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.

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

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 site: https://www.geeksforgeeks.org/linux-tutorial/

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:" 
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
gligar07.gastly.os

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:
gligar07.gastly.os

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
/bin/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:
gligar07.gastly.os

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#

Command	Description
`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#

Command	Description
`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

Editor#

Command	Description
`emacs`
`nano`	Nano's ANOther editor, an enhanced free Pico clone
`vi`	A programmer's text editor

File Commands#

Command	Description
`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#

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

Network Commands#

Command	Description
`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 an ICMP packet if the host responds. This command is useful to check whether your computer is connected or not.

Other Commands#

Command	Description
`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#

Command	Description
`&`	In order to execute a command in the background, place an ampersand (`&`) at the end of the command line. A user job number (in brackets) and a system process number are displayed. The system process number identifies the job, while the user job number is used by the user.
`at`	Executes commands at a specified time
`bg`	Places a suspended job in the background
`crontab`	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 either the user job number or the system process number as an argument
`ps`	Reports a snapshot of the current processes
`top`	Displays Linux tasks

User Account Commands#

Command	Description
`chmod`	Modify properties for users