Structured data access annotations for massively parallel computations

We describe an approach aimed at addressing the issue of joint exploitation of control (stream) and data parallelism in a skeleton based parallel programming environment, based on annotations and refactoring. Annotations drive efficient implementation of a parallel computation. Refactoring is used to transform the associated skeleton tree into a more efficient, functionally equivalent skeleton tree. In most cases, cost models are used to drive the refactoring process. We show how sample use case applications/kernels may be optimized and discuss preliminary experiments with FastFlow assessing the theoretical results. © 2013 Springer-Verlag.

Autonomic scheduling of tasks from data parallel patterns to CPU/GPU core mixes

We propose a methodology for optimizing the execution of data parallel (sub-)tasks on CPU and GPU cores of the same heterogeneous architecture. The methodology is based on two main components: i) an analytical performance model for scheduling tasks among CPU and GPU cores, such that the global execution time of the overall data parallel pattern is optimized; and ii) an autonomic module which uses the analytical performance model to implement the data parallel computations in a completely autonomic way, requiring no programmer intervention to optimize the computation across CPU and GPU cores. The analytical performance model uses a small set of simple parameters to devise a partitioning-between CPU and GPU cores-of the tasks derived from structured data parallel patterns/algorithmic skeletons. The model takes into account both hardware related and application dependent parameters. It computes the percentage of tasks to be executed on CPU and GPU cores such that both kinds of cores are exploited and performance figures are optimized. The autonomic module, implemented in FastFlow, executes a generic map (reduce) data parallel pattern scheduling part of the tasks to the GPU and part to CPU cores so as to achieve optimal execution time. Experimental results on state-of-the-art CPU/GPU architectures are shown that assess both performance model properties and autonomic module effectiveness. © 2013 IEEE.

Model checking support for conflict resolution in multiple non-functional concern management

When implementing autonomic management of multiple non-functional concerns a trade-off must be found between the ability to develop independently management of the individual concerns (following the separation of concerns principle) and the detection and resolution of conflicts that may arise when combining the independently developed management code. Here we discuss strategies to establish this trade-off and introduce a model checking based methodology aimed at simplifying the discovery and handling of conflicts arising from deployment-within the same parallel application-of independently developed management policies. Preliminary results are shown demonstrating the feasibility of the approach.

Managing grid computations: An ORC-based approach

In this paper a model of grid computation that supports both heterogeneity and dynamicity is presented. The model presupposes that user sites contain software components awaiting execution on the grid. User sites and grid sites interact by means of managers which control dynamic behaviour. The orchestration language ORC [9,10] offers an abstract means of specifying operations for resource acquisition and execution monitoring while allowing for the possibility of non-responsive hardware. It is demonstrated that ORC is sufficiently expressive to model typical kinds of grid interactions.

A Case Study of OpenMP applied to Map/Reduce-style Computations

As data analytics are growing in importance they are also quickly becoming one of the dominant application domains that require parallel processing. This paper investigates the applicability of OpenMP, the dominant shared-memory parallel programming model in high-performance computing, to the domain of data analytics. We contrast the performance and programmability of key data analytics benchmarks against Phoenix++, a state-of-the-art shared memory map/reduce programming system. Our study shows that OpenMP outperforms the Phoenix++ system by a large margin for several benchmarks. In other cases, however, the programming model is lacking support for this application domain.

Exploiting Significance of Computations for Energy-Constrained Approximate Computing

Approximate execution is a viable technique for environments with energy constraints, provided that applications are given the mechanisms to produce outputs of the highest possible quality within the available energy budget. This paper introduces a framework for energy-constrained execution with controlled and graceful quality loss. A simple programming model allows developers to structure the computation in different tasks, and to express the relative importance of these tasks for the quality of the end result. For non-significant tasks, the developer can also supply less costly, approximate versions. The target energy consumption for a given execution is specified when the application is launched. A significance-aware runtime system employs an application-specific analytical energy model to decide how many cores to use for the execution, the operating frequency for these cores, as well as the degree of task approximation, so as to maximize the quality of the output while meeting the user-specified energy constraints. Evaluation on a dual-socket 16-core Intel platform using 9 benchmark kernels shows that the proposed framework picks the optimal configuration with high accuracy. Also, a comparison with loop perforation (a well-known compile-time approximation technique), shows that the proposed framework results in significantly higher quality for the same energy budget.

The SPHERE Study: Secondary prevention of heart disease in general practice: protocol of a randomised controlled trial of tailored practice and patient care plans with parallel qualitative, economic and policy analyses. [ISRCTN24081411]

Background: The aim of the SPHERE study is to design, implement and evaluate tailored practice and personal care plans to improve the process of care and objective clinical outcomes for patients with established coronary heart disease (CHD) in general practice across two different health systems on the island of Ireland.CHD is a common cause of death and a significant cause of morbidity in Ireland. Secondary prevention has been recommended as a key strategy for reducing levels of CHD mortality and general practice has been highlighted as an ideal setting for secondary prevention initiatives. Current indications suggest that there is considerable room for improvement in the provision of secondary prevention for patients with established heart disease on the island of Ireland. The review literature recommends structured programmes with continued support and follow-up of patients; the provision of training, tailored to practice needs of access to evidence of effectiveness of secondary prevention; structured recall programmes that also take account of individual practice needs; and patient-centred consultations accompanied by attention to disease management guidelines.

Methods: SPHERE is a cluster randomised controlled trial, with practice-level randomisation to intervention and control groups, recruiting 960 patients from 48 practices in three study centres (Belfast, Dublin and Galway). Primary outcomes are blood pressure, total cholesterol, physical and mental health status (SF-12) and hospital re-admissions. The intervention takes place over two years and data is collected at baseline, one-year and two-year follow-up. Data is obtained from medical charts, consultations with practitioners, and patient postal questionnaires. The SPHERE intervention involves the implementation of a structured systematic programme of care for patients with CHD attending general practice. It is a multi-faceted intervention that has been developed to respond to barriers and solutions to optimal secondary prevention identified in preliminary qualitative research with practitioners and patients. General practitioners and practice nurses attend training sessions in facilitating behaviour change and medication prescribing guidelines for secondary prevention of CHD. Patients are invited to attend regular four-monthly consultations over two years, during which targets and goals for secondary prevention are set and reviewed. The analysis will be strengthened by economic, policy and qualitative components.

Partial structure of the phylloxin gene from the giant monkey frog, Phyllomedusa bicolor: parallel cloning of precursor cDNA and genomic DNA from lyophilized skin secretion

Phylloxin is a novel prototype antimicrobial peptide from the skin of Phyllomedusa bicolor. Here, we describe parallel identification and sequencing of phylloxin precursor transcript (mRNA) and partial gene structure (genomic DNA) from the same sample of lyophilized skin secretion using our recently-described cloning technique. The open-reading frame of the phylloxin precursor was identical in nucleotide sequence to that previously reported and alignment with the nucleotide sequence derived from genomic DNA indicated the presence of a 175 bp intron located in a near identical position to that found in the dermaseptins. The highly-conserved structural organization of skin secretion peptide genes in P. bicolor can thus be extended to include that encoding phylloxin (plx). These data further reinforce our assertion that application of the described methodology can provide robust genomic/transcriptomic/peptidomic data without the need for specimen sacrifice.

Application-Specific Instruction Set Processor for SoC implementation of Modern Signal Processing Algorithms

A novel application-specific instruction set processor (ASIP) for use in the construction of modern signal processing systems is presented. This is a flexible device that can be used in the construction of array processor systems for the real-time implementation of functions such as singular-value decomposition (SVD) and QR decomposition (QRD), as well as other important matrix computations. It uses a coordinate rotation digital computer (CORDIC) module to perform arithmetic operations and several approaches are adopted to achieve high performance including pipelining of the micro-rotations, the use of parallel instructions and a dual-bus architecture. In addition, a novel method for scale factor correction is presented which only needs to be applied once at the end of the computation. This also reduces computation time and enhances performance. Methods are described which allow this processor to be used in reduced dimension (i.e., folded) array processor structures that allow tradeoffs between hardware and performance. The net result is a flexible matrix computational processing element (PE) whose functionality can be changed under program control for use in a wider range of scenarios than previous work. Details are presented of the results of a design study, which considers the application of this decomposition PE architecture in a combined SVD/QRD system and demonstrates that a combination of high performance and efficient silicon implementation are achievable. © 2005 IEEE.

CORDIC based application-specific instruction set processor for QRD/SVD

An application specific programmable processor (ASIP) suitable for the real-time implementation of matrix computations such as Singular Value and QR Decomposition is presented. The processor incorporates facilities for the issue of parallel instructions and a dual-bus architecture that are designed to achieve high performance. Internally, it uses a CORDIC module to perform arithmetic operations, with pipelining of the internal recursive loop exploited to multiplex the two independent micro-rotations onto a single piece of hardware. The net result is a flexible processing element whose functionality can be changed under program control, which combines high performance with efficient silicon implementation. This is illustrated through the results of a detailed silicon design study and the applications of the techniques to a combined SVD/QRD system.