HPC-tutorial

A set of tutorials using & running simulations on the HPC at Imperial, our group workstation.

Outline of repo:

• HPC introduction
  • logging in
  • common linux commands
  • tips and tricks
  • file structure & transferring files
  • the resource manager & running jobs on the HPC (PBS scripting)
  • downloading software to use on the HPC
• Setting up oxDNA
• Running oxDNA simulations
  • oxDNA input file
  • PBS input file
• Analysing oxDNA simulations
  • DNAanalysis (written alongside oxDNA input files)
  • oxDNA analysis tools (source code)

Useful resources:

• Research Computing Service - Official Introduction to the HPC - use this the main resource