Linux Terminal Tutorial - Introduction

Introduction

Mastering the Linux terminal interface is fundamental to working efficiently in the HPC space. This tutorial is designed to help you take that first step on this journey.

For this tutorial it is preferable to log in to the UFS HPC login node using either your UFS HPC account details or the training account details provided to you.

However, it is possible to do this tutorial on a local linux machine - simply skip steps that are relevant to being logged into a UFS HPC.

Notes and Tips

Note

Commands displayed should be typed in WITHOUT the $. The $ is simply a representation of the terminal prompt

Note

Any text starting with # should not be retyped into the terminal as the text with the prefix # denotes a comment.

Tip

If you are typing a command into the terminal and you wish to discard everything you've typed, press Ctrl + C to start fresh with on a new line

Getting Started

  1. Login to the UFS HPC. If using a VNC session, open a terminal.

  2. You should now be in your home directory

  3. Download this archive.

  4. Upload the archive to your home directory

    Alternatively, download the archive directly to your home directory using wget:

    $ wget https://docs.hpc.ufs.ac.za/getting-started/files/tutorial.tar.gz

  5. In your home directory, extract the contents of the directory:

    $ tar -xvf tutorial.tar.gz

Background on the directory used

The directory used in this tutorial (Tutorial) contains files from a single Molecular Dynamics (MD) experiment. A MD experiment has two equilibration phases: a NVT phase and a NPT phase. After the NPT phase a system is equilibrated and a production run (where one would capture data for analysis) is then performed. A shorthand for this final run is simply MD.

Thus, the sub-directories are:

  • nvt_expr_1
  • npt_expr_1
  • md_expr_1

With all files in the directories above being related to the sub-experiment that was performed as part of Experiment 1 (expr_1).

Throughout this tutorial there will be reference to the main directories, which are the directories listed above.

Note that many files have been stripped of their contents to reduce their size (one file is over 500 GB). The reason this file set was chosen, is because it allows for plenty opportunities to practice the commands found in Linux 101. It also shows an example of organising files in directories with meaningful prefixes that will allow one to efficiently navigate and use them in the terminal environment.