Simulation of diffusion in dense molecular systems on ARUZ-Massively-parallel FPGA-based machine

In this paper, the implementation of a molecular diffusion model named Dynamic Lattice Liquid (DLL) is discussed. Two algorithms, sequential and parallel, implementing this model are examined. The presented theoretical considerations indicate some limitations of the sequential approach. The proposed parallel algorithm overcomes these limitations, but it requires dedicated hardware. An example of such hardware, the FPGA-based HPC system named ARUZ, is presented. (c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Automated summary

This paper discusses the implementation of the molecular diffusion model called Dynamic Lattice Liquid (DLL). Two algorithms, sequential and parallel, are examined for implementing this model. The theoretical considerations presented indicate limitations of the sequential approach. The proposed parallel algorithm overcomes these limitations but requires dedicated hardware. An example of such hardware, the FPGA-based HPC system called ARUZ, is presented.