Title
Parallelizing Molecular Dynamics Programs for Distributed Memory Machines:
An Application of the CHAOS Runtime Support Library

Authors
Yuan-Shin Hwang, Raja  Das, Joel  Saltz
Department of Computer Science, University of Maryland,
College Park, MD 20742

Bernard Brooks, Milan Hodoscek
Molecular Graphics & Simulation Laboratory, DCRT, National Institutes of Health
Bethesda, MD 20892

Abstract
CHARMM (Chemistry at Harvard Macromolecular Mechanics) is a program
that is widely used to model and simulate macromolecular systems.
CHARMM has been parallelized by using the CHAOS 
runtime support library on distributed memory architectures. 
This implementation distributes both data and computations over processors. 
This data-parallel strategy should make it possible to simulate 
very large molecules on large numbers of processors.

In order to minimize communication among processors
and to balance computational load,
a variety of partitioning approaches are employed to distribute the atoms
and computations over processors.
In this implementation, atoms are partitioned based on geometrical
positions and computational load by using unweighted or weighted
recursive coordinate bisection. The experimental results reveal that
taking computational load into account is essential.
The performance of two iteration partitioning algorithms,
atom decomposition and force decomposition, is also compared.
A new irregular force decomposition algorithm is introduced and implemented.

The CHAOS library is designed to facilitate parallelization of
irregular applications. This library (1) couples partitioners to the
application programs, (2) remaps data and partitions work among processors,
and (3) optimizes interprocessor communications. This paper
presents an application of {\sc Chaos} that can be used to support efficient
execution of irregular problems on distributed memory machines.