Introduction
Welcome!
There is a rather new documentation for python at UPPMAX at: https://uppmax.uu.se/support/user-guides/python-user-guide/
We hope that it will be helpful for your future reference.
We will approximately follow the outline of it today.
We hope also to identify improvements of the page for today´s interactions with you!
Learning outcomes
load and run python
find installed packages
install package with pip
install package with conda
Understand and create virtual environments
best practice
Collabration document HackMD
Use the HackMD page for the workshop with your questions.
- Depending on how many helpers we’ll see how fast there are answers.
Some answers may come after workshop.
- Type in left frame
“-” means new bullet and <tab> indents the level.
don’t focus too much on the formattiong if you are new to “Markdown” language!
Have a try with the Icebreaker question
Your expectations?
find best practices for using Python at UPPMAX
using Conda
using Bianca
Not covered
improve python coding skills
Tetralith
Kebnekaise
Warning
It is good to have a familiarity with the LINUX command line.
Short introductions may be found here: https://uppsala.instructure.com/courses/67267/pages/using-the-command-line-bash?module_item_id=455632
UPPMAX software library: https://uppsala.instructure.com/courses/67267/pages/uppmax-basics-software?module_item_id=455641
Whole intro course material can be reached here: https://www.uppmax.uu.se/support/courses-and-workshops/introductory-course-winter-2022/
Prepare your environment now!
Please log in to Rackham or other cluster. e.g.
ssh <user>@rackham.uppmax.uu.seCreate a working directory (e.g. “pythonUPPMAX”) where you can code along.
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. …“
Documentation is found here https://www.python.org/doc/ .
Python forum is found here https://python-forum.io/ .
A nice introduction to packages can be found here: https://aaltoscicomp.github.io/python-for-scicomp/dependencies/
CodeRefinery develops and maintains training material on software best practices for researchers that already write code. Ther material addresses all academic disciplines and tries to be as programming language-independent as possible. https://coderefinery.org/lessons/
And, if you feel a little unfamiliar to the LINUX world, have a look at the Introduction to UPPMAX course material here: https://www.uppmax.uu.se/support/courses-and-workshops/introductory-course-winter-2022/
More python?
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. https://coderefinery.org/lessons/
Introduction to Python at https://www.uppmax.uu.se/support/courses-and-workshops/introductory-course-winter-2022/
Introduction to HPC (High performance computing) python at UPPMAX and HPC2N in September. More info to come!
Python at UPPMAX
The python application at UPPMAX comes with several preinstalled packages.
A very small selection of these are:
Numpy, Pandas, Scipy, Matplotlib, Jupyter notebook, pip, cython, ipython
Questions
What to do if you need other packages?
How does it work on Bianca without internet?
What if I have projects with different requirements in terms of python and packages versions?
Objectives
We will:
guide through the python ecosystem on UPPMAX
look at the package handlers pip and conda
explain how to create isolated environment
Warning
At UPPMAX we call the applications available via the module system modules. https://www.uppmax.uu.se/resources/software/module-system/
To distinguish these modules from the python modules that work as libraries we refer to the later ones as packages.
Outline
Loading and running Python
Packages/modules
How to install packages
Isolated environments
- Not this time: jupyter notebook & parallel jobs
Check the next SNIC training letter about new collaboration workshop in beginning of September.