bootCampEx: My practical guide to running simulations on a computing cluster

I developed these notes and exercises as part of a tutorial on how to use the Kao Group’s computing cluster. Although some of the details are specific to this specific cluster, much of the material could be useful for anyone getting started in computational physics, so I thought I would share it here. The materials are posted on and the best place to start is by reading

Who is this for?

If you’re already experienced with the command line and using HPC queuing systems, you probably already know all this stuff. I wrote this tutorial for new students in our group. This is a beginner’s guide for someone who has limited experience with the linux command line or who has never used a queue on a remote shared computing resource (a ‘cluster’ or supercomputer you log into with the terminal). I’ve tried to focus on including the little practical details of being a computational physicist that no one ever explicitly teaches you.

Through lecture notes, example and practical exercises, this tutorial will teach you the basics of using a linux-based computing cluster such as:

  • Logging into a remote machine
  • Navigate using the command line (bash)
  • Creating and running basic shell scripts
  • Starting and monitoring compute jobs using a queuing system (in this case, Sun Grid Engine)

Here’s that link one more time:
Just click and follow the instructions in




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