Implementation and Evaluation of Multiple GridRPC Services for Molecular Dynamics Simulations of Proteins
Implementation and Evaluation of Multiple GridRPC Services for Molecular Dynamics Simulations of Proteins
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DOI：
10.2197/ipsjdc.2.573
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发表时间：
2006-09
期刊：
影响因子：
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通讯作者：
T. Amisaki;S. Fujiwara
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文献类型：
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作者：
T. Amisaki;S. Fujiwara
本文报道了一个蛋白质模拟网格，使用网格远程过程调用（GridRPC）的一个专用集群机的分子动力学模拟。该网格是使用Ninf-G、Torque、LAM和Globus Toolkit实现的。为了避免单个GridRPC会话使用集群的所有节点的低效率，我们设计了网格，以便在多个GridRPC会话共享集群时有效地工作。这是通过将专用节点（带有特殊计算板的PC）置于Torque系统的管理下来完成的，从而使管理员能够动态配置具有所需数量的专用节点的集群。此外，Globus工具包中添加了新的作业类型，Ninf-G中添加了新的后端过程。Ninf-G桩与实际在专用节点上执行力评估的过程分离。两种蛋白质的模拟给出了有希望的结果。使用四节点集群和100 Mbps LAN进行GridRPC会话的模拟比在本地客户端PC上进行的相同模拟快4.6-17.0倍，而它们的通信开销不到总执行时间的20%。即使在两个不同的蛋白质模拟之间共享四节点集群机器时，两个GridRPC通信也不会相互干扰。这显示了多个GridRPC会话的有效性。
This paper reports a protein-simulation grid that uses grid remote procedure calls (GridRPCs)to a special-purpose cluster machine for molecular dynamics simulations. The grid was implemented using Ninf-G, Torque, LAM, and the Globus Toolkit. To avoid the inefficiency of a single GridRPC session using all the nodes of the cluster, we designed the grid so that it works efficiently when multiple GridRPC sessions share the cluster. This was done by putting the dedicated nodes(PCs with special computation boards)under the management of the Torque system, thus enabling the manager to dynamically configure a cluster with the requested number of dedicated nodes. In addition, a new job type was added to the Globus toolkit and new backend procedure was added to Ninf-G. The Ninf-G stub was separated from processes that actually perform the force evaluation on the dedicated nodes. Simulations for two proteins gave promising results. Simulations performed using a four-node cluster and a 100-Mbps LAN for GridRPC sessions were 4.6-17.0 times faster than the same simulation performed on the local client PC, while their communication overhead was less than 20% of total execution time. Even when the the four-node cluster machine was shared between two distinct simulations of proteins, the two GridRPC communications did not interfere with each other. This showed the efficacy of multiple GridRPC sessions.