Article

Parallel molecular dynamics on a multi signalprocessor system

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8092 Zürich, Switzerland; Electronics Laboratory, Swiss Federal Institute of Technology, CH-8092 Zürich, Switzerland; Seminar for Applied Mathematics, Swiss Federal Institute of Technology, CH-8092 Zürich, Switzerland
Computer Physics Communications (Impact Factor: 2.41). 01/1993; 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.

0 Bookmarks
 · 
52 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: Dynamic properties of a binary Lennard-Jones mixture at various temperatures and two densities are studied using a molecular dynamics computer simulation starting from mixed and separated initial configurations. After deriving an analytical correction term for finite size effects, the rate of separation is determined as a function of temperature, which is influenced by two counteracting trends: at higher particle velocities demixing becomes faster, but with increasing temperature the separated state becomes less stable. At both densities studied, we observe an increase in the rate of separation with increasing temperature. In a second step, a small number of a third type of particle representing a crude model of an amphiphilic molecule is added and the results are compared with those of the binary mixture case. Owing to a dip in the density at the binary fluid interface, the amphiphilic molecules collect in a slit and as a result, no effect on the separation behaviour of the system is observed. At those temperatures for which the separated configuration is stable, the typical behaviour of the individual particle is analysed.
    Molecular Physics 01/1994; 82(5):1049-1062. · 1.67 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    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.
    01/1997;
  • [Show abstract] [Hide abstract]
    ABSTRACT: The purpose of the paper is to describe a new semi-automated design space exploration method based on genetic programming. A new control/dataflow specification method is proposed as well as appropriate models for hardware parts and algorithms. With this method we are able to test many different hardware architec- tures and algorithms against cost, speed, computation time and other constraints within very short time. The remaining manual work is to exploit the model parameters of the components of the architecture and the algorithm. In contrast to other approaches our method is suited for embedded and distributed systems. The method, models and application are explained in detail by means of a comprehensive case study.