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Linux is an open-source operating system based on UNIX. Linux is highly versatile and is used in a wide range of applications. Desktop Linux is Linux with a GUI (like Microsoft Windows or Mac OS X); Desktop Linux is popular in niche markets, and it is used widely in developing countries.

Linux is the most widely used operating system for web servers. In CSE330, we will be interacting with Linux from the command line. This article covers the tools you need to make the best use of Linux.

Linux Distributions

The open-source community is responsible for the development of many different distributions of Linux. Distributions, or distros, are different "flavors" of the Linux operating system with different objectives.

There are hundreds of distributions of Linux. Three of the main banches are Debian, SuSE (based on Slackware), and Red Hat Enterprise Linux (RHEL). The Linux Lab in Lopata Hall uses Fedora Linux, a desktop distribution based on RHEL.

The Amazon EC2 Linux AMI is a distribution of Linux based on RHEL. The CSE330 wiki assumes that you have an instance running the Amazon EC2 Linux AMI, although you may use any distribution that you want.

Files and Permissions

At the core of a Unix-based operating system is a directory structure with files and permissions.

Filesystem Hierarchy

The root directory of Linux contains a dozen or so subdirectories, each with a specific purpose:

  • /bin contains binaries used by all users
  • /sbin contains system binaries typically used only by the system administrator
  • /lib contains libraries for the binaries found in /bin and /sbin
  • /etc contains configuration files
  • /dev contains device files
  • /proc contains information on currently running processes
  • /var contains files whose contents is expected to change
    • /var/log contains system log files
    • /var/lib contains packages and database files
    • /var/spool contains print queues
  • /tmp contains temporary files that are deleted at system reboot
  • /usr contains user programs
    • /usr/bin contains binaries for user programs
    • /usr/sbin contains binaries for system administrators
    • /usr/lib contains libraries for /usr/bin and /usr/sbin
    • /usr/local contains programs that you install from source
  • /home contains users' home directories
  • /boot contains boot loader files (do not touch unless you know what you are doing!)
  • /opt contains optional add-on applications
  • /mnt is where system administrators can mount filesystems
  • /media contains links to removable media devices (for example, CDs)
  • /srv contains site-specific data which are served by the system

For more information, see the Wikipedia article on the Filesystem Hierarchy Standard.

File Permissions

Every file in Linux has permissions that define which users can Read, Write, and Execute it. Every file has an owner and a group. The permissions for a file are set on three levels: User (owner), Group, and Other.

Symbolic Notation

When you view the permissions of a file in Linux, they will most often be displayed in symbolic notation. Symbolic notation consists of 10 characters: the first defines the file type, and then there are three characters each for User, Group, and Other permissions.

  • -r--r--r-- is a normal file that is readable by all users but writable or executable by no one.
  • -rwxr-xr-x is a normal file that is readable and executable by everyone but only writable by User (the file's owner). This is the most common permission set.

Viewing File Permissions

To view the permissions of all files in a certain directory, run the binary ls -l in Bash:

$ ls -l   # displays a list of all files in a directory with their permissions in symbolic notation
total 16
lrwxr-xr-x  1 sffc  wheel   6 Aug  9 09:13 link -> myfile.txt
-rwxr--r--  1 sffc  wheel  12 Aug  9 09:13 myfile.txt
$ ls -l myfile.txt   # displays the permissions of only myfile.txt
-rwxr--r--  1 sffc  wheel  12 Aug  9 09:13 myfile.txt

Setting File Permissions

Linux comes with several useful binaries for setting file permissions.

  • chmod is used for setting permissions
  • chown is used for setting a file's owner
  • chgrp is used for setting a file's group

Some examples are shown below.

$ chmod a+x myfile.txt   # turns on the Execute option for all users
$ chmod o-w myfile.txt   # turns off the Write option for Other users
$ chmod u+wx-r myfile.txt   # turns on the Write and Execute options for User (the file's owner) and also turns off the Read option for User
$ chown todd myfile.txt   # sets the owner of myfile.txt to the user todd.  Note: First comes the user, then comes the filename: not the other way around!
$ chgrp staff myfile.txt   # sets the group of myfile.txt to usergroup staff

The . and .. Directories

The . directory is a reference to the current directory. The .. directory brings you one level up in the filesystem.

$ pwd
$ cd projects
$ pwd
$ cd ./
$ pwd
$ cd ../
$ pwd

Symbolic Links

A symbolic link, or symlink, is basically a link from one spot in the filesystem to another. You can think of them like aliases in Mac OS X. To create a a symlink, use the ln -s command:

$ ln -s /path/to/file.txt /path/to/link   # creates a symlink to file.txt at /path/to/link

# Example:
$ ln -s /home/todd/instructions.doc /var/www/public_html/classes/instructions.doc   # creates a symlink in the web server to instructions.doc
$ vi /var/www/public_html/classes/instructions.doc   # changes to the symbolic link will be reflected in the original file


Bash is the default shell environment in Linux; that is, it is the interface in which you will be interacting with your Linux server. Bash is a derivative of sh, one of the first shells. Other popular shells include csh and tcsh, shells with c-like syntax for scripting, and zsh a bash-like shell which focuses on extending the capabilities of the shell environment.

Displaying a Value

To display a value at the shell prompt, use the command echo.

$ echo "Hello World" # displays Hello World
Hello World

Note: In examples, code written at the prompt is conventionally denoted by a line starting with a currency symbol. Lines without a currency symbol represent output.

Seeing the contents of a file

If you want to see the contents of a file, use the cat command.

$ cat myfile.txt
Hello World

cat is one of a number of useful Linux command-line binaries, the rest of which we will see later.


Bash supports the use of variables. There are system-defined variables, and you can also define your own custom variables.

Defining and Accessing Variables

$ MYVARIABLE="Hello World"    # assigns the value Hello World to the variable MYVARIABLE
$ echo $MYVARIABLE     # notice that you need to put a currency symbol in front of the variable in order to access its value
Hello World
$ export $MYVARIABLE     # allows MYVARIABLE to be accessed in child processes (e.g., in a program you call from the shell)
$ export MYVARIABLE="Hello Moon"     # a shortcut for defining a variable and exporting it to subprocesses
$ set     # displays a list of all currently set variables

System Variables

Bash comes pre-loaded with certain environment variables. Some of the variables with which you may find yourself interacting include:

  • PATH: search path for the commands
  • PWD: name of the current directory
  • SHELL: type of shell
  • TERM: type of the terminal
  • USER: the account name
  • HOME: the user's home directory
  • PS1: the prompt at command line
  • $$: the process id of current shell
  • $RANDOM: a random value
  • $?: the return value of the last command
  • $_: the last argument of the previous command
  • $#: where # is a number, the value of the #th argument
  • IFS: input field separator

Try echoing some of the system variables to examine your current environment.

Running Programs

To run an executable file, simply enter its filename into the shell prompt:

$ /usr/bin/perl -v   # runs the binary executable located at /usr/bin/perl with the flag -v
This is perl 5, version 12, subversion 3 (v5.12.3)
$ ../mydir/myprogram   # runs the binary located one level up in the file system, then in mydir/myprogram
You just ran myprogram!

Many commonly-used executable binaries are located in /bin, /usr/bin, and similar directories. In order to avoid typing paths to these directories every time you want to execute a command, you define these directories in your PATH system variable:

$ echo $PATH   # displays the current value of the PATH variable
$ PATH=$PATH:/my/favorite/bin   # adds a directory to your PATH variable
$ echo $PATH

Notice that the different PATH directories are separated by colons. Now, when you execute a command, Bash will scan all of the directories in your PATH variable. To see the path to the binary that Bash found, use the which command.

$ perl -v
This is perl 5, version 12, subversion 3 (v5.12.3)
$ which perl

Note: it is unwise to have . in your PATH. Instead, if you want to run an executable in the current directory, do so by calling ./myprogram:

$ ./myprogram
You just ran myprogram!
$ myprogram
-bash: myprogram: command not found

Foreground and Background Processes

A program runs in the foreground (unless it detaches itself from the terminal) by default. You can run a program in the background by adding & at the end of the command (after arguments). In this case, the shell would fork a process for that program and enable the command prompt back for input. At any time, jobs command can be used to see the processes running at the background. fg command brings the specified process back to foreground. A program running in the background can be stopped by typing ctrl-c in most cases. Typing ctrl-z interrupts a program running in the foreground. If a program is interrupted, it will not continue executing until it is resumed. An interrupted program can be brought back to foreground by fg, or it could be send to background by bg.

$ ./myprogram
You just ran myprogram!
I'm taking a long time to run.
$ jobs
$ ./myprogram
You just ran myprogram!
I'm taking a long time to run.
[1]+  Stopped                 ./myprogram
$ jobs
[1]+  Stopped                 ./myprogram
$ bg
[1]+ ./myprogram &
$ jobs
[1]+  Running                 ./myprogram &
$ fg
$ jobs
$ ./myprogram &
[1] 64741
$ jobs
[1]+  Running                 ./myprogram &

Killing Processes

A process can be killed by using the kill command: kill process-number

In some cases the kill signal can be ignored, so it may be necessary to force kill the program by sending an absolute KILL signal: kill -9 process-number

The current processes can be listed using the ps command.

$ ps   # list currently running processes in the current shell
  PID TTY           TIME CMD
19107 ttys000    0:00.75 -bash
 1873 ttys001    0:00.05 -bash
57267 ttys002    0:00.20 -bash
50721 ttys003    0:00.55 -bash
$ ps -eaf   # list all currently running processes
  UID   PID  PPID   C STIME   TTY           TIME CMD
    0     1     0   0 31Dec00 ??         3:24.45 /sbin/launchd
    0 19106   327   0  1Aug12 ttys000    0:00.03 login -pfl sffc /bin/bash -c exec -la bash /bin/bash
  501 19107 19106   0  1Aug12 ttys000    0:00.75 -bash
    0  1872   327   0 31Jul12 ttys001    0:00.02 login -pfl sffc /bin/bash -c exec -la bash /bin/bash
  501  1873  1872   0 31Jul12 ttys001    0:00.05 -bash
    0 57266   327   0 Mon05AM ttys002    0:00.08 login -pfl sffc /bin/bash -c exec -la bash /bin/bash
  501 57267 57266   0 Mon05AM ttys002    0:00.20 -bash
    0 64747 57267   0  9:58AM ttys002    0:00.00 ps -eaf
    0 50720   327   0 Fri12AM ttys003    0:00.03 login -pfl sffc /bin/bash -c exec -la bash /bin/bash
  501 50721 50720   0 Fri12AM ttys003    0:00.55 -bash

Directing Output

A program's standard output can be send to a file by typing >filename at the end. Similarly, >> appends to a file. In Linux, there are three default file handlers, standard input or STDIN, standard output or STDOUT, and standard error or STDERR. STDOUT has a file handler number 1 and STDERR has a number of 2. In bash, you can direct either of these handlers to a file. You can also redirect one file handler to another.

$ ./myprogram >filename.txt   # redirects all output to filename.txt
$ cat filename.txt
You just ran myprogram!
$ ./myprogram >>filename.txt   # appends the output to filename.txt
$ cat filename.txt
You just ran myprogram!
You just ran myprogram!
$ ./myprogram 1>filename.txt   # redirects the standard output to filename.txt
$ cat filename.txt
You just ran myprogram!
$ ./myprogram 2>filename.txt   #redirects the error output to filename.txt
You just ran myprogram!
$ ./myprogram 2>&1   # STDERR is redirected to STDOUT
You just ran myprogram!

Output of one program can be redirected to the input of another program using pipes.

$ ./program1 | ./program2   # send program1's output as an input to program2
You just ran program2 with the input: You just ran program1!

Redirection is possible for STDIN too. A program can get its input by redirecting STDIN using <

$ ./myprogram < inputfile.txt
You just ran myprogram with input from inputfile.txt!

Finally, ` (a backtick) can be used to capture the output of a program, and use it as a string such as in setting a variable

$ MYVARIABLE=`./myprogram`
You just ran myprogram!

Programming in the Shell

As bash is nothing but a command interpreter, it actually comes with a built-in programming language. Users can take advantage of this powerful language to simplify and automate various tasks. Programs written in shell languages (and other interpreted languages) are referred to as scripts. They can be run from the command line like any other program using the correct shell program as the interpreter. The scripts themselves are just text files with lists of commands. For example,

$ bash commandfile
You just ran commandfile!

reads and executes the commands from the text file named commandfile. A better approach is to make commandfile executable and run it as if it were a compiled program. For this to work, you must also specify the interpreter of commandfile on the first line of the script file, starting with #! (pronounced sha-bang).

$ cat commandfile
echo "You just ran $0!"
$ chmod a+x commandfile
$ ./commandfile 
You just ran commandfile!


Any line in a bash script is a program to be executed. Lines are broken with ;

Conditional statements

Bash supports if statements. The format is




CONDITION could be a logical statement or it could be a test (run man test for more details). For example

if [ $val = 5 ]


if [ $val -eq 5 ]; then
	echo value is 5
if [ somefile1 -ot somefile2 ]; then
	echo somefile1 is older than somefile2

Bash also has case statements. The format is

case $mywar in

In this case, ;; means end of a case block and * means catch anything.

In general, you will nearly always put string variables in quotes, ". To see why, remember that shell variables are simply expanded to their content when used. For example,

myvar="Some very good text was here. Now it is gone and all that is left is this boring message"
if [ $myvar = "This is very good text" ]

would fail with an error message as $myvar would be expanded to its content, like this:

if [ Some very good text was here. Now it is gone and all that is left is this boring message = "This is very good text" ]

To avoid this, you should have the statement as

if [ "$myvar" = "This is very good text" ]

Loop statements

Bash provides standard loop statements, for, while, until. They can be executed in a script or it could be typed at the command prompt.

The format of for statement is

for VAR in somevalue1 somevalue2 .... somevaluen

This loop will execute the for block for each value of VAR. For example,

for i in 1 2 3 4 5 6 7 8 9 10

would sum numbers from 1 to 10. We can also use other techniques in for line, e.g. replacing for in the above code with

for i in `seq 1 1000`

would get the sum from 1 to 1000. Note the usage of `

The format of while and until are very similar

while [ CONDITION ]
	execute some command

until [ CONDITION ]
	execute some command

For both of these commands, CONDITION is the same as for the if statement.


Bash also provides functions. They could be defined at the command prompt and then can be called from command prompt. The structure of a function is similar to most modern languages.

	execute some commands

The function can then be called with:


You can send parameters to the function by adding them next to the function name:

myfunction arg1 arg2 ....

Within a function, you can access the arguments using $#, i.e., $1 for first argument, $2 for second argument, etc.

Additional Information

Advanced Bash-Scripting Guide.