Porting Molecular Dynamics simulation to heterogeneous multi-core architecture

MD (Molecular Dynamics) simulation is widely used for biology and chemistry study and requires computing power several orders of magnitude beyond today's commonly available computing systems. While the heterogeneous multi-core system offers substantial computation power with both lower cost and lower power consumption, its unconventional hardware architecture poses significant challenges to programmers for enabling existing applications to run efficiently on the system. Due to the complexity of applications, especially for MD applications, it is difficult to reorganize a new parallel schema for application to exploit task level parallelism on heterogeneous multi-core system during the application porting process. Instead of the common porting method that requires reorganizing the parallel schema of the application to accelerate the hotspots of the computation, a porting method which exploits task parallelism of MD software on heterogeneous multi-core system by substituting system-level communication library and remaining application's original parallel decomposition strategy unchanged was proposed in this paper. Besides preserving the integrity of the MD applications and avoiding additional cost of code modification, the experimental result of porting MD software named Moldy to IBM CBE architecture shows that the ported MD software based on our proposed porting method obtains both higher speedup ratio and higher performance.