Studies in Rheology: Molecular Simulation and Theory

With an enormous advance in the capability of computers during the last fewdecades, the computer simulation has become an important tool for scientific researches in many areas such as physics, chemistry, biology, and so on. In particular, moleculardynamics (MD) simulations have been proven to be of a great help in understanding the rheology of complex fluids from the fundamental microscopic viewpoint. There are two important standard flows in rheology: shear flow and elongational flow. While there exist suitable nonequilibrium MD (NEMD) algorithms of shear flows, such as the Lees-Edwards purely boundary-driven algorithm and the so-called SLLOD algorithm as a field-driven algorithm, a proper NEMD algorithm for elongational flow has been lacking. The main difficulty of simulating elongational flow lies in the limited simulation time available due to the contraction of one or two dimensions dictated by itskinematics. This problem, however, has been partially resolved by Kraynik and Reinelt’s ingenious discovery of the temporal and spatial periodicity of lattice vectors in planar elongational flow (PEF). Although there have been a few NEMD simulations of PEF using their idea, another serious defect has recently been reported when using the SLLOD algorithm in PEF: for adiabatic systems, the total linear momentum of the system in the contracting direction grows exponentially with time, which eventually leads to an aphysical phase transition.This problem has been completely resolved by using the so-called ‘proper-SLLOD’ or ‘p-SLLOD’ algorithm, whose development has been one of the mainaccomplishments of this study. The fundamental correctness of the p-SLLOD algorithm has been demonstrated quite thoroughly in this work through detailed theoretical analyses together with direct simulation results. Both theoretical and simulation works achieved in this research are expected to play a significant role in advancing the knowledge of rheology, as well as that of NEMD simulation itself for other types of flow in general. Another important achievement in this work is the demonstration of the possibility of predicting a liquid structure in nonequilibrium states by employing a concept of ‘hypothetical’ nonequilibrium potentials. The methodology developed in this work has been shown to have good potential for further developments in this field

Queueing networks: solutions and applications

During the pasttwo decades queueing network models have proven to be a versatile tool for computer system and computer communication system performance evaluation. This chapter provides a survey of th field with a particular emphasis on applications. We start with a brief historical retrospective which also servesto introduce the majr issues and application areas. Formal results for product form queuenig networks are reviewed with particular emphasis on the implications for computer systems modeling. Computation algorithms, sensitivity analysis and optimization techniques are among the topics covered. Many of the important applicationsof queueing networks are not amenableto exact analysis and an (often confusing) array of approximation methods have been developed over the years. A taxonomy of approximation methods is given and used as the basis for for surveing the major approximation methods that have been studied. The application of queueing network to a number of areas is surveyed, including computer system cpacity planning, packet switching networks, parallel processing, database systems and availability modeling.Durante as últimas duas décadas modelos de redes de filas provaram ser uma ferramenta versátil para avaliação de desempenho de sistemas de computação e sistemas de comunicação. Este capítulo faz um apanhado geral da área, com ênfase em aplicações. Começamos com uma breve retrospectiva histórica que serve também para introduzir os pontos mais importantes e as áreas de aplicação. Resultados formais para redes de filas em forma de produto são revisados com ênfase na modelagem de sistemas de computação. Algoritmos de computação, análise de sensibilidade e técnicas de otimização estão entre os tópicos revistos. Muitas dentre importantes aplicações de redes de filas não são tratáveis por análise exata e uma série (frequentemente confusa) de métodos de aproximação tem sido desenvolvida. Uma taxonomia de métodos de aproximação é dada e usada como base para revisão dos mais importantes métodos de aproximação propostos. Uma revisão das aplicações de redes de filas em um número de áreas é feita, incluindo planejamento de capacidade de sistemas de computação, redes de comunicação por chaveamento de pacotes, processamento paralelo, sistemas de bancos de dados e modelagem de confiabilidade

Investigation of hybrid message-passing and shared-memory architectures for parallel computer : a case study : turbonet

Several DSP (Digital Signal Processing) algorithms are developed for the MIT TurboNet parallel computer. In contrast to other parallel computers that implement exclusively in hardware either the message-passing or the shared-memory communication paradigm, or employ distributed shared-memory architectures characterized by inefficient implementation of the shared-memory paradigm, the hybrid architecture of TurboNet supports direct, efficient implementation of both paradigms. Three versions of each algorithm are developed, if possible, corresponding to message-passing, shared-memory, and hybrid communications, respectively. Theoretical and experimental comparisons of algorithms are employed in the analysis of performance. The results prove that the hybrid versions generally achieve better performance than the other two versions. The main conclusion of this research is that small-scale and medium-scale parallel computers should implement directly in hardware both communication paradigms, for high performance, robustness in relation to the application space, and ease of algorithm development. To facilitate theoretical comparisons, a methodology is developed for highly accurate prediction of algorithm performance. The success of this methodology proves that such prediction is possible for complex parallel computers, such as TurboNet, if enough information is provided by the data dependence graphs

White-box methodologies, programming abstractions and libraries

EXCESS deliverable D2.2. More information at http://www.excess-project.eu/This deliverable reports the results of white-box methodologies and early results ofthe first prototype of libraries and programming abstractions as available by projectmonth 18 by Work Package 2 (WP2). It reports i) the latest results of Task 2.2on white-box methodologies, programming abstractions and libraries for developingenergy-efficient data structures and algorithms and ii) the improved results of Task2.1 on investigating and modeling the trade-off between energy and performance ofconcurrent data structures and algorithms. The work has been conducted on two mainEXCESS platforms: Intel platforms with recent Intel multicore CPUs and MovidiusMyriad1 platform

Static and Dynamic Scheduling for Effective Use of Multicore Systems

Multicore systems have increasingly gained importance in high performance computers. Compared to the traditional microarchitectures, multicore architectures have a simpler design, higher performance-to-area ratio, and improved power efficiency. Although the multicore architecture has various advantages, traditional parallel programming techniques do not apply to the new architecture efficiently. This dissertation addresses how to determine optimized thread schedules to improve data reuse on shared-memory multicore systems and how to seek a scalable solution to designing parallel software on both shared-memory and distributed-memory multicore systems. We propose an analytical cache model to predict the number of cache misses on the time-sharing L2 cache on a multicore processor. The model provides an insight into the impact of cache sharing and cache contention between threads. Inspired by the model, we build the framework of affinity based thread scheduling to determine optimized thread schedules to improve data reuse on all the levels in a complex memory hierarchy. The affinity based thread scheduling framework includes a model to estimate the cost of a thread schedule, which consists of three submodels: an affinity graph submodel, a memory hierarchy submodel, and a cost submodel. Based on the model, we design a hierarchical graph partitioning algorithm to determine near-optimal solutions. We have also extended the algorithm to support threads with data dependences. The algorithms are implemented and incorporated into a feedback directed optimization prototype system. The prototype system builds upon a binary instrumentation tool and can improve program performance greatly on shared-memory multicore architectures. We also study the dynamic data-availability driven scheduling approach to designing new parallel software on distributed-memory multicore architectures. We have implemented a decentralized dynamic runtime system. The design of the runtime system is focused on the scalability metric. At any time only a small portion of a task graph exists in memory. We propose an algorithm to solve data dependences without process cooperation in a distributed manner. Our experimental results demonstrate the scalability and practicality of the approach for both shared-memory and distributed-memory multicore systems. Finally, we present a scalable nonblocking topology-aware multicast scheme for distributed DAG scheduling applications

The exploitation of parallelism on shared memory multiprocessors

PhD ThesisWith the arrival of many general purpose shared memory multiple processor (multiprocessor) computers into the commercial arena during the mid-1980's, a rift has opened between the raw processing power offered by the emerging hardware and the relative inability of its operating software to effectively deliver this power to potential users. This rift stems from the fact that, currently, no computational model with the capability to elegantly express parallel activity is mature enough to be universally accepted, and used as the basis for programming languages to exploit the parallelism that multiprocessors offer. To add to this, there is a lack of software tools to assist programmers in the processes of designing and debugging parallel programs. Although much research has been done in the field of programming languages, no undisputed candidate for the most appropriate language for programming shared memory multiprocessors has yet been found. This thesis examines why this state of affairs has arisen and proposes programming language constructs, together with a programming methodology and environment, to close the ever widening hardware to software gap. The novel programming constructs described in this thesis are intended for use in imperative languages even though they make use of the synchronisation inherent in the dataflow model by using the semantics of single assignment when operating on shared data, so giving rise to the term shared values. As there are several distinct parallel programming paradigms, matching flavours of shared value are developed to permit the concise expression of these paradigms.The Science and Engineering Research Council

Approximation and Relaxation Approaches for Parallel and Distributed Machine Learning

Large scale machine learning requires tradeoffs. Commonly this tradeoff has led practitioners to choose simpler, less powerful models, e.g. linear models, in order to process more training examples in a limited time. In this work, we introduce parallelism to the training of non-linear models by leveraging a different tradeoff--approximation. We demonstrate various techniques by which non-linear models can be made amenable to larger data sets and significantly more training parallelism by strategically introducing approximation in certain optimization steps. For gradient boosted regression tree ensembles, we replace precise selection of tree splits with a coarse-grained, approximate split selection, yielding both faster sequential training and a significant increase in parallelism, in the distributed setting in particular. For metric learning with nearest neighbor classification, rather than explicitly train a neighborhood structure we leverage the implicit neighborhood structure induced by task-specific random forest classifiers, yielding a highly parallel method for metric learning. For support vector machines, we follow existing work to learn a reduced basis set with extremely high parallelism, particularly on GPUs, via existing linear algebra libraries. We believe these optimization tradeoffs are widely applicable wherever machine learning is put in practice in large scale settings. By carefully introducing approximation, we also introduce significantly higher parallelism and consequently can process more training examples for more iterations than competing exact methods. While seemingly learning the model with less precision, this tradeoff often yields noticeably higher accuracy under a restricted training time budget