Available code

The tutorial requires three Python scripts, which are listed here for references and convenience. In order to obtain the scripts, clone the GitHub repository as described under Installing Input Files and Scripts.

Map-reduce scripts

These scripts form the map-reduce algorithm. rp_psa.py implements the map logic at the radical.pilot level and drives the computation with mdanalysis_psa_partial.py. psa_reduce.py combines the partial results and performs the analysis.

Helper scripts

  • util/generate_file_list.py is used in this tutorial to generate comprehensive input files in JSON format. It is specifically written for this tutorial with these specific data. Users will need to adapt their own approaches to manage their trajectories and communicate topology/trajectory pairs to the rp_psa.py script.

  • rp/mdanalysis_psa.py is a complete serial implementation of the PSA distance matrix calculation; it is provided for comparison purposes.