Gromacs with Apptainer

Owned by Alan Chapman, created
Last updated: May 15, 2024 by rahull1
1 min read

Overview

https://catalog.ngc.nvidia.com/orgs/hpc/containers/gromacs

We have Gromacs readily available on Sol as a container, which can easily be used with apptainer. Our platform offers various methods to access it, including via the interactive command.

Interactively use Gromacs

To find the name of the container you should use, follow the steps outlined here - Apptainer usage | Step 1: Identify the Apptainer Image for Use

SIMG=gromacs_2022.3.sif interactive -G 1

This command will grant you access to the Parabricks container on a physical node, with a single GPU.

If you receive the following warning, you likely did not use the -G sbatch option to request a GPU.

WARNING: Could not find any nv files on this host!
ERROR Failed to verify GPU driver: Failed to detect host CUDA driver version: nvml init failed: NVML Not Initialized, unable to determine error!
FATAL Please double check that GPU passthrough is enabled: --nv (Singularity), --gpus all (Docker)

Additional Help

 

Arizona State University