User Guide

pmda implements a simple map-reduce scheme for parallel trajectory analysis [Khoshlessan2017] for MDAnalysis [Gowers2016] [Michaud-Agrawal2011]. The trajectory is partitioned into blocks and analysis is performed separately and in parallel on each block (“map”). The results from each block are gathered and combined (“reduce”). pmda contains a number of pre-defined analysis classes (see Pre-defined parallel analysis tasks) that are modelled after functionality in MDAnalysis.analysis and that can be used right away. However, often it can be almost as easy to write your own parallel class.

• Using the pmda analysis classes
• Parallelization
• Writing new parallel analysis