Parallelizing molecular dynamics programs for distributed memory machines: an application of the CHAOS runtime support library
Yuan‐Shin Hwang, Raja Das, Joel Haskin Saltz, Bernard R. Brooks, Milan Hodošček · 1994
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 compa...