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.

The influence of hilly terrain on canopy-atmosphere carbon dioxide exchange

Topography influences many aspects of forest-atmosphere carbon exchange; yet only a small number of studies have considered the role of topography on the structure of turbulence within and above vegetation and its effect on canopy photosynthesis and the measurement of net ecosystem exchange of CO2 (N-ee) using flux towers. Here, we focus on the interplay between radiative transfer, flow dynamics for neutral stratification, and ecophysiological controls on CO2 sources and sinks within a canopy on a gentle cosine hill. We examine how topography alters the forest-atmosphere CO2 exchange rate when compared to uniform flat terrain using a newly developed first-order closure model that explicitly accounts for the flow dynamics, radiative transfer, and nonlinear eco physiological processes within a plant canopy. We show that variation in radiation and airflow due to topography causes only a minor departure in horizontally averaged and vertically integrated photosynthesis from their flat terrain values. However, topography perturbs the airflow and concentration fields in and above plant canopies, leading to significant horizontal and vertical advection of CO2. Advection terms in the conservation equation may be neglected in flow over homogeneous, flat terrain, and then N-ee = F-c, the vertical turbulent flux of CO2. Model results suggest that vertical and horizontal advection terms are generally of opposite sign and of the same order as the biological sources and sinks. We show that, close to the hilltop, F-c departs by a factor of three compared to its flat terrain counterpart and that the horizontally averaged F-c-at canopy top differs by more than 20% compared to the flat-terrain case.

Dynamical influences on European climate: an uncertain future

Climate science is coming under increasing pressure to deliver projections of future climate change at spatial scales as small as a few kilometres for use in impacts studies. But is our understanding and modelling of the climate system advanced enough to offer such predictions? Here we focus on the Atlantic–European sector, and on the effects of greenhouse gas forcing on the atmospheric and, to a lesser extent, oceanic circulations. We review the dynamical processes which shape European climate and then consider how each of these leads to uncertainty in the future climate. European climate is unique in many regards, and as such it poses a unique challenge for climate prediction. Future European climate must be considered particularly uncertain because (i) the spread between the predictions of current climate models is still considerable and (ii) Europe is particularly strongly affected by several processes which are known to be poorly represented in current models.

Nutritional implications on the fertility of high yielding dairy cows

This paper reviews energy utilisation in high yielding Holsteins and draws attention to the competing forces within the cow for nutrients to support different physiological processes. These comprise; meeting obligatory maintenance costs, providing essential nutrients for milk synthesis, maintenance of satisfactory milk composition, regulation of body tissue metabolism and body condition score and the establishment of reproductive cyclity after calving, followed by a successful pregnancy. Interrelationships between nutritional state and the partition of nutrients to these competing forces is discussed, with emphasis on the fertility of high yielding multiparous cows, aiming to determine the origins of some of the abnormal cycles and compromised fertility noted in such cows. A further analysis with primaparous heifers is provided and finally a number of strategies are identified that could be undertaken, to improve nutritional state and the overall fertility of high yielding cows. It is concluded that development of improved nutritional strategies represents a more reliable means of improving the overall productivity, along with the fertility of high yielding cows, than an increased focus on genetic selection, where predictability of response has often been disappointing.

Determinants of fruit and vegetable intake in England: a re-examination based on quantile regression

Objective To examine die sociodemographic determinants of fruit and vegetable (F&V) consumption in England and determine the differential effects of socioeconomic variables at various parts of the intake distribution, with a special focus on severely inadequate intakes Design Quantile regression, expressing F&V intake as a function of sociodemographic variables, is employed. Here, quantile regression flexibly allows variables such as ethnicity to exert effects on F&V intake that. vary depending oil existing levels of intake. Setting The 2003 Health survey of England. Subjects Data were from 11044 adult individuals. Results The influence of particular sociodemographic variables is found to vary significantly across the intake distribution We conclude that women consume more F&V than men, Asians and Hacks mole dian Whites, co-habiting individuals more than single-living ones Increased incomes and education also boost intake However, the key general finding of the present study is that the influence of most variables is relatively weak in the area of greatest concern, i e among those with the most inadequate intakes in any reference group. Conclusions. Our findings emphasise the importance of allowing the effects of socio-economic drivers to vary across the intake distribution The main finding, that variables which exert significant influence on F&V Intake at other parts Of the conditional distribution have a relatively weak influence at the lower tail, is cause for concern. It implies that in any defined group, those consuming the lease F&V are hard to influence using compaigns or policy levers.

Song development in birds: the role of early experience and its potential effect on rehabilitation success

Environmental conditions during the early life stages of birds can have significant effects on the quality of sexual signals in adulthood, especially song, and these ultimately have consequences for breeding success and fitness. This has wide-ranging implications for the rehabilitation protocols undertaken in wildlife hospitals which aim to return captive-reared animals to their natural habitat. Here we review the current literature on bird song development and learning in order to determine the potential impact that the rearing of juvenile songbirds in captivity can have on rehabilitation success. We quantify the effects of reduced learning on song structure and relate this to the possible effects on an individual's ability to defend a territory or attract a mate. We show the importance of providing a conspecific auditory model for birds to learn from in the early stages post-fledging, either via live- or tape-tutoring and provide suggestions for tutoring regimes. We also highlight the historical focus on learning in a few model species that has left an information gap in our knowledge for most species reared at wildlife hospitals.

Response to comments on "On the regulation of populations of mammals, birds, fish, and insects"

The technical comments by Getz and Lloyd-Smith, Ross, and Doncaster focus on specific aspects of our analysis and estimation and do not demonstrate any results opposing our key conclusion-that, contrary to what was previously believed, the relation between a population's growth rate (pgr) and its density is generally concave.

Repeated challenge with prion disease: The risk of infection and impact on incubation period

Natural exposure to prion disease is likely to occur throughout successive challenges, yet most experiments focus on single large doses of infectious material. We analyze the results from an experiment in which rodents were exposed to multiple doses of feed contaminated with the scrapie agent. We formally define hypotheses for how the doses combine in terms of statistical models. The competing hypotheses are that only the total dose of infectivity is important (cumulative model), doses act independently, or a general alternative that interaction between successive doses occurs (to raise or lower the risk of infection). We provide sample size calculations to distinguish these hypotheses. In the experiment, a fixed total dose has a significantly reduced probability of causing infection if the material is presented as multiple challenges, and as the time between challenges lengthens. Incubation periods are shorter and less variable if all material is consumed on one occasion. We show that the probability of infection is inconsistent with the hypothesis that each dose acts as a cumulative or independent challenge. The incubation periods are inconsistent with the independence hypothesis. Thus, although a trend exists for the risk of infection with prion disease to increase with repeated doses, it does so to a lesser degree than is expected if challenges combine independently or in a cumulative manner.

Aziridine synthesis via nucleophilic attack of carbene equivalents on imines: the aza-Darzens reaction

The development of new methods for the efficient synthesis of aziridines has been of considerable interest to researchers for more than 60 years, but no single method has yet emerged as uniformly applicable, especially for asymmetric synthesis of chiral aziridines. One method which has been intensely examined and expanded of late involves the nucleophilic addition to imines by anions bearing a-leaving groups; by analogy with the glycidate epoxide synthesis, these processes are often described as "aza-Darzens reactions". This Microreview gives a summary of the area, with a focus on contemporary developments. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

The impact of ICT on the work patterns of managers and their organisations

Purpose – The main aim of this paper is to present the results of a study examining managers' attitudes towards the deployment and use of information and communications technology (ICT) in their organisations. The study comes at a time when ICT is being recognised as a major enabler of innovation and new business models, which have the potential to have major impact on western economies and jobs. Design/methodology/approach – A questionnaire was specially designed to collect data relating to three research questions. The questionnaire also included a number of open-ended questions. A total of 181 managers from a wide range of industries across a number of countries participated in the electronic survey. The quantitative responses to the survey were analysed using SPSS. Exploratory factor analysis using Varimax rotation was used and ANOVA to compare responses by different groups. Findings – The survey showed that many of the respondents appeared equipped to work “any place, any time”. However, it also highlighted the challenges managers face in working in a connected operation. Also, the data suggested that many managers were less than confident about their companies' policies and practices in relation to information management. Originality/value – A next step from this exploratory research could be the development of a model exploring the impact of ICT on management and organisational performance in terms of personal characteristics of the manager, the role performed, the context and the ICT provision. Also, further research could focus on examining in more detail differences between management levels.

Visualizing knowledge in project-based work

This article considers how visual practices are used to manage knowledge in project-based work. It compares project-based work in a capital goods manufacturer and an architectural firm. Visual representations are used extensively in both cases, but the nature of visual practice differs significantly between the two. The research explores the kinds of knowledge that are (and aren't) developed and made visible in strategizing and planning activities. For example, whereas the emphasis of project-based work in the former firm is on exploitation of knowledge and it visualizes its project context largely in commercial and processual terms, the emphasis in the latter is on exploration and it uses a wide range of visual materials to understand physical interdependencies across the project boundary. We contend particular kinds of visual tools can help project teams step between exploration and exploitation within a project, and articulate the types of representations, foci of attention and patterns of interaction involved. The findings suggest that business managers can make more deliberate choices about how knowledge is made visible, and can change visual practice to align the project with exploring and exploiting opportunities. It raises the question: What don't you see within your organization? The work contributes to academic debates about managing through projects, strategising and organizing, while the focus on visual representation disrupts the tacit-codified dichotomy in the broad debate on knowledge and learning, and highlights the craft skills central to strategizing and organizing.

The impact of EPA and DHA on blood lipids and lipoprotein metabolism: influence of apoE genotype

Fish and fish oil-rich sources of long-chain n-3 fatty acids have been shown to be cardio-protective, through a multitude of different pathways including effects on arrythymias, endothelial function, inflammation and thrombosis, as well as modulation of both the fasting and postprandial blood lipid profile. To date the majority of studies have examined the impact of EPA and DHA fed simultaneously as fish or fish oil supplements. However, a number of recent studies have compared the relative biopotency of EPA v. DHA in relation to their effect on blood lipid levels. Although many beneficial effects of fish oils have been demonstrated, concern exists about the potential deleterious impact of EPA and DHA on LDL-cholesterol, with a highly-heterogenous response of this lipid fraction reported in the literature. Recent evidence suggests that apoE genotype may be in part responsible. In the present review the impact of EPA and DHA on cardiovascular risk and the blood lipoprotein profile will be considered, with a focus on the apoE gene locus as a possible determinant of lipid responsiveness to fish oil intervention.

Multiple stressors on biotic interactions: how climate change and alien species interact to affect pollination

Global change may substantially affect biodiversity and ecosystem functioning but little is known about its effects on essential biotic interactions. Since different environmental drivers rarely act in isolation it is important to consider interactive effects. Here, we focus on how two key drivers of anthropogenic environmental change, climate change and the introduction of alien species, affect plant–pollinator interactions. Based on a literature survey we identify climatically sensitive aspects of species interactions, assess potential effects of climate change on these mechanisms, and derive hypotheses that may form the basis of future research. We find that both climate change and alien species will ultimately lead to the creation of novel communities. In these communities certain interactions may no longer occur while there will also be potential for the emergence of new relationships. Alien species can both partly compensate for the often negative effects of climate change but also amplify them in some cases. Since potential positive effects are often restricted to generalist interactions among species, climate change and alien species in combination can result in significant threats to more specialist interactions involving native species.

Housing supply and planning controls: the impact of development control processing times on housing supply in England

The National Housing and Planning Advice Unit commissioned Professor Michael Ball of Reading University to undertake empirical research into how long it was taking to obtain planning consent for major housing sites in England. The focus on sites as opposed to planning applications is important because it is sites that generate housing.

The effect of cleft lip on socio-emotional functioning in school-aged children

Background: Children with cleft lip are known to be at raised risk for socio-emotional difficulties, but the nature of these problems and their causes are incompletely understood; longitudinal studies are required that include comprehensive assessment of child functioning, and consideration of developmental mechanisms. Method: Children with cleft lip (with and without cleft palate) (N = 93) and controls (N = 77), previously studied through infancy, were followed up at 7 years, and their socio-emotional functioning assessed using teacher and maternal reports, observations of social interactions, and child social representations (doll play). Direct and moderating effects of infant attachment and current parenting were investigated, as was the role of child communication difficulties and attractiveness. Results: Children with clefts had raised rates of teacher-reported social problems, and anxious and withdrawn-depressed behaviour; direct observations and child representations also revealed difficulties in social relationships. Child communication problems largely accounted for these effects, especially in children with cleft palate as well as cleft lip. Insecure attachment contributed to risk in both index and control groups, and a poorer current parenting environment exacerbated the difficulties of those with clefts. Conclusions: Children with clefts are at raised risk for socio-emotional difficulties in the school years; clinical interventions should focus on communication problems and supporting parenting; specific interventions around the transition to school may be required. More generally, the findings reflect the importance of communication skills for children’s peer relations.