Parallel Molecular Dynamics: Communication Requirements for Massively Parallel Machine

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. Many implementations of parallel molecular dynamics have been developed , but few groups have addressed issues related to the use of massively parallel machines with 100K to 1M processors for small to modest size systems in the range of 50K atoms. This is important for problems in which the goal is to reduce the execution time required to simulate millions of time steps on a modest size problem. In this paper we address two main issues: a good decomposition method that can take advantage of a massively parallel system and the communication requirements needed to achieve 30-40% eeciency on MPPs. We developed an analytical model of a benchmark program that simulates a system with helium atom executing on the Intel Touchstone Delta using an interaction decomposition method. Based upon this model, we determine that for an MPP arranged as a four-dimensional mesh with 400 MHz processors, the communication startup time should be approximately 30 clock cycles and the network bandwidth should be 2.3GB/s. The 300 clock cycle startup time should be available to the user at the level of a high-level language. This connguration results in 30-40% eeciency of the MPP for a problem with 50K atoms executing on 50K processors.