A self-mobile skeleton in the presence of external loads

Multicore clusters provide cost-effective platforms for running CPU-intensive and data-intensive parallel applications. To effectively utilise these platforms, sharing their resources is needed amongst the applications rather than dedicated environments. When such computational platforms are shared, user applications must compete at runtime for the same resource so the demand is irregular and hence the load is changeable and unpredictable. This thesis explores a mechanism to exploit shared multicore clusters taking into account the external load. This mechanism seeks to reduce runtime by finding the best computing locations to serve the running computations. We propose a generic algorithmic data-parallel skeleton which is aware of its computations and the load state of the computing environment. This skeleton is structured using the Master/Worker pattern where the master and workers are distributed on the nodes of the cluster. This skeleton divides the problem into computations where all these computations are initiated by the master and coordinated by the distributed workers. Moreover, the skeleton has built-in mobility to implicitly move the parallel computations between two workers. This mobility is data mobility controlled by the application, the skeleton. This skeleton is not problem-specific and therefore it is able to execute different kinds of problems. Our experiments suggest that this skeleton is able to efficiently compensate for unpredictable load variations. We also propose a performance cost model that estimates the continuation time of the running computations locally and remotely. This model also takes the network delay, data size and the load state as inputs to estimate the transfer time of the potential movement. Our experiments demonstrate that this model takes accurate decisions based on estimates in different load patterns to reduce the total execution time. This model is problem-independent because it considers the progress of all current computations. Moreover, this model is based on measurements so it is not dependent on the programming language. Furthermore, this model takes into account the load state of the nodes on which the computation run. This state includes the characteristics of the nodes and hence this model is architecture-independent. Because the scheduling has direct impact on system performance, we support the skeleton with a cost-informed scheduler that uses a hybrid scheduling policy to improve the dynamicity and adaptivity of the skeleton. This scheduler has agents distributed over the participating workers to keep the load information up to date, trigger the estimations, and facilitate the mobility operations. On runtime, the skeleton co-schedules its computations over computational resources without interfering with the native operating system scheduler. We demonstrate that using a hybrid approach the system makes mobility decisions which lead to improved performance and scalability over large number of computational resources. Our experiments suggest that the adaptivity of our skeleton in shared environment improves the performance and reduces resource contention on nodes that are heavily loaded. Therefore, this adaptivity allows other applications to acquire more resources. Finally, our experiments show that the load scheduler has a low incurred overhead, not exceeding 0.6%, compared to the total execution time

Autonomic behavioural framework for structural parallelism over heterogeneous multi-core systems.

With the continuous advancement in hardware technologies, significant research has been devoted to design and develop high-level parallel programming models that allow programmers to exploit the latest developments in heterogeneous multi-core/many-core architectures. Structural programming paradigms propose a viable solution for e ciently programming modern heterogeneous multi-core architectures equipped with one or more programmable Graphics Processing Units (GPUs). Applying structured programming paradigms, it is possible to subdivide a system into building blocks (modules, skids or components) that can be independently created and then used in di erent systems to derive multiple functionalities. Exploiting such systematic divisions, it is possible to address extra-functional features such as application performance, portability and resource utilisations from the component level in heterogeneous multi-core architecture. While the computing function of a building block can vary for di erent applications, the behaviour (semantic) of the block remains intact. Therefore, by understanding the behaviour of building blocks and their structural compositions in parallel patterns, the process of constructing and coordinating a structured application can be automated. In this thesis we have proposed Structural Composition and Interaction Protocol (SKIP) as a systematic methodology to exploit the structural programming paradigm (Building block approach in this case) for constructing a structured application and extracting/injecting information from/to the structured application. Using SKIP methodology, we have designed and developed Performance Enhancement Infrastructure (PEI) as a SKIP compliant autonomic behavioural framework to automatically coordinate structured parallel applications based on the extracted extra-functional properties related to the parallel computation patterns. We have used 15 di erent PEI-based applications (from large scale applications with heavy input workload that take hours to execute to small-scale applications which take seconds to execute) to evaluate PEI in terms of overhead and performance improvements. The experiments have been carried out on 3 di erent Heterogeneous (CPU/GPU) multi-core architectures (including one cluster machine with 4 symmetric nodes with one GPU per node and 2 single machines with one GPU per machine). Our results demonstrate that with less than 3% overhead, we can achieve up to one order of magnitude speed-up when using PEI for enhancing application performance

Structured arrows : a type-based framework for structured parallelism

This thesis deals with the important problem of parallelising sequential code. Despite the importance of parallelism in modern computing, writing parallel software still relies on many low-level and often error-prone approaches. These low-level approaches can lead to serious execution problems such as deadlocks and race conditions. Due to the non-deterministic behaviour of most parallel programs, testing parallel software can be both tedious and time-consuming. A way of providing guarantees of correctness for parallel programs would therefore provide significant benefit. Moreover, even if we ignore the problem of correctness, achieving good speedups is not straightforward, since this generally involves rewriting a program to consider a (possibly large) number of alternative parallelisations. This thesis argues that new languages and frameworks are needed. These language and frameworks must not only support high-level parallel programming constructs, but must also provide predictable cost models for these parallel constructs. Moreover, they need to be built around solid, well-understood theories that ensure that: (a) changes to the source code will not change the functional behaviour of a program, and (b) the speedup obtained by doing the necessary changes is predictable. Algorithmic skeletons are parametric implementations of common patterns of parallelism that provide good abstractions for creating new high-level languages, and also support frameworks for parallel computing that satisfy the correctness and predictability requirements that we require. This thesis presents a new type-based framework, based on the connection between structured parallelism and structured patterns of recursion, that provides parallel structures as type abstractions that can be used to statically parallelise a program. Specifically, this thesis exploits hylomorphisms as a single, unifying construct to represent the functional behaviour of parallel programs, and to perform correct code rewritings between alternative parallel implementations, represented as algorithmic skeletons. This thesis also defines a mechanism for deriving cost models for parallel constructs from a queue-based operational semantics. In this way, we can provide strong static guarantees about the correctness of a parallel program, while simultaneously achieving predictable speedups.“This work was supported by the University of St Andrews (School of Computer Science); by the EU FP7 grant “ParaPhrase:Parallel Patterns Adaptive Heterogeneous Multicore Systems” (n. 288570); by the EU H2020 grant “RePhrase: Refactoring Parallel Heterogeneous Resource-Aware Applications - a Software Engineering Approach” (ICT-644235), by COST Action IC1202 (TACLe), supported by COST (European Cooperation Science and Technology); and by EPSRC grant “Discovery: Pattern Discovery and Program Shaping for Manycore Systems” (EP/P020631/1)” -- Acknowledgement

Accelerating and simulating detected physical interations

The aim of this doctoral thesis is to present a body of work aimed at improving performance and developing new methods for animating physical interactions using simulation in virtual environments. To this end we develop a number of novel parallel collision detection and fracture simulation algorithms. Methods for traversing and constructing bounding volume hierarchies (BVH) on graphics processing units (GPU) have had a wide success. In particular, they have been adopted widely in simulators, libraries and benchmarks as they allow applications to reach new heights in terms of performance. Even with such a development however, a thorough adoption of techniques has not occurred in commercial and practical applications. Due to this, parallel collision detection on GPUs remains a relatively niche problem and a wide number of applications could benefit from a significant boost in proclaimed performance gains. In fracture simulations, explicit surface tracking methods have a good track record of success. In particular they have been adopted thoroughly in 3D modelling and animation software like Houdini [124] as they allow accurate simulation of intricate fracture patterns with complex interactions, which are generated using physical laws. Even so, existing methods can pose restrictions on the geometries of simulated objects. Further, they often have tight dependencies on implicit surfaces (e.g. level sets) for representing cracks and performing cutting to produce rigid-body fragments. Due to these restrictions, catering to various geometries can be a challenge and the memory cost of using implicit surfaces can be detrimental and without guarantee on the preservation of sharp features. We present our work in four main chapters. We first tackle the problem in the accelerating collision detection on the GPU via BVH traversal - one of the most demanding components during collision detection. Secondly, we show the construction of a new representation of the BVH called the ostensibly implicit tree - a layout of nodes in memory which is encoded using the bitwise representation of the number of enclosed objects in the tree (e.g. polygons). Thirdly, we shift paradigm to the task of simulating breaking objects after collision: we show how traditional finite elements can be extended as a way to prevent frequent re-meshing during fracture evolution problems. Finally, we show how the fracture surface–represented as an explicit (e.g. triangulated) surface mesh–is used to generate rigid body fragments using a novel approach to mesh cutting

Prototyping parallel functional intermediate languages

Non-strict higher-order functional programming languages are elegant, concise, mathematically sound and contain few environment-specific features, making them obvious candidates for harnessing high-performance architectures. The validity of this approach has been established by a number of experimental compilers. However, while there have been a number of important theoretical developments in the field of parallel functional programming, implementations have been slow to materialise. The myriad design choices and demands of specific architectures lead to protracted development times. Furthermore, the resulting systems tend to be monolithic entities, and are difficult to extend and test, ultimatly discouraging experimentation. The traditional solution to this problem is the use of a rapid prototyping framework. However, as each existing systems tends to prefer one specific platform and a particular way of expressing parallelism (including implicit specification) it is difficult to envisage a general purpose framework. Fortunately, most of these systems have at least one point of commonality: the use of an intermediate form. Typically, these abstract representations explicitly identify all parallel components but without the background noise of syntactic and (potentially arbitrary) implementation details. To this end, this thesis outlines a framework for rapidly prototyping such intermediate languages. Based on the traditional three-phase compiler model, the design process is driven by the development of various semantic descriptions of the language. Executable versions of the specifications help to both debug and informally validate these models. A number of case studies, covering the spectrum of modern implementations, demonstrate the utility of the framework

Staged Methodologies for Parallel Programming

This thesis presents a parallel programming model based on the gradual introduction of implementation detail. It comprises a series of decision stages that each fix a different facet of the implementation. The initial stages of the model elide many of the parallelisation concerns, while later stages allow low-level control over the implementation details. This allows the programmer to make decisions about each concern at an appropriate level of abstraction. The model provides abstractions not present in single-view explicitly parallel languages; while at the same time allowing more control and freedom of expression than typical high-level treatments of parallelism. A prototype system, called PEDL, was produced to evaluate the effectiveness of this programming model. This system allows the derivation of distributed-memory SPMD implementations for array based numerical computations. The decision stages are structured as a series of related languages, each of which presents a more explicit model of the parallel machine. The starting point is a high-level specification of the computational portion of the algorithm from which a low-level implementation is derived that describes all the parallelisation detail. The derivation proceeds by transforming the program from one language to the next, adding implementation detail at each stage. The system is amenable to producing correctness proofs of the transformations, although this is not required. All languages in the system are executable: programs undergoing derivation can be checked and tested to provide the programmer with feedback. The languages are implemented by embedding them within a host functional language. Their structure is represented within the type system of the host language. This allows programs to be expressed in languages from a combination of stages, which is useful during derivation, while still being able to distinguish the different languages. Once all the parallelisation details have been fixed the final implementation is generated by a process of transformation and translation. This implementation is a conventional imperative program in which communication is provided by the MPI library. The thesis presents case studies of the use of the system: programs undergoing derivation were found to be clear and concise, and it was found that the use of this system introduces little overhead into the final implementation

Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

Phylogeny and phylogeography of the Chacma Baboon (Papio ursinus): the role of landscape in shaping contemporary genetic structure in the southern African baboon

Includes abstract.Includes bibliographical references (leaves 146-175).This thesis contributes to our understanding of the role of climate and landscape change in structuring diversity within chacma baboons (Papio ursinus). The data set comprises molecular sequences from two mitochondrial DNA markers: the Brown region and the hypervariable D-loop. DNA was extracted from faecal samples of 261 free living chacma baboons across southern Africa. Phylogenetic and phylogeographic techniques, including coalescent modeling, were used to examine past and present population dynamics of chacma baboon populations. Bayesian tree constructions provide a timeline of diversification for the sample. Although the ecological drivers of ongoing differentiation remain unclear, it was shown that population contractions and expansions have also played a significant role in driving regional genetic structure within the species