A Very Short Intro To Linux: Laura Alisic October 8, 2008

A very short intro to Linux
Laura Alisic
October 8, 2008
This document is a very short summary of some basic commands, enough to get you started
for the problem sets in Ge161. For a nice and more thorough overview, have a look at the text
Eun-Seo Choi wrote. It is located in:
/home/datalib/Resource_Class/Unix_2007/linux_intro_all.pdf
The best way to learn working with Linux (or any programming language) is doing it!
Introduction Linux is an operating system, and is a flavor of UNIX. Almost everyone in the
Seismolab works on a Linux machine; some people work on MacOS which is also based on
UNIX. The reason to use UNIX-like systems is the ease with which one can write software and
run it. Programming in Windows will mostly give you nightmares! A UNIX/Linux/MacOS
system is very easily maintained and operated using the terminal, which is a window that has
a command line in it. If you enter commands in the terminal, the system will interpret them
and execute them. The general syntax is as follows:
command -option1 -option2 ... <filename>
Below, you can find some of the most common commands and their usage, the ones that
you will use very often when working in Linux. If you master these, you will be able to move
around in your file system, manipulate files and directories, perform simple file editing, make
an executable of a script and execute it from anywhere you want.
Navigating between files and directories
pwd: current directory
ls: list files in current directory
ls *.sh: list all files in current directory that end with .sh, the * is a wildcard for any
number of characters
ls output?.dat: list files in current directory that have the form output.dat, the ? is a
wildcard for one character (i.e. output1.dat, outputx.dat, etc.).
cd: move to other directory
cd ..: move one directory up
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Manipulating files and directories

cp: copy files
cp -r: copy directory with files in it (recursively)
mv: rename and move files (technically equivalent)
rm: remove files (BE CAREFUL!! NO UNDO)
rm -r: remove directory recursively (BE CAREFUL!! NO UNDO)
mkdir: make directory
Example: type on the command line after opening a terminal: (% indicates a new terminal line)
%
%
%
%
%
pwd
ls
mkdir tutorial
cd tutorial
mv /home/datalib/Resource_Class/Unix_2007/linux_intro_all.pdf .
You have just determined where you are in the file system, what files and directories are
present in your current directory. You created a directory tutorial in your home directory,
and copied a linux manual into it. Remember the directory /home/datalib, it contains many
datasets that are very useful for this class (or anything in geophysics really).
Some special characters in Linux
.
..
: current directory
: directory up one level
~ : equivalent to your home directory

; : ending command line, separates commands
& : after a command causes it to run in the background. This is equivalent to pressing
Ctrl+z when a a process is running which suspends it, and then entering bg which keeps
it running in the background. To bring something back to the foreground, enter fg.
Editing files Editing files in Linux can very easily be done in the terminal. It takes a little
practice, but you will see it works much faster than any editor with a graphical user interface (GUI), such as Word. Another reason to use a command line-based editor is that Word
and similar programs put in formatting characters which are unreadable by the terminal and
hence not usable to write scripts with. There are various programs available for command line
editing, of which the best known are Vi and Emacs. Here we will use Vi.
% vi helloworld.sh
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This opens a new file in your current directory, named helloworld.sh. If you already had
a file with that name there, it would open that one for editing. Now you will see an empty
screen. Vi works with two modes, move-around-mode and insert-mode. When you open
a file, it opens in the move-around-mode and you cant type any new text. Here is a list of
common commands in Vi:
:i : switches from move-around-mode to insert-mode, now you can edit your file
esc button: switches back to move-around-mode
:w : saves your file
:q : quits your file and Vi, will complain if you havent saved it first
:q!
: quits your file and Vi without saving
Now try to put this on the first line of your helloworld.sh file, save it and quit Vi:
echo hello world
Creating executables Now you have a file with a command in it. You can try the command
just on the command line to see what it does. You can also run the file as an executable, so
that the computer reads the file and executes it for you. For a one-line command this seems
like a hassle, but you will soon find out that many tasks in Linux take multiple lines and are
far easier done using scripts like this. In order to run the script, you need to tell the computer
that it is an executable. This is done by changing the file permissions:
% chmod +x helloworld.sh
Now if you type:
% ./helloworld.sh
the script executes the command it contains. Its output is directed to the standard output, being the terminal command line here. For more complicated programs, ones that e.g. produce
lists with tables, you may want to redirect the output to a file:
% ./helloworld.sh > output.dat
If you open output.dat with e.g. Vi, you can see that it contains the output you first saw on
the screen. A good thing to know is that you can interrupt any running script using Ctrl+c in
that terminal.
Environment variables Another feature that can be very useful for scripts is being able to
run them from any directory, not just the one that contains the actual script. You can achieve
this by setting environment variables, in this case putting the directory that contains the script
in your PATH. First find out if your terminal is of the bash or csh flavor:
% cd ~
% ls -a
3
This command lists all files in your home directory, also the hidden ones that start with a dot.
If you have files starting with .bash in that list, you have the bash flavor. Similarly with .csh,
you have the csh variety. To set your environment variables in bash, add a line in .bashrc,
e.g. at the bottom of the file:
% vi .bashrc
:i
export PATH=~/tutorial:$PATH
:wq
% source ~/.bashrc
To set your environment variables in csh, add a line in .cshrc:
% vi .cshrc
:i
setenv PATH ~/tutorial:${PATH}
:wq
% source ~/.cshrc
Now you can run any executable scripts you put in the directory tutorial from anywhere! A
little more explanation on what you have just done: .bashrc or .cshrc is read in by the system
every time you open a terminal. It can contain environment variables just like above, or it can
contain aliases which are command substutions that you provide yourself (e.g. if you want
to use ls -a every time you enter ls, you can specify that). This file is a very important one,
so be careful when you edit it! Backing it up when you make many changes cant hurt.
Every time you make a change to this file, you will need to source it, meaning that your
current terminal has to re-read the file or it will not recognize that you made changes to it.
A terminal window that you open after making changes to an rc file will have read in the
modified file and should be fine.
Some other handy things
To open a ps or pdf file in linux, use gv with file name.
To find in which directory an executable script is located, use which with the script name.
To print a file, use e.g.:
% lp -d 366sm_hp_2side file
To find more information about a command, use man command. Also typing the command followed with --help or -h quite often works.
These days, Linux systems contain many GUI-based programs which are equivalent to what
you are familiar with on Windows system. There is Open Office, which is similar to Windows
Office. Also image editing software such as Gimp and Inkscape are extremely useful. Just go
explore!

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A very short intro to Linux

Manipulating files and directories

~ : equivalent to your home directory

: quits your file and Vi without saving

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