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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?

See this YouTube video for 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.

Content

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

Content

  • 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

Prefer a video?

See the YouTube video 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

Content

  • 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.

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'