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Linux

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

Questions

  • What is Linux?
  • How to use the command line?

Objectives

  • We'll briefly get an overview of Linux
  • How the command line works
  • Some text editors
  • Things to be aware of
Want a video?

Here is video that gives an introduction to Linux

What is Linux?

Tux

  • 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.

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

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  • 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

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Local Linux environment

  • You may sometimes benefit from having a local Linux environment.
  • Examples:
    • Mimic cluster environment to work with your local files and data as on the Cluster
    • get used to Linux (!)
  • Mac is UNIX and very Linux-like
  • Windows requires WSL (Windows subsystem for Linux)
For windows users who wants to get started with WSL (not covered here)

Using the command line

Below usage of the command line is discussed in text. If you prefer video, here is how to use the command-line on the UPPMAX Bianca cluster.

Command line with bash (Bourne Again Shell)

  • A Unix shell and command language.
  • Often default shell

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  • 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)

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The prompt

[info]$ word1 word2 word3 [...]

  • [info] is configurable, and usually tells you who you are, on what system, and where in the file system.

    • Example:
    [bjornc@rackham3 linux_tutorial]$

folders

Example bash command

mv inbox

program flags

  • Terminal screen shows

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Tab Completion

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  • 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

Edit

To edit files, you will use a text editor. The UPPMAX HPC clusters have multiple text editors installed, which are described at the UPPMAX 'Text editors' page here.

Example

Start nano and save a file called first.txt

$ nano first.txt
  • Type test text
  • End and save with <ctrl>-X followed by Y and <enter>.

Typical sources of error

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Warning

  • 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.

Caution

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Warning

  • There is no undo for:
    • copy (cp),
    • move (mv), and
    • remove (rm).
  • Beware of overwriting files and deleting the wrong ones.

Tip

    • Within a session: Type in the command prompt

      alias rm='rm -i'

    Tip: make "rm" ask if you really want to erase:

    • 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!

Note

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

Keypoints

  • Linux Operating system is a UNIX-like and UNIX compatible Operating system.
  • Typical command: $ program word1 word2 word3 […]
  • Use text editors to edit files
  • Tips
    • use Tab completion
    • capitalization and spaces matters
    • no undo:s for copying, moving and removing
      • Solution: alias rm='rm -i'