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.

Deforming glassy polystyrene: Influence of pressure, thermal history, and deformation mode on yielding and hardening

The toughness of a polymer glass is determined by the interplay of yielding, strain softening, and strain hardening. Molecular-dynamics simulations of a typical polymer glass, atactic polystyrene, under the influence of active deformation have been carried out to enlighten these processes. It is observed that the dominant interaction for the yield peak is of interchain nature and for the strain hardening of intrachain nature. A connection is made with the microscopic cage-to-cage motion. It is found that the deformation does not lead to complete erasure of the thermal history but that differences persist at large length scales. Also we find that the strain-hardening modulus increases with increasing external pressure. This new observation cannot be explained by current theories such as the one based on the entanglement picture and the inclusion of this effect will lead to an improvement in constitutive modeling.

Microscopic Mechanisms of Strain Hardening in Glassy Polymers

The mechanisms underlying the increase in stress for large mechanical strains of a polymer glass, quantified by the strain-hardening modulus, are still poorly understood. In the present paper we aim to elucidate this matter and present new mechanisms. Molecular-dynamics simulations of two polymers with very different strain-hardening moduli (polycarbonate and polystyrene) have been carried out. Nonaffine displacements occur because of steric hindrances and connectivity constraints. We argue that it is not necessary to introduce the concept of entanglements to understand strain hardening, but that hardening is rather coupled with the increase in the rate of nonaffine particle displacements. This rate increases faster for polycarbonate, which has the higher strain-hardening modulus. Also more nonaffine chain stretching is present for polycarbonate. It is shown that the inner distances of such a nonaffinely deformed chain can be well described by the inner distances of the worm-like chain, but with an effective stiffness length (equal to the Kuhn length for an infinite worm-like chain) that increases during deformation. It originates from the finite extensibility of the chain. In this way the increase in nonaffine particle displacement can be understood as resulting from an increase in the effective stiffness length of the perturbed chain during deformation, so that at larger strains a higher rate of plastic events in terms of nonaffine displacement is necessary, causing in turn the observed strain hardening in polymer glasses.

Simultaneous observations of reconnection pulses at Cluster and their effects on the cusp aurora seen at Chinese Yellow River Station

While the Cluster spacecraft were located near the high-latitude magnetopause, between 10:10 and 10:40 UT on 16 January 2004, three typical flux transfer event (FTE) signatures were observed. During this interval, simultaneous and conjugated all-sky camera measurements, recorded at Yellow River Station, Svalbard, are available at 630.0 and 557.7nm that show poleward-moving auroral forms (PMAFs), consistent with magnetic reconnection at dayside magnetopause. Simultaneous FTEs seen at the magnetopause mainly move northward, but having duskward (eastward) and tailward velocity components, roughly consistent with the observed direction of motion of the PMAFs in all-sky images. Between the PMAFs meridional keograms, extracted from the all-sky images, show intervals of lower intensity aurora which migrate equatorward just before the PMAFs intensify. This is strong evidence for an equatorward eroding and poleward moving open-closed boundary (OCB) associated with a variable magnetopause reconnection rate under variable IMF conditions. From the durations of the PMAFs we infer that the evolution time of FTEs is 5-11 minutes from its origin on magnetopause to its addition to the polar cap.

Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

It is known that germin, which is a marker of the onset of growth in germinating wheat, is an oxalate oxidase, and also that germins possess sequence similarity with legumin and vicilin seed storage proteins. These two pieces of information have been combined in order to generate a 3D model of germin based on the structure of vicilin and to examine the model with regard to a potential oxalate oxidase active site. A cluster of three histidine residues has been located within the conserved beta-barrel structure. While there is a relatively low level of overall sequence similarity between the model and the vicilin structures, the conservation of amino acids important in maintaining the scaffold of the beta-barrel lends confidence to the juxtaposition of the histidine residues. The cluster is similar structurally to those found in copper amine oxidase and other proteins, leading to the suggestion that it defines a metal-binding location within the oxalate oxidase active site. It is also proposed that the structural elements involved in intermolecular interactions in vicilins may play a role in oligomer formation in germin/oxalate oxidase.

The syntheses, structures and redox properties of phosphine-gold(I) and triruthenium-carbonyl cluster derivatives of tolans

The syntheses of several ethynyl-gold(I) phosphine substituted tolans (1,2-diaryl acetylenes) of general form [Au(C=CC6H4C=CC6H4X)(PPh3)] are described [X = Me (2a), OMe (2b), CO2Me (2c), NO2 (2d), CN (2e)]. These complexes react readily with [Ru-3(CO) 10(mu-dppm)] to give the heterometallic clusters [Ru3(mu-AuPPh3)(mu-eta(1), eta(2)-C2C6H4C, CC6H4X)(CO)(7)(mu-dppm)] (3a-e). The crystallographically determined molecular structures of 2b, 2d, 2e and 3a-e are reported here, that of 2a having been described on a previous occasion. Structural, spectroscopic and electrochemical studies were conducted and have revealed little electronic interaction between the remote substituent and the organometallic end-caps. (C) 2007 Elsevier B. V. All rights reserved.

Synthesis of a Mn-6 cluster and its self-assembly of an azido-bridged polymer

A rare mu(6)-oxo-centered Mn-6 mixed-valent cluster (1) is prepared and used as a secondary building unit for the self-assembly of its azido-bridged polymeric analogue (2) in a systematic way with the retention of the Mn-6 core of (1). Both complexes are characterized by X-ray single-crystal structure determination. The complex 1 was crystallized in a monoclinic system, space group P2(1), a = 11.252(5) A, b = 20.893(9) A, c = 12.301(6) A, and beta = 115.853(7)degrees, whereas the polymeric analogue was crystallized in an orthorhombic system, space group P2(1)2(1)2(1), a = 13.1941(8) A, b = 14.9897(9) A, and c = 27.8746(14) A. Variable-temperature magnetic behavior showed the presence of strong antiferromagnetic interaction in both cases.

A new tetrameric Cu-II cluster with square topology exhibiting ferro- and antiferromagnetic magnetic pathways: which is which?

[Cu4L2(bpy)(4)(H2O)(3)](ClO4)(4).2.5H(2)O, 1, a new tetranuclear Cu-II cluster showing square planar geometry, formed with aspartate bridging ligand (L) has been synthesized. The global magnetic coupling is ferromagnetic but theoretical DFT/B3LYP calculations are necessary to assign which Cu-L-Cu side is ferro or antiferromagnetically coupled.

Building cluster and shading in urban canyon for hot dry climate - Part 1: Air and surface temperature measurements

Under low latitude conditions, minimization of solar radiation within the urban environment may often be a desirable criterion in urban design. The dominance of the direct component of the global solar irradiance under clear high sun conditions requires that the street solar access must be small. It is well known that the size and proportion of open spaces has a great influence on the urban microclimate This paper is directed towards finding the interaction between urban canyon geometry and incident solar radiation. The effect of building height and street width on the shading of the street surfaces and ground for different orientations have been examined and evaluated. It is aimed to explore the extent to which these parameters affect the temperature in the street. This work is based on air and surface temperature measurements taken in different urban street canyons in EL-Oued City (hot and and climate), Algeria. In general, the results show that there are less air temperature variations compared to the surface temperature which really depends on the street geometry and sky view factor. In other words, there is a big correlation between the street geometry, sky view factor and surface temperatures.