 Mon Jul 27 16:52:20 2020, Alex M, Daily Update 7/27/20
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Name
Update
Plans for Tomorrow
Aelx
M
Leo, Julie, and I merged the two dev branches (Antenna_Database and asymBicone) onto master. I think I resolved all of the conflicts
and successfully merged. I'm going to start testing by running each setting (original, database, and asymmetric) through generation 1 to make sure |
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Thu Jul 30 15:36:54 2020, Alex M, Daily Update 7/30/20
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Name
Update
Plans for Tomorrow
Alex
M
Tested the database setting for the symmetric loop. It ran well and gave correct results, so all that's left to test is the
asymmetric loop (going to start that momentarily). |
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Mon Aug 3 16:39:56 2020, Alex M, Daily Update 8/3/20
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Name
Update
Plans for Tomorrow
Alex
M
I fixed the issues I outlined a little while ago that we needed to resolve before starting a real run. I started a real run with 10 individuals
for up to 20 generations using the database for a symmetric bicone. The name of the run is Machtay_20200803_Master_Symmetric_Database_Real (whew!). Right |
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Tue Aug 4 17:30:09 2020, Alex M, Daily Update 8/4/20
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Name
Update
Plans for tomorrow
Alex
M
I've continued the run I started yesterday. I ran into a bug where the LRT plots weren't being made but it should be fixed now.
The loop is on generation 10, but it hasn't really converged or shown a clear pattern. We'll keep this run going until at least gen 15 probably.
If |
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Wed Aug 5 16:08:40 2020, Alex M, Daily Update 8/5/20
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Name
Update
Plans for Tomorrow
Alex
M
Continued running the loop up to gen 15. I also adjusted the LRTPlot script so that it can slightly spread the points along the
generation axis so that you can see overlapping points, but I still need to implement this in the loop. |
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Fri Aug 7 14:16:01 2020, Alex M, Daily Update 8/7/20
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Name
Update
Plans for Monday
Alex
M
Alex P |
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Mon Aug 10 16:12:28 2020, Alex M, Daily Update 8/10/20
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Name
Update
Plans for Tomorrow
Alex
M
Over the weekend I tried making some fixes we discussed. I fixed the roulette algorithm (the symmetric version) so that the random number
generator is only set once and then passed to functions. It will now print the values in the generator to files to be plotted. I tried running the loop |
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Tue Aug 11 19:56:45 2020, Alex M, Daily Update
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Name
Update
Plans for tomorrow
Alex
M
I worked on fixing the AraSim issue today. I think I have it resolved. Essentially, I made a second set of flags that the loop will
look for and use the first set of flags to tell the loop which error files to look at to look for the phrase "segmentation fault." If it sees |
Fri Aug 28 16:31:56 2020, Alex M, First Results Slides 
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Here's a power point I showed today at the GENETIS meeting for the two most recent runs we did. The first run was symmetric and we ended it at 15
generations. The second one is ongoing and is shown up through generation 9 on the power point. |
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Mon Aug 31 18:32:21 2020, Alex M, Daily Update 8/31/20
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Name
Update
Plans for tomorrow
Alex
M
I started working on the slides for our meeting with Wolfgang this Friday. I'll share it via one drive/email/slack tomorrow
for comments from everyone. |
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Wed Sep 9 17:28:54 2020, Alex M, Update 9/9/20
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Name
Update
Plans for tomorrow
Alex
M
I've been working on readying the loop for the transition to slurm. OSC is switching from its current job managing software
(torque/moab) to slurm, which uses some different commands but is functionally similar. Since we have places where jobs are called in the script, I've |
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Mon Sep 14 17:23:26 2020, Alex M, GENETIS Update 9/14/20
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I just wanted to give an update on what I've been doing today for GENETIS. I went ahead and recorded myself running the loop. It should be useful
for new people we're onboarding but I also went through a whole generation, which I think is interesting for everyone to understand the timescale of
each part of the loop. I'm making a small edit (I have no clue how to edit videos haha) so once I'm done I'll try to send it via email and |
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Fri Nov 20 17:50:05 2020, Alex M, Working Meeting 11/20/20
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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: |
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Wed Dec 2 15:24:39 2020, Alex M, Guide for Loop Errors
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Attached is a .txt file you can find in the Evolutionary_Loop directory as Loop_Error_List.txt. It's a list of the current errors we sometimes experience
in the loop, along with how to fix them if you encounter them while running. If people encounter errors that aren't in the list, let everyone know
in the #genstudents chat on slack and update the file with the error message and when it was encountered (what state the loop was in) and the possible |
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Mon Dec 7 22:51:08 2020, Alex M, Important Runs
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Today I removed some of the run directories which had very little or no data or weren't worth keeping around. There are still a few that I think
can be removed, but I'm keeping them until we can get a consensus that they can definitely be removed. Below I listed the names and descriptions of
the runs that I think we should definitely preserve going forward. In general, the more data contained in the run directory, the more important it is to |
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Tue Jan 19 19:00:30 2021, Alex M, Latest Run Details/Running on Slurm
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OSC managed to figure out our issue with running XF from an interactive job on Slurm. Previously, we were losing our connection to x11 forwarding. The
solution is to use sinteractive instead of srun to obtain an interactive job. Here's the syntax:
sinteractive -A PAS0654 -t <time> -N 1 -n 8 -p serial |
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Fri Jan 29 15:59:21 2021, Alex M, Loop Demonstration Video
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Here's the video I made a few months ago demonstrating how to run the loop. There might be some changes that have been made since then, but they'll
generally be minor so it should still be representative of what running the loop looks like. It might need to be shared with you through the Microsoft
drive service OSU gives us in order to view it, so either message me on Slack or email me at machtay.1@osu.edu and I'll share the link through there. |
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Thu Mar 11 15:41:52 2021, Alex M, Running The Loop Updated
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Because of issues we were having with XF when running at the command line, we've shifted to running through a Pitzer VDI (see here: https://ondemand.osc.edu/pun/sys/dashboard/batch_connect/sys/bc_desktop/vdi/session_contexts/new).
The VDI will give you a mirror of a desktop running on OSC's side, so things like XF will run much faster. You can open a terminal by clicking
the black box at the bottom of the screen and then run the loop like normal (./Asym_XF_Loop.sh). This has the added benefit of making it possible to exit |
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Mon Mar 15 13:05:22 2021, Alex M, Current Run
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We are currently running the loop using the improved parameters. The parameters are as follows:
50 individuals
80/20 Roulette/Tournament
6% Reproduction, 72% Crossover, 22% Mutation
Also note that individual 5 of generation
1 had its fitness score altered because one of its AraSim jobs didn't finish in time (and we would have had to wait 5 hours for it to rerun). |
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Fri Mar 19 17:39:47 2021, Alex M, New Run
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We began a new run using the same parameters as the previous one (see the last ELOG entry). The previous one ran for 8 generations. The difference between
this run and the last one is that we have added in the polarity fix for AraSim Brian and Jorge gave us (copying the correct Report.cc and Report.h files
into our AraSim version). Here are the run parameters: |