Design and implementation of flexible, robust and efficient Grid-enabled hybrid QM/MD simulation

摘要

This paper describes the implementation of Grid-enabled hybrid Quantum Mechanics/Classical Molecular Dynamics (QM/MD) Simulation. The Grid-enabled QM/MD simulation is capable of (1) dynamic resource allocation and migration, (2) automatic recovery from faults, and (3) managing large number of CPUs in geographically distributed sites. In the implementation, both GridRPC and MPI are used to complement each other, that is, GridRPC allows dynamic resource allocation and migration and automatic recovery from faults while MPI provides high-performance parallel processing on each cluster. We ran the hybrid QM/MD simulation on an international Grid testbed in the Asia Pacific Region for about 52 days. The experimental results indicated that the hybrid QM/MD simulation could (1) adapt to the dynamic behavior of the simulation and can change the number of CPUs and the number of clusters, (2) adapt to unstable Grid infrastructure and recovers from faults automatically, and (3) manage hundreds to thousands of CPUs on distributed locations, and (4) survive for several weeks without interrupting manual operation. This paper reports on the details of the implementation, strategies for long-run, and experimental results.