Fault-tolerant parallel applications using a network of workstations

PhD thesisIt is becoming common to employ a Network Of Workstations, often referred to as a NOW, for general purpose computing since the allocation of an individual workstation offers good interactive response. However, there may still be a need to perform very large scale computations which exceed the resources of a single workstation. It may be that the amount of processing implies an inconveniently long duration or that the data manipulated exceeds available storage. One possibility is to employ a more powerful single machine for such computations. However, there is growing interest in seeking a cheaper alternative by harnessing the significant idle time often observed in a NOW and also possibly employing a number of workstations in parallel on a single problem. Parallelisation permits use of the combined memories of all participating workstations, but also introduces a need for communication. and success in any hardware environment depends on the amount of communication relative to the amount of computation required. In the context of a NOW, much success is reported with applications which have low communication requirements relative to computation requirements. Here it is claimed that there is reason for investigation into the use of a NOW for parallel execution of computations which are demanding in storage, potentially even exceeding the sum of memory in all available workstations. Another consideration is that where a computation is of sufficient scale, some provision for tolerating partial failures may be desirable. However, generic support for storage management and fault-tolerance in computations of this scale for a NOW is not currently available and the suitability of a NOW for solving such computations has not been investigated to any large extent. The work described here is concerned with these issues. The approach employed is to make use of an existing distributed system which supports nested atomic actions (atomic transactions) to structure fault-tolerant computations with persistent objects. This system is used to develop a fault-tolerant "bag of tasks" computation model, where the bag and shared objects are located on secondary storage. In order to understand the factors that affect the performance of large parallel computations on a NOW, a number of specific applications are developed. The performance of these applications is ana- lysed using a semi-empirical model. The same measurements underlying these performance predictions may be employed in estimation of the performance of alternative application structures. Using services provided by the distributed system referred to above, each application is implemented. The implement- ation allows verification of predicted performance and also permits identification of issues regarding construction of components required to support the chosen application structuring technique. The work demonstrates that a NOW certainly offers some potential for gain through parallelisation and that for large grain computations, the cost of implementing fault tolerance is low.Engineering and Physical Sciences Research Counci

Cluster Computing Review

In the past decade there has been a dramatic shift from mainframe or ‘host−centric’ computing to a distributed ‘client−server’ approach. In the next few years this trend is likely to continue with further shifts towards ‘network−centric’ computing becoming apparent. All these trends were set in motion by the invention of the mass−reproducible microprocessor by Ted Hoff of Intel some twenty−odd years ago. The present generation of RISC microprocessors are now more than a match for mainframes in terms of cost and performance. The long−foreseen day when collections of RISC microprocessors assembled together as a parallel computer could out perform the vector supercomputers has finally arrived. Such high−performance parallel computers incorporate proprietary interconnection networks allowing low−latency, high bandwidth inter−processor communications. However, for certain types of applications such interconnect optimization is unnecessary and conventional LAN technology is sufficient. This has led to the realization that clusters of high−performance workstations can be realistically used for a variety of applications either to replace mainframes, vector supercomputers and parallel computers or to better manage already installed collections of workstations. Whilst it is clear that ‘cluster computers’ have limitations, many institutions and companies are exploring this option. Software to manage such clusters is at an early stage of development and this report reviews the current state−of−the−art. Cluster computing is a rapidly maturing technology that seems certain to play an important part in the ‘network−centric’ computing future

System support for object replication in distributed systems

Distributed systems are composed of a collection of cooperating but failure prone system components. The number of components in such systems is often large and, despite low probabilities of any particular component failing, the likelihood that there will be at least a small number of failures within the system at a given time is high. Therefore, distributed systems must be able to withstand partial failures. By being resilient to partial failures, a distributed system becomes more able to offer a dependable service and therefore more useful. Replication is a well known technique used to mask partial failures and increase reliability in distributed computer systems. However, replication management requires sophisticated distributed control algorithms, and is therefore a labour intensive and error prone task. Furthermore, replication is in most cases employed due to applications' non-functional requirements for reliability, as dependability is generally an orthogonal issue to the problem domain of the application. If system level support for replication is provided, the application developer can devote more effort to application specific issues. Distributed systems are inherently more complex than centralised systems. Encapsulation and abstraction of components and services can be of paramount importance in managing their complexity. The use of object oriented techniques and languages, providing support for encapsulation and abstraction, has made development of distributed systems more manageable. In systems where applications are being developed using object-oriented techniques, system support mechanisms must recognise this, and provide support for the object-oriented approach. The architecture presented exploits object-oriented techniques to improve transparency and to reduce the application programmer involvement required to use the replication mechanisms. This dissertation describes an approach to implementing system support for object replication, which is distinct from other approaches such as replicated objects in that objects are not specially designed for replication. Additionally, object replication, in contrast to data replication, is a function-shipping approach and deals with the replication of both operations and data. Object replication is complicated by objects' encapsulation of local state and the arbitrary interaction patterns that may exist among objects. Although fully transparent object replication has not been achieved, my thesis is that partial system support for replication of program-level objects is practicable and assists the development of certain classes of reliable distributed applications. I demonstrate the usefulness of this approach by describing a prototype implementation and showing how it supports the development of an example toy application. To increase their flexibility, the system support mechanisms described are tailorable. The approach adopted in this work is to provide partial support for object replication, relying on some assistance from the application developer to supply application dependent functionality within particular collators for dealing with processing of results from object replicas. Care is taken to make the programming model as simple and concise as possible

Probabilistic Graphical Models on Multi-Core CPUs using Java 8

In this paper, we discuss software design issues related to the development of parallel computational intelligence algorithms on multi-core CPUs, using the new Java 8 functional programming features. In particular, we focus on probabilistic graphical models (PGMs) and present the parallelisation of a collection of algorithms that deal with inference and learning of PGMs from data. Namely, maximum likelihood estimation, importance sampling, and greedy search for solving combinatorial optimisation problems. Through these concrete examples, we tackle the problem of defining efficient data structures for PGMs and parallel processing of same-size batches of data sets using Java 8 features. We also provide straightforward techniques to code parallel algorithms that seamlessly exploit multi-core processors. The experimental analysis, carried out using our open source AMIDST (Analysis of MassIve Data STreams) Java toolbox, shows the merits of the proposed solutions.Comment: Pre-print version of the paper presented in the special issue on Computational Intelligence Software at IEEE Computational Intelligence Magazine journa

Smart Distributed Processing Technologies For Hedge Fund Management

Distributed processing cluster design using commodity hardware and software has proven to be a technological breakthrough in the field of parallel and distributed computing. The research presented herein is the original investigation on distributed processing using hybrid processing clusters to improve the calculation efficiency of the compute-intensive applications. This has opened a new frontier in affordable supercomputing that can be utilised by businesses and industries at various levels. Distributed processing that uses commodity computer clusters has become extremely popular over recent years, particularly among university research groups and research organisations. The research work discussed herein addresses a bespoke-oriented design and implementation of highly specific and different types of distributed processing clusters with applied load balancing techniques that are well suited for particular business requirements. The research was performed in four phases, which are cohesively interconnected, to find a suitable solution using a new type of distributed processing approaches. The first phase is an implementation of a bespoke-type distributed processing cluster using an existing network of workstations as a calculation cluster based on a loosely coupled distributed process system design that has improved calculation efficiency of certain legacy applications. This approach has demonstrated how to design an innovative, cost-effective, and efficient way to utilise a workstation cluster for distributed processing. The second phase is to improve the calculation efficiency of the distributed processing system; a new type of load balancing system is designed to incorporate multiple processing devices. The load balancing system incorporates hardware, software and application related parameters to assigned calculation tasks to each processing devices accordingly. Three types of load balancing methods are tested, static, dynamic and hybrid, which each of them has their own advantages, and all three of them have further improved the calculation efficiency of the distributed processing system.   The third phase is to facilitate the company to improve the batch processing application calculation time, and two separate dedicated calculation clusters are built using small form factor (SFF) computers and PCs as separate peer-to-peer (P2P) network based calculation clusters. Multiple batch processing applications were tested on theses clusters, and the results have shown consistent calculation time improvement across all the applications tested. In addition, dedicated clusters are built using SFF computers with reduced power consumption, small cluster size, and comparatively low cost to suit particular business needs. The fourth phase incorporates all the processing devices available in the company as a hybrid calculation cluster utilises various type of servers, workstations, and SFF computers to form a high-throughput distributed processing system that consolidates multiple calculations clusters. These clusters can be utilised as multiple mutually exclusive multiple clusters or combined as a single cluster depending on the applications used. The test results show considerable calculation time improvements by using consolidated calculation cluster in conjunction with rule-based load balancing techniques. The main design concept of the system is based on the original design that uses first principle methods and utilises existing LAN and separate P2P network infrastructures, hardware, and software. Tests and investigations conducted show promising results where the company’s legacy applications can be modified and implemented with different types of distributed processing clusters to achieve calculation and processing efficiency for various applications within the company. The test results have confirmed the expected calculation time improvements in controlled environments and show that it is feasible to design and develop a bespoke-type dedicated distributed processing cluster using existing hardware, software, and low-cost SFF computers. Furthermore, a combination of bespoke distributed processing system with appropriate load balancing algorithms has shown considerable calculation time improvements for various legacy and bespoke applications. Hence, the bespoke design is better suited to provide a solution for the calculation of time improvements for critical problems currently faced by the sponsoring company

Optimal use of computing equipment in an automated industrial inspection context

This thesis deals with automatic defect detection. The objective was to develop the techniques required by a small manufacturing business to make cost-efficient use of inspection technology. In our work on inspection techniques we discuss image acquisition and the choice between custom and general-purpose processing hardware. We examine the classes of general-purpose computer available and study popular operating systems in detail. We highlight the advantages of a hybrid system interconnected via a local area network and develop a sophisticated suite of image-processing software based on it. We quantitatively study the performance of elements of the TCP/IP networking protocol suite and comment on appropriate protocol selection for parallel distributed applications. We implement our own distributed application based on these findings. In our work on inspection algorithms we investigate the potential uses of iterated function series and Fourier transform operators when preprocessing images of defects in aluminium plate acquired using a linescan camera. We employ a multi-layer perceptron neural network trained by backpropagation as a classifier. We examine the effect on the training process of the number of nodes in the hidden layer and the ability of the network to identify faults in images of aluminium plate. We investigate techniques for introducing positional independence into the network's behaviour. We analyse the pattern of weights induced in the network after training in order to gain insight into the logic of its internal representation. We conclude that the backpropagation training process is sufficiently computationally intensive so as to present a real barrier to further development in practical neural network techniques and seek ways to achieve a speed-up. Weconsider the training process as a search problem and arrive at a process involving multiple, parallel search "vectors" and aspects of genetic algorithms. We implement the system as the mentioned distributed application and comment on its performance

A Review of Commercial and Research Cluster Management Software

In the past decade there has been a dramatic shift from mainframe or ‘host-centric’ computing to a distributed ‘client-server’ approach. In the next few years this trend is likely to continue with further shifts towards ‘network-centric’ computing becoming apparent. All these trends were set in motion by the invention of the mass-reproducible microprocessor by Ted Hoff of Intel some twenty-odd years ago. The present generation of RISC microprocessors are now more than a match for mainframes in terms of cost and performance. The long-foreseen day when collections of RISC microprocessors assembled together as a parallel computer could outperform the vector supercomputers has finally arrived. Such high-performance parallel computers incorporate proprietary interconnection networks allowing low-latency, high bandwidth inter-processor communications. However, for certain types of applications such interconnect optimization is unnecessary and conventional LAN technology is sufficient. This has led to the realization that clusters of high-performance workstations can be realistically used for a variety of applications either to replace mainframes, vector supercomputers and parallel computers or to better manage already installed collections of workstations. Whilst it is clear that ‘cluster computers’ have limitations, many institutions and companies are exploring this option. Software to manage such clusters is at an early stage of development and this report reviews the current state-of-the-art. Cluster computing is a rapidly maturing technology that seems certain to play an important part in the ‘network-centric’ computing future

An agent-based visualisation system.

This thesis explores the concepts of visual supercomputing, where complex distributed systems are used toward interactive visualisation of large datasets. Such complex systems inherently trigger management and optimisation problems; in recent years the concepts of autonomic computing have arisen to address those issues. Distributed visualisation systems are a very challenging area to apply autonomic computing ideas as such systems are both latency and compute sensitive, while most autonomic computing implementations usually concentrate on one or the other but not both concurrently. A major contribution of this thesis is to provide a case study demonstrating the application of autonomic computing concepts to a computation intensive, real-time distributed visualisation system. The first part of the thesis proposes the realisation of a layered multi-agent system to enable autonomic visualisation. The implementation of a generic multi-agent system providing reflective features is described. This architecture is then used to create a flexible distributed graphic pipeline, oriented toward real-time visualisation of volume datasets. Performance evaluation of the pipeline is presented. The second part of the thesis explores the reflective nature of the system and presents high level architectures based on software agents, or visualisation strategies, that take advantage of the flexibility of the system to provide generic features. Autonomic capabilities are presented, with fault recovery and automatic resource configuration. Performance evaluation, simulation and prediction of the system are presented, exploring different use cases and optimisation scenarios. A performance exploration tool, Delphe, is described, which uses real-time data of the system to let users explore its performance

A grid and cloud-based framework for high throughput bioinformatics

Recent advances in genome sequencing technologies have unleashed a flood of new data. As a result, the computational analysis of bioinformatics data sets has been rapidly moving from a labbased desktop computer environment to exhaustive analyses performed by large dedicated computing resources. Traditionally, large computational problems have been performed on dedicated clusters of high performance machines that are typically local to, and owned by, a particular institution. The current trend in Grid computing has seen institutions pooling their computational resources in order to offload excess computational work to remote locations during busy periods. In the last year or so, commercial Cloud computing initiatives have matured enough to offer a viable remote source of reliable computational power. Collections of idle desktop computers have also been used as a source of computational power in the form of ‘volunteer Grids’. The field of bioinformatics is highly dynamic, with new or updated versions of software tools and databases continually being developed. Several different tools and datasets must often be combined into a coherent, automated workflow or pipeline. While existing solutions are available for constructing workflows, there is a clear need for long-lived analyses consisting of many interconnected steps to be able to migrate among Grid and cloud computational resources dynamically. This project involved research into the principles underlying the design and architecture of flexible, high-throughput bioinformatics processes. Following extensive research into requirements gathering, a novel Grid-based platform, Microbase, has been implemented that is based on service-oriented architectures and peer-to-peer data transfer technology. This platform has been shown to be amenable to utilising a wide range of hardware from commodity desktop computers, to high-performance cloud infrastructure. The system has been shown to drastically reduce the bandwidth requirements of bioinformatics data distribution, and therefore reduces both the financial and computational costs associated with cloud computing. The system is inherently modular in nature, comprising a service based notification system, a data storage system scheduler and a job manager. In keeping with e-Science principles, each module can operate in physical isolation from each other, distributed within an intranet or Internet. Moreover, since each module is loosely coupled via Web services, modules have the potential to be used in combination with external service oriented components or in isolation as part of another system. In order to demonstrate the utility of such an open source system to the bioinformatics community, a pipeline of inter-connected bioinformatics applications was developed using the Microbase system to form a high throughput application for the comparative and visual analysis of microbial genomes. This application, Automated Genome Analyser (AGA) has been developed to operate without user interaction. AGA exposes its results via Web-services which can be used by further analytical stages within Microbase, by external computational resources via a Web service interface or which can be queried by users via an interactive genome browser. In addition to providing the necessary infrastructure for scalable Grid applications, a modular development framework has been provided, which simplifies the process of writing Grid applications. Microbase has been adopted by a number of projects ranging from comparative genomics to synthetic biology simulations.EThOS - Electronic Theses Online ServiceGBUnited Kingdo