For a detailed explanation of the current implementation of parallel analysis in MDAnalysis, check out the documentation. The core idea is that trajectory analysis is often trivially parallelizable. You can analyze all frames independently and then merge the results into a single object.
Since this implementation is still in the develop branch (it was just merged in early August 2024), we’re actively seeking contributors to help us refine it and enhance its user-friendliness. This is also a fantastic opportunity to integrate parallel capabilities into your own analysis code!
To get started, you’ll need to install the develop version of MDAnalysis. You can do so by following the installation guide.
The MDAnalysis core developers are here to assist you as you contribute to implementing parallel analysis for existing analysis classes and your own custom analysis code.
Currently, the parallel analysis framework is integrated into the RMSD class as an example. We’d love to see this framework extended and tested across all other analysis classes. Pick your favorite analysis class and implement parallel analysis for it! Guidelines for adding parallelization to existing analysis classes can be found in the documentation.
For an example, see this issue.
We maintain a list of known issues and areas for improvement that we’d like to see addressed. These are tracked in the issue tracker under the parallelization label.
If you have your own analysis code that you’d like to parallelize, we provide guidelines for doing so in the documentation. This is a great way to enhance the performance of your analysis tools while contributing to the broader MDAnalysis community.