Scalable online comparative genomics of mononucleosomes: a BigJob

Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery Pub Date : 2013-07-22 DOI:10.1145/2484762.2484819

Jack A. Smith, Y. E. Khamra, Melissa Romanus, T. Bishop, P. Mantha, S. Jha

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引用次数: 5

Abstract

Our goal is to develop workflows for simulating arbitrary collections of mononucleosomes in atomic detail as an on demand analysis tool for online comparative genomics. The limiting factor is resource availability. The aim of this paper is to document and share our experiences in providing a general-purpose, easy-to-use and extensible solution for such computations. At the core it involves supporting the execution of high-throughput workloads of high-performance biomolecular simulations on one or more XSEDE machines. Although conceptually simple, it is still a difficult practical problem to solve, especially in a flexible, robust, scalable manner. Specifically, we employ BigJob-- an interoperable Pilot-Job. The bulk of this paper is about our experience in executing a very large number of ensembles including the associated non-trivial data management problem. Our experience suggests that although a nascent and fledgling technology, BigJob provides a flexible and scalable Pilot-Job to support workloads that were hitherto not easy.

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单核小体的可扩展在线比较基因组学:一项大工作

我们的目标是开发工作流程，以模拟原子细节的任意单核小体集合，作为在线比较基因组学的随需应变分析工具。限制因素是资源的可用性。本文的目的是记录和分享我们在为此类计算提供通用、易于使用和可扩展的解决方案方面的经验。其核心是支持在一台或多台XSEDE机器上执行高性能生物分子模拟的高吞吐量工作负载。虽然概念上很简单，但它仍然是一个难以解决的实际问题，特别是以灵活、健壮、可扩展的方式解决。具体来说，我们使用了BigJob——一个可互操作的Pilot-Job。本文的大部分内容是关于我们在执行大量集成方面的经验，包括相关的重要数据管理问题。我们的经验表明，尽管BigJob是一项新兴的技术，但它提供了一个灵活的、可扩展的Pilot-Job来支持迄今为止并不容易的工作负载。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery

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