Re: [Genesis-sim-users] question about Genesis via batch systems

[Jaeger, D. <dj...@em...>]

Dear Susan,

Genesis can certainly be run as a batch job.  We have  been doing this for many years.  First, use nxgenesis to get rid of the graphics.  Second,  if you want to use different parameters for each job while using the same .g command file, use environment variables to transmit the parameters. I am attaching a script that does reads environment variables (actually 2 versions of this), and also puts the parameter values in the file names so that one can tell what is what afterwards (the Genesis binary data format carries no metainformation unfortunately).  For a systematic parameter manipulation package, see  https://github.com/cengique/param-search-neuro maintained by Cengiz Gunay.  He first started this software as a postdoc in my lab and it has since been used on a variety of cluster configurations.  It is also becoming available as Genesis simulation toolkit on the NSG (https://www.nsgportal.org/).   We have just started to use the NSG instead of a local cluster.

-Dieter

-----Original Message-----
From: Susan Chacko [mailto:su...@he...]
Sent: Monday, June 05, 2017 4:19 PM
To: gen...@li...
Subject: [Genesis-sim-users] question about Genesis via batch systems

Hi all,

I've installed Genesis on a cluster here at the NIH (see https://hpc.nih.gov/apps/genesis.html). I can see how to run it in an interactive session, as I've documented on our webpage. Can Genesis be run as a detached batch job? I looked through the Genesis documentation, but I couldn't see how to make that work. We run the Slurm batch system here, and I'd like to add instructions for running batch jobs, to guide our users in the right direction.

Any info or suggestions much appreciated, Susan Chacko.

--
Susan Chacko, Ph.D.
HPC @ NIH Staff


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