Molecular dynamics simulation on a parallel computer.

For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer with a systolic loop architecture, based on Transputers as computational units, and have programmed it in Occam 11. The computational nodes of the computer are linked together in a systolic ring. The program based on this .topology for large biopolymers increases its computational throughput nearly linearly with the number of computational nodes. The program developed is closely related to the simulation programs CHARMM and XPLOR, the input files required (force field, protein structure file, coordinates) and output files generated (sets of atomic coordinates representing dynamic trajectories and energies) are compatible with the corresponding files of these programs. Benchmark results of simulations of biopolymers comprising 66, 568, 3 634, 5 797 and 12 637 atoms are compared with XPLOR simulations on conventional computers (Cray, Convex, Vax). These results demonstrate that the software and hardware developed provide extremely cost effective biopolymer simulations. We present also a simulation (equilibrium of X-ray structure) of the complete photosynthetic reaction center of Rhodopseudomonus viridis (12 637 atoms). The simulation accounts for the Coulomb forces exactly, i.e. no cut-off had been assumed

Domain growth in alloys

This thesis describes Monte-Carlo computer simulations of binary alloys, with comparisons between small angle neutron scattering (SANS) data, and numerically integrated solutions to the Cahn-Hilliard-Cook (CHC) equation. Elementary theories for droplet growth are also compared with computer simulated data. Monte-Carlo dynamical algorithms are investigated in detail, with special regard for universal dynamical times. The computer simulated systems are Fourier transformed to yield partial structure functions which are compared with SANS data for the binary Iron-Chromium system. A relation between real time and simulation time is found. Cluster statistics are measured in the simulated systems, and compared to droplet formation in the Copper-Cobalt system. Some scattering data for the complex steel PE16 is also discussed. The characterisation of domain size and its growth with time are investigated, and scaling laws fitted to real and simulated data. The simple scaling law of Lifshitz and Slyozov is found to be inadequate, and corrections such as those suggested by Huse, are necessary. Scaling behaviour is studied for the low-concentration nucleation regime and the high-concentration spinodal-decomposition regime. The need for multi-scaling is also considered. The effect of noise and fluctuations in the simulations is considered in the MonteCarlo model, a cellular-automaton (CA) model and in the Cahn-Billiard-Cook equation. The Cook noise term in the CHC equation is found to be important for correct growth scaling properties

Centre for Information Science Research Annual Report, 1987-1991

Annual reports from various departments of the AN

Parallelisation of algorithms

Most numerical software involves performing an extremely large volume of algebraic computations. This is both costly and time consuming in respect of computer resources and, for large problems, often super-computer power is required in order for results to be obtained in a reasonable amount of time. One method whereby both the cost and time can be reduced is to use the principle "Many hands make light work", or rather, allow several computers to operate simultaneously on the code, working towards a common goal, and hopefully obtaining the required results in a fraction of the time and cost normally used. This can be achieved through the modification of the costly, time consuming code, breaking it up into separate individual code segments which may be executed concurrently on different processors. This is termed parallelisation of code. This document describes communication between sequential processes, protocols, message routing and parallelisation of algorithms. In particular, it deals with these aspects with reference to the Transputer as developed by INMOS and includes two parallelisation examples, namely parallelisation of code to study airflow and of code to determine far field patterns of antennas. This document also reports on the practical experiences with programming in parallel

Director's discretionary fund report for FY 1991

The Director's Discretionary Fund (DDF) at the Ames Research Center was established to fund innovative, high-risk projects in basic research which would otherwise be difficult to initiate, but which are essential to our future programs. Here, summaries are given of individual projects within this program. Topics covered include scheduling electric power for the Ames Research Center, the feasibility of light emitting diode arrays as a lighting source for plant growth chambers in space, plasma spraying of nonoxide coatings using a constricted arcjet, and the characterization of vortex impingement footprint using non-intrusive measurement techniques

Development of a collision table for three dimensional lattice gases

Bibliography: pages 92-95.A lattice gas is a species of cellular automaton used for numerically simulating fluid flows. TransGas [9], the lattice gas code currently in use at the CSIR, is based on the FHP-I model [5], and is used to perform various two-dimensional flow simulations. In order to broaden the scope of the applications in which lattice gases can be used locally, the development of a three-dimensional lattice gas capability is required. The first major task in setting up a three dimensional-lattice gas is the construction of an efficient collision rule generator which will determine collision outcomes. For suitability to local applications, the collision rules should be chosen in such a way as to maximise the Reynolds coefficient of the flow, while conserving quantities such as mass and momentum. Part of the task thus becomes an optimisation problem. When expanding from two to three dimensions, the number of possible collision rules increases from 64 to 16777216. If a complete collision rule table is used for determining collision outcomes, storage problems are encountered on the available hardware. Selection and optimisation of collision rules cannot be done by hand when there are so many rules to choose from. Selection of rules is thus non-trivial. The work outlined in this thesis provides the CSIR with a 3-D lattice gas collision table which is well suited to the available hardware capabilities. The necessary theoretical background is considered, and a survey of the literature is presented. Based on the findings of this literature study, various methods of collision outcome determination are implemented which are considered to be suitable to the local needs, while remaining within the constraints set by hardware availability. An isometric collision algorithm, and a reduced collision table are generated and tested. A measure of the overall efficiency of a lattice gas model is determined by two factors, namely the computational efficiency and the implementation efficiency. In testing a collision table, the first is characterised by the rate at which post-collision states can be determined, and depends on the hardware and programming techniques. The second factor can be expressed by means of a number called the Reynolds coefficient, which is defined and discussed in the following chapters. The higher the Reynolds coefficient of a model, the greater the scope of flow regimes which may be simulated using it. Another advantage of having a high Reynolds coefficient is that the simulation time required for a given flow regime decreases as the Reynolds coefficient of the model increases. The overall efficiency of the isometric model is too low to be of practical use, but a significant improvement is obtained by using the method of reduced tables. In the isometric case, the number of collision outcomes that can be determined per second is similar to that of the reduced table, but the Reynolds coefficient is very much lower. Simulation of a flow regime with a Reynolds number of about 100, on a lattice of size 128³, over 20 thousand timesteps, making use of the isometric model, would take of the order of a few years to complete on the currently available hardware. Since the simulation parameters mentioned above are typical of the local requirements for lattice gas simulations, this method is obviously unsatisfactory. The isometric method does however serve as a useful introduction to three-dimensional lattice gas collision rule methods. The reduced collision table has been constructed so that it maintains semi-detailed balance, and the Boltzmann Reynolds coefficient has been calculated. In the reduced collision table model, the efficiency is higher than the isometric case in respect of both the rate at which collision outcomes can be determined, and in terms of the Reynolds coefficient. As a result of these improvements, the simulation time for the exact case mentioned above would reduce to the order of days, on the same hardware. This simulation time is sufficiently low for immediate practical application in the local environment

An Object-Oriented Programming Environment for Parallel Genetic Algorithms

This thesis investigates an object-oriented programming environment for building parallel applications based on genetic algorithms (GAs). It describes the design of the Genetic Algorithms Manipulation Environment (GAME), which focuses on three major software development requirements: flexibility, expandability and portability. Flexibility is provided by GAME through a set of libraries containing pre-defined and parameterised components such as genetic operators and algorithms. Expandability is offered by GAME'S object-oriented design. It allows applications, algorithms and genetic operators to be easily modified and adapted to satisfy diverse problem's requirements. Lastly, portability is achieved through the use of the standard C++ language, and by isolating machine and operating system dependencies into low-level modules, which are hidden from the application developer by GAME'S application programming interfaces. The development of GAME is central to the Programming Environment for Applications of PArallel GENetic Algorithms project (PAPAGENA). This is the principal European Community (ESPRIT III) funded parallel genetic algorithms project. It has two main goals: to provide a general-purpose tool kit, supporting the development and analysis of large-scale parallel genetic algorithms (PGAs) applications, and to demonstrate the potential of applying evolutionary computing in diverse problem domains. The research reported in this thesis is divided in two parts: i) the analysis of GA models and the study of existing GA programming environments from an application developer perspective; ii) the description of a general-purpose programming environment designed to help with the development of GA and PGA-based computer programs. The studies carried out in the first part provide the necessary understanding of GAs' structure and operation to outline the requirements for the development of complex computer programs. The second part presents GAME as the result of combining development requirements, relevant features of existing environments and innovative ideas, into a powerful programming environment. The system is described in terms of its abstract data structures and sub-systems that allow the representation of problems independently of any particular GA model. GAME's programming model is also presented as general-purpose object-oriented framework for programming coarse-grained parallel applications. GAME has a modular architecture comprising five modules: the Virtual Machine, the Parallel Execution Module, the Genetic Libraries, the Monitoring Control Module, and the Graphic User Interface. GAME's genetic-oriented abstract data structures, and the Virtual Machine, isolates genetic operators and algorithms from low-level operations such as memory management, exception handling, etc. The Parallel Execution Module supports GAME's object- oriented parallel programming model. It defines an application programming interface and a runtime library that allow the same parallel application, created within the environment, to run on different hardware and operating system platforms. The Genetic Libraries outline a hierarchy of components implemented as parameterised versions of standard and custom genetic operators, algorithms and applications. The Monitoring Control Module supports dynamic control and monitoring of simulations, whereas the Graphic User Interface defines a basic framework and graphic 'widgets' for displaying and entering data. This thesis describes the design philosophy and rationale behind these modules, covering in more detail the Virtual Machine, the Parallel Execution Module and the Genetic Libraries. The assessment discusses the system's ability to satisfy the main requirements of GA and PGA software development, as well as the features that distinguish GAME from other programming environments