Using an interactive parallelisation toolkit to parallelise an ocean modelling code

This paper describes an interactive parallelisation toolkit that can be used to generate parallel code suitable for either a distributed memory system (using message passing) or a shared memory system (using OpenMP). This study focuses on how the toolkit is used to parallelise a complex heterogeneous ocean modelling code within a few hours for use on a shared memory parallel system. The generated parallel code is essentially the serial code with OpenMP directives added to express the parallelism. The results show that substantial gains in performance can be achieved over the single thread version with very little effort.

The semi-automatic parallelisation of scientific application codes using a computer aided parallelisation toolkit

The shared-memory programming model can be an effective way to achieve parallelism on shared memory parallel computers. Historically however, the lack of a programming standard using directives and the limited scalability have affected its take-up. Recent advances in hardware and software technologies have resulted in improvements to both the performance of parallel programs with compiler directives and the issue of portability with the introduction of OpenMP. In this study, the Computer Aided Parallelisation Toolkit has been extended to automatically generate OpenMP-based parallel programs with nominal user assistance. We categorize the different loop types and show how efficient directives can be placed using the toolkit's in-depth interprocedural analysis. Examples are taken from the NAS parallel benchmarks and a number of real-world application codes. This demonstrates the great potential of using the toolkit to quickly parallelise serial programs as well as the good performance achievable on up to 300 processors for hybrid message passing-directive parallelisations.

Automatic relative debugging of OpenMP programs

In this work we show how automatic relative debugging can be used to find differences in computation between a correct serial program and an OpenMP parallel version of that program that does not yield correct results. Backtracking and re-execution are used to determine the first OpenMP parallel region that produces a difference in computation that may lead to an incorrect value the user has indicated. Our approach also lends itself to finding differences between parallel computations, where executing with M threads produces expected results but an N thread execution does not (M, N > 1, M ≠ N). OpenMP programs created using a parallelization tool are addressed by utilizing static analysis and directive information from the tool. Hand-parallelized programs, where OpenMP directives are inserted by the user, are addressed by performing data dependence and directive analysis.

An environment for OpenMP code parallelization

This chapter discusses the code parallelization environment, where a number of tools that address the main tasks, such as code parallelization, debugging, and optimization are available. The parallelization tools include ParaWise and CAPO, which enable the near automatic parallelization of real world scientific application codes for shared and distributed memory-based parallel systems. The chapter discusses the use of ParaWise and CAPO to transform the original serial code into an equivalent parallel code that contains appropriate OpenMP directives. Additionally, as user involvement can introduce errors, a relative debugging tool (P2d2) is also available and can be used to perform near automatic relative debugging of an OpenMP program that has been parallelized either using the tools or manually. In order for these tools to be effective in parallelizing a range of applications, a high quality fully inter-procedural dependence analysis, as well as user interaction is vital to the generation of efficient parallel code and in the optimization of the backtracking and speculation process used in relative debugging. Results of parallelized NASA codes are discussed and show the benefits of using the environment.

When the shift hits the critical fan: a Foucauldian analysis

In the past 15 years in the UK, the state has acquired powers, which mark a qualitative shift in its relationship to higher education. Since the introduction and implementation of the Further and Higher Education Act 1992, the Teaching and Higher Education Act 1998 and the Higher Education Act 2004, a whole raft of changes have occurred which include the following: Widening participation; the development of interdisciplinary, experiential and workplace-based learning focused on a theory-practice dialogue; quality assurance; and new funding models which encompass public and private partnerships. The transformation of higher education can be placed in the context of New Labour’s overall strategies for overarching reform of public services, as set out in the Prime Minister’s Strategy Unit’s discussion paper The UK Government’s Approach to Public Service Reform (2006). An optimistic view of changes to higher education is that they simultaneously obey democratic and economic imperatives. There is an avowed commitment through the widening participation agenda to social inclusion and citizenship, and to providing the changing skills base necessary for the global economy. A more cynical view is that, when put under critical scrutiny, as well as being emancipatory, in some senses these changes can be seen to mobilise regulatory and disciplinary practices. This paper reflects on what kinds of teaching and learning are promoted by the new relationship between the state and the university. It argues that, whilst governmental directives for innovations and transformations in teaching and learning allegedly empower students and put their interests at the centre, reforms can also be seen to consist of supervisory and controlling mechanisms with regard both to our own practices as teachers and the knowledge/ learning we provide for the students.

Operational monitoring and forecasting of bathing water quality through exploiting satellite Earth observation and models: The AlgaRisk demonstration service

Coastal zones and shelf-seas are important for tourism, commercial fishing and aquaculture. As a result the importance of good water quality within these regions to support life is recognised worldwide and a number of international directives for monitoring them now exist. This paper describes the AlgaRisk water quality monitoring demonstration service that was developed and operated for the UK Environment Agency in response to the microbiological monitoring needs within the revised European Union Bathing Waters Directive. The AlgaRisk approach used satellite Earth observation to provide a near-real time monitoring of microbiological water quality and a series of nested operational models (atmospheric and hydrodynamic-ecosystem) provided a forecast capability. For the period of the demonstration service (2008–2013) all monitoring and forecast datasets were processed in near-real time on a daily basis and disseminated through a dedicated web portal, with extracted data automatically emailed to agency staff. Near-real time data processing was achieved using a series of supercomputers and an Open Grid approach. The novel web portal and java-based viewer enabled users to visualise and interrogate current and historical data. The system description, the algorithms employed and example results focussing on a case study of an incidence of the harmful algal bloom Karenia mikimotoi are presented. Recommendations and the potential exploitation of web services for future water quality monitoring services are discussed.

A comparison of the degree of implementation of marine biodiversity indicators by European countries in relation to the Marine Strategy Framework Directive (MSFD)

The degree of development and operability of the indicators for the Marine Strategy Framework Directive (MSFD) using Descriptor 1 (D1) Biological Diversity was assessed. To this end, an overview of the relevance and degree of operability of the underlying parameters across 20 European countries was compiled by analysing national directives, legislation, regulations, and publicly available reports. Marked differences were found between countries in the degree of ecological relevance as well as in the degree of implementation and operability of the parameters chosen to indicate biological diversity. The best scoring EU countries were France, Germany, Greece and Spain, while the worst scoring countries were Italy and Slovenia. No country achieved maximum scores for the implementation of MSFD D1. The non-EU countries Norway and Turkey score as highly as the top-scoring EU countries. On the positive side, the chosen parameters for D1 indicators were generally identified as being an ecologically relevant reflection of Biological Diversity. On the negative side however, less than half of the chosen parameters are currently operational. It appears that at a pan-European level, no consistent and harmonized approach currently exists for the description and assessment of marine biological diversity. The implementation of the MSFD Descriptor 1 for Europe as a whole can therefore at best be marked as moderately successful.

A review of climate change and the implementation of marine biodiversity legislation in the United Kingdom

1. Marine legislation, the key means by which the conservation of marine biodiversity is achieved, has been developing since the 1960s. In recent decades, an increasing focus on ‘holistic’ policy development is evident, compared with earlier ‘piecemeal’ sectoral approaches. Important marine legislative tools being used in the United Kingdom, and internationally, include the designation of marine protected areas and the Marine Strategy Framework Directive (MSFD) with its aim of meeting ‘Good Environmental Status’ (GES) for European seas by 2020. 2. There is growing evidence of climate change impacts on marine biodiversity, which may compromise the effectiveness of any legislation intended to promote sustainable marine resource management. 3. A review of key marine biodiversity legislation relevant to the UK shows climate change was not considered in the drafting of much early legislation. Despite the huge increase in knowledge of climate change impacts in recent decades, legislation is still limited in how it takes these impacts into account. There is scope, however, to account for climate change in implementing much of the legislation through (a) existing references to environmental variability; (b) review cycles; and (c) secondary legislation and complementary policy development. 4. For legislation relating to marine protected areas (e.g. the EC Habitats and Birds Directives), climate change has generally not been considered in the site-designation process, or for ongoing management, with the exception of the Marine (Scotland) Act. Given that changing environmental conditions (e.g. rising temperatures and ocean acidification) directly affect the habitats and species that sites are designated for, how this legislation is used to protect marine biodiversity in a changing climate requires further consideration. 5. Accounting for climate change impacts on marine biodiversity in the development and implementation of legislation is vital to enable timely, adaptive management responses. Marine modelling can play an important role in informing management decisions.

Identifying species and ecosystem sensitivities.

Executive Summary The programme of work was commissioned in September 1998 to supply information to underpin the UK’s commitments to protection and conservation of the ecosystems and biodiversity of the marine environment under the 1992 OSPAR Convention on the Protection of the Marine Environment of the North East Atlantic. The programme also provided support for the implementation of the Biodiversity Convention and the EU Habitats Directive. The MarLIN programme initiated a new approach to assessing sensitivity and recoverability characteristics of seabed species and biotopes based on structures (such as the seabed biotopes classification) and criteria (such as for assessing rarity and defining ‘sensitivity’) developed since 1997. It also developed tools to disseminate the information on the Internet. The species researched were those that were listed in conventions and directives, included in Biodiversity Action Plans, or were nationally rare or scarce. In addition, species were researched if they maintained community composition or structure and/or provided a distinctive habitat or were special to or especially abundant in a particular situation or biotope At its conclusion in August 2001, the work carried out under the contract with DETR/DEFRA had: · Developed protocols, criteria and structures for identifying ‘sensitivity’ and ‘recoverability’, which were tested by a programme management group. · Developed a database to hold research data on biology and sensitivity of species and biotopes. · Defined the link between human activities and the environmental factors likely to be affected by those activities. · Developed a user-friendly Web site to access information from the database, on the sensitivity and recoverability characteristics of over 100 species and basic information on over 200 species. Additionally, the project team have: · Brought together and facilitated discussion between current developers and users of electronic resources for environmental management, protection and education in the conference ‘Using Marine Biological Information in the Electronic Age’ (19-21 July 1999). · Contributed to the development of Ecological Quality Objectives for the North Sea (Scheveningen, 11- 3 September 1999 and subsequent papers). · Provided detailed information on species as a supplement to the National Biodiversity Network Gateway demonstration www.searchnbn.net. · Developed a peer-reviewed approach to electronic publication of updateable information. · Promoted the contract results and the MarLIN approach to the support of marine environmental management and protection at European research fora and, through the web site, internationally. The information available through the Web site is now being used by consultants and Government agencies. The DEFRA contract has been of critical importance in establishing the Marine Life Information Network (MarLIN) programme and has encouraged support from other organisations. Other related work in the MarLIN programme is on-going, especially to identify sensitivity of biotopes to support management of SACs (contract from English Nature in collaboration with Scottish Natural Heritage), to access data sources (in collaboration with the National Biodiversity Network) and to establish volunteer recording schemes for marine life. The results of the programme are best viewed on the Web site (www.marlin.ac.uk). Three reports have been produced during the project. A final report detailing the work undertaken, a brochure ‘Identifying the sensitivity of seabed ecosystems’ and a CD-ROM describing the programme and demonstrating the Web site have been delivered as final products in addition to the Web site.

Cross-Border Environmental Governance and EC Law

This article examines the nature and scope of emerging cross-border participatory rights under European Community environmental law. It reviews the legal and political forces that have stimulated the development of such rights and also the specific nature of the rights conferred by three major legislative initiatives: the Community Directives on Environmental Impact Assessment, Integrated Pollution Prevention and Control, and the Water Framework Directive. The article concludes with a case study on Ireland which assesses the likely significance of these cross-border participatory rights for transboundary environmental governance in Ireland.

Scientifi c discourses on chronic pain without organic cause Incorporating gender perspective for pain resignifyng-repoliticizing

Chronic pain, without any organic or physical cause (DC), which in psycho-medical terminology is known as fi bromyalgia, (FM), is diagnosed each year to a considerable number of women in capitalistic societies. Our main interest in the following paper is to go in depth in the elaboration of this symptom, its treatment and the psychosocial effects, both in the social order as well as in the lives of the people who suffer from it. Our main goal in the following paper is to look deeper in the elaboration (conceptualization) of this symptom, its treatment and psychological affects, both in the social order as well as in the lives of the people who suffer from it, we are using linked speeches in Spanish magazines publications. The result has been the emergence of three hegemonic discourse positions: One position “scientist”, one “therapeutic of the conformity” position and one “economic and legalistic” position. Each of these has a specifi c feature, but on the whole, is enhanced, producing effects such as the absence of social context to explain the disease; disregard of gender differences in the management and treatment; the instrumentalization of pain to legitimize their practices and the subjection of women to the “psycho-biomedical” paradigm. In that way, a new signifi cance and politicization of the concept of pain is proposed.

Ion-Atom/Argon - Calculation of ionization cross sections by fast ion impact for neutral target atoms ranging from hydrogen to argon

A FORTRAN 90 program is presented which calculates the total cross sections, and the electron energy spectra of the singly and doubly differential cross sections for the single target ionization of neutral atoms ranging from hydrogen up to and including argon. The code is applicable for the case of both high and low Z projectile impact in fast ion-atom collisions. The theoretical models provided for the program user are based on two quantum mechanical approximations which have proved to be very successful in the study of ionization in ion-atom collisions. These are the continuum-distorted-wave (CDW) and continuum-distorted-wave eikonal-initial-state (CDW-EIS) approximations. The codes presented here extend previously published. codes for single ionization of. target hydrogen [Crothers and McCartney, Comput. Phys. Commun. 72 (1992) 288], target helium [Nesbitt, O'Rourke and Crothers, Comput. Phys. Commun. 114 (1998) 385] and target atoms ranging from lithium to neon [O'Rourke, McSherry and Crothers, Comput. Phys. Commun. 131 (2000) 129]. Cross sections for all of these target atoms may be obtained as limiting cases from the present code. Title of program: ARGON Catalogue identifier: ADSE Program summary URL: http://cpc.cs.qub.ac.uk/cpc/summaries/ADSE Program obtainable from: CPC Program Library Queen's University of Belfast, N. Ireland Licensing provisions: none Computer for which the program is designed and others on which it is operable: Computers: Four by 200 MHz Pro Pentium Linux server, DEC Alpha 21164; Four by 400 MHz Pentium 2 Xeon 450 Linux server, IBM SP2 and SUN Enterprise 3500 Installations: Queen's University, Belfast Operating systems under which the program has been tested: Red-hat Linux 5.2, Digital UNIX Version 4.0d, AIX, Solaris SunOS 5.7 Compilers: PGI workstations, DEC CAMPUS Programming language used: FORTRAN 90 with MPI directives No. of bits in a word: 64, except on Linux servers 32 Number of processors used: any number Has the code been vectorized or parallelized? Parallelized using MPI No. of bytes in distributed program, including test data, etc.: 32 189 Distribution format: tar gzip file Keywords: Single ionization, cross sections, continuum-distorted-wave model, continuum- distorted-wave eikonal-initial-state model, target atoms, wave treatment Nature of physical problem: The code calculates total, and differential cross sections for the single ionization of target atoms ranging from hydrogen up to and including argon by both light and heavy ion impact. Method of solution: ARGON allows the user to calculate the cross sections using either the CDW or CDW-EIS [J. Phys. B 16 (1983) 3229] models within the wave treatment. Restrictions on the complexity of the program: Both the CDW and CDW-EIS models are two-state perturbative approximations. Typical running time: Times vary according to input data and number of processors. For one processor the test input data for double differential cross sections (40 points) took less than one second, whereas the test input for total cross sections (20 points) took 32 minutes. Unusual features of the program: none (C) 2003 Elsevier B.V All rights reserved.

The importance of stakeholder engagement in invasive species management: A cross-jurisdictional perspective in Ireland

The management of invasive non-native species is a frequent cause of conflict in the field of biodiversity conservation because perceptions of their costs and benefits differ among stakeholder groups. A lack of cohesion between scientific researchers, the commercial sector and policy makers lies at the root of a widespread failure to develop and implement sustainable management practices for invasive species. The crisis of this situation is intensified by drivers stemming from international conventions and directives to address invasive species issues. There are further direct conflicts between legislative instruments promoting biodiversity conservation on the one hand while liberalizing trade at the national, European and global level on the other. The island of Ireland provides graphic illustration of the importance of cross-jurisdictional approaches to biological invasions. Using primarily Irish examples in this review, we emphasize the importance of approaching risk assessment, risk reduction and control or eradication policies from a cost-efficient, highly flexible perspective, incorporating linkages between environmental, economic and social objectives. The need for consolidated policies between Northern Ireland and the Republic of Ireland is particularly acute, though few model cross-border mechanisms for such consolidation are available. The importance of engaging affected stakeholders through positive interactions is discussed with regard to reducing the currently fragmented nature of invasive species management between the two jurisdictions.

Grassroots mobilisations against waste disposal sites in Greece

The government of Greece has gained notoriety for its failure to implement EU environmental directives in general, and is criticised specifically for its lack of an effective plan for the safe disposal of waste. Local mobilisations against a series of planned 'Sanitary Waste Disposal Sites' (HETAs) in three municipalities of Attica are examined. Should such protests be classified as NIMBY (not in my backyard)? Or do they present broader claims of justice and equity? Qualitative analysis of the protesters' on-line campaign material reveals that while these mobilisations do demonstrate some NIMBY characteristics, such campaigns should rather be perceived as ad hoc mobilisations reflective of tensions of late modernity. The public's mistrust of science and concerns about democratic deficit and accountability, as well as different perceptions of risk, are prominent.

The growing visibility of creationism in Northern Ireland: are new science teachers equipped to deal with the issues?

The growing visibility of various forms of creationism in Northern Ireland raises issues for science education. Attempts have been made at political levels to have such “alternatives” to evolution taught in the science classroom, and the issue has received coverage in local press and media. A sample of 112 pre-service science teachers answered a survey on attitudes toward evolution. Preliminary analysis revealed many of these new teachers held views contrary to scientific consensus—over one fifth doubt the evidence for human evolution, and over one quarter dispute the common ancestry of life. Over two thirds indicated a preference for teaching a “range of theories” regarding these issues in science. In addition, 49 pre-service biology teachers viewed a DVD resource promoting “intelligent design” and completed an evaluation of it. The biology teachers also took part in either focus groups or additional questionnaires. A majority took the resource at face value and made positive comments regarding its utility. Many articulated views contrary to the stated positions of science academies, professional associations, and the UK government teaching directives regarding creationism. Most indicated a perception that intelligent design is legitimate science and that there is a scientific “controversy” regarding the legitimacy of evolution. Concern is raised over the ability of these new teachers to distinguish between scientific and non-scientific theories. The suggestion is made that the issue should be addressed directly with pre-service science teachers to make clear the status of such “alternatives.” The paper raises implications for science education and questions for further research.