What Is Apptainer?

What Is Apptainer?#

Apptainer is a container runtime designed specifically for HPC (High-Performance Computing). It provides the same core functionality as Docker—packaging your software and environment into a portable, reproducible container—but it is built to work without root privileges, which is essential in shared supercomputing environments.

It is:

  • Open-source, governed by the Linux Foundation

  • The successor to Singularity (the project was renamed starting in 2021)

  • The standard on HPC systems, where Docker is typically prohibited

Most people in HPC still casually say “Singularity,” but the modern software stack and project name is Apptainer.

Why HPC Uses Apptainer Instead of Docker#

Supercomputers do not allow root access or privileged daemons. Docker requires:

  • A root-owned daemon (dockerd)

  • Privileged operations (namespaces, cgroups, mounts)

This is unsafe on multi-user HPC clusters.

Apptainer, however:

  • Runs containers as the user, with the same permissions the user already has

  • Does not require a daemon

  • Plays nicely with job schedulers like Slurm, PBS, LSF, etc.

  • Integrates with shared filesystems (Lustre, GPFS, NFS)

This makes Apptainer the “official container runtime” for academic HPC.

How an Apptainer Container Works#

An Apptainer container is typically a single immutable .sif file:

mycontainer.sif

This file contains:

  • A full Linux filesystem (like an OS image)

  • Installed software/packages

  • Executables, libraries, Python environments, etc.

You run it like this:

apptainer run mycontainer.sif

or:

apptainer exec mycontainer.sif python script.py

It feels like Docker, but the security model and execution model are very different.

Apptainer vs Docker (quick comparison)#

Feature

Docker

Apptainer

Requires root?

Yes

No

Designed for HPC?

❌ No

✔ Yes

Runs under Slurm?

Not allowed

Standard

File is a single .sif?

No

Yes

Can import Docker images?

—

✔ Yes, converts to .sif

User isolation

Strong

User-level, HPC-safe

Supports GPUs, MPI?

Yes (but not on HPC)

Yes, HPC-native

Big point: Apptainer can pull and convert Docker images:

apptainer build my.sif docker://pytorch/pytorch

This makes it the bridge between Docker ecosystems and HPC ecosystems.

How This Relates to Tapis Apps on DesignSafe#

When your Tapis app specifies:

"runtime": "SINGULARITY"

…it is essentially running through Apptainer on Stampede3 or Frontera.

The app’s:

"containerImage": "/work/.../myapp.sif"

is the Apptainer/Singularity image file.

Inside the job, Tapis runs something like:

apptainer run myapp.sif args...

(Older docs say “singularity run,” but on TACC systems the backend is now Apptainer.)

When You Should Use Apptainer in Your Apps#

Use Apptainer (runtime = SINGULARITY) when:

  • You want a self-contained, portable environment

  • You want to ensure the software stack is the same everywhere

  • Your app needs custom Python/conda, exotic libraries, or OS-level dependencies

  • You want to run the same container on Jetstream2, TACC, and another cluster

Do not use it if:

  • You want extremely fast iteration and don’t want to rebuild images

  • You’re happy with TACC modules → in this case, use ZIP runtime instead

Simple definition you can include in your documentation#

Apptainer (formerly Singularity) is the container engine used on HPC systems because it runs securely without root privileges. It packages your application and its full software environment into a single portable .sif image and executes entirely within user space, making it the standard container runtime for Tapis apps on DesignSafe’s HPC resources.

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