Model@Home: distributed computing in bioinformatics using a screensaver based approach
Model@Home: distributed computing in bioinformatics using a screensaver based approach
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DOI：
10.1093/bioinformatics/18.2.315
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发表时间：
2002-02-01
期刊：
影响因子：
5.8
通讯作者：
Vriend, G
中科院分区：
文献类型：
--
作者：
Krieger, E;Vriend, G
动机：由于生物信息学和相关科学学科的计算需求稳步增长，人们被迫优化利用现有资源。一个直接的解决方案是建立一个由空闲计算机组成的网络，让每台计算机处理一个科学挑战的一小部分，就像世界上最大的分布式计算项目Seti@Home （http://setiathome.berkeley.edu）所做的那样。结果：我们开发了一个普遍适用的分布式计算解决方案，它使用类似于Seti@Home的屏幕保护程序系统。该软件利用了典型生物信息学项目的粗粒度特性。设计的三个主要考虑因素是：(1)通常需要许多不同的程序，而缺乏时间来并行化它们。Models@Home可以并行运行任何程序而无需修改源代码；(2)与Seti项目相比，生物信息学应用通常对失业更为敏感。因此，Models@Home包含对作业调度的严格控制；(3)为了允许在异构环境中使用，基于Linux和Windows的工作站可以与专用pc机组合以构建同构集群。本文介绍了Models@Home在30台pc上运行WHAT IF和YASARA建模程序的三个实际应用：力场参数化、分子动力学对接和数据库维护。
Motivation: Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project.Results: We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster.We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.