Connecting to Karolina HPC and Using Apptainer

Because Apptainer does not run within a Docker Codespace, you’ll need to connect to the Karolina HPC system (EuroHPC) to work with Apptainer. In this section, we’ll cover:

  • How to SSH into Karolina.

  • How to remotely log in to GHCR.

  • How to pull, inspect, and run your Apptainer (SIF) image.

  • How to bind host directories and launch an interactive shell.

Connecting to Karolina HPC

First, connect to the Karolina HPC system. Replace your_username and adjust the hostname as needed:

ssh your_username@karolina.it4i.cz

I use the follow ssh configuration to connect to Karolina HPC:

Host karolina
    Hostname karolina.it4i.cz
    User it4i-<login>
    ForwardAgent Yes

and of course I have my SSH key added to the ssh-agent and the public key added to the ~/.ssh/authorized_keys file on the Karolina HPC system using the ssh-copy-id command. In vscode with the Remote - SSH extension, I can connect to Karolina HPC by selecting the karolina host. In a terminal, I can connect to Karolina HPC by running ssh karolina.

Remote Login to GitHub Container Registry

Before pulling your image, you need to log in to GHCR using Apptainer’s remote login command. Replace <username> and <GHCR_PAT> with your GitHub username and Personal Access Token respectively:

apptainer remote login -u <username> -p <GHCR_PAT> oras://ghcr.io

Pulling and Inspecting the Docker Package as a SIF Image

Pull the Docker image (from GHCR) and convert it to an Apptainer SIF file:

apptainer pull -F myapp.sif docker://ghcr.io/<username>/myapp:latest

After pulling, inspect the SIF image to verify its contents:

apptainer inspect myapp.sif

Running the Apptainer Container

You can run your container in several ways on Karolina:

  • Interactive Mode (Shell):

apptainer shell myapp.sif

  • Default Command:

apptainer run myapp.sif

  • MPI Batch Execution:

mpirun -np 4 apptainer exec myapp.sif ./my_mpi_app

Mounting Directories and Using an Interactive Shell

Often in HPC, you need to access data stored on the host. Use the --bind option to mount directories into your container. For example, to mount /data from the host to /mnt/data inside the container and then launch a Bash shell:

apptainer exec --bind /data:/mnt/data myapp.sif /bin/bash

This command allows you to interact with your data within the container environment.

Conclusion

In this section, you learned how to: - Connect to the Karolina HPC system via SSH. - Remotely log in to GHCR to retrieve your Docker-based Apptainer image. - Pull, inspect, and run your Apptainer SIF image. - Bind host directories and launch an interactive shell within the container.

These steps ensure that your HPC applications run in a reproducible, containerized environment on Karolina HPC.

Questions? Let’s discuss how to integrate these steps into your HPC workflows!