Customized Plug-in Modules in Metascheduler CSF4 for Life Sciences Applications
Customized Plug-in Modules in Metascheduler CSF4 for Life Sciences Applications
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DOI：
10.1007/s00354-007-0024-6
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发表时间：
2007-08
影响因子：
2.6
通讯作者：
Zhaohui Ding;Xiaohui Wei;Yuan Luo;Da Ma;P. Arzberger;Wilfred W. Li
中科院分区：
文献类型：
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作者：
Zhaohui Ding;Xiaohui Wei;Yuan Luo;Da Ma;P. Arzberger;Wilfred W. Li
随着越来越多的生命科学研究人员开始在他们的工作中利用网格技术，对健壮且易于使用的元数据库或资源代理的需求也在增加。在本文中，我们扩展了元数据库CSF 4，提供了一个虚拟作业模型（VJM）的跨域并行作业的同步资源协同分配。VJM消除了使用MPICH-G2编译的多集群并行应用程序的死锁并提高了资源使用率。利用CSF 4的可扩展调度器插件模型，可以为生命科学应用程序开发定制的元数据存储策略。作为一个例子，我们为AutoDock和Blast等令人愉快的并行应用程序开发了一个数组作业调度器插件。VJM的性能进行了评估，通过实验与mpiBLAST-g2使用Gfarm数据网格测试床。此外，还发布了一个CSF 4 portlet，为透明的网格访问提供图形用户界面，并使用Gfarm进行数据分级和简化数据管理。该平台在sourceforge.net/projects/gcsf/上是开源的，并已被My WorkSphere和PRAGMA Biosciences Portal等项目部署在生命科学网关中。VJM支持在不久的将来开发对更复杂的工作流和元数据库策略的支持。
As more and more life science researchers start to take advantages of grid technologies in their work, the demand increases for a robust yet easy to use metascheduler or resource broker. In this paper, we have extended the metascheduler CSF4 by providing a Virtual Job Model (VJM) to synchronize the resource co-allocation for cross-domain parallel jobs. The VJM eliminates dead-locks and improves resource usage for multi-cluster parallel applications compiled with MPICH-G2. Taking advantage of the extensible scheduler plug-in model of CSF4, one may develop customized metascheduling policies for life sciences applications. As an example, an array-job scheduler plug-in is developed for pleasantly parallel applications such as AutoDock and Blast. The performance of the VJM is evaluated through experiments with mpiBLAST-g2 using a Gfarm data grid testbed. Furthermore, a CSF4 portlet has been released to provide a graphical user interface for transparent grid access, with the use of Gfarm for data staging and simplified data management. The platform is open source at sourceforge.net/projects/gcsf/ and has been deployed in life science gateways by projects such as My WorkSphere, and PRAGMA Biosciences Portal. The VJM enables the development of support for more sophisticated workflows and metascheduling policies in the near future.