Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

Controlling nitrate pollution: an integrated approach

The introduction of the EU Water Framework Directive requires policy to address non-point source pollution as part of an overall integrated strategy to improve the ecological status of water bodies. In this paper, we combine an economic optimisation framework with a dynamic simulation model of N transport in the Kennet Catchment to link decisions taken at the farm level to reductions in nitrate concentrations in the River Kennet. We examine a variety of policies targeted at reducing fertiliser use and changing the way in which farm land is used. We find that a tax on nitrogen emerges as the best policy both in terms of cost- and environmental effectiveness. Such a policy involves a considerable reduction in fertiliser use, as well as, a restructuring of land-use away from arable towards increased use of set-aside. Budgetary implications of such a radical move towards set-aside would be huge and hence unlikely to be politically palatable given the objective of reducing the EU budgetary allocation to agriculture. Additionally, the current rise in world demand for food may also mitigate calls for increasing the proportion of land taken out of agricultural production. Although the study succeeds in establishing a link between actions on the farm and nitrate concentrations in the stream water, further work is required to explore the effect of the retention of nitrates in the unsaturated zone and groundwater on this link.

Diversity and difference in the everyday lives of Ugandan street children: The significance of age and gender for understanding the use of space

Childhood is characterised by diversity and difference across and within societies. Street children have a unique relationship to the urban environment evident through their use of the city. The everyday geographies that street children produce are diversified through the spaces they frequent and the activities they engage in. Drawing on a range of children-centred qualitative methods, this article focuses on street children's use of urban space in Kampala, Uganda. The article demonstrates the importance of considering variables such as gender and age in the analysis of street children's socio-spatial experiences, which, to date, have rarely been considered in other accounts of street children's lives. In addition the article highlights the need for also including street children's individuality and agency into understanding their use of space. The article concludes by arguing for policies to be sensitive to the diversity that characterises street children's lives and calls for a more nuanced approach where policies are designed to accommodate street children's age and gender differences, and their individual needs, interests and abilities.

Managing land-use conflict around urban centres: Australian poultry farmer attitudes towards relocation

In analysing the release of agricultural land to urban development, the urban fringe literature has not focused on whether farmers are able to relocate from the urban fringe to remoter rural areas. Through interviews with representatives from the poultry industry in two Australian states, this paper identifies that poultry farm relocation strategies are constrained by off-farm economic relations, the land-use planning system and financial considerations. Closely aligned to these constraints on relocation is the on-going process of poultry farm intensification, which is seen as presenting rising problems for land-use management around expanding metropolitan centres in Australia. Of particular concern is the potential for amenity complaints and associated land-use conflicts, which have not been comprehensively investigated. Recognising that existing environmental and land-use planning controls are ineffective in producing amicable solutions when conflict involving poultry farming is at its most intense, the paper calls for improvements to the regulatory system, including greater consideration for how the process of relocation can be encouraged. (c) 2005 Elsevier Ltd. All rights reserved.

Diversity and difference in the everyday lives of Ugandan street children: The significance of age and gender for understanding the use of space

Childhood is characterised by diversity and difference across and within societies. Street children have a unique relationship to the urban environment evident through their use of the city. The everyday geographies that street children produce are diversified through the spaces they frequent and the activities they engage in. Drawing on a range of children-centred qualitative methods, this article focuses on street children's use of urban space in Kampala, Uganda. The article demonstrates the importance of considering variables such as gender and age in the analysis of street children's socio-spatial experiences, which, to date, have rarely been considered in other accounts of street children's lives. In addition the article highlights the need for also including street children's individuality and agency into understanding their use of space. The article concludes by arguing for policies to be sensitive to the diversity that characterises street children's lives and calls for a more nuanced approach where policies are designed to accommodate street children's age and gender differences, and their individual needs, interests and abilities.

Feminist geography, prehistory of

The article traces the beginnings and early history of feminist geography in the United Kingdom through the memories and personal narratives of two women who were heavily involved in this field of geographical research, in the 1970s, and were founder members of the Women and Geography Study Group of the Institute of British Geographers. The article begins by considering the context (both political and academic) within which feminist geography was born. Second-wave feminism and the rise of the women’s movement, initially in the United States, is seen as a major influence on the development of feminist geography. In the academic world, it was the dominance of quantitative geography in the 1960s, and the related opposition to this positivist paradigm by humanistic and socialist geographers, which led to calls for a recognition of the inequalities faced by women in society and an understanding of the differences in men’s and women’s lives. Through personal narratives, the authors seek to illustrate the obstacles and disagreements, as well as the encouragements and opportunities, which led to the birth of UK-feminist geography. Many individual geographers, influential to the story, are referred to, seen through the eyes of the authors at that time.

Impact of coronal mass ejections, interchange reconnection, and disconnection on heliospheric magnetic field strength

An update of Owens et al. (2008) shows that the relationship between the coronal mass ejection (CME) rate and the heliospheric magnetic field strength predicts a field floor of less than 4 nT at 1 AU. This implies that the record low values measured during this solar minimum do not necessarily contradict the idea that open flux is conserved. The results are consistent with the hypothesis that CMEs add flux to the heliosphere and interchange reconnection between open flux and closed CME loops subtracts flux. An existing model embracing this hypothesis, however, overestimates flux during the current minimum, even though the CME rate has been low. The discrepancy calls for reasonable changes in model assumptions.

What is the new medicines use review ‘patient survey’ attempting to capture in the context of existing patient satisfaction with pharmacy questionnaires and a new conceptual framework?

The community pharmacy service medicines use review (MUR) was introduced in 2005 ‘to improve patient knowledge, concordance and use of medicines’ through a private patient–pharmacist consultation. The MUR presents a fundamental change in community pharmacy service provision. While traditionally pharmacists are dispensers of medicines and providers of medicines advice, and patients as recipients, the MUR considers pharmacists providing consultation-type activities and patients as active participants. The MUR facilitates a two-way discussion about medicines use. Traditional patient–pharmacist behaviours transform into a new set of behaviours involving the booking of appointments, consultation processes and form completion, and the physical environment of the patient–pharmacist interaction moves from the traditional setting of the dispensary and medicines counter to a private consultation room. Thus, the new service challenges traditional identities and behaviours of the patient and the pharmacist as well as the environment in which the interaction takes place. In 2008, the UK government concluded there is at present too much emphasis on the quantity of MURs rather than on their quality.[1] A number of plans to remedy the perceived imbalance included a suggestion to reward ‘health outcomes’ achieved, with calls for a more focussed and scientific approach to the evaluation of pharmacy services using outcomes research. Specifically, the UK government set out the main principal research areas for the evaluation of pharmacy services to include ‘patient and public perceptions and satisfaction’as well as ‘impact on care and outcomes’. A limited number of ‘patient satisfaction with pharmacy services’ type questionnaires are available, of varying quality, measuring dimensions relating to pharmacists’ technical competence, behavioural impressions and general satisfaction. For example, an often cited paper by Larson[2] uses two factors to measure satisfaction, namely ‘friendly explanation’ and ‘managing therapy’; the factors are highly interrelated and the questions somewhat awkwardly phrased, but more importantly, we believe the questionnaire excludes some specific domains unique to the MUR. By conducting patient interviews with recent MUR recipients, we have been working to identify relevant concepts and develop a conceptual framework to inform item development for a Patient Reported Outcome Measure questionnaire bespoke to the MUR. We note with interest the recent launch of a multidisciplinary audit template by the Royal Pharmaceutical Society of Great Britain (RPSGB) in an attempt to review the effectiveness of MURs and improve their quality.[3] This template includes an MUR ‘patient survey’. We will discuss this ‘patient survey’ in light of our work and existing patient satisfaction with pharmacy questionnaires, outlining a new conceptual framework as a basis for measuring patient satisfaction with the MUR. Ethical approval for the study was obtained from the NHS Surrey Research Ethics Committee on 2 June 2008. References 1. Department of Health (2008). Pharmacy in England: Building on Strengths – Delivering the Future. London: HMSO. www. official-documents.gov.uk/document/cm73/7341/7341.pdf (accessed 29 September 2009). 2. Larson LN et al. Patient satisfaction with pharmaceutical care: update of a validated instrument. JAmPharmAssoc 2002; 42: 44–50. 3. Royal Pharmaceutical Society of Great Britain (2009). Pharmacy Medicines Use Review – Patient Audit. London: RPSGB. http:// qi4pd.org.uk/index.php/Medicines-Use-Review-Patient-Audit. html (accessed 29 September 2009).

The 2002 US Farm Bill: what's in it for CAP reform?

The 2002 U.S. Farm Bill (the Farm Security and Rural Investment Act or FSRIA) provides considerably more government subsidies for U.S. agriculture than Congress envisaged when it passed the preceding 1996–2002 FAIR Act. We review the FAIR record, showing how government subsidies increased greatly beyond those originally scheduled. For FSRIA, we outline key commodity, trade, and conservation and environmental provisions. We expect that the commodity programmes will: (a) encourage production when the market calls for less; (b) significantly increase subsidies over FAIR baseline subsidies; (c) press against current WTO and possible Doha Round support limits; and (d) aggravate trading partners. Finally, we suggest two lessons from the U.S. policy experience that might benefit those working on CAP and WTO reform. First, past research shows that farm programmes have little to do with the economic health of rural communities. Second, programme transparency, and especially public disclosure of the level of payments going to individual farmers, by name, influences the farm policy debate. Personalized data show what economists have long maintained—that the bulk of programme benefits go to a relatively few, large, producers—but do so in a way that captures the public and policy-makers' attention

Phylloxera and the grapevine: a sense of common purpose?

The purpose of life is its continuation: survival is the reason things live. Here we explore this 'basic' of biology, by reference to the extraordinary life-cycle of the aphid-like pest phylloxera, and the complexity of its relationship with its host the grapevine. The effort and ingenuity that phylloxera employs to continue itself leads to a doubt that survival alone is sufficient reason. It has frequently been suggested that the reduction of life to a catalogue of facts (by science) creates this doubt, because it robs existence of its essence (which is something other than its mechanics). The part that science is said to steal is what Robert Pirsig calls Quality-the harmonious balance of things. Pirsig seems to imply that this is something inherent in things-and independent from us. A more mundane explanation is that the difference between facts and the complete reality is us-the tendency of mind to connect freely between different kinds of information. This possibility is briefly illustrated here by a myth based on the facts of phylloxera.