Bash Scripting and Working on the UCI HPC

Presentation by Stacey Borrego

Presentation Material

Working on the HPC: Bash Scripting

What is in a .bashrc?

Topics for this Meeting

1. How to write a bash script
   • Recommended reading
     • BASH Structure - basic layout and structure of a Bash Shell Script
     • Bash Scripting Cheatsheet
2. Running a job on the HPC with a bash script
   • Recommended reading
     • Running Jobs on the HPC cluster at least up to the 'Batch Job Parallel' section
     • Batch Jobs Serial - following this example will be helpful
3. Personalize your shell by setting aliases in your .bashrc script
   • Recommended reading
     • What Is The Bashrc File Used For?
4. The Biostar Handbook: A Beginner's Guide to Bioinformatics
   • Seven subscriptions remaining

Helpful HPC Commands

Once you have logged on the HPC these commands may be useful

• This is a cheat sheet that lists some HPC specific commands and information pages
  • $ cat /data/help/cheat-sheet.txt
• This will list all of the groups you belong to
  • $ groups
• See where you are
  • $ pwd

A short video introducing the command line text editor "nano"