hpci

You can't spell reproducibility without CI

hpci is a tool to integrate Continuous Integration (CI) with High Performance Compute (HPC).

Install hpci on your CI runner, and hpci can schedule and monitor jobs on HPC. When you job has finished, the job's exit status code is recorded.

hpci will copy log files from HPC to the CI runner, print these to the CI logs. Then hpci will exit will the same exit status code as the job on HPC, therefore CI will crash if the job on HPC fails.

hpci is designed to be easily used with different CI platforms and different HPC clusters.

How to use hpci

1. Download hpci to your CI runner. You can either add hpci to your deployed runner vm, or include a download step as part of your CI workflow. You can also download it locally for testing, but it is intended to be used on CI runner.

  wget https://github.com/Garvan-Data-Science-Platform/hpci/releases/download/v0.0.5/hpci-exe

Either add the binary to your path, or download to a specific location by using wget with --directory-prefix=. For this README, I'll use /usr/local/bin/ as example location

2. Ensure binary is executable

chmod +x /usr/local/bin/hpci-exe

3. Run hpci

/usr/local/bin/hpci-exe followed by the following required arguments:

• --user username on remote system
• --host IP address or domain name or remote host
• --port port declaration - typically 22
• --publickey local filepath for ssh public key
• --privatekey local filepath for ssh private key schedule to schedule a job on HPC
• --script local filepath of job scheduler script
• --logFile remote filepath of logfile produced by job scheduler script to copy back to local system
• -c Optional Configuration in the form of KEY1=VALUE1,KEY2=VALUE2 that is passed to job scheduler when submitting the job

Security

I recommend creating an ssh key specifically for use with hpci so you can easily revoke access, and cycle keys.

Other steps you can take to increase security:

• use self-hosted, ephemeral runners
• use CI secrets for as many variables as possible (e.g. username, host)
• use a cloud secret manager to store ssh-keys

Acknowlegements

This repo was initialised with template-haskell