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The command-line on Bianca

Objectives

  • Being able to navigate to home folder, project folder and wharf
  • Extra: Being able to view/create/move/delete files
Notes for teachers

Teaching goals:

  • The learners demonstrate they can navigate to home folder, project folder and wharf
  • Extra: The learners demonstrate they can create, move and delete files
  • Extra: The learners demonstrate they can create and delete folders

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

Why?

You need the command-line to start calculations.

Introduction

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.

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

Extra: 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

Extra: 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

Extra: 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

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.

The video, however, follows a different order.

flowchart TD

  classDef minimal_node fill:#fdd,color:#000,stroke:#f00
  classDef extra_node fill:#ffd,color:#000,stroke:#ff0

  exercise_1[1.file navigation]:::minimal_node
  exercise_2[2.view help]:::extra_node
  exercise_3[3.folder management]:::extra_node
  exercise_4[4.file management]:::extra_node

  exercise_1 --> exercise_2 --> exercise_3 --> exercise_4

Exercises for this session. Red nodes: minimal, needed in other sessions. Yellow nodes: extra, useful in general.

Exercise 1: file navigation

  • Navigate to your home folder
Answer

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 ~
  • Navigate to the project folder of this course
Don't know the project code?

In our case, the project code is sens2023598, hence the project folder is /proj/sens2023598.

To go there:

cd /proj/sens2023598

The wharf is an important folder: it is the only folder where files can be transferred to/from.

  • Navigate to the wharf folder of the project of this course
Cannot find it?

Go to the UPPMAX documentation about the wharf folder

Still cannot find it?

It is at /proj/nobackup/[project_id]/wharf/[user_name]/[user_name]-[project_id], hence, /proj/nobackup/sens2023598/wharf/[user_name]/[user_name]-sens2023598, or, for a user with username sven, at /proj/nobackup/sens2023598/wharf/sven/sven-sens2023598

To go there:

cd /proj/nobackup/sens2023598/wharf/sven/sven-sens2023598

Extra: Exercise 2: view help

View the help of the command cd

Answer

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.

Extra: Exercise 3: folder management

  • Create a folder /proj/sens2023598/workshop/[your_login_name], for example, /proj/sens2023598/workshop/richel"
Answer 
mkdir /proj/sens2023598/workshop/richel

Or navigate there first:

cd /proj/sens2023598/workshop/
mkdir richel

Extra: Exercise 4: file management

  • Create a file, e.g. richel.txt
Answer 
nano richel.txt

or alternatively:

touch richel.txt
  • Copy the file (e.g. to richel_again.txt)
Answer 
cp richel.txt richel_again.txt
  • Move the copied file (e.g. move it one folder up to ../richel_again.txt)
Answer 
mv richel_again.txt ../
  • Delete the copied file
Answer 
rm ../richel_again.txt

or:

cd ..
rm richel_again.txt

Extra material

Other useful commands

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

Command name Purpose
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
> Write to file (removes existing content if any)
>> Append to file

A command that cannot be put in a Markdown table:

  • |: pipe, the output of one command to serve as input for the next

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