Linux command line Basics

The command line in Linux is referred to as a shell. The shell is a program that allows the user to interact with Linux at the command line. Most work to be done on the cluster will be done using the command line (shell). Once you logged in to the cluster using SSH, you will be in your home directory on a shell prompt (username@server:~$_). The following are some of the commands for system operations via the shell

Man pages

Man pages refers to manual pages on Linux. They provide the help guide for most commands and applications on linux. Most Linux files and commands have pretty good man pages to explain their use. Type man followed by a command (for which you want help) and start reading. Press q to quit the man page. sample below:

username@allot:~$ man whoami (shows manual page for the command whoami)
username@allot:~$ man syslog.config (shows the manual page for a configuration file)
username@allot:~$ man syslogd (show the manual for a daemon (background program))

Working with directories

The Linux filesystem is based around files and directories. Users issue commands to navigate around the filesystem. The common file system commands to work with include pwd, cd, ls, mkdir, cp, touch etc . These commands are available on any Linux system.

This section will also discuss absolute and relative paths and path completion in the bash shell.

pwd

The pwd (Print Working Directory) command basically displays the current directory you are in. This would appear as:

username@allot:~$ pwd
/home/username

cd

On the command line cd (or change directory) changes your current directory to the one specified:

There is also a shortcut back to your home directory by typing the character ~ (tilda) which has the same effect as typing (for example) /home/user.

username@allot:~$ cd ~
username@allot:~$ pwd
/home/user

The filesystem is usually organized as hierarchies, To go to the directory above (higher hierarchy or parent directory), we use the characters ..

username@allot:~$ pwd
/home/user
username@allot:~$ cd ..
username@allot:~$ pwd
/home

There is also the character. which means the current directory. This is not useful for the cd command but is very useful for copying files to your current directory.

Absolute and relative paths

Important to note that When you type a path starting with a slash (/), then the root of the file tree is assumed. If you don’t start your path with a slash, then the current directory is the assumed starting point.

/directory1/directory2 is not the same as directory1/directory2

/ on linux systems is known as ROOT Directory, Which signifies the beginning of the file-system hierarchy

Absolute path:

username@allot:~$ pwd
/home/user
user@allot:~$ cd /var
user@allot:~$ pwd
/var

Relative path

username@allot:~$ pwd
/home/user
username@allot:~$ cd myfiles
username@allot:~$ pwd
/home/user/myfiles

The command line will help you in typing a path without errors. If you type a partial command such as:

username@allot:~$ cd /home/user/my

Pressing the TAB key on your keyboard will fill in the rest of the directory name (or filename/program) depending on the uniqueness, or presence.

username@allot:~$ cd /home/user/myfiles

ls

This command lists the contents of a directory:

username@allot:~$ ls
myfile1.txt myfile2.txt workdirectory1

ls has a number of useful different options to format the output listing.

username@allot:~$ ls –l (show a long listing with more information)
username@allot:~$ ls –a (show all files including those that are hidden)
username@allot:~$ ls –la (combines both of the options above)

mkdir

This commands creates a directory (folder) in the current (or specified) directory:

username@allot:~$ mkdir workdirectory1
username@allot:~$ cd workdirectory1
username@allot:~$ pwd
/home/user/workdirectory1

rmdir

This command removes the specified directory, note the directory must be empty and must not be the directory you are currently in:

username@allot:~$ rmdir workdirectory1

Working with files

Working on the linux shell would require you to carry out file operations using commands to create, remove, copy, move and rename files.

When working with files on linux you have to know that MYFILE1 is not the same as MYfile1 or myfile1 due to case sentivity. Also Linux treats everything on Linux as a file. A directory is a special kind of file, but it is still a (case sensitive!) file. Each terminal window (for example /dev/pts/4), any hard disk or partition (for example /dev/sdb1), and any process are all represented somewhere in the file system as a file. It is important to note that not all files or directories are accessible to every user. File and directory access is dependent on the permissions on the latter. As with most commands in linux, options can be specified while executing any given command e.g. ls -l

file

This command determines the file type. Unlike Windows, Linux does not determine the file type from the extension but from examining the file header/contents itself.

username@allot:~$ file mypicture.png
pic33.png: PNG image data, 3840 x 1200, 8-bit/color RGBA, non-interlaced
username@allot:~$ file parallel.c
parallel.c: ASCII C program text

touch

This creates an empty file, which can be useful for various uses.

username@allot:~$ touch newfile.c
username@allot:~$ ls
newfile.c

rm

Remove a file, as always be very careful with this command and without a backup, this file will be lost forever.

username@allot:~$ rm –rf mydirectory (works recursively down the specified directory to remove non-empty directories with the –f option which means force. This is a very powerful option which must be used with extreme care!)

As with many Linux commands there are a few options with can be used with rm (these can be view by typing man rm).

cp

Copy files or directories from a source to a destination:

Command syntax is ‘cp SOURCE DESTINATION’

username@allot:~$ cp workfile.c mybackup.c (copies workfile.c to mybackup.c)
username@allot:~$ cp workfile.c mydirectory1 (copies workfile.c to mydirectory1)
username@allot:~$ cp \*c backupdirectory/ (copies all \*.c files to backupdirectory)
username@allot:~$ cp –r mydirectory1 mydirectory2 (copies one directory to another, note the option –r for recursive copying)

As with many Linux commands there are a few options with can be used with cp (these can be view by typing man cp).

mv

Move files from a source to a destination. A versatile command that can rename a file too:

username@allot:~$ mv file1.c testfile.c (rename file1.c to testfile.c)
username@allot:~$ mv directory1 directory2 (rename directory)
username@allot:~$ mv file1.c /home/user/myrepo (mv file1.c to /home/user/myrepo/file1.c)

rename

Although preferably to use the mv command, this command does exist to rename files

Working with file contents

This section will look at working with file contents themselves, such commands are head, tail, cat, tac, more and less.

head

By default, the head command will show the first ten lines of a file.

username@allot:~$ head /etc/passwd
root:x:0:0:root:/root:/bin/bash
daemon:x:1:1:daemon:/usr/sbin:/bin/sh

tail

Similar to head but this time it will show the last 10 lines of the file by default.

username@allot:~$ tail /etc/services
vboxd 20012/udp
binkp 24554/tcp             # binkp fidonet protocol
asp 27374/tcp               # Address Search Protocol
asp 27374/udp
csync2 30865/tcp            # cluster synchronization tool
dircproxy 57000/tcp         # Detachable IRC Proxy
tfido 60177/tcp             # fidonet EMSI over telnet
fido 60179/tcp              # fidonet EMSI over TCP

cat

The cat command (short for concatenate) one of the most universal tools, yet all it does is copy standard input to standard output. In combination with the shell, this can be very powerful and diverse. Some examples will give a glimpse into the possibilities.

username@allot:~$ cat /etc/resolv.conf
domain example.com
search example.com
nameserver 192.168.1.42
username@allot:~$ cat file1.c file2.c >file3.all (concatenate c files into file3.all)

tac

Works the same as cat but will show you the file backwards:

username@allot:~$ cat numbers
one
two
three

username@allot:~$ tac numbers
three
two
one

more

The more command is useful for displaying files that take up more than one screen. More will allow you to see the contents of the file page by page. Use the space bar to see the next page, or q to quit. Some people prefer the less command to more.

less

Very similar to more but with some additional features

Basic Linux Tools

This chapter introduces commands to find or locate files and to compress files, together with other common tools that were not discussed before.

find

This command is very useful to find files, more options are provided on the command line by typing man find. Here are some useful examples below:

username@allot:~$ find /etc (find all files in the /etc directory) username@allot:~$ find . –name “*.conf” (find all files that end in .conf from the current directory) username@allot:~$ find . –newer file1.c (find all files newer than file1.c) username@allot:~$ find /etc >etcfiles.txt (find all files but this time put them in (pipe) to the file etcfiles.txt)

date

The date command can display the date, time, time zone, and more.

username@allot:~$ date
Tue Jan 14 12:18:58 PM WAT 2025

cal

The cal command displays the current month, with the current day highlighted.

sleep

The sleep command is sometimes used in scripts to wait a number of seconds. This example shows a five-second sleep.

username@allot:~$ sleep 5 (five seconds later)
username@allot:~$

sort

The command sort will sort lines of text files. By default, the output is to the screen but this can be piped to a file or another program.

username@allot:~$ sort myfile.txt
apple
banana
cherry

gzip – gunzip

This is a useful compression program (like zip which also exists in Linux). The gzip command can make files take up less space.

username@allot:~$ gzip myfile.c (will create myfile.c.gz)
username@allot:~$ gunzip myfile.c.gz (will create myfile.c again)

bzip2 – bunzip2

Files can also be compressed with bzip2 which takes a little more time than gzip, but compresses better.

username@allot:~$ bzip2 myfile.c (will create myfile.c.bz2)
username@allot:~$ bunzip2 myfile.c.bz2 (will create myfile.c again)

zip – unzip

A compression program which is compatible with other zip programs found in MS Windows and other OSes.

username@allot:~$ zip myfile.c (will create myfile.c.zip)
username@allot:~$ unzip myfile.c.zip (will create myfile.c again)

grep

The grep filter is famous among Linux (and UNIX) users. The most common use of grep is to filter lines of text containing (or not containing) a certain string.

username@allot:~$ grep “word” /folder/file

As with most Linux commands, there are also a large number of useful options that will go with each command and grep is certainly no exception here

username@allot:~$ grep –i “Word” /folder/file (search in a case insensitive way)
username@allot:~$ grep –r “Word” /folder/folder (search recursively down any directories too)
username@allot:~$ grep –v “Word” /folder/file (search for everything not containing “Word”)

wc

Counting words, lines, and characters are easy with wc.

username@allot:~$ wc myfile.c (show number of words, lines, and characters)
5 10 100 tennis.txt

File Permissions

Introduction

Similar to many other operating systems Linux uses a method of access rights on files and directories. These can be view by using the ls command

username@allot:~$ ls –l (option l is for long listing)

-rwx–x–x 1 hpcuser001 hpcuser001 68 Jan 14 12:15 newfile.sh -rwxr-xr-x 1 hpcuser001 hpcuser001 265 Jan 13 11:45 script_slurm_hostname.sh -rwx—— 1 hpcuser001 hpcuser001 235 Jan 13 12:49 script_slurm_jupyterlab.sh -rw–r–r– 1 hpcuser001 hpcuser001 147 Jan 13 11:50 slurm-778.out -rwx—— 1 hpcuser001 hpcuser001 3415 Jan 13 11:54 slurm-779.out -rwx—— 1 hpcuser001 hpcuser001 2580 Jan 13 12:51 slurm-787.out drwx—— 2 hpcuser001 hpcuser001 2 Jan 14 12:12 workdirectory1

Each file and directory has access rights that are associated with each one. When we look at the 10 symbol string above on the left-hand side (e.g. drwxr-xr-x).

The first letter present whether the file is a directory or not.
The next three represent the file permission for the user that owns that file (i.e. dbird in this example).
The next three represent the file permission of the group to whom that user belongs (i.e. group admin).
The last three represent the file permissions for everyone else (i.e. all users).

For each of the permission parts the letters mean the following in their groups:

r indicates read permission to read and copy the file, its absence indicates this is not available.
w indicates write permission to write the file, its absence indicates this is not available.
x indicates execution permission to allow the file to be executed, its absence indicates this is not available.

Using the example above would mean:

Example (1) has read/write access for user dbird and read access only for everyone else.
Example (2) is a directory with full access for user dbird and read access for only users in the admin group.
Example (3) is an application which is only accessible by the user dbird, note not only is it read and write but it also has its ‘execution’ permission set for that user also.

Changing access rights

This command allows the user to change file (and directory) permissions.

u User
g Group
o Other
a All
r Read
w Write (and erase)
x Execution (and access directory
- Add permission
- Remove permission

username@allot:~$ chmod go-rwx myfile.c (remove read, write and execute permissions removed for group and other)
username@allot:~$ chmod u+x myapp.pl (make the program myapp.pl executable to the user (i.e. the owner of the file))

Text editing

In order to edit files on linux terminal, programs such as vim, emacs, nano can be used.

username@allot:~$ nano myfile1.c (opens a new file in the nano text editor)

Environment variables

The following variables are automatically available after you log in:

$USER your account name
$HOME your home directory
$PWD your current directory

You can use these variables on the command line or in shell scripts by typing $USER, $HOME, etc. For instance: ‘echo $USER’. A complete listing of the defined variables and their meanings can be obtained by typing ‘printenv ‘.

You can define (and redefine) your own variables by typing:

export VARIABLE=VALUE

Aliases

If you frequently use a command that is long and has for example many options to it, you can put an alias (abbreviation) for it in your ~/.bashrc file. For example, if you normally prefer a long listing of the contents of a directory with the command ‘ls -laF | more’, you can put following line in your ~/.bashrc file:

alias ll='ls -laF \| more'

You must run ‘source ~/.bashrc’ to update your environment and to make the alias effective, or log out and in :-). From then on, the command ‘ll’ is equivalent to ‘ls -laF | more’. Make sure that the chosen abbreviation is not already an existing command, otherwise you may get unexpected (and unwanted) behavior. You can check the existence and location of a program, script, or alias by typing:

which [command]
whereis [command]

~/bin

If you frequently use a self-made or self-installed program or script that you use in many different directories, you can create a directory ~/bin in which you put this program/script. If that directory does not already exist, you can do the following. Suppose your favorite little program is called ‘myscript’ and is in your home ($HOME) directory:

mkdir -p $HOME/bin cp myscript $HOME/bin export PATH=$PATH:$HOME/bin

PATH is a colon-separated list of directories that are searched in the order in which they are specified whenever you type a command. The first occurrence of a file (executable) in a directory in this PATH variable that has the same name as the command will be executed (if possible). In the example above, the ‘export’ command adds the ~/bin directory to the PATH variable and any executable program/script you put in the ~/bin directory will be recognized as a command. To add the ~/bin directory permanently to your PATH variable, add the above ‘export’ command to your ~/.bashrc file and update your environment with ‘source ~/.bashrc’.

Make sure that the names of the programs/scripts are not already existing commands, otherwise you may get unexpected (and unwanted) behaviour. You can check the contents of the PATH variable by typing:

printenv PATH
echo $PATH