Re: Running NAMD Singularity container on GPU multinode cluster with Omnipath

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 21 2022 - 06:51:11 CST

Is that the container you are referring to?
https://urldefense.com/v3/__https://singularityhub.github.io/singularity-hpc/r/nvcr.io-hpc-namd/__;!!DZ3fjg!u-YD25AJAGUx75c_0CMzOP2hYx6hS6ln-BUKAzkCMeN56LiDWicxNqbph-fkqkRGBA$
Because in that case, it quite clearly says "SingleNode" in the version
label.

At any rate, for a cluster it is generally better to build the Charm++
library (which NAMD uses to achieve multi-node parallelism) to be better
integrated with the cluster's software configuration.

Multi-node, however, will also require the older, hybrid CPU-GPU scheme and
does not support the pure-GPU scheme of 3.0. With the latter you are
limited to running one replica over one node at most, and perhaps do
replica-based methods across multiple nodes (all is explained in the NAMD
3.0 alpha webpage).

Giacomo

On Fri, Jan 21, 2022 at 4:17 AM Almeida-Hern√°ndez, Yasser, Dr. <
yasser.almeida-hernandez_at_uni-due.de> wrote:

> Dear all,
>
>
> I want to run NAMD on several GPU nodes in a cluster with an Omnipath
> network. I thought to run the NVIDIA Singularity container. Does the
> container support the Omnipath network?
>
>
> Best,
>
> Yasser
>
>
>

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