A model for composible and extensible parallel architectural skeletons

Application of pattern-based approaches to parallel programming is an active area of research today. The main objective of pattern-based approaches to parallel programming is to facilitate the reuse of frequently occurring structures for parallelism whereby a user supplies mostly the application specific code-components and the programming environment generates most of the code for parallelization. Parallel Architectural Skeleton (PAS) is such a pattern-based parallel programming model and environment. The PAS model provides a generic way of describing the architectural/structural aspects of patterns in message-passing parallel computing. Application development using PAS is hierarchical, similar to conventional parallel programming using MPI, however with the added benefit of re-usability and high level patterns. Like most other pattern-based parallel programming models, the benefits of PAS were offset by some of its drawbacks such as difficulty in: (1) extending PAS and (2) skeleton composition. SuperPAS is an extension of PAS that addresses these issues. SuperPAS provides a skeleton description language to describe a skeleton in a generic way. Using SuperPAS, a skeleton developer can extend PAS by adding new skeletons to the skeleton repository (i.e., extensibility). SuperPAS also makes the PAS system more flexible by defining composition of skeletons. In this thesis, we describe the model and description language for SuperPAS and elaborate its use through examples

EXA2PRO programming environment:Architecture and applications

The EXA2PRO programming environment will integrate a set of tools and methodologies that will allow to systematically address many exascale computing challenges, including performance, performance portability, programmability, abstraction and reusability, fault tolerance and technical debt. The EXA2PRO tool-chain will enable the efficient deployment of applications in exascale computing systems, by integrating high-level software abstractions that offer performance portability and efficient exploitation of exascale systems' heterogeneity, tools for efficient memory management, optimizations based on trade-offs between various metrics and fault-tolerance support. Hence, by addressing various aspects of productivity challenges, EXA2PRO is expected to have significant impact in the transition to exascale computing, as well as impact from the perspective of applications. The evaluation will be based on 4 applications from 4 different domains that will be deployed in JUELICH supercomputing center. The EXA2PRO will generate exploitable results in the form of a tool-chain that support diverse exascale heterogeneous supercomputing centers and concrete improvements in various exascale computing challenges

On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag

A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures

Scientific problems that depend on processing large amounts of data require overcoming challenges in multiple areas: managing large-scale data distribution, co-placement and scheduling of data with compute resources, and storing and transferring large volumes of data. We analyze the ecosystems of the two prominent paradigms for data-intensive applications, hereafter referred to as the high-performance computing and the Apache-Hadoop paradigm. We propose a basis, common terminology and functional factors upon which to analyze the two approaches of both paradigms. We discuss the concept of "Big Data Ogres" and their facets as means of understanding and characterizing the most common application workloads found across the two paradigms. We then discuss the salient features of the two paradigms, and compare and contrast the two approaches. Specifically, we examine common implementation/approaches of these paradigms, shed light upon the reasons for their current "architecture" and discuss some typical workloads that utilize them. In spite of the significant software distinctions, we believe there is architectural similarity. We discuss the potential integration of different implementations, across the different levels and components. Our comparison progresses from a fully qualitative examination of the two paradigms, to a semi-quantitative methodology. We use a simple and broadly used Ogre (K-means clustering), characterize its performance on a range of representative platforms, covering several implementations from both paradigms. Our experiments provide an insight into the relative strengths of the two paradigms. We propose that the set of Ogres will serve as a benchmark to evaluate the two paradigms along different dimensions.Comment: 8 pages, 2 figure

Advanced Grid programming with components: a biometric identification case study

Component-oriented software development has been attracting increasing attention for building complex distributed applications. A new infrastructure supporting this advanced concept is our prototype component framework based on the Grid component model. This paper provides an overview of the component framework and presents a case study where we utilise the component-oriented approach to develop a business process application for a biometric identification system. We then introduce the tools being developed as part of an integrated development environment to enable graphical component-based development of Grid applications. Finally, we report our initial findings and experiences of efficiently using the component framework and set of software tools

Quality-aware model-driven service engineering

Service engineering and service-oriented architecture as an integration and platform technology is a recent approach to software systems integration. Quality aspects ranging from interoperability to maintainability to performance are of central importance for the integration of heterogeneous, distributed service-based systems. Architecture models can substantially influence quality attributes of the implemented software systems. Besides the benefits of explicit architectures on maintainability and reuse, architectural constraints such as styles, reference architectures and architectural patterns can influence observable software properties such as performance. Empirical performance evaluation is a process of measuring and evaluating the performance of implemented software. We present an approach for addressing the quality of services and service-based systems at the model-level in the context of model-driven service engineering. The focus on architecture-level models is a consequence of the black-box character of services

Pattern Operators for Grid Environments

The definition and programming of distributed applications has become a major research issue due to the increasing availability of (large scale) distributed platforms and the requirements posed by the economical globalization. However, such a task requires a huge effort due to the complexity of the distributed environments: large amount of users may communicate and share information across different authority domains; moreover, the “execution environment” or “computations” are dynamic since the number of users and the computational infrastructure change in time. Grid environments, in particular, promise to be an answer to deal with such complexity, by providing high performance execution support to large amount of users, and resource sharing across different organizations. Nevertheless, programming in Grid environments is still a difficult task. There is a lack of high level programming paradigms and support tools that may guide the application developer and allow reusability of state-of-the-art solutions. Specifically, the main goal of the work presented in this thesis is to contribute to the simplification of the development cycle of applications for Grid environments by bringing structure and flexibility to three stages of that cycle through a commonmodel. The stages are: the design phase, the execution phase, and the reconfiguration phase. The common model is based on the manipulation of patterns through pattern operators, and the division of both patterns and operators into two categories, namely structural and behavioural. Moreover, both structural and behavioural patterns are first class entities at each of the aforesaid stages. At the design phase, patterns can be manipulated like other first class entities such as components. This allows a more structured way to build applications by reusing and composing state-of-the-art patterns. At the execution phase, patterns are units of execution control: it is possible, for example, to start or stop and to resume the execution of a pattern as a single entity. At the reconfiguration phase, patterns can also be manipulated as single entities with the additional advantage that it is possible to perform a structural reconfiguration while keeping some of the behavioural constraints, and vice-versa. For example, it is possible to replace a behavioural pattern, which was applied to some structural pattern, with another behavioural pattern. In this thesis, besides the proposal of the methodology for distributed application development, as sketched above, a definition of a relevant set of pattern operators was made. The methodology and the expressivity of the pattern operators were assessed through the development of several representative distributed applications. To support this validation, a prototype was designed and implemented, encompassing some relevant patterns and a significant part of the patterns operators defined. This prototype was based in the Triana environment; Triana supports the development and deployment of distributed applications in the Grid through a dataflow-based programming model. Additionally, this thesis also presents the analysis of a mapping of some operators for execution control onto the Distributed Resource Management Application API (DRMAA). This assessment confirmed the suitability of the proposed model, as well as the generality and flexibility of the defined pattern operatorsDepartamento de Informática and Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa; Centro de Informática e Tecnologias da Informação of the FCT/UNL; Reitoria da Universidade Nova de Lisboa; Distributed Collaborative Computing Group, Cardiff University, United Kingdom; Fundação para a Ciência e Tecnologia; Instituto de Cooperação Científica e Tecnológica Internacional; French Embassy in Portugal; European Union Commission through the Agentcities.NET and Coordina projects; and the European Science Foundation, EURESCO