Breakthrough Molecular Dynamics Research via an Anton2 Supercomputer

通过 Anton2 超级计算机进行突破性分子动力学研究

• 批准号: 9187833
• 负责人: Philip D. Blood
• 金额: $ 43.24万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-12-01 至 2020-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9187833
• 关键词: Architecture; Award; Biological; Biomedical Research; Chemicals; Communities; Computer Systems; Data Analyses; Data Files; Documentation; Drug Interactions; Educational workshop; Event; Funding; Future; Generations; Gifts; Goals; Investigation; Ion Channel; Letters; Longevity; Membrane Proteins; Molecular; Names; Nucleic Acids; Performance; Persons; Prize; Proteins; Publications; Research; Research Infrastructure; Research Project Grants; Resources; Running; Sales; Science; Scientist; Signal Transduction; Speed; Supercomputing; System; Training; base; biomedical resource; biomedical scientist; computing resources; cost; design; drug development; drug discovery; molecular dynamics; next generation; price lists; protein folding; public health relevance; response; simulation; success; supercomputer; symposium

 DESCRIPTION (provided by applicant): This project represents the continuation of a longstanding, ongoing and very productive partnership between the Pittsburgh Supercomputing Center (PSC) and D. E. Shaw Research (DESRES). The project's overarching goal is to provide the biomedical research community access to a truly unique supercomputing resource, Anton, designed and developed by DESRES. Anton's performance exceeds that of present general-purpose supercomputer systems by approximately two orders of magnitude, and allows biomedical scientists to conduct routine long timescale molecular dynamics (MD) simulations at an unprecedented scale. Recently, the next-generation Anton 2 architecture was publicly unveiled at the 2014 Supercomputing Conference and, like Anton 1, was awarded the prestigious ACM Gordon Bell Prize. Since October 2010, DESRES has made a 512-node Anton 1 machine available without cost at the PSC for not-for-profit use. This machine can simulate systems with tens of thousands of atoms at rates above 10 µs/day - roughly two orders of magnitude greater than typically achieved by state-of-the-art parallel MD simulation packages running on the fastest general-purpose machines. So far 229 research projects by 120 unique PIs have been conducted on this exceptional resource. The range of investigation possible on Anton is as broad as that of the MD research community itself, and includes protein folding, ion channel selectivity and gating, protein-membrane signaling, and drug interactions with proteins, to name but a few. This breadth is reflected in the range of projects that to date have been accomplished on the machine. Use of the Anton at PSC by the scientific community has already resulted in a significant number of important research findings and high impact publications that we believe would not have been possible otherwise. Here, we propose to continue to make an Anton machine available to the biomedical research community. Since the Anton at PSC is the only machine outside of the DESRES lab, this project represents a unique opportunity for scientists to access this resource for conducting the longest timescale MD simulations currently possible. Importantly, in Year 2 of the award we plan to upgrade Anton 1 with a 128-node Anton 2 machine that will provide a significant increase in computational capabilities. As with the current Anton, the Anton 2 machine to be hosted by PSC will be generously made available by DESRES without cost and thus represents a multi-million dollar resource for the biomedical research community for which the PSC is only requesting funds to cover operating expenses, user support, file storage and basic infrastructure costs. This upgrade will provide roughly a 4-fold increase in simulation speed and, importantly, will allow scientists to simulate system sizes of up to 700,000 atoms, compared to the Anton 1 limit of 150,000 atoms. Thus, Anton 2 will provide biomolecular scientists across the nation with unparalleled simulation capabilities, enabling the study of biological hypotheses not otherwise possible.

 描述（由申请人提供）：该项目代表了匹兹堡超级计算中心 (PSC) 和 D. E. Shaw Research (DESRES) 之间长期、持续且富有成效的合作伙伴关系的延续。该项目的总体目标是为生物医学研究界提供访问权限。 Anton 是一种真正独特的超级计算资源，由 DESRES 设计和开发，其性能比目前的通用超级计算机系统高出大约两个数量级，并允许生物医学科学家进行计算。最近，下一代 Anton 2 架构在 2014 年超级计算大会上亮相，并与 Anton 1 一样，自 2010 年 10 月起公开授予著名的 ACM Gordon Bell 奖。在 PSC 上免费提供了一台 512 节点 Anton 1 机器，供非营利用途使用。该机器可以以高于 10 的速率模拟具有数万个原子的系统。微秒/天 - 比在最快的通用机器上运行的最先进的并行 MD 仿真包通常实现的速度大约高两个数量级，到目前为止，120 个独特的 PI 已在这一特殊资源上开展了 229 个研究项目。 Anton 的研究范围与 MD 研究界本身一样广泛，包括蛋白质折叠、离子通道选择性和门控、蛋白质膜信号传导以及药物与蛋白质的相互作用等。迄今为止，科学界使用 Anton 在 PSC 上完成的一系列项目已经体现了这一点，我们认为，如果不使用 Anton，这是不可能实现的大量重要研究成果和高影响力的出版物。在这里，我们建议继续向生物医学研究界提供 Anton 机器，由于 PSC 的 Anton 是 DESRES 实验室之外的唯一机器，因此该项目为科学家提供了一个独特的机会来访问该资源以进行最长的时间尺度。重要的是，目前可以进行 MD 模拟。在奖项的第 2 项中，我们计划使用 128 节点 Anton 2 机器升级 Anton 1，这将显着提高计算能力，与当前的 Anton 一样，由 PSC 托管的 Anton 2 机器将由 DESRES 慷慨提供。无需成本，因此为生物医学研究界提供了数百万美元的资源，而 PSC 仅要求资金用于支付运营费用、用户支持、文件存储和基本基础设施成本。此次升级将使生物医学研究界的成本增加大约 4 倍。模拟速度重要的是，与 Anton 1 的 150,000 个原子的限制相比，它将允许科学家模拟多达 700,000 个原子的系统大小。因此，Anton 2 将为全国的生物分子科学家提供无与伦比的模拟能力，从而使生物假设的研究成为可能。否则可能。