Re: Error while simulating on NAMD

From: Anirvinya Gururajan (
Date: Mon Mar 21 2022 - 08:53:39 CDT

Hey Josh!

Thanks for the reply. I do ask for GPUs in my batch script (PFA). Error dumped by slurm and the NAMD stdout output is attached in the previous message.

Anirvinya G
From: Josh Vermaas <>
Sent: 21 March 2022 18:52
To: <>; Anirvinya Gururajan <>
Subject: Re: namd-l: Error while simulating on NAMD

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).

Anirvinya G

Josh Vermaas
Assistant Professor
MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology
Michigan State University;!!DZ3fjg!sahpKfVO-tEtsbSszh9awlxQUC7lG1IfFyszJxkEY79c_Bj40OdOpmWcAcs9HebRKQ$ 

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