (could be 2GPU if we choose to edit it so). <ol> <li>WHY WE ARE DOING THIS: <ol> <li>Remember that we only need an interactive job when XF initializes and reads in the DNA for each individual. The GUI closes once the simulations start and we no longer need an interactive job. </li> <li>We were requesting a 1GPU interactive job and just running XF from the command line; however, OSC has been SUPER busy lately and we haven't been getting them (especially since we need long wall times if we are running the full simulations over many generations within the interactive job). However, we realized that if we submit an interactive job at a CPU (so that XF can allow the GUI to pop up), and then run the simulations by requesting 1-2GPUs we can then request a much smaller wall time and it will be quicker for the simulations to run --- ie we would be requesting a wall time of about 10 minutes using 1-2GPUs per simulation for each job submission versus 5+ hour wall time of an interactive job using 1-2GPUs.</li> <li><strong>WE HAVE NOT TESTED OUR .SH JOB SUBMISSION SCRIPTS!<span style="background-color:#FFFF00"> JULIE </span>WILL DO IT THIS WEEKEND!</strong></li> </ol> </li> </ol> </li> <li> <p dir="ltr"><u>Parallelize the AraActualBicone job.</u></p> <ol> <li> <p dir="ltr">The AraSim run in Gen 0 that gets Veff for the ARA actual bicone input file is not currently being parallelized. <span style="background-color:#FFFF00">(ALEX M)</span></p> </li> </ol> </li> <li> <p dir="ltr"><u>Comment code thoroughly <span style="background-color:#FFFF00">(Everyone needs to help with this)</span></u></p> </li> <li> <p dir="ltr"><u>Get new proposal results for March 12th deadline.</u></p> </li> </ol>
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