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Apptainer, Docker, and Containers

TLDR

Turing uses Apptainer as its container system. After module load apptainer you can load perbuilt docker images using apptainer run --userns docker://organization/container:version. Turing does NOT support docker directly.

What is a Container?

A container is a portable software package that includes everything needed to run an application: code, libraries, and dependencies. It ensures consistency across environments, making it ideal for running software with specific requirements.

When to Use a Container

If the software you need is not available as a module on the Turing cluster, consider using a container. Containers provide flexibility by isolating the software environment, allowing you to run applications without relying on system-wide installations.

Using Containers on Turing

The Turing cluster uses Apptainer to run containers. It supports Docker containers and is optimized for HPC environments.

Running Prebuilt Containers

You can often find the software you need as a prebuilt container on platforms like Docker Hub. Follow these steps:

  1. Find the Container
    Search for the container on Docker Hub. The container address is included in the docker pull command (e.g., docker://organization/container:version).

  2. Run the Container
    Apptainer can directly run containers available on DockerHub. For example, to run the sylabsio/lolcow:latest container, first run

module load apptainer

Then use the following command to save a public Docker container as a SIF file for later use with Apptainer:

$ apptainer pull docker://sylabsio/lolcow:latest

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 16ec32c2132b done  
Copying blob 5ca731fc36c2 done  
Copying config fd0daa4d89 done  
Writing manifest to image destination
Storing signatures
2024/07/17 14:25:43  info unpack layer: sha256:16ec32c2132b43494832a05f2b02f7a822479f8250c173d0ab27b3de78b2f058
2024/07/17 14:25:44  info unpack layer: sha256:5ca731fc36c28789c5ddc3216563e8bfca2ab3ea10347e07554ebba1c953242e
INFO:    Creating SIF file...

This will save a file lolcow_latest.sif which you can run using 

$ apptainer run --userns lolcow_latest.sif

 ______________________________
< Wed Jul 17 14:25:57 EDT 2024 >
 ------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

More information about using Docker containers with Apptainer can be found at the Apptainer documentation.