title: FEREBUS: Highly parallelized engine for kriging training.
abstract: FFLUX is a novel force field based on quantum topological atoms, combining multipolar electrostatics with IQA intraatomic and interatomic energy terms. The program FEREBUS calculates the hyperparameters of models produced by the machine learning method kriging. Calculation of kriging hyperparameters (θ and p) requires the optimization of the concentrated log-likelihood L̂(θ,p). FEREBUS uses Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms to find the maximum of L̂(θ,p). PSO and DE are two heuristic algorithms that each use a set of particles or vectors to explore the space in which L̂(θ,p) is defined, searching for the maximum. The log-likelihood is a computationally expensive function, which needs to be calculated several times during each optimization iteration. The cost scales quickly with the problem dimension and speed becomes critical in model generation. We present the strategy used to parallelize FEREBUS, and the optimization of L̂(θ,p) through PSO and DE. The code is parallelized in two ways. MPI parallelization distributes the particles or vectors among the different processes, whereas the OpenMP implementation takes care of the calculation of L̂(θ,p), which involves the calculation and inversion of a particular matrix, whose size increases quickly with the dimension of the problem. The run time shows a speed-up of 61 times going from single core to 90 cores with a saving, in one case, of ∼98% of the single core time. In fact, the parallelization scheme presented reduces computational time from 2871 s for a single core calculation, to 41 s for 90 cores calculation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
authors.affiliation: Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain.
authors.forename: Nicodemo
authors.initials: N
authors.lastname: Di Pasquale
authors.affiliation: Research IT, The University of Manchester and High End Compute, http://highendcompute.co.uk, Manchester, M13 0EL.
authors.forename: Michael
authors.initials: M
authors.lastname: Bane
authors.affiliation: Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Davie
authors.affiliation: Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, Great Britain and School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain. paul.popelier@manchester.ac.uk.
authors.forename: Paul L A
authors.initials: PL
authors.lastname: Popelier
keywords: IQA; MPI; OpenMP; QTAIM; differential evolution; force field design; kriging; machine learning; parallellization; particle swarm optimization