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.
- https://hackmd.io/EW_atH_vR5iq-uBFV-CiTw?both
- 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.se - Create a working directory (e.g. "pythonUPPMAX") where you can code along.
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!
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
- 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?
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.