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Flywheel HPC Singularity API key configuration

Version 1.0.2

Purpose

Singularity/Apptainer needs to establish a remote endpoint with your Flywheel instance's Docker repository so that it can pull container images to your HPC system.

Instructions

Create a remote endpoint to your site's Docker registry

Use the command below to login and set up a token for your site's Docker registry. It will prompt you for a password; enter the associated Flywheel API Key (create one if you haven't already).

Note: This user will be the only one that pulls Docker images from your Flywheel site through Singularity/Apptainer. It is recommended that a new Flywheel admin user be created that is not tied to an individual at your institution/company.

singularity remote login --username <flywheel_user_email> docker://<your_flywheel_site_url>

Example:

singularity remote login --username [email protected] docker://ga.ce.flywheel.io

You should see something like the following if the login was succesful:

INFO:    Token stored in /home/<user>/.singularity/remote.yaml

You should also be able to see the new remote endpoint with singularity remote list, under the "Authenticated Logins" section.

Secure the docker json file (Recommended)

As is mentioned in Singularity/Apptainer documentation, the token is stored in the home directory of the user you selected to set up the remote endpoint. It is typically stored in ~/.singularity/docker-config.json (or ~/.apptainer/docker-config.json). It is recommended that the permissions for this file be changed so that only certain users can access it. Here are several options and considerations for each.

Only one user has read & write access

After the HPC Client submits the HPC job through the scheduler (e.g., Slurm), the Flywheel engine will use credentials from the ~/fw-cast/settings/credentials.sh file to get the Flywheel job from your Flywheel site. It wil run it locally on your HPC. Singularity/Apptainer still needs, however, a user to pull the Docker image from your Flywheel site.

By default, the user that submits the job to your HPC scheduler is the one that periodically runs the ~/fw-cast/settings/start-cast.sh file (with the integration method you chose). This user must have access to the docker-config.json file. If it is the same user, then you can just do the following:

chmod 0600 ~/.singularity/docker-config.json

Several users have access (Future feature, not implemented yet)

In future HPC Client releases, there will be an option for different users to submit the scheduler job. With this configuration, HPC resources can be tracked for the user or group that creates the Flywheel job (and subsequent scheduler job). If configuring this, then all users that submit the scheduler job to the HPC must be able to read the docker-config.json file. To give read/write access to the file owner and read permission to a group of users, you can use the following:

chmod 0640 ~/.singularity/docker-config.json