Parallel Programming with Python

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General Information

The eScience Center offers a range of free workshops and training courses, open to all researchers affiliated with Dutch research organizations. We organize workshops covering digital skills needed to put reproducible research into practice. These include online collaboration, reproducible code and good programming practices. We also offer more advanced workshops such as GPU Programming, Parallel Programming and Deep Learning.

Python is one of most widely used languages to do scientific data analysis, visualization, and even modelling and simulation. The popularity of Python is mainly due to the two pillars of a friendly syntax together with the availability of many high-quality libraries. The flexibility that Python offers comes with a few downsides though: code typically doesn’t perform as fast as lower-level implementations in C/C++ or Fortran, and it is not trivial to parallelize Python code to work efficiently on many-core architectures. This workshop addresses both these issues, with an emphasis on being able to run Python code efficiently (in parallel) on multiple cores.

We’ll start with learning to recognize problems that are suitable for parallel processing, looking at dependency diagrams and kitchen recipes. From then on, the workshop is highly interactive, diving straight into the first parallel programs. Participants will be coding along with the instructor in the style of teaching like Software Carpentry. This workshop teaches the principles of parallel programming in Python using Dask, Numba and Snakemake. More importantly, we try to give insight in how these different methods perform and when they should be used.

Where: Science Park 402, 1098 XH Amsterdam. Get directions with OpenStreetMap or Google Maps.

When: May 17 - 18, 2022, 9:30 - 16:30 CEST.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

• The room is wheelchair / scooter accessible.
• Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email or training@esciencecenter.nl for more information.

Code of Conduct

Participants are expected to follow those guidelines:

• Use welcoming and inclusive language
• Be respectful of different viewpoints and experiences
• Gracefully accept constructive criticism
• Focus on what is best for the community
• Show courtesy and respect towards other community members

Syllabus

• Recognizing potential for parallelism
• Dependency diagrams
• Measuring performance
• Working with Dask arrays
• Working with Numba
• Parallel design patterns
• Delayed evaluation
• Dependency based programming using Snakemake

Schedule

Setup

To participate in this workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Software setup

Requirements

• A programming editor, when in doubt we recommend Microsoft VS Code.
• Python version 3.9, we recommend Anaconda or Miniconda if you only use the command-line interface. If you insist on using vanilla Python, see instructions below.
• Git. If you’re on Windows, follow these instructions: Git for Windows.

To follow along with the workshop, you need to prepare an environment. Clone the workshop repository that we prepared:

git clone https://github.com/esciencecenter-digital-skills/parallel-python-workshop.git
cd parallel-python-workshop

You may prepare the environment either in conda or using vanilla Python with poetry.

Conda (recommended)

For most users we recommend that you use conda to install the requirements for the workshop.

conda env create -f environment.yml
conda activate parallel-python
pytest

If the tests pass, you’re all good! Otherwise, please contact us before the workshop.

Poetry

Only follow these instructions if you’re on Linux or Mac and don’t have conda installed. Make sure that you have Python 3.9 installed.

If you’ve never used poetry before, check it out!