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The command-line on Bianca

Using the command line on a computer cluster

Objectives

  • Being able to navigate in/out folders
  • Being able to view/create/move/delete files
  • Create an executable bash script
Notes for teachers

Teaching goals:

  • The learners demonstrate they can use a text editor
  • The learners demonstrate they can create, move and delete files
  • The learners demonstrate they can create and delete folders
  • The learners demonstrate they can create an executable script

Schedule:

gantt
  title Lesson plan Command line
  dateFormat X
  axisFormat %s
  Prior knowledge: prior, 0, 5s
  Theory: theory, after prior, 5s
  Exercises: crit, exercise, after theory, 25s
  Feedback: feedback, after exercise, 10s

Overview

Bianca is a cluster with the Linux operating system. We must use a Linux terminal to work with Bianca, therefore we must learn some Linux commands.

We will learn to:

  • read the manual
  • navigate through the file system
  • work with directories
  • work with files
  • create an executable script

Read the manual

Use man to see the help pages about a command:

man man
man cd
man ls

These command give the help pages about the programs man, cd and ls respectively.

Press q (short for 'quit') to exit man

Like any operating system, Linux has directories (also called 'folders').

Use cd to change directory:

Where to Example command
The root folder cd /
The project folder cd /proj/sens2023598
Your home folder, using full path cd /home/richel
Your home folder, using tilde cd ~
The wharf cd /proj/sens2023598/nobackup/wharf
Up one folder cd ..
Into a folder, using relative path cd myfolder
The previous location cd -

See the content of a folder

Use ls to see the content of a folder

See the current location

Use pwd to see your current location

The Silence Is Golden Rule

When your command 'just works' there is no output (try, for example cd ~). This is due to The Silence Is Golden Rule

Work with directories

Linux can create, move and delete folders.

Do what Example command
Create a folder mkdir myfolder
Move a folder mv from_folder to_folder
Delete an empty folder rmdir myfolder
Delete a folder rm -r myfolder

See the content of a folder

Use ls to see the content of a folder

See the current location

Use pwd to see your current location

See the current real location (advanced)

For sysadmins: use pwd -P to see your real current location on the hardware

Work with files

Linux can create, view, rename, move and delete files. Additionally, there are some text editors that allow one to edit files.

Do what Example command
Create an empty file touch myfile.txt
View a file using cat cat myfile.txt
Edit a file using nano nano myfile.txt
Delete a file rm myfile.txt
Copy a file cp myfile.txt mycopy.txt
Rename a file mv myfile.txt mycopy.txt
Move a file to one folder up mv myfile.txt ../
Move a file to the home folder mv myfile.txt ~
  • Note: nano is one of many text editors. It is the one recommended to beginners, as its interface is closest to what one expects

Create an executable script

Creating an executable script has two steps:

    1. Create a script
    1. Allow the script to execute

As an example, we create a script, called do_it.sh:

nano do_it.sh

Why use a .sh file extension?

Using .sh as a file extension a social convention for how a Bash script is called, as (1) sh is short for 'shell', (2) Bash is short for 'Bourne Again Shell'. A 'shell' in this context is a program that allows working with an operating system.

As an example, copy-paste this content into the script:

#!/bin/bash
echo "Hello!"
ls | rev

What does this program do?

  • The first line is called the shebang, and indicates this is a Bash script
  • The second line displays the text between double quotes
  • The third line displays the files in the folder reversed. The | is called the pipeline operator

Save and close nano.

  • Use CTRL-X to start to exit, then press y to start saving the file, then press enter to use the current filename

Use chmod to make the file executable:

chmod +x do_it.sh
  • +x can be read as: 'add the right to execute'

Create read-only files

If you want to protect your data from being modified accidentally, chmod can create read-only files, by removing the writing rights using chmod -w.

Exercises

Use the materials shown above to answer the questions below.

Video with solutions

There is a video that shows the solution of all these exercises: YouTube

1. View the help of the command cd

Use man to view the help of any command, in this case cd:

man cd
This will fail, because Bianca has (close to) no internet access.

2a. Navigate to the project folder, e.g. /proj/sens2023598 
cd /proj/sens2023598

Don't forget the / at the start.

2b. Navigate to your home folder

The syntax to move to your home folder is:

cd /home/[username]

where [username] is your UPPMAX username, for example:

cd /home/richel

The squiggle/tilde (~) is a shorter notation, that does exactly the same:

cd ~
2c. Navigate to the wharf, e.g. /proj/sens2023598/nobackup/wharf 
cd /proj/sens2023598/nobackup/wharf
3a. Create a folder /proj/sens2023598/workshop/[your_login_name], for example, /proj/sens2023598/workshop/richel 
mkdir /proj/sens2023598/workshop/richel

Or navigate there first:

cd /proj/sens2023598/workshop/
mkdir richel
4a. Create a file, e.g. richel.txt 
touch richel.txt
4b. Copy the file (e.g. to richel_again.txt). 
cp richel.txt richel_again.txt
4c. Move the copied file (e.g. move it one folder up to ../richel_again.txt) 
mv richel_again.txt ../
4d. Delete the copied file 
rm ../richel_again.txt

or:

cd ..
rm richel_again.txt
5. Create an executable script called /proj/sens2023598/workshop/[your_login_name]/do_it.sh, which, upon running, displays a welcome message in text (e.g. Hello!) and does something (e.g. show the files in reverse order)

Edit the script:

nano do_it.sh

Change the text to:

#!/bin/bash
echo "Hello!"
ls | rev

Make the script executable:

chmod +x ./do_it.sh

Run the script:

./do_it.sh

Extra material

Other useful commands

These are some commands that we enjoy, but are not part of the learning objectives.

Command name Purpose
scp Copy file between Bianca and your local computer
cat Show the content of a file
less Navigate through the content of a file
head Show the first lines of a file
tail Show the last lines of a file
less Show the content of a file
wc Count words, lines and/or characters
| Pipe the output of one command to serve as input for the next
> Write to file (removes existing content if any)
>> Append to file

With ls /usr/bin | wc --lines one can see that there are more than 1700 commands on Bianca.

The terminal and the GUI are friends

If you are using the Bianca remote desktop environment, you can see that its file browser and terminal are friends.

On a clean terminal, try typing cd and then drag a folder from the GUI to the terminal.

It types the absolute path for you!

These are some commonly used symbolic links, that will simplify navigation:

cd Desktop
ln -s /proj/sens2023598/ proj
ln -s /proj/sens2023598/nobackup nobackup
ln -s /proj/sens2023598/nobackup/wharf/richel/richel-sens2023598 wharf`
  • Replace sens2023598 by your project
  • Replace richel by your username