Using the Python interpreter¶

Learning outcomes

Practice using the documentation of your HPC cluster
Practice using the Python book How to Think Like a Computer Scientist: Learning with Python 3
To be able to login to your HPC cluster
To be able to load Python
To be able to run a minimal Python program

For teachers

Teaching goals are:

Learners have used the documentation of their HPC cluster
Learners have used the Python book
Learners have used the Python interpreter
Learners have loaded Python

Other goals are:

Verify that learners indeed have learned how to login
Verify that learners indeed have learned how to use the module system

Prior and feedback question:

What is Python?
What are features of the Python language?
What is an interpreted language?
What is a scripting language?
What is an interpreter?
What is an HPC cluster?
What are features of your HPC cluster?
What is a login node?
What is the rule on what to run on a login node?
How to run heavy Python calculations on your HPC cluster?
How to make your Python scripts reproducible?

Lesson plan:

5 mins: prior knowledge
5 mins: presentation
15 mins: challenge
5 mins: feedback

Notes:

For those that use Bianca, it may take some time to get a login node. Encourage those to try Rackham while waiting

Why?¶

You want to make a computer run Python code, for some good reason. Here we do so!

To develop code in Python on your HPC clusters, one needs to:

Login to that HPC cluster, to be able to work on it
Load the Python module, to be able to use a modern Python interpreter
Use the Python interpreter, to run Python code

Luckily, the documentation of your HPC center should allow you to do this by yourself!

These exercises will ensure you are able to run a minimal Python program.

    flowchart TD
        python[[Python]]

        %% Give a white background to all nodes, instead of a transparent one
        classDef node fill:#fff,color:#000,stroke:#000

        subgraph sub_programming_language[Python as a language]
        interpreted_language[Interpreted language]
        programming_language[Programming language]
        scripting_language[Scripting language]
        interpreter[Interpreter]
        %% scripts[Scripts]
        %% text_files[Text files]
        end
        style sub_programming_language fill:#ccf,color:#000,stroke:#fcc


        subgraph sub_naiss[NAISS]
          your_hpc_center[Your HPC center]
          your_hpc_cluster[Your HPC cluster]
          modules[software modules]
          %% text_editors[Text editors]
          %%x_forwarding[X-forwarding]
          %%remote_desktop[Remote desktop]
        end
        style sub_naiss fill:#fcc,color:#000,stroke:#fcc

        python --> |is a| programming_language
        python --> |is a| interpreted_language
        python --> |is a| scripting_language

        %% programming_language --> |uses| text_files
        interpreted_language --> |has a| interpreter
        scripting_language --> |is a|interpreted_language
        %% scripting_language --> |runs| scripts
        %% scripts --> |are| text_files
        %% scripts --> |can use| command_line_arguments

        your_hpc_center --> |has| your_hpc_cluster
        your_hpc_cluster --> |uses| modules
        %%your_hpc_cluster --> |have| text_editors
        %%your_hpc_cluster --> |allow| x_forwarding
        %%your_hpc_cluster --> |has| remote_desktop
        %% modules --> |allow the use of| python_packages
        modules --> |allow the use of| interpreter

        %% text_editors --> |work on|text_files
        %%x_forwarding --> |allows|graphics
        %%remote_desktop --> |allows|graphics


        %% variables ~~~ your_hpc_center

Exercises¶

Enjoy a video?

You can find a video with solutions to these exercises:

HPC Cluster	Login method	Link to video
Alvis	SSH	here
Bianca	SSH	here
COSMOS	SSH	here
Dardel	SSH	here
Kebnekaise	SSH	here
Rackham	SSH	here
Tetralith	SSH	here

Go to the documentation of your HPC cluster and search for the login procedure(s).

Then answer these questions:

Login to your HPC cluster in any way

Answer

The documentation for the your HPC cluster can be found at:

HPC Cluster	Link to documentation
Alvis	here
Bianca	here
COSMOS	here
Dardel	here
Kebnekaise	here
LUMI	here
Rackham	here
Tetralith	here

From there, searching for, for example, 'login', you will find information on how to do so.

HPC Cluster	Link to documentation
Alvis	here
Bianca	here
COSMOS	here
Dardel	here
Kebnekaise	here
LUMI	here and here
Rackham	here
Tetralith	here

means that there is either no direct to the documentation and/or the documentation present is incomplete. You are encouraged to contact your HPC center to help them help you better

Exercise 2: load the Python module¶

Go to the documentation of your HPC cluster and load a Python software module.

Answer

From the documentation of your center, searching for, for example, 'Python module', you will find information on how to load the Python module.

HPC Cluster	Link to documentation	Solution
Alvis	None, closest is here	`module load Python/3.12.3-GCCcore-13.3.0`
Bianca	here	`module load python/3.11.4`
COSMOS	here	`module load GCCcore/13.2.0 Python/3.11.5`
Dardel	here	`module load bioinfo-tools python/3.11.4`
Kebnekaise	here	`module load GCC/12.3.0 Python/3.11.3`
LUMI	here	Unknown
Rackham	here	`module load python`
Tetralith	here	`module load Python/3.10.4-env-hpc2-gcc-2022a-eb`

means that there is either no direct to the documentation and/or the documentation present is incomplete. You are encouraged to contact your HPC center to help them help you better

Exercise 3: start the Python interpreter¶

Go to the documentation of your HPC cluster and start the Python interpreter.

Answer

From the documentation of your center, searching for, for example, 'Python' or 'Python interpreter', you will find information on how to start the Python interpreter.

HPC Cluster	Link to documentation	Solution
Alvis	here	`python`
Bianca	here	`python`
COSMOS	here	`python`
Dardel	here	`python`
Kebnekaise	here	`python`
LUMI	here	Probably: `python`
Rackham	here	`python`
Tetralith	here	`python`

means that there is either no direct to the documentation and/or the documentation present is incomplete. You are encouraged to contact your HPC center to help them help you better

Cannot get this to work?

If there is no time to get this fixed during the course, you are also use Python on your local computer.

Exercise 4: run a 'Hello world' program¶

Copy-paste the following code to the Python interpreter:

print('Hello, world!')

Press enter.

How does that look like?

Answer

You output will look similar to this:

$ python
Python 3.12.3 (main, Nov  6 2024, 18:32:19) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> print('Hello, world!')
Hello, world!
>>>

Congratulations, you've just run a 'Hello world' program

Using the Python interpreter¶

Why?¶

Exercises¶

Exercise 1: login to your HPC cluster¶

Exercise 2: load the Python module¶

Exercise 3: start the Python interpreter¶

Exercise 4: run a 'Hello world' program¶