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:

• 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	Link to video
Alvis	SSH	Here
Bianca	SSH	Here
COSMOS	SSH	Here
Dardel	SSH	Here
Kebnekaise	SSH	Here
LUMI	SSH	Here
Rackham	SSH	Here
Tetralith	SSH	Here

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	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