基于神威太湖之光的NAMD软件的移植与优化
发布时间：2019-06-29 06:56
【摘要】：纳米级粒度分子动力学NAMD是基于Charm++并行编程模型的开源免费分子动力学模拟软件,能够在大规模并行计算机上快速模拟百万原子级别的大分子体系。太湖之光是中国自主研发的超级计算机,峰值性能为125.4Pflop/s,共有1 000多万个核心,整机Linpack效率不低于70%。NAMD在空间上对原子进行划分,在计算上对力进行划分,充分曝露出单步模拟的并行度,并通过CHARM++对负载平衡进行调控。针对NAMD进行模拟计算时的特点,移植并优化了NAMD的核心计算代码,让其能够更好地运行在超级计算机神威太湖之光上,优化后性能提高了近20倍,单个核组的性能较Intel XeonE5-2650v2提高3倍。扩展性方面目前至多可达到325万核的并行度,突破百万核大关。
[Abstract]:Nanometer particle size molecular dynamics NAMD is an open source free molecular dynamics simulation software based on Charm parallel programming model, which can quickly simulate the macromolecular system of one million atoms on a large scale parallel computer. Taihu Lake Light is a supercomputer developed by China, with a peak performance of 125.4 Pflopos, with more than 10 million cores. The Linpack efficiency of the whole machine is not lower than that of 70%.NAMD in space, the force is divided in calculation, the parallelism of one-step simulation is fully exposed, and the load balance is regulated by CHARM. According to the characteristics of NAMD simulation calculation, the core computing code of NAMD is ported and optimized, so that it can run better on the supercomputer Shenwei Taihu Lake Light. The optimized performance is nearly 20 times higher than that of Intel XeonE5-2650v2, and the performance of single kernel group is three times higher than that of Intel XeonE5-2650v2. At present, scalability can reach up to 3.25 million cores of parallelism, breaking through the million nuclear mark.
【作者单位】： 中国科学技术大学计算机系科学与技术学院;
【分类号】：TP311.54;TP338
本文编号：2507634
[Abstract]:Nanometer particle size molecular dynamics NAMD is an open source free molecular dynamics simulation software based on Charm parallel programming model, which can quickly simulate the macromolecular system of one million atoms on a large scale parallel computer. Taihu Lake Light is a supercomputer developed by China, with a peak performance of 125.4 Pflopos, with more than 10 million cores. The Linpack efficiency of the whole machine is not lower than that of 70%.NAMD in space, the force is divided in calculation, the parallelism of one-step simulation is fully exposed, and the load balance is regulated by CHARM. According to the characteristics of NAMD simulation calculation, the core computing code of NAMD is ported and optimized, so that it can run better on the supercomputer Shenwei Taihu Lake Light. The optimized performance is nearly 20 times higher than that of Intel XeonE5-2650v2, and the performance of single kernel group is three times higher than that of Intel XeonE5-2650v2. At present, scalability can reach up to 3.25 million cores of parallelism, breaking through the million nuclear mark.
【作者单位】： 中国科学技术大学计算机系科学与技术学院;
【分类号】：TP311.54;TP338
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