An occam Style Communications System for UNIX Networks

This document describes the design of a communications system which provides occam style communications primitives under a Unix environment, using TCP/IP protocols, and any number of other protocols deemed suitable as underlying transport layers. The system will integrate with a low overhead scheduler/kernel without incurring significant costs to the execution of processes within the run time environment. A survey of relevant occam and occam3 features and related research is followed by a look at the Unix and TCP/IP facilities which determine our working constraints, and a description of the T9000 transputer's Virtual Channel Processor, which was instrumental in our formulation. Drawing from the information presented here, a design for the communications system is subsequently proposed. Finally, a preliminary investigation of methods for lightweight access control to shared resources in an environment which does not provide support for critical sections, semaphores, or busy waiting, is made. This is presented with relevance to mutual exclusion problems which arise within the proposed design. Future directions for the evolution of this project are discussed in conclusion

Parallel algorithms for the solution of elliptic and parabolic problems on transputer networks

This thesis is a study of the implementation of parallel algorithms for solving elliptic and parabolic partial differential equations on a network of transputers. The thesis commences with a general introduction to parallel processing. Here a discussion of the various ways of introducing parallelism in computer systems and the classification of parallel architectures is presented. In chapter 2, the transputer architecture and the associated language OCCAM are described. The transputer development system (TDS) is also described as well as a short account of other transputer programming languages. Also, a brief description of the methodologies for programming transputer networks is given. The chapter is concluded by a detailed description of the hardware used for the research. [Continues.

Alternating-Direction Line-Relaxation Methods on Multicomputers

We study the multicom.puter performance of a three-dimensional Navier–Stokes solver based on alternating-direction line-relaxation methods. We compare several multicomputer implementations, each of which combines a particular line-relaxation method and a particular distributed block-tridiagonal solver. In our experiments, the problem size was determined by resolution requirements of the application. As a result, the granularity of the computations of our study is finer than is customary in the performance analysis of concurrent block-tridiagonal solvers. Our best results were obtained with a modified half-Gauss–Seidel line-relaxation method implemented by means of a new iterative block-tridiagonal solver that is developed here. Most computations were performed on the Intel Touchstone Delta, but we also used the Intel Paragon XP/S, the Parsytec SC-256, and the Fujitsu S-600 for comparison

Lewis Structures Technology, 1988. Volume 1: Structural Dynamics

The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the Structures Division of the Lewis Research Center and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive testing, dynamical systems, fatigue and damage, wind turbines, hot section technology, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics

Structural dynamics branch research and accomplishments for FY 1988

Fiscal year 1988 research highlights from the Structural Dynamics Branch at NASA Lewis Research Center are described. Highlights from the branch's major work areas -- aeroelasticity, vibration control, dynamic systems, and computational structural methods -- are included as well as a complete listing of the FY 88 branch publications

An empirical evaluation of techniques for parallel simulation of message passing networks

209 p.[EN]In the field of computer design, simulation is an essential tool to validate and evaluate architectural proposals. Conventional simulation techniques, designed for their use in sequential computers, are too slow if the system to simulate is large or complex. The aim of this work is to search for techniques to accelerate simulations exploiting the parallelism available in current, commercial multicomputers, and to use these techniques to study a model of a message router. This router has been designed to constitute the communication infrastructure of a (hypothetical) massively parallel computer. Three parallel simulation techniques have been considered: synchronous, asynchronous-conservative and asynchronous-optimistic. These algorithms have been implemented in three multicomputers: a transputer-based Supernode, an Intel Paragon and a network of workstations. The influence that factors such as the characteristics of the simulated models, the organization of the simulators and the characteristics of the target multicomputers have in the performance of the simulations has been measured and characterized. It is concluded that optimistic parallel simulation techniques are not suitable for the considered kind of models, although they may provide good performance in other environments. A network of workstations is not the right platform for our experiments, because the communication demands of the parallel simulators surpass the abilities of local area networks—the granularity is too fine. Synchronous and conservative parallel simulation techniques perform very well in the Supernode and in the Paragon, specially if the model to simulate is complex or large—precisely the worst case for traditional, sequential simulators. This way, studies previously considered as unrealizable, due to their exceedingly high computational cost, can be performed in reasonable times. Additionally, the spectrum of possibilities of using multicomputers can be broadened to execute more than numeric applications.[ES]En el ámbito del diseño de computadores, la simulación es una herramienta imprescindible para la validación y evaluación de cualquier propuesta arquitectónica. Las ténicas convencionales de simulación, diseñadas para su utilización en computadores secuenciales, son demasiado lentas si el sistema a simular es grande o complejo. El objetivo de esta tesis es buscar técnicas para acelerar estas simulaciones, aprovechando el paralelismo disponible en multicomputadores comerciales, y usar esas técnicas para el estudio de un modelo de encaminador de mensajes. Este encaminador está diseñado para formar infraestructura de comunicaciones de un hipotético computador masivamente paralelo. En este trabajo se consideran tres técnicas de simulación paralela: síncrona, asíncrona-conservadora y asíncrona-optimista. Estos algoritmos se han implementado en tres multicomputadores: un Supernode basado en Transputers, un Intel Paragon y una red de estaciones de trabajo. Se caracteriza la influencia que tienen en las prestaciones de los simuladores aspectos tales como los parámetros del modelo simulado, la organización del simulador y las características del multicomputador utilizado. Se concluye que las técnicas de simulación paralela optimista no resultan adecuadas para trabajar con el modelo considerado, aunque pueden ofrecer un buen rendimiento en otros entornos. La red de estaciones de trabajo no resulta una plataforma apropiada para estas simulaciones, ya que una red local no reúne condiciones para la ejecución de aplicaciones paralelas de grano fino. Las técnicas de simulación paralela síncrona y conservadora dan muy buenos resultados en el Supernode y en el Paragon, especialmente si el modelo a simular es complejo o grande—precisamente el peor caso para los algoritmos secuenciales. De esta forma, estudios previamente considerados inviables, por ser demasiado costosos computacionalmente, pueden realizarse en tiempos razonables. Además, se amplía el espectro de posibilidades de los multicomputadores, utilizándolos para algo más que aplicaciones numéricas.Este trabajo ha sido parcialmente subvencionado por la Comisión Interministerial de Ciencia y Tecnología, bajo contrato TIC95-037

Towards Solving the Dopamine G Protein Coupled Receptor Modelling Problem

The overall aim of this work has been to furnish a model of the dopamine (DA) receptor D2. There are currently two sub-groups within the DA family of G protein coupled receptors (GPCRs): D1 sub-group (includes D1 and D5) and the D2 sub-group (includes D2, D3 and D4). Organon (UK) Ltd. supplied a disk containing the PDB atomic co-ordinates of the integral membrane protein bacteriorhodopsin (bRh; Henderson et al., 1975 and 1990) to use as a template to model D2 - the aim being to generate a model of D2 by simply mutating the side-residues of bRh. The assumption being that bRh had homology with members of the supergene class of GPCRs. However, using the GCG Wisconsin GAP algorithm (Devereux et al., 1984) no significant homology was detected between the primary structures of any member of the DA family of GPCRs and bRh. However, given the original brief to carry out homology modelling using bRh as a template (see appendix 1) I felt obliged to carry out further alignments using a shuffling technique and a standard statistical test to check for significant structural homology. The results clearly showed that there is no significant structural homology, on the basis of sequence similarity, between bRh and any member of the DA family of GPCRs. Indeed, the statistical analysis clearly demonstrated that while there is significant structural homology between every catecholamine binding GPCR, there is no structural homology what so ever between any catecholamine binding GPCR and bRh. Hydropathy analysis is frequently used to identify the location of putative transmembrane segments. However, is difficult to predict the end positions of each ptms. To this end a novel alignment algorithm (DH Scan) was coded to exploit transparallel supercomputer technology to provide a basis for identifying likely helix end points and to pinpoint areas of local homology between GPCRs. DH Scan clearly demonstrated characteristic transmembrane homology between different subtype DA GPCRs. Two further homology algorithms were coded (IH Scan and RH Scan) which provided evidence of internal homology. In particular IH Scan independently revealed a repeat region in the 3rd intracellular loop (iIII) of D4 and RH Scan revealed palindromic like short stretches of amino acids which were found to be particularly well represented in predicted ?-helices in each DA receptor subtype. In addition, the profile network prediction algorithm (PHD; Rost et al., 1994) predicted a short alpha-helix at greater than 80% probablility at each end of the third intracellular loop and between the carboxy terminal end of transmembrane VII and a conserved Cys residue in the forth intracellular loop. Fourier analysis of catecholamine binding GPCR primary structures in the form of a multiple-sequence file suggested that the consensus view that only those residues facing the protein interior are conserved is not entirely correct. In particular, transmembrane helices II and III do not exhibit residue conservancy characteristic of an amphipathic helix. It is proposed that these two helices undergo a form of helix interface shear to assist agonist binding to a Asp residue on helix II. This data in combination with information from a number of papers concerning helix shear interface mechanism and molecular dynamic studies of proline containing ?-helices suggested a physically plausible binding mechanism for agonists. While it was evident that homology modelling could not be scientifically justified, the combinatorial approach to protein modelling might be successfully applied to the transmembrane region of the D2 receptor. The probable arrangement of helices in the transmembrane region of GPCRs (Baldwin, 1993) which was based on a careful analysis of a low resolution projection map of rhodopsin (Gebhard et ah, 1993) was used as a guide to model the transmembrane region of D2. The backbone torsion angles of a helix with a middle Pro residue (Sankararamakrishnan et al., 1991) was used to model transmembrane helix V. Dopamine was successfully docked to the putative binding pocket of D2. Using this model as a template, models of D3 and D4 were produced. A separate model of Di was then produced and this in turn was used as a template to model D5

Multiple Track Performance of a Digital Magnetic Tape System : Experimental Study and Simulation using Parallel Processing Techniques

The primary aim of the magnetic recording industry is to increase storage capacities and transfer rates whilst maintaining or reducing costs. In multiple-track tape systems, as recorded track dimensions decrease, higher precision tape transport mechanisms and dedicated coding circuitry are required. This leads to increased manufacturing costs and a loss of flexibility. This thesis reports on the performance of a low precision low-cost multiple-track tape transport system. Software based techniques to study system performance, and to compensate for the mechanical deficiencies of this system were developed using occam and the transputer. The inherent parallelism of the multiple-track format was exploited by integrating a transputer into the recording channel to perform the signal processing tasks. An innovative model of the recording channel, written exclusively in occam, was developed. The effect of parameters, such as data rate, track dimensions and head misregistration on system performance was determined from the detailed error profile produced. This model may be run on a network of transputers, allowing its speed of execution to be scaled to suit the investigation. These features, combined with its modular flexibility makes it a powerful tool that may be applied to other multiple-track systems, such as digital HDTV. A greater understanding of the effects of mechanical deficiencies on the performance of multiple-track systems was gained from this study. This led to the development of a software based compensation scheme to reduce the effects of Lateral Head Displacement and allow low-cost tape transport mechanisms to be used with narrow, closely spaced tracks, facilitating higher packing densities. The experimental and simulated investigation of system performance, the development of the model and compensation scheme using parallel processing techniques has led to the publication of a paper and two further publications are expected.Thorn EMI, Central Research Laboratories, Hayes, Middlese