MIC acceleration of short-range molecular dynamics simulations

Authors:
Qiang Wu;Canqun Yang;Tao Tang;Liquan Xiao
Affiliations:
National University of Defense Technology, Changsha, China;National University of Defense Technology, Changsha, China;National University of Defense Technology, Changsha, China;National University of Defense Technology, Changsha, China
Venue:
Proceedings of the First International Workshop on Code OptimiSation for MultI and many Cores
Year:
2013

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Abstract

Heterogeneous systems containing accelerators such as GPUs or co-processors such as Intel MIC are becoming more prevalent due to their ability of exploiting large-scale parallelism in applications. In this paper, we have developed a hierarchical parallelization scheme for molecular dynamics simulations on CPU-MIC heterogeneous systems. The scheme exploits multi-level parallelism combining (1) task-level parallelism using a tightly-coupled division method, (2) thread-level parallelism employing spatial-decomposition through dynamically scheduled multi-threading, and (3) data-level parallelism via SIMD technology. By employing a hierarchy of parallelism with several optimization methods such as memory latency hiding and data pre-fetching, our MD code running on a CPU-MIC heterogeneous system (one 2.60GHZ eight-core Intel Xeon E5-2670 CPU and one 57-core Intel Knight Corner co-processor) achieves (1) multi-thread parallel efficiency of 72.4% for 57 threads on the co-processor with up to 7.62 times SIMD speedup on each core for the force computation task, and (2) up to 2.25 times speedup on the CPU-MIC system over the pure CPU system, which outperforms our previous work on a CPU-GPU (one NVIDIA Tesla M2050) platform. Our work shows that MD simulations can benefit enormously from the CPU-MIC heterogeneous platforms.