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.

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).

Eiffel assertions and the external structure of classes and objects

The “external structure” in an object oriented system refers here to the  graphs of objects and classes. The class structure graph or class model is derived from the object structure graph or object model, and in this operation structural information is lost, or never made explicit. Although object oriented programming languages capture the class model as declarations,  contradictory assumptions about object model properties may be made introducing faults into the design. Consistent assumptions about the object model can be specified in the code using assertions such as Eiffel’s  invariants, preconditions and postconditions. Three examples specifying the external structure are considered.

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.

BDI4JADE: a BDI layer on top of JADE

Several agent platforms that implement the belief-desire-intention (BDI) architecture have been proposed. Even though most of them are implemented based on existing general purpose programming languages, e.g. Java, agents are either programmed in a new programming language or Domain-specific Language expressed in XML. As a consequence, this prevents the use of advanced features of the underlying programming language and the integration with existing libraries and frameworks, which are essential for the development of enterprise applications. Due to these limitations of BDI agent platforms, we have implemented the BDI4JADE, which is presented in this paper. It is implemented as a BDI layer on top of JADE, a well accepted agent platform.

The use of prolog in the realisation of digital transfer functions

Systems characterised by general graphs are very flexible because of a given application they offer a great number of degrees of freedom and consequently a great possibility of choice to the designer. This can become a drawback in practice when myriads of cases have to be examined analytically and most of them rejected for a variety of heterogeneous reasons. For such design problems, it appears that logic programming languages are ideally suited because they can implement the heterogeneous rules which describe the desired system in a natural way. An application of the Prolog language to the design of active RC biquad circuits investigated by Mouly in his doctoral thesis illustrates the advantages of such a rule-based approach.

Object oriented regular expressions

Regular expressions are used to parse textual data to match patterns and extract variables. They have been implemented in a vast number of programming languages with a significant quantity of research devoted to improving their operational efficiency. However, regular expressions are limited to finding linear matches. Little research has been done in the field of object-oriented results which would allow textual or binary data to be converted to multi-layered objects. This is significantly relevant as many of todaypsilas data formats are object-based. This paper extends our previous work by detailing an algorithmic approach to perform object-oriented parsing, and provides an initial study of benchmarks of the algorithms of our contribution

Generating reusable visual notations using model transformation

Visual notations are a key aspect of visual languages. They provide a direct mapping between the intended information and set of graphical symbols. Visual notations are most often implemented using the low level syntax of programming languages which is time consuming, error prone, difficult to maintain and hardly human-centric. In this paper we describe an alternative approach to generating visual notations using by-example model transformations. In our new approach, a semantic mapping between model and view is implemented using model transformations. The notations resulting from this approach can be reused by mapping varieties of input data to their model and can be composed into different visualizations. Our approach is implemented in the CONVErT framework and has been applied to many visualization examples. Three case studies for visualizing statistical charts, visualization of traffic data, and reuse of a Minard's map visualization's components, are presented in this paper. A detailed user study of our approach for reusing notations and generating visualizations has been provided. 80% of the participants in this user study agreed that the novel approach to visualization was easy and 87% stated that they quickly learned to use the tool support.

Generating reusable visual notations using model transformation

Visual notations are a key aspect of visual languages. They provide a direct mapping between the intended information and set of graphical symbols. Visual notations are most often implemented using the low level syntax of programming languages which is time consuming, error prone, difficult to maintain and hardly human-centric. In this paper we describe an alternative approach to generating visual notations using byexample model transformations. In our new approach, a semantic mapping between model and view is implemented using model transformations. The notations resulting from this approach can be reused by mapping varieties of input data to their model and can be composed into different visualisations. Our approach is implemented in the CONVErT framework and has been applied to many visualisation examples. Two case studies for visualising statistical charts and visualisation of traffic data are presented in this paper. A detailed user study of our approach for reusing notations and generating visualisations has been provided that shows good reusability and general acceptance of the novel approach.

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