Implementation of a macromolecular mechanics program on a cyber 205 supercomputer

We describe the steps involved in the conversion and vectorization of a macromolecular mechanics program on a CYBER 205 supercomputer. Several programming problems that we have encountered in optimizing a molecular mechanics program for a CYBER 205 are discussed including: the effect of vector length on speed, design of alternative algorithms, the migration of bottlenecks and rate differences obtained for logical vs arithmetic operations. The vectorized code for particular subroutines runs more than 200 times faster on the CYBER 205 as compared with a VAX 11/780. Using an enzyme-inhibitor complex, Rhizopus Chinensis carboxyl protease-pepstatin, containing 2,844 atoms as a model for this type of calculation, we have obtained an overall increase in speed of between 80-120 over a VAX 11/780 equipped with floating point accelerator for the evaluation of the conformational energy and forces on the atoms.     

NSEDIT: A syntax-directed editor and testing tool based on Nassi—Shneiderman charts

This paper describes a programming environment for Pascal, called NSEDIT, which runs under VAX/VMS

1 VAX/VMS is a trademark of the Digital Equipment Corporation.

. NSEDIT is based upon the notion of Nassi-Shneiderman charts (abbreviated to N-S charts in this paper) and is designed for ease of use by novice programmers in a teaching situation. A key component of the system is the editor, which enables structural features of Pascal to be manipulated in terms of their N-S chart box representations. Simultaneous editing of more than one program or module is permitted. Another key feature of the system is a semiautomatic interface to the VAX/VMS Pascal compiler, with subsequent display of execution counts as part of the N-S charts. In this way users can obtain immediate feedback on the coverage of program elements by test runs, while still inside an editing session.     

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program

We report our work to parallelize the Particle Mesh Ewald (PME) method to compute the long-range electrostatic interactions in the molecular dynamics program AMBER and to extend the scalability of the PME method to hundreds of processors.     

An interactive FORTRAN program for three-dimensional molecular visualization

An interactive FORTRAN program executable in the VAX/VMS computer environment has been developed for three-dimensional molecular visualization on the Evans & Sutherland Picture System 390. The essential features of this program are described and the FORTRAN source code is available upon request.     

Game: Genetic algorithm for minimization of energy,an interactive program for three-dimensional intermolecular interactions

An interactive FORTRAN-77 program GAME has been developed for three-dimensional intermolecular interactions of molecular clusters or docking problems. In this note the essential features of the program are described. The source code can be compiled and run on most computer environments such as VAX/VMS, Unix and IBM and is available upon request.     

Improving the description of salt bridge strength and geometry in a Generalized Born model

The Generalized Born (GB) solvent model is widely used in molecular dynamics simulations because it can be less computationally expensive and it samples conformational changes more efficiently than explicit solvent simulations. Meanwhile, great efforts have been made in the past to improve its precision and accuracy. Previous studies have shown that reducing intrinsic GB radii of some hydrogen atoms would improve AMBER GB-HCT solvent model's accuracy on salt bridges. Here we present our finding that similar correction also shows dramatic improvement for the AMBER GB-OBC solvent model. Potential of mean force and cluster analysis for small peptide replica exchange molecular dynamics simulations suggested that new radii GB simulation with ff99SB/GB-OBC corrected salt bridge strength and achieved significantly higher geometry similarity with TIP3P simulation. Improved performance in 60 ns HIV-1 protease GB simulation further validated this approach for large systems.     

IPS-2: the second generation of a parallel program measurementsystem

IPS, a performance measurement system for parallel and distributed programs, is currently running on its second implementation. IPS's model of parallel programs uses knowledge about the semantics of a program's structure to provide two important features. First, IPS provides a large amount of performance data about the execution of a parallel program, and this information is organized so that access to it is easy and intuitive. Secondly, IPS provides performance analysis techniques that help to guide the programmer automatically to the location of program bottlenecks. The first implementation of IPS was a testbed for the basic design concepts, providing experience with a hierarchical program and measurement model, interactive program analysis, and automatic guidance techniques. It was built on the Charlotte distributed operating system. The second implementation, IPS-2, extends the basic system with new instrumentation techniques, an interactive and graphical user interface, and new automatic guidance analysis techniques. This implementation runs on 4.3BSD UNIX systems, on the VAX, DECstation, Sun 4, and Sequent Symmetry multiprocessor     

The Cambridge ring and Unix

In March 1980, a VAX 11/780

1 VAX is a trademark of Digital Equipment Corp.

was installed at the Computing Laboratory of the University of Kent. The VAX runs UNIX as a user service. This paper discusses what has been learnt from the integration of an existing operating system (UNIX) into a local area network based on the Cambridge ring. The approach which has been evolved attempts to make the network connections invisible to the operating system so that the utilities running on the system can access the network as if they were talking to standard peripherals. The paper gives an overview of the ring and the protocols in use at Kent; and points to alternative approaches to the implementation which could be used in a different environment.     

多核CPU和GPU加速分子动力学模拟

在多核中央处理器(CPU)—图形处理器(GPU)异构并行体系结构上,采用OpenMP和计算统一设备架构(CUDA)编程实现了基于AMBER力场的蛋白质分子动力学模拟程序。通过合理地将程序划分为CPU单线程、CPU多线程和GPU多线程执行部分,高效地利用了计算机的处理能力。性能测试结果表明,相对于优化后的CPU串行计算,多核CPU-GPU异构并行计算模型有强大的性能优势,特别是将占整个程序执行时间90%的作用力的计算移植到GPU上执行,获得了最高可达12倍的计算加速比。     

Finite element analysis on the BBN butterfly multiprocessor

Applications of the finite element method can easily exhaust CPU and memory resources on conventional uniprocessor machines, and are thus prime candidates for multiprocessor application. In order to investigate various parallel processing methodologies and to evaluate their performance, we have developed a finite element program for the Butterfly Parallel Processor. The overall organization of the program and its data structures are described along with parallel implementations of well-known algorithms for transient and static analysis. Results are presented for two implementations of explicit time integration, and for static analysis using a parallel version of Gaussian elimination. For comparison, results from running the same program on a DEC VAX 11/785 are also included. The transient cases yielded near-linear (within 2.5%) speedup in the full range of 1–64 processors; the static case results showed significant nonlinearity over the same range.     

Gramm-software package for molecular dynamics on graphical processing units

This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from .     

双CPU计算服务器MPI并行环境的实现及其在生物大分子动力学模拟中的应用

在Red Hat Linux 9.0操作系统环境下,通过建立双CPU服务器,并采用MPICH并行技术,实现双CPU的并行计算。采用分子动力学模拟程序Amber 7.0分析双CPU并行系统的计算效率,结果表明:该并行系统能够有效地利用现有计算资源,同时计算效率得到较大幅度地提高。在该系统的基础上,采用分子动力学模拟计算生物大分子核酸与药物小分子复合物,在分子水平上提供了较详细、明确的结构变化情况。     

Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm

We have parallelized the FASTA algorithm for biological sequence comparison using Linda, a machine-independent parallel programming language. The resulting parallel program runs on a variety of different parallel machines. A straight-forward parallelization strategy works well if the amount of computation to be done is relatively large. When the amount of computation is reduced, however, disk I/O becomes a bottleneck which may prevent additional speed-up as the number of processors is increased. The paper describes the parallelization of FASTA, and uses FASTA to illustrate the I/O bottleneck problem that may arise when performing parallel database search with a fast sequence comparison algorithm. The paper also describes several program design strategies that can help with this problem. The paper discusses how this bottleneck is an example of a general problem that may occur when parallelizing, or otherwise speeding up, a time-consuming computation.     

化学结构匹配的探试——回溯算法

本文在建立了新的化学结构机内表示方法的基础上,提出了化学结构匹配的探试—回溯算法,定义了在化学结构上的行走,以及记录这种行走的路径的概念;将化学结构的同构与同态过程在一个算法中统一处理。文中讨论了在最坏情况下搜索空间大小以及回溯对于缩小搜索空间的效果。对于将13个节点的结构匹配到15个节点的结构上的情况下,需要VAX 11/785,CPU 时间0.06秒。     

FRIL: A Support Logic Programming System

FRIL: A Support Logic Programming System is principally an extension of Prolog designed to facilitate the modelling of uncertainty in applications which are suitable for Prolog and need to allow for probabilistic, evidential or vague reasoning. This review was carried out on an Amstrad 1640HD. The product runs on IBM PC, XT, AT and PS/2 computers and compatibles running MS-DOS 3.0 or higher, with 640 Kb RAM. It also runs on a variety of workstations and minicomputers such as the Sun and VAX range. Prices of currently available versions are as follows:

• PC single user: £495

• PC single user with expanded memory (2 Mb): £995

• PC networks (up to ten PCs): £1495

• SUN, Apollo HP300 workstations: £2500

• MicroVax and VAX workstations (UNIX or VMS): £5000

• VAX 11/730, 11/750, 11/780 (UNIX or VMS): £6000.

The product is available from FRIL Systems Ltd, Bristol ITeC, St Anne's House, St Anne's Road, Bristol BS4 4AB, England. Telephone: (0272) 713481. FRIL Systems launched version 4.0 of FRIL in late 1988.     

核磁共振多维谱图处理系统

随着多维NMR谱的出现,计算机处理的数据量迅速增加,而谱仪专用计算机受到容量和速度的限制,对大批量数据的处理能力有限,影响谱仪的使用效率.而目前个人计算机特别是超级小型机和工作站的性能、速度和容量远胜过谱仪专用机,且具有优良的性能价格比,MR数据的脱机处理-NMR数据处理站的建立已成必然.本文初步对我所在国内首次实现MSL-400脉冲傅立叶变换核磁共振谱仪与超级小型机VAX-11/785联机及所建立的NMR数据处理站作一介绍.该站目前对一维谱数据的常规处理软件已经完成.     

基于MapReduce模型的并行量子进化算法

利用MapReduce模型可自动编写串行程序及编程接口简单的优点,实现量子进化算法在MapReduce模型下的并行化,提出基于MapReduce模型的并行量子进化算法MRQEA,并将其部署到Hadoop云计算平台上运行。对0-1背包问题的测试结果证明,MRQEA算法在处理大型数据集时具有良好的加速比和并行效率。     

一种分布式网格计算框架以及在大规模分子动力学模拟中的应用

分子动力学（molecular dynamics）模拟蛋白质等大分子内原子间的相互作用,蛋白质折叠所需的时间通常在微秒（10^-6s）量级，而进行模拟的时间步长在飞秒（10^-15s）量级，并且每步需要计算大量的相互作用（O（n^2），n为原子数），以致于无法模拟足够长时间的折叠过程．现今在满足精确度的需求下没有更好的模拟算法．最近，生物学家研究了一种分布式的动力学方法，使得可以利用分布在Internet上的计算机进行并行模批成为可能,本文的目标是设计并实现在分布式P2P和网格计算环境等多种异构计算资源下进行动力学模拟的可靠框架，以便更大限度地利用计算资源，加快计算过程．我们基于Java和web service技术，已经实现了对应用透明的计算框架，并已将它扩展到我们的网格计算环境,实验表明分子动力学模拟程序在该框架下运行良好．     

Three dimensional singular element

The finite element method has become a powerful tool for computation of stress intensity factors in fracture mechanics. The simulation of singular behavior in the stress field is accomplished using “quarter points,” following the methods of Barsoum[1] and Henshell-Shaw[2]. The analysis has also been extended to cubic elements [3] and transition elements [4]. However, these concepts cannot be easily extended to three dimensional cases without additional conditions. Progress has been hampered firstly due to a variety of possible shapes the element may possess near the singular edge of the crack, and secondly due to the complexity of algebraic expressions that have to be manipulated.

In the present investigation we extensively used MACSYMA[5], a large symbolic manipulation program at MIT, thereby alleviating some of these difficulties. A simple condition between mid-side nodes has been derived which simulates the proper singular behavior along the crack.

In the investigation we first study a simple collapsed brick element. This is then generalized to a curved crack front. A few results are derived which can be used to compute the stress intensity factors. The concept of the transitional element has also been outlined. The stability of singular element has been discussed. Some of these ideas have been applied to a specific problem with unusual crack geometry. The analysis was carried out using ADINA on VAX machine. ADINA was implemented on VAX by W. E. Lorensen.