Re: Error while simulating on NAMD

From: Josh Vermaas (
Date: Mon Mar 21 2022 - 08:22:58 CDT

Hi Anirvinya,

In your slurm script, are you asking for any GPUs on the nodes? It looks
like you are using a GPU-accelerated executable, which requires a GPU to
be present in order to run. With slurm, the typical way to ask for GPUs
to be allocated to the job is something like '#SBATCH --gres=gpu:1'. Do
you have a line like that in your submission script?


On 3/20/22 5:16 PM, Anirvinya Gururajan wrote:
> Hi all,
> Recently, I have been facing trouble with a very specific system that
> I am trying to simulate using NAMD/2.13. PFA the slurm output file
> generated. When I try to simulate it over an interactive job on the
> cluster node, it seems to work fine. But if it is submitted as a batch
> job on the same cluster node, it throws the following error. I am not
> very sure as to where the source of the problem is. The system is
> large and has about 800k atoms (I don't know how irrelevant it is to
> this issue).
> Regards,
> Anirvinya G

Josh Vermaas
Assistant Professor
MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!trLSEbxIddst0McHibfSxszmRixtsvPbOGg3gwF4HtckeuzlvRKLQWZmHJj8hnKJoQ$ 

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