CRPC-TR93356-S

Title:	  Parallelization using Spatial Decomposition for Molecular
 	  Dynamics 

Authors:  T. W. Clark, R. v. Hanxleden*, J. A. McCammon, L. R. Scott

Date:	  May 1994

* student author

Keywords:
  Parallel, Molecular dynamics, Spatial decomposition, Load balancing,
  Scalability 

Abstract:

Several algorithms have been used for parallel molecular dynamics,
including the replicated algorithm and those based on spatial
decompositions.  The replicated algorithm stores the entire system's
coordinates and forces at each processor, and therefore has a low
overhead in maintaining the data distribution.  Spatial decompositions
distribute the data, providing better locality and scalability with
respect to memory and computation.

We present EulerGROMOS, a parallelization of the GROMOS molecular
dynamics program, which is based on a spatial decomposition.
EulerGROMOS parallelizes all molecular dynamics phases, with most data
structures using O(N/P) memory.  This paper focuses on the structure
of EulerGROMOS and analyses its performance using molecular systems of
current interest in the molecular dynamics community.  EulerGROMOS
achieves performance increases with as few as twenty atoms per
processor.  We also compare EulerGROMOS	with an parallelization of
GROMOS, UHGROMOS, which uses the replicated algorithm.

Appeared in:  Scalable High Performance Computing Conference,
 	      Knoxville, TN