Thesis (M. Phil.)--University of Hong Kong, 1999. / Includes bibliographical references (leaves 89-95).

Thesis (M.S.)--Missouri University of Science and Technology, 2009. / Vita. The entire thesis text is included in file. Title from title screen of thesis/dissertation PDF file (viewed November 17, 2009) Includes bibliographical references (p. 61-62).

Advances in computer technology such as faster processors, better data compression schemes, and cheaper audio and video devices have made it possible to integrate multimedia into the computing environment. Desktop conferencing evolved as a plausible result of this multimedia revolution. The bandwidth granted for these conferencing applications is restricted in most cases by the speed of the modem device connected to the network. Poor performance of multimedia conferencing over the Internet can be attributed to two main factors: local and remote induced effects. Local effects are induced by bandwidth sharing between different media components, operating system limitations, or poor design. Remote effects include all Internet related problems such as unfairness, nonguaranteed quality of service, congestion, etc. Both effects are addressed in this study and some solutions are proposed. The primary goal is to maintain audio quality and prevent video from degrading audio performance. We study characteristics of video and audio traffic sources of conferencing applications following the H.323 set of standards defined by the International Telecommunication Union (ITU). The media traffic uses the Real-time Transport Protocol (RTP) and User Datagram Protocol (UDP) as their transport vehicle over IP network protocol. Tradeoffs involved in the choice of multimedia traffic parameters are presented. Our measurements were carried out on audio and video codecs defined in G.723.1 and H.263 specifications respectively, both drafted by the ITU. This dissertation investigates traffic multiplexing issues at the host, and the interaction of conferencing media components as they are multiplexed locally in a shared bandwidth transport medium. Lack of appropriate multiplexing algorithms can lead to one or more media components oversubscribing to the shared bandwidth and penalizing other participants. These local effects can contribute significantly to traffic delay or abuse of the network bandwidth. We propose the “bit rate adjuster” (BRA) algorithm and use it the network bandwidth. We propose the “bit rate adjuster” (BRA) algorithm and use it for regulating media flow. The algorithm compensates for video local effects induced by packet preparation or processing to allow for better audio performance. A new performance qualifier is introduced and used in the evaluation process. Further on the remote side, we investigate reactive mechanisms used to recover media flow performance degradation caused by shared bandwidth traffic effects. We overview feedback mechanisms based on the Real-time Control Protocol (RTCP). We uncover its limitation on applications connected to the Internet through narrow bandwidth pipes. We propose an alternative approach that predicts and prevents the loss of audio packets before it occurs based on local computation of audio jitter. We also propose a mechanism that recovers audio traffic from jitter and latency effects introduced by the Internet shared medium. These approaches improve the audio performance significantly in multimedia conferencing sessions. / Graduate

La croissance exponentielle de la génération de données pour la bioinformatique couplée à une stagnation des fréquences d’horloge des processeurs modernes accentuent la nécessité de fournir des implémentation tirant bénéfice des capacités parallèles des ordinateurs modernes. Cette thèse se concentre sur des algorithmes et implementations pour des problèmes de bioinformatique. Plusieurs types de parallélisme sont décrits et exploités. Cette thèse présente des applications en génétique, avec un outil de détection de QTL paralllisé sur GPU, en comparaison de structures de protéines, avec un outil permettant de trouver des régions similaires entre protéines parallélisé sur CPU, ainsi qu’à l’analyse de larges graphes avec une implémentation multi-GPUs d’un nouvel algorithme pour le problème du «All-Pairs Shortest Path». / The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications in genetics with a GPU parallel tool for QTL detection, in protein structure comparison with a multicore parallel tool for finding similar regions between proteins, and large graph analysis with a multi-GPU parallel implementation for a novel algorithm for the All-Pairs Shortest Path problem.

It was observed, that the RT-PICLS code ran by FWKT on the hypnos cluster was producing an unusual amount of system load, according to Ganglia metrics. Since this may point to an IO-problem in the code, this code was analyzed more closely.

Thesis (M. Phil.)--University of Hong Kong, 1999. / Includes bibliographical references (leaves 71-75).

<p dir="ltr">Graph-structure data is prevalent because of its ability to capture relations between real-world entities. However, graph data analyzing applications, including traditional and machine-learning-based approaches, are highly resource-demanding, necessitating massively parallel hardware like distributed clusters. Domain-specific systems, which aims to hide the hardware complexity from application users, suffers from the communication and computation efficiency problems.</p><p dir="ltr">This thesis tackles the problems with a set of novel specialized system designs for each category of workloads. For graph analytics workloads, we propose to enforce precise loop-carried dependency propagation to reduce redundant communication and computation in our SympleGraph system. SympleGraph achieves up to 2.30x and 7.76x speedups over Gemini and D-Galios, two state-of-the-art systems. For graph pattern mining workloads, we propose to co-design the pattern decomposition algorithm and compilation techniques to improve computation efficiency, and leverage application-characteristics-aware optimizations to reduce and hide communication overhead efficiently in our DecoMine and Khuzdul systems, respectively. Our extensive experiments show that, DecoMine and Khuzdul significantly outperform previous state-of-the-art solutions. For graph neural network training, we propose to introduce pipelined model parallelism for deep model training to reduce the worst-case communication complexity by a factor of model depth. With the proposed technique, our system, GNNPipe, can reduce the communication volume by up to 22.89x and speed up the training by up to 2.45x.</p>

Computer simulations have become a vital tool in modern science. The ability to reliably move beyond the capabilities of experiment has allowed great insights into the nature of matter. To enable the study of a wide range of systems and properties a plethora of simulation techniques have been developed and refined, allowing many aspects of complex systems to be demystified. I have used a range of these to study a variety of systems, utilising the latest technology in high performance computing (HPC) and novel, nanoscale models. Monte Carlo (MC) simulation is a commonly used method to study the properties of system using statistical mechanics and I have made use of it in published work [1] to study the properties of ferrogels in homogeneous magnetic fields using a simple microscopic model. The main phenomena of interest concern the anisotropy and enhancement of the elastic moduli that result from applying uniform magnetic fields before and after the magnetic grains are locked in to the polymer-gel matrix by cross-linking reactions. The positional organization of the magnetic grains is influenced by the application of a magnetic field during gel formation, leading to a pronounced anisotropy in the mechanical response of the ferrogel to an applied magnetic field. In particular, the elastic moduli can be enhanced to different degrees depending on the mutual orientation of the fields during and after ferrogel formation. Previously, no microscopic models have been produced to shed light on this effect and the main purpose of the work presented here is to illuminate the microscopic behaviour. The model represents ferrogels by ensembles of dipolar spheres dispersed in elastic matrices. Experimental trends are shown to be reflected accurately in the simulations of the microscopic model while shedding light on the microscopic mechanism causing these effects. These mechanisms are shown to be related to the behaviour of the dipoles during the production of the gels and caused by the chaining of dipoles in magnetic fields. Finally, simple relationships between the elastic moduli and the magnetization are proposed. If supplemented by the magnetization curve, these relationships yield the dependencies of the elastic moduli on the applied magnetic field, which are often measured directly in experiments. While MC simulations are useful for statistical studies, it can be difficult to use them to gather information about the dynamics of a system. In this case, Molecular Dynamics (MD) is more widely used. MD generally utilises the classical equations of motion to simulate the evolution of a system. For large systems, which are often of interest, and multi-species polymers, the required computer power still poses a challenge and requires the use of HPC techniques. The most recent development in HPC is the use of Graphical Processing Units (GPU) for the fast solution of data parallel problems. In further published work [2], I have used a bespoke MD code utilising GPU acceleration in order to simulate large systems of block copolymers(BC) in solvent over long timescales. I have studied thin films of BC solutions drying on a flat, smooth surface which requires long timescales due to the ’slow’ nature of the process. BC’s display interesting self-organisation behaviour in bulk solution and near surfaces and have a wide range of potential applications from semi-conductors to self-constructing fabrics. Previous studies have shown some unusual behaviour of PI-PEO diblock co-polymers adsorbing to a freshly cleaved mica surface. These AFM studies showed polymers increasing in height over time and proposed the change of affinity of mica to water and the loss of water layers on the surface as a driver for this change. The MD simulation aimed to illuminate the process involved in this phenomena. The process of evaporation of water layers from a surface was successfully simulated and gave a good indication that the process of solvent evaporation from the surface and the ingress of solvent beneath the adsorbed polymer caused the increase in height seen in experiment.

published_or_final_version / Computer Science and Information Systems / Doctoral / Doctor of Philosophy

Finite element analysis is versatile and used widely in a range of engineering andscientific disciplines. As time passes, the problems that engineers and designers areexpected to solve are becoming more computationally demanding. Often theproblems involve the interplay of two or more processes which are physically andtherefore mathematically coupled. Although parallel computers have been availablefor about twenty years to satisfy this demand, finite element analysis is still largelyexecuted on serial machines. Parallelisation appears to be difficult, even for thespecialist. Parallel machines, programming languages, libraries and tools are used toparallelise old serial programs with mixed success. In some cases the serialalgorithm is not naturally suitable for parallel computing. Some argue that rewritingthe programs from scratch, using an entirely different solution strategy is a betterapproach. Taking this point of view, using MPI for portability, a mesh free elementby element method for simple data distribution and the appropriate iterative solvers,a general parallel strategy for finite element analysis is developed and assessed.