NEMO2/Containers

NEMO supports two container runtimes for different use cases. Neither requires root privileges and both integrate with the cluster's shared filesystems (/home, /work).

Overview

	Enroot + Pyxis (recommended)	Apptainer / Singularity
Image source	Docker Hub, NGC, any OCI registry	Apptainer Hub, Docker (via conversion), SIF files
Image format	SquashFS (.sqsh)	SIF (.sif)
Slurm integration	Native via Pyxis plugin (--container-name etc.)	Manual — wrap in batch script
GPU support	Automatic, no extra flags needed	Via --nv flag
Installation	System-wide, always available	System-wide, always available
Best for	Docker-based workflows, GPU workloads, Slurm batch jobs	Existing SIF images, reproducible science, portability

When to use what

Enroot + Pyxis

Use this if you want to run Docker images directly from a registry, submit containerised jobs via srun/sbatch, or need tight GPU integration.

→ Enroot & Pyxis details

Apptainer

Use this if you have an existing .sif image, are working with a workflow that builds Apptainer/Singularity images, or need a self-contained portable image you can copy between systems.

→ Apptainer details

Note on Docker

Plain Docker is not available on NEMO. Use Enroot to pull and run Docker images, or build a .sif with Apptainer on a machine where you have Docker installed and copy it over.