NEMO2/Containers
< NEMO2
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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. Both Enroot and Apptainer can pull Docker/OCI images directly from registries without a local Docker installation.