Introduction to Unix and SGE for beginners

The Shell

The traditional and arguably most effective way to interact with a Unix-like system is through a special programme called "shell". A shell can be used interactively as a command line interface or as a batch processor.

In the following screenshot you can see what a shell environment looks like on MacOS. You see four terminal windows in a graphical user interface, running different shells (a descendent of the original shell sh, and tcsh).


In this tutorial we assume that the popular GNU shell bash is used instead.

What is GNU?

According to the GNU website,

GNU is a Unix-like operating system that is free softwareit respects your freedom. You can install versions of GNU (more precisely, GNU/Linux systems) which are entirely free software.

The GNU Project was launched in 1984 to develop the GNU system. The name “GNU” is a recursive acronym for “GNU's Not Unix!”.

Although GNU is by its own admission "not Unix", the GNU system is one of the most popular modern implementations of a Unix-like system. Many of the GNU applications (including the bash shell) are available for other operating systems as well.

Starting a shell session

We highly recommended that a Unix-like system be used for this course. If this is not an option for you and you are tied to Microsoft Windows, you should install Cygwin, a Unix-like environment for Windows. If you have remote access to a system running a Unix-like operating system such as GNU/Linux, it may be sufficient to install PuTTY, a terminal application for accessing remote systems over the SSH protocol. Many Windows users use PuTTY to connect to remote servers, such as the login node of a cluster.

Let's start a shell session!

  • In Mac OS X, go to "utilities" and start "terminal"
  • In Windows open the Cygwin terminal or use PuTTY to connect to a remote Unix host
  • If you are using GNU/Linux, start your preferred terminal application (e.g. xterm, urxvt, konsole, terminal, etc.)

What are commands?

The shell interprets text as commands. In interactive mode the user inputs text commands on the command line prompt and submits them for processing; the shell reads from the "standard input" stream (connected to the keyboard). In batch processing mode, on the other hand, the shell reads commands from a specified file, called a "script". By default, the shell is configured to print all potential output of the commands to the screen.

Any command line consists of one or more words; the first word is the name of the command itself, whereas anything that follows belongs to the arguments to the command.

Arguments are passed to the command. They can be switches or options (indicated by the - prefix) to modify the behaviour of the command, patterns, the names of files to operate on, etc. The meaning of the arguments depends on the command.

The below example shows the ls command (which lists the files in a given directory) without any arguments and run with the -l option. (The $ stands for the shell prompt and is not part of the command.)

$ ls

$ ls -l
total 0
drwxr-xr-x  22 root    staff   748 May 26 19:08 Documents

As you can see, the -l option changed the output of the ls command.

Getting help

  • Man pages. Type "man commandName", such as man ls. this will return the manual page on the given command. Most unix commands have extensive explanations and examples on those pages. Type q on your keyboard to quit the manual view.
  • Info manuals. All GNU software comes with extensive manuals, called info pages. You can read them with the info programme on the command line or from within Emacs. Type info ls for the ls manual page. The info pages are hypertext documents with a hierarchical structure and links. When in info, type H to learn how to use info. To open info documentation inside of Emacs issue the command "Ctrl-h i".
  • Web search. Search online for the command followed by "+ unix" or "+ linux", this will usually return forums and webpages about the command. Look for example usage and explanations.