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.

Variance estimation with highly stratified sampling designs with unequal probabilities

It is common practice to design a survey with a large number of strata. However, in this case the usual techniques for variance estimation can be inaccurate. This paper proposes a variance estimator for estimators of totals. The method proposed can be implemented with standard statistical packages without any specific programming, as it involves simple techniques of estimation, such as regression fitting.

On-line processing of wh-questions in children with G-SLI and typically developing children

Background: The computational grammatical complexity ( CGC) hypothesis claims that children with G(rammatical)-specific language impairment ( SLI) have a domain-specific deficit in the computational system affecting syntactic dependencies involving 'movement'. One type of such syntactic dependencies is filler-gap dependencies. In contrast, the Generalized Slowing Hypothesis claims that SLI children have a domain-general deficit affecting processing speed and capacity. Aims: To test contrasting accounts of SLI we investigate processing of syntactic (filler-gap) dependencies in wh-questions. Methods & Procedures: Fourteen 10; 2 - 17; 2 G-SLI children, 14 age- matched and 17 vocabulary-matched controls were studied using the cross- modal picturepriming paradigm. Outcomes & Results: G-SLI children's processing speed was significantly slower than the age controls, but not younger vocabulary controls. The G- SLI children and vocabulary controls did not differ on memory span. However, the typically developing and G-SLI children showed a qualitatively different processing pattern. The age and vocabulary controls showed priming at the gap, indicating that they process wh-questions through syntactic filler-gap dependencies. In contrast, G-SLI children showed priming only at the verb. Conclusions: The findings indicate that G-SLI children fail to establish reliably a syntactic filler- gap dependency and instead interpret wh-questions via lexical thematic information. These data challenge the Generalized Slowing Hypothesis account, but support the CGC hypothesis, according to which G-SLI children have a particular deficit in the computational system affecting syntactic dependencies involving 'movement'. As effective remediation often depends on aetiological insight, the discovery of the nature of the syntactic deficit, along side a possible compensatory use of semantics to facilitate sentence processing, can be used to direct therapy. However, the therapeutic strategy to be used, and whether such similar strengths and weaknesses within the language system are found in other SLI subgroups are empirical issues that warrant further research.

Criteria for validation and selection of cognitive tests for investigating the effects of foods and nutrients.

This review is an output of the International Life Sciences Institute (ILSI) Europe Marker Initiative, which aims to identify evidence-based criteria for selecting adequate measures of nutrient effects on health through comprehensive literature review. Experts in cognitive and nutrition sciences examined the applicability of these proposed criteria to the field of cognition with respect to the various cognitive domains usually assessed to reflect brain or neurological function. This review covers cognitive domains important in the assessment of neuronal integrity and function, commonly used tests and their state of validation, and the application of the measures to studies of nutrition and nutritional intervention trials. The aim is to identify domain-specific cognitive tests that are sensitive to nutrient interventions and from which guidance can be provided to aid the application of selection criteria for choosing the most suitable tests for proposed nutritional intervention studies using cognitive outcomes. The material in this review serves as a background and guidance document for nutritionists, neuropsychologists, psychiatrists, and neurologists interested in assessing mental health in terms of cognitive test performance and for scientists intending to test the effects of food or food components on cognitive function.

Parenting difficulties and postnatal depression: implications for primary healthcare assessment and intervention

Postnatal depression (PND) is associated with impairments in the mother–child relationship, and these impairments are themselves associated with adverse child outcomes. Thus, compared to the children of non-depressed mothers, children of mothers with PND are more likely to be insecurely attached, and to have externalising behaviour problems and poor cognitive development. Each of these three child outcomes is predicted by a particular pattern of difficulty in parenting: insecure attachment is related to maternal insensitivity, particularly in relation to infant distress and emotional vulnerability; externalising problems are particularly common in the context of hostile parenting; and poor cognitive development is related to parental difficulties in noticing infant signs of interest and supporting their engagement with the environment. This article sets out procedures for how parenting could be assessed in ways that are sensitive to the domain-specific associations between parenting and child outcome, while remaining sensitive to the child's developmental stage. This set of assessments requires field testing.

Interactive Vector Field Feature Identification

We introduce a flexible technique for interactive exploration of vector field data through classification derived from user-specified feature templates. Our method is founded on the observation that, while similar features within the vector field may be spatially disparate, they share similar neighborhood characteristics. Users generate feature-based visualizations by interactively highlighting well-accepted and domain specific representative feature points. Feature exploration begins with the computation of attributes that describe the neighborhood of each sample within the input vector field. Compilation of these attributes forms a representation of the vector field samples in the attribute space. We project the attribute points onto the canonical 2D plane to enable interactive exploration of the vector field using a painting interface. The projection encodes the similarities between vector field points within the distances computed between their associated attribute points. The proposed method is performed at interactive rates for enhanced user experience and is completely flexible as showcased by the simultaneous identification of diverse feature types.

Developing a Communication link between Agents and cross Platform IDE

The main objective of this thesis work is to develop communication link between Runrev Revolution (IDE) and JADE (Multi-Agent System) through Socket programming using TCP/IP layer. These two independent platforms are connected using socket programming technique. Socket programming is considered to be newly emerging technology among these two platforms, the work done in this thesis work is considered to be a prototype.A Graphical simulation model is developed by salixphere (Company in Hedemora) to simulate logistic problems using Runrev Revolution (IDE). The simulation software/program is called “BIOSIM”. The logistic problems are complex, and conventional optimization techniques are unlikely very successful. “BIOSIM” can demonstrate the graphical representation of logistic problems depending upon the problem domains. As this simulation model is developed in revolution programming language (Transcript) which is dynamically typed and English-like language, it is quite slow compared to other high level programming languages. The object of this thesis work is to add intelligent behaviour in graphical objects and develop communication link between Runrev revolution (IDE) and JADE (Multi-Agent System) using TCP/IP layers.The test shows the intelligent behaviour in the graphical objects and successful communication between Runrev Revolution (IDE) and JADE (Multi-Agent System).

Leveraging new plans in AgentSpeak(PL)

In order to facilitate the development of agent-based software, several agent programming languages and architectures, have been created. Plans in these architectures are often self-contained procedures with an associated triggering event and a context condition, while any further information about the consequences of executing a plan is absent. However, agents designed using such an approach have limited flexibility at runtime, and rely on the designer’s ability to foresee all relevant situations an agent might have to handle. In order to overcome this limitation, we have created AgentSpeak(PL), an interpreter capable of performing state-space planning to generate new high-level plans. As the planning module creates new plans, the plan library is expanded, improving performance over time. However, for new plans to be useful in the long run, it is critical that the context condition associated with new plans is carefully generated. In this paper we describe a plan reuse technique aimed at improving an agent’s runtime performance by deriving optimal context conditions for new plans, allowing an agent to reuse generated plans as much as possible.

Maude Object-Oriented Action Tool

MAIDL, André Murbach; CARVILHE, Claudio; MUSICANTE, Martin A. Maude Object-Oriented Action Tool. Electronic Notes in Theoretical Computer Science. [S.l:s.n], 2008.

Ambiente computacional paradesenvolvimento de aplicações de controladores lógicos programáveis baseado em linguagens SFC e ST

This work proposes an environment for programming programmable logic controllers applied to oil wells with BCP type method of artificially lifting. The environment will have an editor based in the diagram of sequential functions for programming of PLCs. This language was chosen due to the fact of being high-level and accepted by the international standard IEC 61131-3. The use of these control programs in real PLC will be possible with the use of an intermediate level of language based on XML specification PLCopen T6 XML. For the testing and validation of the control programs, an area should be available for viewing variables obtained through communication with a real PLC. Thus, the main contribution of this work is to develop a computational environment that allows: modeling, testing and validating the controls represented in SFC and applied in oil wells with BCP type method of artificially lifting

Uma perspectiva de extensão do modelo de aceitação de tecnologia para explicar o uso de linguagens de desenvolvimento WEB: pesquisa com desenvolvedores Pyton e Java

The spread of the Web boosted the dissemination of Information Systems (IS) based on the Web. In order to support the implementation of these systems, several technologies came up or evolved with this purpose, namely the programming languages. The Technology Acceptance Model TAM (Davis, 1986) was conceived aiming to evaluate the acceptance/use of information technologies by their users. A lot of studies and many applications have used the TAM, however, in the literature it was not found a mention of the use of such model related to the use of programming languages. This study aims to investigate which factors influence the use of programming languages on the development of Web systems by their developers, applying an extension of the TAM, proposed in this work. To do so, a research was done with Web developers in two Yahoo groups: java-br and python-brasil, where 26 Java questionnaires and 39 Python questionnaires were fully answered. The questionnaire had general questions and questions which measured intrinsic and extrinsic factors of the programming languages, the perceived usefulness, the perceived ease of use, the attitude toward the using and the programming language use. Most of the respondents were men, graduate, between 20 and 30 years old, working in the southeast and south regions. The research was descriptive in the sense of its objectives. Statistical tools, descriptive statistics, main components and linear regression analysis were used for the data analysis. The foremost research results were: Java and Python have machine independence, extensibility, generality and reliability; Java and Python are more used by corporations and international organizations than supported by the government or educational institutions; there are more Java programmers than Python programmers; the perceived usefulness is influenced by the perceived ease of use; the generality and the extensibility are intrinsic factors of programming languages which influence the perceived ease of use; the perceived ease of use influences the attitude toward the using of the programming language