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Using the Python interpreter

Learning outcomes

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 using the right Python interpreter and environment
  • 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.

The difficulty of these exercises depends on your HPC cluster:

HPC cluster name Need VPN? Need SSH keys? Need 2FA? Documentation Difficulty
Alvis Yes No No Minimal Medium
Bianca Yes No Yes Excellent Medium
COSMOS No No Yes Good Easy
Dardel No Yes No Minimal Medium
LUMI No Yes No Reasonable Medium
Kebnekaise No No No Good Easy
Rackham No No No Excellent Easy
Tetralith No No Yes Good Easy 
    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
LUMI SSH .
Rackham SSH here
Tetralith SSH here

Exercise 0: pick a Zoom room

We will use breakout rooms, as this is best for learning. Ideally, each breakout room has 2 learners for the same HPC cluster. As it cannot be predicted how many learners show up per cluster, we do this dynamically:

  • Go to the main breakout room of your HPC cluster
HPC cluster name Main breakout room
Alvis Room 1
Bianca Room 2
COSMOS Room 3
Dardel Room 4
Kebnekaise Room 5
LUMI Room 6
Rackham Room 7
Tetralith Room 8
  • When the main breakout room reaches 4 learners, decide upon 2 to move to a free breakout room. Repeat until the group size is below 4.
  • When you are the only one in your main breakout room, the teachers will let you decide to either work in silence or to join another group. You will be taken care of well :-)

Exercise 1: login to your HPC cluster

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

Then answer these questions:

  • Login to an interactive session (e.g. SSH) on your HPC cluster
Answer

The documentation for 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' or 'connecting', 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

Exercise 2: load the Python module

Go to the documentation of your HPC cluster and load a Python software module of the version indicated in the table below.

HPC Cluster Python version
Alvis 3.12.3
Bianca 3.11.4
COSMOS 3.11.5
Dardel 3.11.4
Kebnekaise 3.11.3
LUMI 3.11.7
Rackham 3.12.7
Tetralith 3.10.4
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 short or long 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 and here module load bioinfo-tools python/3.11.4
Kebnekaise here module load GCC/12.3.0 Python/3.11.3
LUMI here module load cray-python/3.11.7
Rackham here module load python/3.12.7
Tetralith here module load Python/3.10.4-env-hpc2-gcc-2022a-eb
  • ⚠ means that the documentation does not clearly answer this question. You may find that you can piece it together easily enough or you may find that you cannot. 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 may find information on how to start the Python interpreter.

HPC Cluster Link to documentation Solution
Alvis ⚠ python
Bianca here python
COSMOS ⚠ python
Dardel ⚠ here python
Kebnekaise ⚠ python
LUMI ⚠ here python
Rackham here python
Tetralith here python
  • ⚠ for this specific question means that the documentation does not answer this (or the answer is hiding in more complicated examples). You may find this an acceptable omission or you may not. 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 can 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

Your 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 👍