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.

A web 2.0 user interface for wide-area resource monitoring

Resource monitoring in distributed systems is required to understand the 'health' of the overall system and to help identify particular problems, such as dysfunctional hardware or faulty system or application software. Monitoring systems such as GridRM provide the ability to connect to any number of different types of monitoring agents and provide different views of the system, based on a client's particular preferences. Web 2.0 technologies, and in particular 'mashups', are emerging as a promising technique for rapidly constructing rich user interfaces, that combine and present data in intuitive ways. This paper describes a Web 2.0 user interface that was created to expose resource data harvested by the GridRM resource monitoring system.

The use of cursor measures for motion-impaired computer users

“Point and click” interactions remain one of the key features of graphical user interfaces (GUIs). People with motion-impairments, however, can often have difficulty with accurate control of standard pointing devices. This paper discusses work that aims to reveal the nature of these difficulties through analyses that consider the cursor’s path of movement. A range of cursor measures was applied, and a number of them were found to be significant in capturing the differences between able-bodied users and motion-impaired users, as well as the differences between a haptic force feedback condition and a control condition. The cursor measures found in the literature, however, do not make up a comprehensive list, but provide a starting point for analysing cursor movements more completely. Six new cursor characteristics for motion-impaired users are introduced to capture aspects of cursor movement different from those already proposed.

Running climate models on grids 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 also involves complicated workflows implemented as shell scripts. A new grid middleware system that is well suited to climate modelling applications is presented in this paper. Grid Remote Execution (G-Rex) allows climate models to be deployed as Web services on remote computer systems and then launched and controlled as if they were running on the user's own computer. 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. G-Rex has a REST architectural style, featuring a Java client program that can easily be incorporated into existing scientific workflow scripts. Some technical details of G-Rex are presented, with examples of its use by climate modellers.

Grid Remote Execution (G-Rex) of Climate Models

G-Rex is light-weight Java middleware that allows scientific applications deployed on remote computer systems to be launched and controlled as if they are running on the user's own computer. G-Rex is particularly suited to ocean and climate modelling applications because output from the model is transferred back to the user while the run is in progress, which prevents the accumulation of large amounts of data on the remote cluster. The G-Rex server is a RESTful Web application that runs inside a servlet container on the remote system, and the client component is a Java command line program that can easily be incorporated into existing scientific work-flow scripts. The NEMO and POLCOMS ocean models have been deployed as G-Rex services in the NERC Cluster Grid, and G-Rex is the core grid middleware in the GCEP and GCOMS e-science projects.

Bringing the target to the cursor: proxy targets for older adults

Studies in the literature have proposed techniques to facilitate pointing in graphical user interfaces through the use of proxy targets. Proxy targets effectively bring the target to the cursor, thereby reducing the distance that the cursor must travel. This paper describes a study which aims to provide an initial understanding of how older adults respond to proxy targets, and compares older with younger users. We found that users in both age groups adjusted to the proxy targets without difficulty, and there was no indication in the cursor trajectories that users were confused about which target, i.e. the original versus the proxy, was to be selected. In terms of times, preliminary results show that for younger users, proxies did not provide any benefits over direct selection, while for older users, times were increased with proxy targets. A full analysis of the movement times, error rates, throughput and subjective feedback is currently underway.

Norms-based simulation for personalised service provision

User interfaces have the primary role of enabling access to information meeting individual users' needs. However, the user-systems interaction is still rigid, especially in support of complex environments where various types of users are involved. Among the approaches for improving user interface agility, we present a normative approach to the design interfaces of web applications, which allow delivering users personalized services according to parameters extracted from the simulation of norms in the social context. A case study in an e-Government context is used to illustrate the implications of the approach.

Perception and haptics

For people with motion impairments, access to and independent control of a computer can be essential. Symptoms such as tremor and spasm, however, can make the typical keyboard and mouse arrangement for computer interaction difficult or even impossible to use. This paper describes three approaches to improving computer input effectivness for people with motion impairments. The three approaches are: (1) to increase the number of interaction channels, (2) to enhance commonly existing interaction channels, and (3) to make more effective use of all the available information in an existing input channel. Experiments in multimodal input, haptic feedback, user modelling, and cursor control are discussed in the context of the three approaches. A haptically enhanced keyboard emulator with perceptive capability is proposed, combining approaches in a way that improves computer access for motion impaired users.

Issues and benefits of using 3D Interfaces: visual and verbal tasks

Spatial memory is important for locating objects in hierarchical data structures, such as desktop folders. There are, however, some contradictions in literature concerning the effectiveness of 3D user interfaces when compared to their 2D counterparts. This paper uses a task-based approach in order to investigate the effectiveness of adding a third dimension to specific user tasks, i.e. the impact of depth on navigation in a 3D file manager. Results highlight issues and benefits of using 3D interfaces for visual and verbal tasks, and introduces the possible existence of a correlation between aptitude scores achieved on the Guilford- Zimmerman Orientation Survey and Electroencephalography- measured brainwave activity as participants search for targets of variable perceptual salience in 2D and 3D environments.

A decadal view of biodiversity informatics: challenges and priorities

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Investigating novel point-select techniques for older people

As the number and proportion of older people worldwide continues to grow, robotic devices can play a role in helping older people continue to live independent and active lives. Graphical user interfaces (GUIs) and interactions that involve pointing to items and selecting them are becoming more common in assistive robots. The authors are currently working on a project investigating techniques to improve point-select interactions for older people. In particular, the project studies how older people respond to expanding and moving targets. The research is ongoing, and this paper describes the methods that will be used in upcoming experiments.

Analysis of the dominant enterprise information assurance mechanisms

The purpose of this study is to analyse current data continuity mechanisms employed by the target group of businesses and to identify any inadequacies in the mechanisms as a whole. The questionnaire responses indicate that 47% of respondents do perceive backup methodologies as important, with a total of 70% of respondents having some backup methodology already in place. Businesses in Moulton Park perceive the loss of data to have a significant effect upon their business’ ability to function. Only 14% of respondents indicated that loss of data on computer systems would not affect their business at all, with 54% of respondents indicating that there would be either a “major effect” (or greater) on their ability to operate. Respondents that have experienced data loss were more likely to have backup methodologies in place (53%) than respondents that had not experienced data loss (18%). Although the number of respondents clearly affected the quality and conclusiveness of the results returned, the level of backup methodologies in place appears to be proportional to the company size. Further investigation is recommended into the subject in order to validate the information gleaned from the small number of respondents.