Strategies for Energy-Efficient Resource Management of Hybrid Programming Models

Many scientific applications are programmed using hybrid programming models that use both message passing and shared memory, due to the increasing prevalence of large-scale systems with multicore, multisocket nodes. Previous work has shown that energy efficiency can be improved using software-controlled execution schemes that consider both the programming model and the power-aware execution capabilities of the system. However, such approaches have focused on identifying optimal resource utilization for one programming model, either shared memory or message passing, in isolation. The potential solution space, thus the challenge, increases substantially when optimizing hybrid models since the possible resource configurations increase exponentially. Nonetheless, with the accelerating adoption of hybrid programming models, we increasingly need improved energy efficiency in hybrid parallel applications on large-scale systems. In this work, we present new software-controlled execution schemes that consider the effects of dynamic concurrency throttling (DCT) and dynamic voltage and frequency scaling (DVFS) in the context of hybrid programming models. Specifically, we present predictive models and novel algorithms based on statistical analysis that anticipate application power and time requirements under different concurrency and frequency configurations. We apply our models and methods to the NPB MZ benchmarks and selected applications from the ASC Sequoia codes. Overall, we achieve substantial energy savings (8.74 percent on average and up to 13.8 percent) with some performance gain (up to 7.5 percent) or negligible performance loss.

Paraphrasing:Generating parallel programs using refactoring

Refactoring is the process of changing the structure of a program without changing its behaviour. Refactoring has so far only really been deployed effectively for sequential programs. However, with the increased availability of multicore (and, soon, manycore) systems, refactoring can play an important role in helping both expert and non-expert parallel programmers structure and implement their parallel programs. This paper describes the design of a new refactoring tool that is aimed at increasing the programmability of parallel systems. To motivate our design, we refactor a number of examples in C, C++ and Erlang into good parallel implementations, using a set of formal pattern rewrite rules. © 2013 Springer-Verlag Berlin Heidelberg.

The ParaPhrase Project:Parallel patterns for adaptive heterogeneous multicore systems

This paper describes the ParaPhrase project, a new 3-year targeted research project funded under EU Framework 7 Objective 3.4 (Computer Systems), starting in October 2011. ParaPhrase aims to follow a new approach to introducing parallelism using advanced refactoring techniques coupled with high-level parallel design patterns. The refactoring approach will use these design patterns to restructure programs defined as networks of software components into other forms that are more suited to parallel execution. The programmer will be aided by high-level cost information that will be integrated into the refactoring tools. The implementation of these patterns will then use a well-understood algorithmic skeleton approach to achieve good parallelism. A key ParaPhrase design goal is that parallel components are intended to match heterogeneous architectures, defined in terms of CPU/GPU combinations, for example. In order to achieve this, the ParaPhrase approach will map components at link time to the available hardware, and will then re-map them during program execution, taking account of multiple applications, changes in hardware resource availability, the desire to reduce communication costs etc. In this way, we aim to develop a new approach to programming that will be able to produce software that can adapt to dynamic changes in the system environment. Moreover, by using a strong component basis for parallelism, we can achieve potentially significant gains in terms of reducing sharing at a high level of abstraction, and so in reducing or even eliminating the costs that are usually associated with cache management, locking, and synchronisation. © 2013 Springer-Verlag Berlin Heidelberg.

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.