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Learning how to use HPC infrastructure (part II: Choosing software, editing files, writing scripts)

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CYCL09b (Louvain-la-Neuve)

CYCL09b

Louvain-la-Neuve

Chemin du cyclotron,2 1348 Louvain-la-Neuve Belgium
Description
We will continue to learn the fundamental tool needed to use a cluster. We will cover how to choose/activate the (version) of software that you need, how to edit a file on any HPC cluster, how to script simple tasks.

Contents:

  • Choosing and activating software with system modules on CECI clusters
  • Writing and editing text files with Vim
  • Bash scripting

Prerequisite:

  • Being able to use SSH with private keys 
Type: Lecture Hands-on
Target audience: Rookie
Must: This session is a must-have for anyone.
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    • 1
      Choosing and activating software with system modules on CECI clusters

      Software installed on the clusters is organised and managed with environment modules that allow choosing a specific version of a software package compiled with a given compiler, linked to chosen libraries, etc. This session explains how modules are used on the clusters.

      Contents:

      • The installed software
      • The modules command
      • What is Easybuild
      • What are the different toolchains
      • how to install software by yourself

      Prerequisite:

      • Being able to use SSH with private keys 
      • Being familiar with a text editor 
      • Mastering the Linux command line and the GNU utilities (mkdir, cp, scp, etc.)

      Type: Hands-on
      Target audience: Everyone
      Must: This session is a must for anyone.
      Speaker: Bernard Van Renterghem (UCL CISM)
      modules.pdf
    • 2
      Writing and editing text files with Vim

      Vim is a very powerful text editor installed on all Unix systems, including Mac OSX, and used by many programs as default text editor. Knowing the basics is crucial on HPC. Mastering it will dramatically speed up tasks like the edition of submition scripts, configuration files, code, ...

      Contents:

      • Why use VIM on user interfaces ?
      • VIM modes
      • Movement and action commands
      • Macros
      • Plugins

      Prerequisite:

      • Being able to use SSH with private keys 

      Type: Hands-on
      Target audience: Everyone
      Must: This session is a must for anyone.
      Speaker: Jérôme de Favereau (UCLouvain/IRMP/CP3)
      cthulhu.txt
      formation-vim.pdf
    • 3
      Bash Scripting

      Come here to learn the baisc on how to create small scripts to simplify your workflow.

      Bash is the default shell on many systems and allows writing scripts to automate things. This session gives a basic introduction to programming with Bash.

      Speakers: Mr Jérôme de Favereau (UCLouvain/IRMP/CP3), Mr Pierre-Yves Barriat (UCL/ELIC)
      Bash-1.pdf
      link to the presentation page