The HPC cluster

Obtaining DCCN account

You will receive a pair of username/password (the DCCN account) after completing the DCCN registraion procedure (a.k.a. DCCN check-in). If you do not have a account, ask the TG helpdesk.

Note

The DCCN account is NOT the account issued by the Radboud University central IT.

Accessing the cluster

• Requirements
  • Setup eduVPN
• Web access
  • Connect
  • HPC Terminal
  • HPC Desktop
• Terminal access with SSH
  • Use system terminal
  • Use PUTTY
• Desktop access with VNC
  • Set VNC password
  • Start new VNC server
  • Connect VNC server
  • Disconnect VNC server
  • Terminate VNC server

Using the cluster

• Slurm cluster
  • What is the Slurm cluster?
  • Migrating from Torque/PBS to Slurm
  • Resource sharing and job prioritization
  • The slurm module
  • Interactive job
  • Batch job
  • Job status and information
  • Job deletion
  • Output streams of the job
  • Specifying resource requirements
  • Estimating resource requirements
• Using supported software
  • Using environment modules
  • Using utility scripts
• Using IDE for coding
  • Using PyCharm
  • Using VSCode
• Using GenAI for coding
  • Ollama
• Maintaining supported software
  • Software maintainer
  • Software modules How-to
• Best practices
  • Avoid massive short jobs
  • Utilise the scratch drive on the compute node
  • Avoid massive output to STDOUT
  • Calculate your carbon footprint

Application software

• Environment modules
• Matlab
• Freesurfer
• Python
• R

Exercises

• Interactive job
• Batch job
• Data analysis in parallel