• The “operating system” of the UPPMAX and most of the other clusters is Linux.


  • What is Linux?

  • How to use the command line?


  • We’ll briefly get an overview of Linux

    • How the command line works

    • Some text editors

    • Things to be aware of

What is Linux?


  • Daily speaking: The Linux Operating system is a UNIX like and UNIX compatible Operating system.

  • Linux is a “Kernel” on which many different programs can run.

  • The shell (bash, sh, ksh, csh, tcsh and many more) is one such program.


  • Actually, for it to be an OS, it is supplied with GNU software and other additions giving us the name GNU/Linux.

    • [Linux naming controversy]((


  • Linux has a multiuser platform at its base which means permissions and security comes easy.

Linux comes in different distributions, dialects or, say, flavours.

  • UPPMAX runs CentOS and RedHat


Using the command line

Command line with bash (Bourne Again Shell)

  • A Unix shell and command language.

  • Often default shell


  • The command-line interface: the bash prompt $

  • bash can be seen as a program that finds and runs other programs

  • bash is scripting language that is referred to as a shell

    • (because it sits around the kernel making it easy to interact with)


The prompt

[info]$ program word1 word2 word3 […]


Example bash command

mv inbox

program flags

  • Terminal screen shows


Tab Completion


  • Whenever you’re writing a path or filename on the bash prompt, you can strike the ‘tab’ key to ask Bash to complete what you’re writing.

  • Get in the habit of this — it will save you many hours!

Editing files with file/text editors



  • graphical user interface — GUI, needs X-server

  • Also graphical editor within MobaXterm


The graphical editors

  • When starting the graphical versions of an editor, add & to be able to use the command line while program is open.

    • Ex: gedit &

    • If not, you can <Ctrl>+z and type bg to send program to background.

Try out later!

Try them out and pick one favorite editor!

Typical sources of error



  • Capitalization matters in file names and program names

  • Spaces matter.

    • Always have a space after the program name.

    • Don’t add spaces within file names.

  • Check that you are in the right place in the file system.

  • File permissions. Check that the right read, write and execute permission are set. See next session.




  • There is no undo for:

    • copy (cp),

    • move (mv), and

    • remove (rm).

  • Beware of overwriting files and deleting the wrong ones.


  • Tip: make “rm” ask if you really want to erase:

    • Within a session: Type in the command prompt

      alias rm='rm -i'
    • Override asking with

      rm –f <>
    • Edit file .bashrc in home directory by adding the alias line for this to start everytime.

  • This will also work for mv and cp!


  • If you do destroy your data, email UPPMAX support, we may be able to help.


  • Linux Operating system is a UNIX-like and UNIX compatible Operating system.

  • Typical command: $ program word1 word2 word3 […]

  • Example of file editors

    • terminal

      • nano

      • vim

      • emacs

    • graphical:

      • gedit

  • Tips

    • use Tab completion

    • capitalization and spaces matters

    • no undo:s for copying, moving and removing

      • Solution: alias rm='rm -i'