The HPC cluster

Obtaining an user account

You should receive a pair of username/password after following the ICT check-in at DCCN. If you do not have a account, ask the TG helpdesk.

Note

The user account here is NOT the account (e.g. u-number) given by the Radboud University.

Accessing the cluster

• Inside DCCN
  • SSH login with Putty
  • SSH logout
  • VNC for graphic desktop
  • Disconnect VNC server
  • Terminate VNC server
• Outside DCCN
  • Using eduVPN

Using the cluster

• Torque cluster
  • What is the Torque cluster?
  • Resource sharing and job prioritisation
  • Job management workflow
  • Batch job submission
  • Interactive computation in text mode
  • Interactive computation in graphic mode
  • Checking job status
  • Cancelling jobs
  • Output streams of the job
  • Specifying resource requirement
  • Estimating resource requirement
  • Cluster tools
• Slurm cluster
  • What is the Slurm cluster?
  • Migrating from Torque/PBS to SLURM
  • Resource sharing and job prioritisation
  • The slurm module
  • Interactive job
  • Batch job
  • Job status and information
  • Job deletion
  • Output streams of the job
  • Specifying resource requirement
  • Estimating resource requirement
• Using supported software
  • Using environment modules
  • Using utility scripts
• Using IDE for coding
  • Using PyCharm
  • Using VSCode
• 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

Application software

• Environment modules
• Matlab
• Freesurfer
• Python
• R

Exercises

• Interactive job
• Batch job
• Resource estimation
• Data analysis in parallel