Gromacs Overview

We have Gromacs readily available on as a container from Gromacs | Nvidia NGC. Our platform offers various methods to access it, most simply via the interactive command.

Interactive

Use the instructions listed here to identify the apptainer filename to use.

SIMG=gromacs_2022.3.sif classic-interactive -G 1

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

Common Errors

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)**