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.

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.

Large-scale and synoptic meteorology in the south-east Pacific during the observations campaign VOCALS-REx in austral Spring 2008

We present a descriptive overview of the meteorology in the south eastern subtropical Pacific (SEP) during the VOCALS-REx intensive observations campaign which was carried out between October and November 2008. Mainly based on data from operational analyses, forecasts, reanalysis, and satellite observations, we focus on spatio-temporal scales from synoptic to planetary. A climatological context is given within which the specific conditions observed during the campaign are placed, with particular reference to the relationships between the large-scale and the regional circulations. The mean circulations associated with the diurnal breeze systems are also discussed. We then provide a summary of the day-to-day synoptic-scale circulation, air-parcel trajectories, and cloud cover in the SEP during VOCALS-REx. Three meteorologically distinct periods of time are identified and the large-scale causes for their different character are discussed. The first period was characterised by significant variability associated with synoptic-scale systems interesting the SEP; while the two subsequent phases were affected by planetary-scale disturbances with a slower evolution. The changes between initial and later periods can be partly explained from the regular march of the annual cycle, but contributions from subseasonal variability and its teleconnections were important. Across the whole of the two months under consideration we find a significant correlation between the depth of the inversion-capped marine boundary layer (MBL) and the amount of low cloud in the area of study. We discuss this correlation and argue that at least as a crude approximation a typical scaling may be applied relating MBL and cloud properties with the large-scale parameters of SSTs and tropospheric temperatures. These results are consistent with previously found empirical relationships involving lower-tropospheric stability.

Dispersion Experiments in Central London: The 2007 DAPPLE project

In the event of a release of toxic gas in the center of London, the emergency services would need to determine quickly the extent of the area contaminated. The transport of pollutants by turbulent flow within the complex street and building architecture of cities is not straightforward, and we might wonder whether it is at all possible to make a scientifically-reasoned decision. Here we describe recent progress from a major UK project, ‘Dispersion of Air Pollution and its Penetration into the Local Environment’ (DAPPLE, www.dapple.org.uk). In DAPPLE, we focus on the movement of airborne pollutants in cities by developing a greater understanding of atmospheric flow and dispersion within urban street networks. In particular, we carried out full-scale dispersion experiments in central London (UK) during 2003, 2004, 2007, and 2008 to address the extent of the dispersion of tracers following their release at street level. These measurements complemented previous studies because (i) our focus was on dispersion within the first kilometer from the source, when most of the material was expected to remain within the street network rather than being mixed into the boundary layer aloft, (ii) measurements were made under a wide variety of meteorological conditions, and (iii) central London represents a European, rather than North American, city geometry. Interpretation of the results from the full-scale experiments was supported by extensive numerical and wind tunnel modeling, which allowed more detailed analysis under idealized and controlled conditions. In this article, we review the full-scale DAPPLE methodologies and show early results from the analysis of the 2007 field campaign data.

'Thou glorious kingdome, thou chiefe of empires': Persia in seventeenth-century travel literature

Bringing together a range of little-considered materials, this article assesses the portrayal of Persia in seventeenth-century travel literature and drama. In particular it argues that such texts use their awareness of Islamic sectarian division to portray Persia as a good potential trading partner in preference to the Ottoman Empire. A close reading of John Day, William Rowley and George Wilkins’ The Travailes of the Three English Brothers (1607) demonstrates how the play develops a fantasy model of how relations between Persia and England might function. The potential unity between England and Persia, imagined in terms of both religion and trade, demonstrates how Persia figured as a model ‘other England’ in early modern literature.

Does short termism affect the quality of urban design in the UK?

This paper follows the report on the “Quality of Urban Design: Study of the Influence of Private Property Decision Maker in Urban Design” (RICS 1996). It focuses on one of the findings in the report, namely that decisions made in development, investment and occupation seemed overly influenced by short term considerations. In this paper, the authors review the Report and examine the concept of short termism as it affects urban design decisions. The paper concludes that although it is difficult to establish whether or not short termism exists in many decisions, there are grounds for believing that a priori short termism might particularly influence property orientated decisions. The paper ends with some implications for policy both at the economy and local level.

Community involvement in urban design: help or hindrance?

This paper examines the realities of community involvement in urban design in the context of a study of the West Itchen Neighbourhood of Southampton, a diverse inner city area accommodating some 7,000 households and 18,000 people. The findings are based on a literature review of community involvement in urban design and case study research into three government supported regeneration projects all located within the study area: a Neighbourhood Renewal Area - designated in 1994; an Estate Action Scheme - implemented between 1993 and 1996; and a Single Regeneration Budget programme - following a successful bid in 1995. The research was undertaken by Helen Gregory in 1997/8 as the basis of a dissertation, supervised by Alan Rowley, submitted for the award of an MPhil in Environmental Planning and Development from The University of Reading.

Calciferols and bait shyness in the laboratory rat

Rodenticides with delayed action are generally more effective than fast-acting compounds because of the phenomenon of bait shyness. Calciferols have a stop-feed effect quite soon after dosing, and physiological effects are measurable within one day of dosing. We investigated whether bait shyness might result from these fairly rapid effects in the laboratory rat. We found evidence of bait shyness following recovery from sub-lethal dosing with two forms of calciferol. Use of intubation as well as feeding showed that the response was to the bait carrier rather than to detection of calciferols per se.

Role of the two-component regulator CpxAR in the virulence of Salmonella entetica serotype typhimurium

The CpxAR (Cpx) two-component regulator controls the expression of genes in response to a variety of environmental cues. The Cpx regulator has been implicated in the virulence of several gram-negative pathogens, although a role for Cpx in vivo has not been demonstrated directly. Here we investigate whether positive or negative control of gene expression by Cpx is important for the pathogenesis of Salmonella enterica serotype Typhimurium. The Cpx signal pathway in serotype Typhimurium was disrupted by insertional inactivation of the cpxA and cpxR genes. We also constitutively activated the Cpx pathway by making an internal in-frame deletion in cpxA (a cpxA* mutation). Activation of the Cpx pathway inhibited induction of the envelope stress response pathway controlled by the alternative sigma factor sigma(E) (encoded by rpoE). Conversely, the Cpx pathway was highly up-regulated (>40-fold) in a serotype Typhimurium rpoE mutant. The cpxA* mutation, but not the cpxA or the cpxR mutation, significantly reduced the capacity of serotype Typhimurium to adhere to and invade eucaryotic cells, although intracellular replication was not affected. The cpxA and cpxA* mutations significantly impaired the ability of serotype Typhimurium to grow in vivo in mice. To our knowledge, this is the first demonstration that the Cpx system is important for a bacterial pathogen in vivo.

'Thou glorious kingdome, thou chiefe of empires': Persia in seventeenth-century travel literature

This article discusses a series of texts by or about travellers to Safavid Persia in the early seventeenth century, and in particular the literature surrounding the Sherley brothers. It looks at the ways in which, in order to encourage support for the voyages they described, English travel writers emphasised the potential for closer Anglo-Persian relations. In doing so, such narratives took advantage of a developing awareness of sectarian division within Islam in order to differentiate Persia from the Ottoman Empire. The article then examines how The Travailes of the Three English Brothers (1607) by Day, Rowley and Wilkins, built on the possibilities suggested by the travel writings, and specifically their recognition of Islamic sectarian division, to develop an idealised model of how relations between Persia and England might function. More broadly, these texts demonstrate travellers’ interest in looking for potential correlation between Christian and Muslim identities during this period.

Multimodel assessment of the upper troposphere and lower stratosphere: tropics and global trends

The performance of 18 coupled Chemistry Climate Models (CCMs) in the Tropical Tropopause Layer (TTL) is evaluated using qualitative and quantitative diagnostics. Trends in tropopause quantities in the tropics and the extratropical Upper Troposphere and Lower Stratosphere (UTLS) are analyzed. A quantitative grading methodology for evaluating CCMs is extended to include variability and used to develop four different grades for tropical tropopause temperature and pressure, water vapor and ozone. Four of the 18 models and the multi-model mean meet quantitative and qualitative standards for reproducing key processes in the TTL. Several diagnostics are performed on a subset of the models analyzing the Tropopause Inversion Layer (TIL), Lagrangian cold point and TTL transit time. Historical decreases in tropical tropopause pressure and decreases in water vapor are simulated, lending confidence to future projections. The models simulate continued decreases in tropopause pressure in the 21st century, along with ∼1K increases per century in cold point tropopause temperature and 0.5–1 ppmv per century increases in water vapor above the tropical tropopause. TTL water vapor increases below the cold point. In two models, these trends are associated with 35% increases in TTL cloud fraction. These changes indicate significant perturbations to TTL processes, specifically to deep convective heating and humidity transport. Ozone in the extratropical lowermost stratosphere has significant and hemispheric asymmetric trends. O3 is projected to increase by nearly 30% due to ozone recovery in the Southern Hemisphere (SH) and due to enhancements in the stratospheric circulation. These UTLS ozone trends may have significant effects in the TTL and the troposphere.

A strategy for process-oriented validation of coupled chemistry–climate models

Evaluating CCMs with the presented framework will increase our confidence in predictions of stratospheric ozone change.