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Title: An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities
Author: Law, Timothy R.
ISNI:       0000 0004 7657 756X
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2017
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We develop the projection sorting algorithm, used to compute pairwise short-range interaction forces between particles in molecular dynamics simulations. We contrast this algorithm to the state of the art and discuss situations where it may be particularly effective. We then explore the efficient implementation of the projection sorting algorithm in both on-node (shared memory parallel) and off-node (distributed memory parallel) environments. We provide AVX, AVX2, KNC and AVX-512 intrinsic implementations of the force calculation kernel. We use the modern multi- and many-core architectures: Intell Haswell, Broadwell Knights Corner (KNC) and Knights Landing (KNL), as representative slice of modern High Performance Computing (HPC) installations. In the course of implementation we use our algorithm as a means of optimising a contemporary biophysical molecular dynamics simulation of chromosome condensation. We compare state-of-the-art Molecular Dynamics (MD) algorithms and projection sorting, and experimentally demonstrate the performance gains possible with our algorithm. These experiments are carried out in single- and multi-node configurations. We observe speedups of up to 5x when comparing our algorithm to the state of the art, and up to 10x when compared to the original unoptimised simulation. These optimisations have directly affected the ability of domain scientists to carry out their work.
Supervisor: Not available Sponsor: Engineering and Physical Sciences Research Council ; Intel Corporation
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QA76 Electronic computers. Computer science. Computer software