www.neuron.yale.edu

Everyone,

I'd like to introduce the software utility SimAgent, a community developed tool created to facilitate submission of jobs to NSG from your laptop. SimAgent directly interfaces your laptop with NSG resources to run NEURON-based network simulations, MATLAB scripts and python code. Tyler Banks, Neural Engineering Laboratory, Electrical Engineering & Computer Science, University of Missouri-Columbia, Columbia MO 65211. https://engineering.missouri.edu/academics/eecs/neuro/



Features

SimAgent has two core functions, automated job submission and parameter sweep. The automated job submission feature is a point and click interface that accepts any project directory, submits the project to run remotely and watches it until completion with live updates to the user. The parameter sweep feature allows the same functionality with the added ability to specify sections of code to automatically change with each run. You will be able to specify a range of values for a parameter to take on, run each simulation in a parallel configuration and determine the optimal output for your needs. It currently supports connections to the NSG-R restful API and connections using SSH to servers running Slurm. While sweep capabilities are possible in any programming language, SimAgent removes the need for complex parameter sweep loops and replaces them with an easy to use point and click interface requiring no coding.

Download and Instructions

If you are interested in learning more see the quickstart YouTube videos to get started.

Download at: https://tylerbanks.net/SimAgentMPI/

Informational Videos:
Part 1 (Installation): https://www.youtube.com/watch?v=ZaqqbNzprAY
Part 2 (Sample Model/Usage): https://www.youtube.com/watch?v=_AsOgrTj7TE

Help

SimAgent was originally developed by the Neural Engineering Lab at the University of Missouri as an internal tool but has since been released to the public as open source code.

Users with proprietary issues may contact the author directly at tbanks@mail.missouri.edu, but it would be best to post other questions to the SimAgent section here on the Neuron forum (viewforum.php?f=47).



Contributions to the project or bug reports can also be made via SimAgent's main GitHub page at https://github.com/tjbanks/SimAgentMPI

Thanks, Tyler very much,
I have used the tool, it did help increaseing my productivity instead of uploading and downloading the simulations files from the html portal one by one.

the tool is easy to use, and saved me a lot of time, thank you very much.

@Mohamed_Hisham

Of course! Thanks for your kind words. Please let me know if there are any additional features you'd like to see or if you run into any bugs.

Tyler

Thanks, Tyler very much.

Yes, one of the features that will make this tool my right hand is working offline, I mean my simulation takes usually more than one day to run, so usually I send the jobs to the NSG and let them work overnight, but using the SimAgent, I am not sure , should I keep SimAgent also running overnight, or I can turn it off and open it back the next day to follow up on the simulations

Thanks, Tyler very much for the nice work

@Mohamed_Hisham

Absolutely, SimAgent works offline. I regularly close the application while I wait for jobs to finish. Once you reopen SimAgent and re-select your project folder SimAgent should automatically reach back out to NSG for updates. Let me know if you run into any issues!

Tyler

tyler wrote: ↑Fri Nov 08, 2019 11:20 pm @Mohamed_Hisham

Absolutely, SimAgent works offline. I regularly close the application while I wait for jobs to finish. Once you reopen SimAgent and re-select your project folder SimAgent should automatically reach back out to NSG for updates. Let me know if you run into any issues!

Tyler

That's Great Tyler, I was afraid to turn it off, Thanks , I will try it and let you know