Introduction Python
- Welcome page and syllabus
Also link at House symbol 🏠 at top of page
Learning outcomes
Load Python modules and site-installed Python packages
Create a virtual environment
Install Python packages with pip (Kebnekaise, Rackham, Snowy)
Write a batch script for running Python
Exercises FIX
You can download the exercises from the course GitHub repo, under the “Exercises” directory: https://github.com/UPPMAX/R-python-julia-HPC
Your expectations?
Find best practices for using Python at UPPMAX and HPC2N
Packages
Use the HPC performance with Python
Not covered
Improve python coding skills
Other clusters (though they work in a mostly very similar way)
Schedule
Time |
Topic |
Teacher(s) |
---|---|---|
9:00 |
First login |
BB + PO + RB + RP |
9:45 |
Break |
. |
10:00 |
Syllabus |
RP |
10:10 |
Python in general |
RP |
10:20 |
Load modules and run |
RP |
10:50 |
Break |
. |
11:05 |
Packages |
RB |
11:35 |
Isolated environments 1 |
RB |
12:00 |
Lunch |
. |
13:00 |
Isolated environments 2 |
RB |
13:35 |
Batch |
BB |
14:05 |
Break |
. |
14:20 |
GPU |
BB |
14:40 |
Simulataneous sessions |
BB * RB * RP |
15:10 |
Break |
. |
15:25 |
Parallel and multi-threaded functions |
PO |
16:00 |
Summary and evaluation |
RB |
16:15 |
End of the day |
. |
Simultaneous session:
Kebnekaise: Jupyter, by BB
Rackham: Interactive session and Jupyter, by RB
LUNARC, by RP
What is python?
As you probably already know…
“Python combines remarkable power with very clear syntax.
It has modules, classes, exceptions, very high level dynamic data types, and dynamic typing.
There are interfaces to many system calls and libraries, as well as to various windowing systems. …“
In particular, what sets Python apart from other languages is its fantastic open-source ecosystem for scientific computing and machine learning with libraries like NumPy, SciPy, scikit-learn and Pytorch.
Official Python documentation is found here https://www.python.org/doc/ .
Python forum is found here https://python-forum.io/ .
Material for improving your programming skills
First level
The Carpentries teaches basic lab skills for research computing.
Second level
CodeRefinery develops and maintains training material on software best practices for researchers that already write code. Their material addresses all academic disciplines and tries to be as programming language-independent as possible.
Aalto Scientific Computing
Third level
ENCCS (EuroCC National Competence Centre Sweden) is a national centre that supports industry, public administration and academia accessing and using European supercomputers. They give higher-level training of programming and specific software.
The youtube video Thinking about Concurrency is a good introduction to writing concurrent programs in Python
The book High Performance Python is a good resource for ways of speeding up Python code.
Other NAISS centres
Objectives
We will:
Teach you how to navigate the module system
Show you how to find out which versions of Python and packages are installed
Use the package handler pip
Explain how to create and use virtual environments
Show you how to run batch jobs
Show some examples with parallel computing and using GPUs
Most of this will be the same or very similar to how it is done at other HPC centres in Sweden