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

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dc.contributor.authorNicolas-Barreales, Gonzaloen_US
dc.contributor.authorNovalbos, Marcosen_US
dc.contributor.authorOtaduy, Miguel Ángelen_US
dc.contributor.authorSánchez, Albertoen_US
dc.contributor.editorGarcía-Fernández, Ignacio and Ureña, Carlosen_US
dc.date.accessioned2018-06-26T13:59:25Z
dc.date.available2018-06-26T13:59:25Z
dc.date.issued2018
dc.description.abstractParallel 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.en_US
dc.description.sectionheadersAnimation and Simulation
dc.description.seriesinformationSpanish Computer Graphics Conference (CEIG)
dc.identifier.doi10.2312/ceig.20181149
dc.identifier.isbn978-3-03868-067-3
dc.identifier.pages25-28
dc.identifier.urihttps://doi.org/10.2312/ceig.20181149
dc.identifier.urihttps://diglib.eg.org:443/handle/10.2312/ceig20181149
dc.publisherThe Eurographics Associationen_US
dc.subjectComputing methodologies
dc.subjectMassively parallel algorithms
dc.subjectGraphics processors
dc.subjectApplied computing
dc.subjectMolecular structural biology
dc.titleA Prototype of a Scalable Multi-GPU Molecular Dynamics Simulator for Large Molecular Systemsen_US
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