provide a singularity container for running SIMON

You found maybe a bug in SIMON or you're missing a major feature? Just ask and discuss
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Posts: 1
Joined: Thu May 06, 2021 7:37 am

Thu May 06, 2021 7:46 am


First of all, great work with SIMON! I really like the concept and how it can facilitate and automate ML applications for biological problems.
Currently, you only offer a docker image to run SIMON. Unfortunately, only singularity is available in our cluster and I suspect this situation may affect other users as well since many cluster admins prefer singularity over docker.
I've tried using your docker image with singularity through automatic conversion, but despite my efforts, I was unable to start SIMON.
After some adjustments to bind all the needed paths, it seems there are still issues with permissions when the startup script in the container tries to configure the requested folders. Thus, the various tools can not run properly.

Any suggestion on how to run this using singularity or any plan to provide a singularity image?

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Posts: 16
Joined: Wed Feb 13, 2019 7:47 pm
Location: Palo Alto, CA

Tue May 11, 2021 1:11 pm

Hi @gedoardo83,

I understand your issue. As you can imagine currently the most easiest way is to scale SIMON is vertically. SIMON has experimental horizontal scaling back-end developed but it currently only supports and OpenStack backend scaling API.
In any case I think scaling is not your question here, rather pure installation of it for your users? Unfortunately, having in mind current workload, I cannot see that we will add singularity support at least until we pass v1. In any case if you succeed to make some adjustment and add support for it I will gladly welcome your PR request.
“We can not solve our problems with the same level of thinking that created them” A.E.
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