Parallel molecular dynamics on a multi signalprocessor system

Electronics Laboratory, Swiss Federal Institute of Technology, CH-8092 Zürich, Switzerland
Computer Physics Communications (Impact Factor: 2.41). 04/1993; 75(1-2):65-86. DOI: 10.1016/0010-4655(93)90165-9

ABSTRACT This paper gives an overview of a parallel computer architecture called MUSIC (Multi Signalprocessor System with Intelligent Communication), which has been developed at the Swiss Federal Institute of Technology. The current version achieves a peak performance of 3.8 GFlops. We discuss the system software and tools used to program the system and then present our implementation of a molecular dynamics simulation program which uses the architecture of MUSIC in an efficient way. We demonstrate the correctness of our implementation and give measurements of the performance of the system. To the best of our knowledge, MUSIC outperforms the most powerful present-day vector supercomputers.

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    ABSTRACT: In this report the work of the first 18 months of the Polyproject "Parallel Computing in Quantum and Classical Molecular Dynamical Simulation" is summarized. The project is planned for a total dura-tion of three years. Four labs of the ETH attend the project: IGC (Computational Chemistry Group, head of the project), IFE (Electronics Lab), TIK (Computer Engineering and Networks Lab) and IWR (Scientific Computing Lab). GROMOS (GROningen MOlecular Simulation package) is a computer simulation tool which is distributed and supported in various versions by the Computational Chemistry Group. The main goal of the project is to accelerate the simulation of molecules in liquids by a factor of ten. To achieve the goal dedicated hardware must be developed to speed-up the Gromos software. The main topics in this report are as follows: First we present profiling results of the Gromos program, per-formed on different workstations and processors. Then we give an overview on existing hardware accelerators. New modelling techniques for the molecular dynamics algorithm are presented as well as models for different new parallel hardware solutions. With these models a design space exploration was performed using techniques such as system synthesis using Evolutionary Algorithms.