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Useful Linux Commands#

Basic Linux Usage#

All the HPC clusters run some variant of the "Red Hat Enterprise Linux" operating system. This means that, when you connect to one of them, you get a command line interface, which looks something like this:

vsc40000@ln01[203] $

When you see this, we also say you are inside a "shell". The shell will accept your commands, and execute them.

ls Shows you a list of files in the current directory
cd Change current working directory
rm Remove file or directory
nano Text editor
echo Prints its parameters to the screen

Most commands will accept or even need parameters, which are placed after the command, separated by spaces. A simple example with the "echo" command:

$ echo This is a test
This is a test

Important here is the "$" sign in front of the first line. This should not be typed, but is a convention meaning "the rest of this line should be typed at your shell prompt". The lines not starting with the "$" sign are usually the feedback or output from the command.

More commands will be used in the rest of this text, and will be explained then if necessary. If not, you can usually get more information about a command, say the item or command "ls", by trying either of the following:

$ ls --help 
$ man ls
$  info ls 

(You can exit the last two "manuals" by using the "q" key.) For more exhaustive tutorials about Linux usage, please refer to the following sites:

How to get started with shell scripts#

In a shell script, you will put the commands you would normally type at your shell prompt in the same order. This will enable you to execute all those commands at any time by only issuing one command: starting the script.

Scripts are basically non-compiled pieces of code: they are just text files. Since they don't contain machine code, they are executed by what is called a "parser" or an "interpreter". This is another program that understands the command in the script, and converts them to machine code. There are many kinds of scripting languages, including Perl and Python.

Another very common scripting language is shell scripting. In a shell script, you will put the commands you would normally type at your shell prompt in the same order. This will enable you to execute all those commands at any time by only issuing one command: starting the script.

Typically in the following examples they'll have on each line the next command to be executed although it is possible to put multiple commands on one line. A very simple example of a script may be:

echo "Hello! This is my hostname:" 

You can type both lines at your shell prompt, and the result will be the following:

$ echo "Hello! This is my hostname:"
Hello! This is my hostname:
$ hostname

Suppose we want to call this script "foo". You open a new file for editing, and name it "foo", and edit it with your favourite editor

$ nano foo

or use the following commands:

$ echo "echo Hello! This is my hostname:" > foo
$ echo hostname >> foo

The easiest ways to run a script is by starting the interpreter and pass the script as parameter. In case of our script, the interpreter may either be "sh" or "bash" (which are the same on the cluster). So start the script:

$ bash foo
Hello! This is my hostname:

Congratulations, you just created and started your first shell script!

A more advanced way of executing your shell scripts is by making them executable by their own, so without invoking the interpreter manually. The system can not automatically detect which interpreter you want, so you need to tell this in some way. The easiest way is by using the so called "shebang" notation, explicitly created for this function: you put the following line on top of your shell script "#!/path/to/your/interpreter".

You can find this path with the "which" command. In our case, since we use bash as an interpreter, we get the following path:

$ which bash

We edit our script and change it with this information:

#!/bin/bash echo \"Hello! This is my hostname:\" hostname

Note that the "shebang" must be the first line of your script! Now the operating system knows which program should be started to run the script.

Finally, we tell the operating system that this script is now executable. For this we change its file attributes:

$  chmod +x foo

Now you can start your script by simply executing it:

$ ./foo
Hello! This is my hostname:

The same technique can be used for all other scripting languages, like Perl and Python.

Most scripting languages understand that lines beginning with "#" are comments, and should be ignored. If the language you want to use does not ignore these lines, you may get strange results ...

Linux Quick reference Guide#

Archive Commands#

tar An archiving program designed to store and extract files from an archive known as a tar file.
tar -cvf foo.tar foo/ compress the contents of foo folder to foo.tar
tar -xvf foo.tar extract foo.tar
tar -xvzf foo.tar.gz extract gzipped foo.tar.gz

Basic Commands#

ls Shows you a list of files in the current directory
cd Change the current directory
rm Remove file or directory
mv Move file or directory
echo Display a line or text
pwd Print working directory
mkdir Create directories
rmdir Remove directories


nano Nano's ANOther editor, an enhanced free Pico clone
vi A programmers text editor

File Commands#

cat Read one or more files and print them to standard output
cmp Compare two files byte by byte
cp Copy files from a source to the same or different target(s)
du Estimate disk usage of each file and recursively for directories
find Search for files in directory hierarchy
grep Print lines matching a pattern
ls List directory contents
mv Move file to different targets
rm Remove files
sort Sort lines of text files
wc Print the number of new lines, words, and bytes in files

Help Commands#

man Displays the manual page of a command with its name, synopsis, description, author, copyright etc.

Network Commands#

hostname show or set the system's host name
ifconfig Display the current configuration of the network interface. It is also useful to get the information about IP address, subnet mask, set remote IP address, netmask etc.
ping send ICMP ECHO_REQUEST to network hosts, you will get back ICMP packet if the host responds. This command is useful when you are in a doubt whether your computer is connected or not.

Other Commands#

logname Print user's login name
quota Display disk usage and limits
which Returns the pathnames of the files that would be executed in the current environment
whoami Displays the login name of the current effective user

Process Commands#

& In order to execute a command in the background, place an ampersand (&) on the command line at the end of the command. A user job number (placed in brackets) and a system process number are displayed. A system process number is the number by which the system identifies the job whereas a user job number is the number by which the user identifies the job
at executes commands at a specified time
bg Places a suspended job in the background
crontab crontab is a file which contains the schedule of entries to run at specified times
fg A process running in the background will be processed in the foreground
jobs Lists the jobs being run in the background
kill Cancels a job running in the background, it takes argument either the user job number or the system process number
ps Reports a snapshot of the current processes
top Display Linux tasks

User Account Commands#

chmod Modify properties for users