A Prototype of a Scalable Multi-GPU Molecular Dynamics Simulator for Large Molecular Systems

Nicolas-Barreales, GonzaloNovalbos, MarcosOtaduy, Miguel ÁngelSánchez, AlbertoGarcía-Fernández, Ignacio and Ureña, Carlos2018-06-262018-06-262018978-3-03868-067-3https://doi.org/10.2312/ceig.20181149https://diglib.eg.org:443/handle/10.2312/ceig20181149Parallel architectures, in the form of multi-core or multiple computers, have produced a major impact in the field of information technology. GPU devices, as an extreme example of parallel architectures, have been adapted to enable generic computation in massively parallel architectures. Molecular dynamics is a problem that fits perfectly such architectures, as it relies on the computation of many similar interactions between atoms. Moreover, large molecular systems require resources that exceed those available in a single computer, even multi-GPU computers. Therefore, the ideal architecture to simulate molecular dynamics is a distributed multi-GPU cluster, which consists of multiple interconnected computers with one or more GPUs each. A molecular dynamics simulation usually needs days, and even weeks of computation time to produce results that represent only a few microseconds of atom interactions. In contrast, distributed multi-GPU clusters allows us to develop an efficient and scalable simulator. This paper aims to develop a prototype of a molecular dynamics simulator for large molecular systems. It uses the GPU as the main computing device, using only the CPU to control the workflow. We have implemented parallel processing techniques to develop a fully scalable system.Computing methodologiesMassively parallel algorithmsGraphics processorsApplied computingMolecular structural biologyA Prototype of a Scalable Multi-GPU Molecular Dynamics Simulator for Large Molecular Systems10.2312/ceig.2018114925-28