GSOC 2018: Improvements in distance search methods

We are pleased to announce another successful year of Google Summer of Code with the NumFOCUS organization, thanks to Richard Gowers and Jonathan Barnoud for mentoring the GSoC students. This year one of the projects was to improve the performance of pairwise distance computations, which is used quite frequently in MDAnalysis in different forms.

MDAnalysis v0.19.0 and higher now include the new functions MDAnalysis.lib.distances.capped_distance and MDAnalysis.lib.distances.self_capped_distance which offer a much faster way to calculate all pairwise distances up to a certain maximum distance. By only considering distances up to a certain maximum, we can use various algorithms to optimise the number of pairwise comparisons that are performed. Behind the scenes, these functions are using one of three different algorithms: bruteforce which is a naive pairwise distance calculation algorithm, pkdtree which is a wrapper method around Scipy’s KD tree search algorithm and nsgrid which is an implementation of cell-list algorithm. This last algorithm uses the new MDAnalysis.lib.nsgrid module which was implemented with the help of Sebastien Buchoux.

For more information on these algorithms the reader is encouraged to read @ayushsuhane’s blog, which includes a comparison of these approaches and their performance in different conditions.

The GSoC project

One of the major bottleneck in various analysis routines in MDAnalysis (and typically in molecular dynamics studies) is the evaluation of pairwise distances among the particles.

The primary problem revolves around fixed radius neighbor search algorithms. MDAnalysis offers a suite of algorithms including brute force method, tree-based binary search algorithms to solve such problems. While these methods are suitable for a variety of analysis functions using pairwise distances in MDAnalysis, one of the question was whether one can improve the performance of distance calculations using other established neighbor search methods.

This question led to the inception of a Google Summer of Code project with NumFOCUS. Ayush Suhane completed the project and was able to demonstrate performance improvements for specific cases of distance selections, identification of bonds, and radial distribution function in the analysis module of MDAnalysis. More details on the commit history, PR’s and blog posts can be found in the final report submitted to GSoC. Real-time benchmarks for specific modules in MDAnalysis can be found here.

The new capped_distance() function

The major highlight of the project is the introduction of MDAnalysis.lib.distances.capped_distance which allows automatic selection of methods based on predefined set of rules to evaluate pairs of atoms in the neighborhood of any particle. It allows a user-friendly interface for the developers to quickly implement any new algorithm throughout MDAnalysis modules. To test any new algorithm, one must comply with the following API:

def newmethod_capped(reference, configuration, max_cutoff, min_cutoff=None, box=None, return_distance=True):
        An Algorithm to evaluate pairs between reference and configuration atoms
        and corresponding distances
    return pairs, distances

Once the method is defined, register the function name in _determine_method in MDAnalysis.lib.distances as:

from MDAnalysis.lib import distances
distances_methods['newmethod'] = newmethod_capped

That’s it. The new method is ready to be tested across functions which use capped_distance. For any specific application, it can be called as capped_distance(ref, conf, max_dist, method='newmethod') from the function.

Treatment of periodic boundary conditions

While implementing any new algorithm for Molecular dynamics trajectories, one additional requirement is to handle the periodic boundary conditions. A combination of versatile function augment_coordinates and undo_augment can be used with any algorithm to handle PBC. The main idea is to extend the box by generating duplicate particles in the vicinity of the box by augment_coordinates. These duplicates, as well as the original particles, can now be used with any algorithm to evaluate the nearest neighbors. After the operation, the duplicate particles can be reverted back to their original particle indices using undo_augment. These functions are available in MDAnalysis.lib._augment. We encourage the interested readers to try different algorithms using these functions. Hopefully, you can help us improve the performance further with your feedback. As a starting point, the skeleton to enable PBC would take the following form:

def newmethod_search(coords, centers, radius, box=None):
    aug, mapping = augment_coordinates(coords, box, radius)
    all_coords = no.concatenate([coords, aug])
        Perform operations for distance evaluations
        with **all_coords** using the new algorithm 
        and obtain the result in indices
    indices = undo_augment(indices, mapping, len(coords))
    return indices

Finally, this function can be tested with capped_distance to check the performance against already implemented algorithms in MDAnalysis.

Performance improvements

As a final note, we managed to get a speed improvement of

The performance is also found to improve with larger datasets but is not reported in benchmarks. Any motivated reader is welcome to submit their feedbacks about the performance of the above-mentioned functions on their data, and/or a benchmark which we would be happy to showcase to the world.

This was a flavor of what work was done during GSoC’18. Apart from performance improvements, it is envisioned that this internal functionality will reduce the burden from the user to understand all the technical details of distance search algorithms and instead allow a user to focus on their analysis, as well as allow future developers to easily implement any new algorithm which can exceed the present performance benchmarks.

Ayush Suhane, Richard Gowers