Tutorial · 9 min read

Containers on Regulated HPC Clusters

Containers are the fastest way to share environments across labs, but compliance officers still expect airtight controls. Follow this workflow to ship GPU-ready images that pass security reviews on ORNL, Argonne, and pharma clusters.

Toolchain snapshot

• Apptainer 1.3/1.4 for SIF signing and overlay support.
• NVIDIA Container Toolkit 1.16 for GH200/H100 MIG awareness.
• ROCm Container Toolkit 6.x for MI300A/X support.
• Cosign 2.x for Sigstore-based signing.

Build + sign workflow

apptainer build --fakeroot climate.sif climate.def
cosign sign --key k8s://hcp/signing climate.sif
cosign verify --key hcp/signing.pub climate.sif

Keep definition files in git for diffable review and store signing keys in an HSM-backed vault.

Granting GPU + network access

apptainer run --nv \
  --bind /lus:/lus,/scratch:/scratch \
  climate.sif python run.py

Use --nv or --rocm runtime flags, bind only required directories, and rely on Slurm job_container or burst-buffer stages for inputs/outputs.

Policy enforcement

1. Maintain allow-list registries/digests via /etc/containers/policy.json.
2. Scan images with Trivy/Grype before promotion.
3. Monitor runtime with Falco/eBPF for unexpected syscalls.

Troubleshooting

• Permission denied? Avoid needing cap_sys_admin; rewrite definitions to minimize mounts.
• Slow performance? Check for double encryption and extra bind mounts.
• Missing GPUs? Ensure host driver versions match container CUDA/ROCm versions.

Compliance talking points

• Signed images + attested pipelines prove provenance.
• Containers inherit the host kernel—document patch cadence.
• Archive SBOMs and vulnerability reports with each release.

References

• Apptainer 1.4 security hardening guide (Sept 2024).
• NVIDIA GH200 container best practices (SC24).
• EuroHPC JU policy templates for containerized workloads.