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.

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.

Global hydrology modelling and uncertainty: running multiple ensembles with a campus grid.

Uncertainties associated with the representation of various physical processes in global climate models (GCMs) mean that, when projections from GCMs are used in climate change impact studies, the uncertainty propagates through to the impact estimates. A complete treatment of this ‘climate model structural uncertainty’ is necessary so that decision-makers are presented with an uncertainty range around the impact estimates. This uncertainty is often underexplored owing to the human and computer processing time required to perform the numerous simulations. Here, we present a 189-member ensemble of global river runoff and water resource stress simulations that adequately address this uncertainty. Following several adaptations and modifications, the ensemble creation time has been reduced from 750 h on a typical single-processor personal computer to 9 h of high-throughput computing on the University of Reading Campus Grid. Here, we outline the changes that had to be made to the hydrological impacts model and to the Campus Grid, and present the main results. We show that, although there is considerable uncertainty in both the magnitude and the sign of regional runoff changes across different GCMs with climate change, there is much less uncertainty in runoff changes for regions that experience large runoff increases (e.g. the high northern latitudes and Central Asia) and large runoff decreases (e.g. the Mediterranean). Furthermore, there is consensus that the percentage of the global population at risk to water resource stress will increase with climate change.

A preliminary investigation of the running digit span as a test of working memory

The objective of this study was to compare performance on different versions of the running span task, and to examine the relationship between task performance and tests of episodic memory and executive function. We found that the average capacity of the running span was approximately 4 digits, and at long sequence lengths, performance was no longer affected by varying the running span window. Both episodic and executive function measures correlated with short and long running spans. suggesting that a simple dissociation between immediate memory and executive processes in short and long running digit span tasks may not be warranted.

Unifying syntactic theory and sentence processing difficulty through a connectionist minimalist parser

Syntactic theory provides a rich array of representational assumptions about linguistic knowledge and processes. Such detailed and independently motivated constraints on grammatical knowledge ought to play a role in sentence comprehension. However most grammar-based explanations of processing difficulty in the literature have attempted to use grammatical representations and processes per se to explain processing difficulty. They did not take into account that the description of higher cognition in mind and brain encompasses two levels: on the one hand, at the macrolevel, symbolic computation is performed, and on the other hand, at the microlevel, computation is achieved through processes within a dynamical system. One critical question is therefore how linguistic theory and dynamical systems can be unified to provide an explanation for processing effects. Here, we present such a unification for a particular account to syntactic theory: namely a parser for Stabler's Minimalist Grammars, in the framework of Smolensky's Integrated Connectionist/Symbolic architectures. In simulations we demonstrate that the connectionist minimalist parser produces predictions which mirror global empirical findings from psycholinguistic research.

Financial implications for companies running standby generators in support of a smart grid

Integrating renewable energy into built environments requires additional attention to the balancing of supply and demand due to their intermittent nature. Demand Side Response (DSR) has the potential to make money for organisations as well as support the System Operator as the generation mix changes. There is an opportunity to increase the use of existing technologies in order to manage demand. Company-owned standby generators are a rarely used resource; their maintenance schedule often accounts for a majority of their running hours. DSR encompasses a range of technologies and organisations; Sustainability First (2012) suggest that the System Operator (SO), energy supply companies, Distribution Network Operators (DNOs), Aggregators and Customers all stand to benefit from DSR. It is therefore important to consider impact of DSR measures to each of these stakeholders. This paper assesses the financial implications of organisations using existing standby generation equipment for DSR in order to avoid peak electricity charges. It concludes that under the current GB electricity pricing structure, there are several regions where running diesel generators at peak times is financially beneficial to organisations. Issues such as fuel costs, Carbon Reduction Commitment (CRC) charges, maintenance costs and electricity prices are discussed.

Characterization of Metal and Trace Element Contents of Particulate Matter (PM10) Emitted by Vehicles Running on Brazilian FuelsHydrated Ethanol and Gasoline with 22% of Anhydrous Ethanol

Emission of fine particles by mobile sources has been a matter of great concern due to its potential risk both to human health and the environment. Although there is no evidence that one sole component may be responsible for the adverse health outcomes, it is postulated that the metal particle content is one of the most important factors, mainly in relation to oxidative stress. Data concerning the amount and type of metal particles emitted by automotive vehicles using Brazilian fuels are limited. The aim of this study was to identify inhalable particles (PM10) and their trace metal content in two light-duty vehicles where one was fueled with ethanol while the other was fueled with gasoline mixed with 22% of anhydrous ethanol (gasohol); these engines were tested on a chassis dynamometer. The elementary composition of the samples was evaluated by the particle-induced x-ray emission technique. The experiment showed that total emission factors ranged from 2.5 to 11.8 mg/km in the gasohol vehicle, and from 1.2 to 3 mg/km in the ethanol vehicle. The majority of particles emitted were in the fine fraction (PM2.5), in which Al, Si, Ca, and Fe corresponded to 80% of the total weight. PM10 emissions from the ethanol vehicle were about threefold lower than those of gasohol. The elevated amount of fine particulate matter is an aggravating factor, considering that these particles, and consequently associated metals, readily penetrate deeply into the respiratory tract, producing damage to lungs and other tissues.

Circadian Pattern of Wheel-Running Activity of a South American Subterranean Rodent (Ctenomys cf knightii)

Circadian rhythms are regarded as essentially ubiquitous features of animal behavior and are thought to confer important adaptive advantages. However, although circadian systems of rodents have been among the most extensively studied, most comparative biology is restricted to a few related species. In this study, the circadian organization of locomotor activity was studied in the subterranean, solitary north Argentinean rodent, Ctenomys knightii. The genus, Ctenomys, commonly known as Tuco-tucos, comprises more than 50 known species over a range that extends from 12S latitude into Patagonia, and includes at least one social species. The genus, therefore, is ideal for comparative and ecological studies of circadian rhythms. Ctenomys knightii is the first of these to be studied for its circadian behavior. All animals were wild caught but adapted quickly to laboratory conditions, with clear and precise activity-rest rhythms in a light-dark (LD) cycle and strongly nocturnal wheel running behavior. In constant dark (DD), the rhythm expression persisted with free-running periods always longer than 24h. Upon reinstatement of the LD cycle, rhythms resynchronized rapidly with large phase advances in 7/8 animals. In constant light (LL), six animals had free-running periods shorter than in DD, and 4/8 showed evidence of splitting. We conclude that under laboratory conditions, in wheel-running cages, this species shows a clear nocturnal rhythmic organization controlled by an endogenous circadian oscillator that is entrained to 24h LD cycles, predominantly by light-induced advances, and shows the same interindividual variable responses to constant light as reported in other non-subterranean species. These data are the first step toward understanding the chronobiology of the largest genus of subterranean rodents.

Effects of voluntary running on spatial memory and mature brain-derived neurotrophic factor expression in mice hippocampus after status epilepticus

Voluntary physical activity improves memory and learning ability in rodents, whereas status epilepticus has been associated with memory impairment. Physical activity and seizures have been associated with enhanced hippocampal expression of BDNF, indicating that this protein may have a dual role in epilepsy. The influence of voluntary physical activity on memory and BDNF expression has been poorly studied in experimental models of epilepsy. In this paper, we have investigated the effect of voluntary physical activity on memory and BDNF expression in mice with pilocarpine-incluced epilepsy. Male Swiss mice were assigned to four experimental groups: pilocarpine sedentary (PS), pilocarpine runners (PRs), saline sedentary (SS) and saline runners (SRs). Two days after pilocarpine-induced status epilepticus, the affected mice (PR) and their running controls (SR) were housed with access to a running wheel for 28 days. After that, the spatial memory and the expression of the precursor and mature forms of hippocampal BDNF were assessed. PR mice performed better than PS mice in the water maze test. In addition, PR mice had a higher amount of mature BDNF (14 kDa) relative to the total BDNF (14 kDa + 28 kDa + 32 kDa forms) content when compared with PS mice. These results show that voluntary physical activity improved the spatial memory and increased the hippocampal content of mature BDNF of mice with pilocarpine-induced status epilepticus. (C) 2009 Elsevier B.V. All rights reserved.

Performance results of running parallel applications on the InteGrade

The InteGrade middleware intends to exploit the idle time of computing resources in computer laboratories. In this work we investigate the performance of running parallel applications with communication among processors on the InteGrade grid. As costly communication on a grid can be prohibitive, we explore the so-called systolic or wavefront paradigm to design the parallel algorithms in which no global communication is used. To evaluate the InteGrade middleware we considered three parallel algorithms that solve the matrix chain product problem, the 0-1 Knapsack Problem, and the local sequence alignment problem, respectively. We show that these three applications running under the InteGrade middleware and MPI take slightly more time than the same applications running on a cluster with only LAM-MPI support. The results can be considered promising and the time difference between the two is not substantial. The overhead of the InteGrade middleware is acceptable, in view of the benefits obtained to facilitate the use of grid computing by the user. These benefits include job submission, checkpointing, security, job migration, etc. Copyright (C) 2009 John Wiley & Sons, Ltd.

Antipanic procedures reduce the strychnine-facilitated wild running of rats

Wild running (WR) behavior of rats seen in response to intense acoustic stimulation of audiogenic seizure-paradigm is very similar to the panic flight and can be facilitated by subconvulsive doses of strychnine. The present work aimed to test whether antipanic procedures, such as dorsal periaqueductal gray (dPAG) lesion and imipramine treatments, affect the strychnine-facilitated WR. In study 1, six Wistar male adult rats with electrolytic lesion of dPAG had their WR completely blocked, whereas it was facilitated in 50% of sham-lesioned control rats by a dose of 0.5 mg/kg of strychnine administered intraperitoneal. This effect was not reproduced with a higher strychnine dose (1.0 mg/kg). In study 2, the effects of imipramine were investigated by testing 36 rats under a dose of strychnine that induces WR in 50% of subjects. They were assigned into three experimental groups: imipramine treatments of 5.0 and 10.0 mg/kg, and infusions of saline. All these treatments were subchronical with three intraperitoneal injections within 24h. Imipramine (10.0mg/kg) reduced the incidence of WR in comparison to the saline results. It is concluded that strychnine-facilitated WR is reduced by antipanic procedures and, therefore, can be viewed as a manifestation closely related to panic. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Correlation between the fighting rates of REM sleep-deprived rats and susceptibility to the 'wild running' of audiogenic seizures

Sleep-deprived rats exhibit defensive fighting as well as explosive flights very similar to the wild-running of audiogenic seizures. In order to determine why sleep deprivation is a common factor that facilitates both panic and convulsive manifestations, the present study was undertaken to investigate whether rats that display sleep deprivation-induced fighting (SDIF) are the same as those that are susceptible to audiogenic wild-running (WR). Twenty-eight male adult Wistar rats were divided into two groups assigned to two e-sleep deprivation for 5 days and had their SDIF evaluated in social experimental schemes. In the first, 18 subjects were submitted to REM grouping. After 1 week for recovery, their susceptibility to WR was tested in an acoustic stimulation trial ( 104 dB, 200 Hz, 60 S). Rats that did not present WR received a lactate infusion and were tested again by acoustic stimulation 40 min later. In the second experimental scheme, 10 subjects were initially evaluated for WR susceptibility and the number of SDIF was recorded in social grouping after I week. Three categories of WR-susceptibility were determined: WR-sensitive rats, intermediate WR-sensitive rats and WR-insensitive rats. T'he number of SDIF in each category was significantly different and there was a high positive correlation (r=0.89; Spearman test) between the number of SDIF and the level of WR-susceptibility. We conclude that the reasons why sleep deprivation exerts facilitatory effects on both panic and convulsive manifestations are due to overlappings of neural pathways responsible for both behavioral patterns and for the property of sleep deprivation to increase neuronal excitability. (C) 2002 Elsevier B.V. B.V. All rights reserved.