Linux

Table of Contents

Shell

Shell

The command line interface is called a shell and on Ubuntu, the default shell is bash.

After logging in, you will be in your HOME directory. Usually, it is in '/home/username' but on this cluster, your home will be inside '/home_nfs/username'.

This directory is stored on the storage array of the head node of the cluster and its content will be shared over the network.

Whichever server you log in, you will always get into your home folder (represented by a ~ in the prompt).

Here is the meaning behind the prompt look :

[demo@datamaster ~]$          (1)
[user@hostname   directory]$  (2)

1	You are the user demo and you are in your home directory on the datamaster server.
2	User@Server directory

Table 1. Comparison between Windows and Linux
	Windows	Linux
Root	c:\	/
User’s directory	C:\Users\username	/home_nfs/username
Programs path	c:\Program Files\	/usr/bin/

How to move in the filesystem tree

Here is an example that shows how to move in the filesystem tree :

[demo@datamaster ~]$ pwd
/home_nfs/demo

[demo@datamaster ~]$ mkdir scripts
[demo@datamaster ~]$ cd scripts
[demo@datamaster scripts]$ pwd
/home_nfs/demo/scripts

[demo@datamaster scripts]$ cd ..
[demo@datamaster ~]$ pwd
/home_nfs/demo/

[demo@datamaster ~]$ mkdir -p sources/python
[demo@datamaster ~]$ cd /home_nfs/demo/sources/python
[demo@datamaster python]$ pwd
/home_nfs/demo/sources/python

Table 2. Command change directory
Return to your home	cd	cd ~
Go up in the tree	cd ..
Return to last dir	cd -
Move to a relative path	cd ../../usr/local/share
Move to an absolute path	cd /usr/local/share

Creating files and directories

You can create files in several ways.

The touch command, which is used to modify the timestamps of a file, also allows you to create an empty file if no file with the name passed as argument exists in the current folder.

Creating an empty file with touch

$ touch hello.txt
$ ls hello.txt -l
-rw-rw-r--. 1 demo demo 0 26 jun 11:50 hello.txt

This file can be opened with a test editor like nano or vim.

Opening a file with nano

$ nano hello.txt (1)

$ cat hello.txt
Hello World !
...
$ ls hello.txt -l
-rw-rw-r--. 1 demo demo 342 26 jun 11:50 hello.txt

1	See capture below.

Figure 1. Nano

A file can be created by redirecting a stream :

Streams Redirections

$ ls /usr/lib/ -l >> apps.txt

$ ls -lh apps.txt
-rw-rw-r--. 1 guttadauriaa guttadauriaa 44K 26 jun 12:07 apps.txt

A double >> adds the stream to the end of an existing file but a single one > will replace the existing content by the new one.

Erasing files and folders

The rm command allows you to delete files.

Erasing files

$ rm hello.txt
$ ls hello.txt -l
-rw-rw-r--. 1 demo demo 0 26 jun 11:50 hello.txt

The rmdir command allows you to delete empty directories.

Erasing a folder

$ mkdir files/
$ touch files/hello.txt
$ ls hello.txt -l
-rw-rw-r--. 1 demo demo 0 26 jun 11:50 hello.txt
$ rmdir files
rmdir: cannot delete 'files': The directory is not empty
$ rm files/*.txt
$ rmdir files

Programs and Environment Variables

In POSIX systems like Linux, applications are mainly installed in the /usr/bin directory for users and /usr/sbin for system commands. Applications can share code with dynamic libraries which are stored in /usr/lib or /usr/lib64.

You can run a program by entering its full path in a terminal :

Running applications

$ /usr/bin/g++ --version
g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0

For not having to enter full paths to applications, a variable named PATH is defined. It contains a list of directories where are stored the system’s apps.

Thanks to it, you can run these apps by entering their names :

Variable $PATH

$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

$ gcc --version
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0

$ which gcc
/usr/bin/gcc

This works out of the box for the apps installed from the software manager of the system but not for the programs you downloaded or built in your home directory.

For these, you will need to add their directories in the PATH :

Adding a directory to the PATH

# Downloading Go language
$ wget https://dl.google.com/go/go1.18.6.linux-amd64.tar.gz
$ tar -xf go1.18.6.linux-amd64.tar.gz -C ~/bin/

# Adding its directory in the PATH
$ export PATH=$HOME/bin/go/bin:$PATH
/home_nfs/demo/bin/go/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

$ go version
go version go1.18.6 linux/amd64

$ which go
/home_nfs/demo/bin/go/bin/go

The modified PATH variable will only be active for the current session and will revert after exiting. In order to preserve this change, you can add this line in your ~/.bashrc ou ~/.bash_profile file.

$ echo 'export PATH=$HOME/bin/go/bin:$PATH' >> ~/.bashrc

This use case is really simple but often software needs dynamic libraries (.so on Linux, .dll on Windows). Then, you need to add their folders to another variable named $LD_LIBRARY_PATH. Furthermore, other environment variables could be necessary at execution or when compiling a framework.

Then comes another problem. What happens when, for example, you need to use different versions of OpenMPI for different projects ? Of course, you can add several directories leading to the mpirun command in the PATH variable but only the first occurence would be used.

Modifying theses variables can be tedious and are sources of errors. This is the reason why the environment modules have been created.

Scripts

A script is a file containing a set of instructions in an interpreted language like bash, Python or Ruby as examples.

Here is a bash script that write "Hello World !" on the standard output :

Content of my_script.sh

#!/bin/bash
NAME=$1

if [[ -n $NAME ]]; then
    echo "Hello $NAME !"
    exit
fi

echo "Hello World !"

[demo@datamaster ~]$ ls scripts
my_script.sh
[demo@datamaster ~]$ ./scripts/my_script.sh Adriano  (1)
Hello Adriano !
[demo@datamaster ~]$ cd scripts
[demo@datamaster scripts]$ ./my_script.sh    (1)
Hello World !
[demo@datamaster scripts]$ cd -
[demo@datamaster ~]$ /home_nfs/demo/scripts/my_script.sh (2)
Hello World !

1	Called from a relative path with an argument
2	Called from an absolute path (from the root '/' of the tree)

The script need to be executable in order to call it directly.

Here is how you can verify if it has the execution permission :

[demo@datamaster scripts]$ ls -l script.sh
-rw-rw-r--. 1 demo demo 104 29 jun 15:05 script.sh

[demo@datamaster scripts]$ chmod u+x script.sh

[demo@datamaster scripts]$ ls -l script.sh
-rwxrw-r--. 1 demo demo 104 29 jun 15:05 script.sh

Bash scripting cheatsheet

Here is a list of commands

ls: List files
cd: Change directory : move around the file systems
pwd: Present working directory : print where you are.
mkdir: Make directory : Create a new directory
rm: Remove file : Delete a file
rmdir: Remove directory : delete an empty directory
file: Give information on a file
nano: edit a file (simple)
vim: edit a file (advanced)
ssh: Secure Shell : go to another server through an encrypted connection
htop: Show computer status (quit with 'q')
chmod: Change modificator : change permissions on a file or directory
chown: Change owner : change the owner or group owner of a file
man: Manual : display the manual of a command