The Linux / Unix operating system

Shells

A shell is a program that allows you to interact with the operating system. In this class you will mainly use the BASH shell. You are probably already familiar with the Matlab shell (or ‘’Matlab command window’’ if you are using a GUI version of Matlab.)

In the shell you will have a prompt (usually denoted by $ or >>) where you can type in commands to the operating system. For example if you have forgotten, you can ask $ whoami. There are other commands that are a bit more useful:

pwd, cd, mkdir, ls

The command pwd prints the working directory, i.e. where your prompt is located in the directory structure. If you want to change the directory you use cd. For example if I am stainding in /home/appelo/ and want to change to /home/appelo/repos/math471 I would just type $ cd repos and then $ cd math471 or alternatively I could type $ cd repos/math471 and change two levels at one. The command cd (and most other commands) can take a relative (as above) or absolute path. The absolute path starts from the root directory / so we could also type $ cd /home/appelo/repos/math471 with the same result as above. If you want to go up (towards the root) you can use $ cd .. which brings you up one level.

If you need to make a new directory use $ mkdir dir_name.

A very useful command is ls which lists files and directories

$ls
README.rst      notes           slides

The command ls can be executed with a lot of different flags (see man ls), I find the flags -ltr which provides a long listing with the latest modified file/directory at the bottom:

$ls -ltr
total 8
-rw-r--r--   1 appelo  staff  451 Aug  4 16:04 README.rst
drwxr-xr-x  10 appelo  staff  340 Aug 18 08:59 slides
drwxr-xr-x  21 appelo  staff  714 Aug 18 15:28 notes

Displaying the content of files

The commands less, more, head and tail can all be used to display the contents of files. less is somewhat more than more as it can scroll both up and down. The commands head and tail displays the first and last lines of a file. The default number of lines is 10 but that can be adjusted to, say, 21 by giving the flag $ tail -n 21, where -n sets the number of lines to be displayed.

Copy, move and delete

The commands that copy, move and delete files and directories are cp, mv and rm. Typically you would do something like $ cp original.txt copy.txt

These commands also come with many options, for example if you want to copy a directory and all its sub-directories you will have to use the flag -r, that is: $ cp -r odir cdir. The move command mv works very much like the copy command.

To remove files the command to use is rm, again with the option to be executed with flags such as -f for force or -r for descending into sub-directories.

Logging in to a remote computer

To login to a remote computer you can use the secure shell, for example to login to linux.unm.edu you would type:

ssh -X appelo@linux.unm.edu

Here the -X starts the X-server so you can open windows locally on your machine. The result of the above command is the following (angry) message

========================================================================
=                       WARNING NOTICE TO USERS                        =
=                        Authorized uses only.                         =
=             All activity may be monitored and reported.              =
========================================================================
appelo@linux.unm.edu's password:
Last login: Wed Aug 21 15:54:53 2013 from valhall.math.unm.edu


         ---------------------------------------
              linux.unm.edu  ftp.unm.edu
         ---------------------------------------


   Popular Packages:

   SAS 9.2  | Matlab  R2011a |  Maple  v12 | Subversion 1.6
   Java 1.6 | PINE: ALPINE (which is PINE)
   GCC, G++ and GNU Fortran, Ruby, Perl, Python, GNU assembler

Environment variables

The bash shell uses environment variables to keep track of various information. These can be displayed by the command printenv or simply env. Executing this may give an output that looks something like this:

[appelo@mizar ~]$ printenv
HOSTNAME=mizar.unm.edu
SHELL=/bin/bash
USER=appelo
PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/nfs/user/a/appelo/bin
PWD=/nfs/user/a/appelo
HOME=/nfs/user/a/appelo
LOGNAME=appelo
_=/usr/bin/printenv

The environment variables can be accessed through the dollar sign, for example ls -ltr $PWD would list the content of the current directory. The underscore environment variable holds the last command you executed and can be useful, if you don’t want to type in a long command again just type $_.

The search path

The variable PATH is a list of the directories where the shell searches for the commands you are trying to execute. So if you install some software in a new location, say HOME/newbin, you may want to append PATH by using the export command

export PATH=$PATH:$HOME/newbin

The search paths are separated by a colon. If you want the added directory to be searched first you can prepend the PATH instead

export PATH=$HOME/newbin:$PATH

The .bashrc file

Whenever you open a new terminal the file $HOME/.bashrc is executed so if you always want to append the PATH variable or do other permanent changes you can add them to the .bashrc file. For example you can redefine ls to color the output by adding the line alias ls='ls -G'.

A good resource for reading more about shells and Linux/Unix is software-carpentry.