A Workstation Cluster for High Performance Computing in Structural Biology

本提案的目标是继续发展通过异步传输模式（ATM）交换机耦合的高性能工作站网络，以便在计算结构生物学中有效利用。所要求的资金将补充（匹配）从惠普公司获得的资金，用于建立一个基于PA-RISC 7200处理器的16个惠普工作站集群（8个由NSF资助），为该集群获取通信骨干（基于ATM或光纤通道技术，将在购买时决定），并升级现有16个工作站集群的ATM交换机。这两个集群将用于：(1)与实验实验室正在进行的合作项目，涉及超大规模的超分子系统建模（膜、磷酸脂肪酶A2膜复合物、g -肌动蛋白到f -肌动蛋白的聚合、基因V蛋白与单链DNA的结合、核受体蛋白与DNA的复合物、光收集系统等）；(2)用于核磁共振蛋白结构/功能研究；(3)用于研究氧化还原蛋白中的电子转移路径和预测蛋白质结构（蛋白质折叠）。其中一个集群将允许用户池化少量工作站（1-4），另一个集群将允许池化8-16个工作站。16个工作站集群的峰值功率也将用于实时建模。为了有效的跨簇并行计算，分子动力学程序（namd, vmd）已经开发出来，并正在进一步改进。这项工作由美国国立卫生研究院资源拨款和美国国家科学基金会大挑战应用小组拨款资助。实时建模将基于一个新的图形程序（vmd），用于大屏幕立体投影和3D交互设备。除了三位主要研究人员外，16位实验研究人员将从本提案中寻求的计算资源中受益。两名计算机科学教员与我们合作研究分子动力学算法和并行计算软件。计算工作的部分资金来自卡弗慈善信托基金，该基金为操作集群和实验实验室的计算小组之间的项目提供了6名研究生和2个博士后职位。

The objective of this proposal is to continue the development of a network of high performance workstations coupled through an Asynchronous Transfer Mode (ATM) switch for effective utilization in computational structural biology. The funds requested will complement (matching) funds to be obtained from Hewlett-Packard Comp. to build a cluster of sixteen (8 to be funded through NSF) Hewlett-Packard workstations based on PA-RISC 7200 processors, to acquire a communication backbone for this cluster (based either on an ATM or on fibre channel technology, which will be decided at the time of purchase), and to upgrade the ATM switch of an existing cluster of 16 workstations. The two clusters will be used: (1) for ongoing collaborative projects with experimental laboratories which involve very large scale modeling of supramolecular systems (membranes, phopspho lipase A2 - membrane complexes, polymerization of G-actin to F-actin and association of gene V protein with single stranded DNA, complexes of nuclear receptor proteins with DNA, light harvesting systems, and others); (2) for NMR protein structure/function studies; (3) for studies of electron transfer paths in redox proteins and for the prediction of protein structures (protein folding). One of the clusters will allow users to pool small numbers of workstations (1-4), the other will allow a pooling of 8-16 workstations. The peak power of a 16 workstation cluster will also be utilized for real time modeling. For effective parallel computing across the clusters molecular dynamics programs (namd, vmd) have been developed and are being further improved. The effort is funded through an NIH Resource grant and through an NSF Grand Challenge Applications Group grant. Real time modeling will be based on a new graphics program (vmd) for large screen stereo projections and 3D interactive devices. Besides the three principle investigators, sixteen experimental investigators will benefit from the computational resources sought in this proposal. Two computer science faculty members collaborate with us on molecular dynamics algorithms and parallel computing software. The computational work is partially funded through a grant from the Carver Charitable Trust which has provided six graduate students and two postdoctoral positions for projects between the computational group operating the clusters and experimental laboratories.