Sivagnanam Subhashini, Majumdar Amit, Yoshimoto Kenneth, Astakhov Vadim, Bandrowski Anita, Martone MaryAnn, Carnevale Nicholas T
University of California San Diego, La Jolla, CA, USA.
Yale School of Medicine, New Haven, CT, USA.
Concurr Comput. 2015 Feb 1;27(2):473-488. doi: 10.1002/cpe.3283.
The last few decades have seen the emergence of computational neuroscience as a mature field where researchers are interested in modeling complex and large neuronal systems and require access to high performance computing machines and associated cyber infrastructure to manage computational workflow and data. The neuronal simulation tools, used in this research field, are also implemented for parallel computers and suitable for high performance computing machines. But using these tools on complex high performance computing machines remains a challenge because of issues with acquiring computer time on these machines located at national supercomputer centers, dealing with complex user interface of these machines, dealing with data management and retrieval. The Neuroscience Gateway is being developed to alleviate and/or hide these barriers to entry for computational neuroscientists. It hides or eliminates, from the point of view of the users, all the administrative and technical barriers and makes parallel neuronal simulation tools easily available and accessible on complex high performance computing machines. It handles the running of jobs and data management and retrieval. This paper shares the early experiences in bringing up this gateway and describes the software architecture it is based on, how it is implemented, and how users can use this for computational neuroscience research using high performance computing at the back end. We also look at parallel scaling of some publicly available neuronal models and analyze the recent usage data of the neuroscience gateway.
在过去几十年里,计算神经科学已发展成为一个成熟的领域,研究人员对复杂的大型神经元系统建模感兴趣,并需要使用高性能计算机及相关网络基础设施来管理计算工作流程和数据。该研究领域所使用的神经元模拟工具也是为并行计算机实现的,适用于高性能计算机。但是,由于在国家超级计算机中心获取这些机器的计算时间、处理这些机器复杂的用户界面、处理数据管理和检索等问题,在复杂的高性能计算机上使用这些工具仍然是一项挑战。神经科学网关正在开发中,以减轻和/或消除计算神经科学家面临的这些入门障碍。从用户角度来看,它隐藏或消除了所有管理和技术障碍,使并行神经元模拟工具在复杂的高性能计算机上易于获取和使用。它负责处理作业运行以及数据管理和检索。本文分享了建立这个网关的早期经验,并描述了其基于的软件架构、实现方式,以及用户如何利用它在后端使用高性能计算进行计算神经科学研究。我们还研究了一些公开可用的神经元模型的并行扩展性,并分析了神经科学网关的近期使用数据。