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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:

  • On an HPC cluster, what are software modules?
  • On an HPC cluster, which problem do software modules solve?
  • On an HPC cluster, why don't we let users install all software themselves?
  • What does it mean that Python is an interpreted language?
  • What is an interpreter?

Notes:

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

Why software modules are important

Software modules allows users of any HPC cluster to activate their favorite software of any version. This helps to assure reproducible research.

Why the Python interpreter is important

flowchart TD
  a_letter[A letter to do something]
  employee[Employee]
  something_done[Something is done]
  a_letter --> employee --> something_done

  code[Code] 
  interpreter[Interpreter]
  machine_code[Machine code]
  code --> interpreter --> machine_code

The Python interpreter is the program that lets your Python code do something. It is at the heart of using Python: without it, you cannot do Python programming.

Exercises

Enjoy a video?

You can find a video with solutions to these exercises:

HPC Cluster Login method Videos
Alvis SSH Video
Bianca SSH Video
COSMOS SSH Video
Dardel SSH Video
Kebnekaise SSH Video
LUMI SSH Video
Rackham SSH Video
Tetralith SSH Video

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

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 Documentation
Alvis Documentation
Bianca Documentation
COSMOS Documentation
Dardel Documentation
Kebnekaise Documentation
LUMI Documentation
Rackham Documentation
Tetralith Documentation

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

HPC Cluster Documentation
Alvis Documentation
Bianca Documentation
COSMOS Documentation
Dardel Documentation
Kebnekaise Documentation
LUMI Documentation and more documentation
Rackham Documentation
Tetralith Documentation

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 Documentation Solution
Alvis Short documentation or long documentation module load Python/3.12.3-GCCcore-13.3.0
Bianca Documentation module load python/3.11.4
COSMOS Documentation module load GCCcore/13.2.0 Python/3.11.5
Dardel ⚠ Documentation and more documentation module load bioinfo-tools python/3.11.4
Kebnekaise Documentation module load GCC/12.3.0 Python/3.11.3
LUMI Documentation module load cray-python/3.11.7
Rackham Documentation module load python/3.12.7
Tetralith Documentation 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 Documentation Solution
Alvis ⚠ python
Bianca Documentation python
COSMOS ⚠ python
Dardel ⚠ Documentation python
Kebnekaise ⚠ python
LUMI ⚠ Documentation python
Rackham Documentation python
Tetralith Documentation 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 👍