Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
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DOI：
10.1016/j.cpc.2011.02.013
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发表时间：
2011-06-01
影响因子：
6.3
通讯作者：
Hamada, Tsuyoshi
中科院分区：
文献类型：
--
作者：
Yokota, Rio;Bardhan, Jaydeep P.;Hamada, Tsuyoshi
我们提出了通过算法和硬件加速相结合实现的万亿次浮点级生物分子静电计算。算法加速是通过快速多极法 (FMM) 结合连续静电模型的边界元法 (REM) 公式以及 BEM 的 BIBEE 近似来实现的。硬件加速是通过图形处理器opus实现的。我们展示了我们的算法和软件在计算溶液中生物分子之间的静电相互作用方面的强大功能。展示的应用包括蛋白质-药物结合的静电学以及由数百到数千个溶菌酶分子副本组成的数百万个原子系统。该软件的并行可扩展性在长崎高级计算中心的集群中进行了研究，该集群使用 128 个节点，每个节点配备 4 个 GPU。精细的调整带来了强大的扩展能力，256 个 GPU 的并行效率为 0.8，512 个 GPU 的并行效率为 0.5。最大的应用程序运行包含超过 2000 万个原子和 10 亿个未知数，在 512 个 GPU 上只需要一分钟。我们目前正在调整 BEM 软件来求解稀离子溶液的线性化泊松-玻尔兹曼方程，并且它的设计也足够灵活，可以扩展到各种积分方程问题，从泊松问题到电磁学和声学中的亥姆霍兹问题，再到高雷诺数流。 (C) 2011 Elsevier B.V. 保留所有权利。
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (REM) formulation of the continuum electrostatic model, as well as the BIBEE approximation to BEM. The hardware acceleration is achieved through graphics processors, opus. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. The applications demonstrated include the electrostatics of protein-drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of lysozyme molecules. The parallel scalability of the software was studied in a cluster at the Nagasaki Advanced Computing Center, using 128 nodes, each with 4 GPUS. Delicate tuning has resulted in strong scaling with parallel efficiency of 0.8 for 256 and 0.5 for 512 GPUS. The largest application run, with over 20 million atoms and one billion unknowns, required only one minute on 512 GPUS. We are currently adapting our BEM software to solve the linearized Poisson-Boltzmann equation for dilute ionic solutions, and it is also designed to be flexible enough to be extended for a variety of integral equation problems, ranging from Poisson problems to Helmholtz problems in electromagnetics and acoustics to high Reynolds number flow. (C) 2011 Elsevier B.V. All rights reserved.